Natronomonas pharaonis (DSM 2160, ATCC 35678, Gabara)

Name: Natronomonas pharaonis (DSM 2160, ATCC 35678, Gabara)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5896

Type strain

Strain Designation Gabara

Culture col. no. DSM 2160 ATCC 35678 Gabara JCM 8858 CCM 3872 5 more

NCBI tax ID(s) 348780 2257

Special Collections DSMZ JCM CIP

Links

Natronomonas pharaonis Gabara is a mesophilic, Gram-negative, motile prokaryote that was isolated from water sample.

Gram-negative motile rod-shaped mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 41222

ATCC 35678,DSM 2160,ATCC 43656,CIP 103997,IFO 14720,JCM 8858,CCM 3872,NCIMB 2260,VKM B-1749,NBRC 14720,CECT 4578,CGMCC 1.1965

@ref 20215

Last LPSN update 2025-12-16 09:48:10

Domain Methanobacteriati

Phylum Methanobacteriota

Class Halobacteria

Order Halobacteriales

Family Halobacteriaceae

Genus Natronomonas

Species Natronomonas pharaonis

Full scientific name Natronomonas pharaonis (Soliman and Trüper 1983) Kamekura et al. 1997

Synonyms (2)

Halobacterium pharaonis
Natronobacterium pharaonis

BacDive ID	Other strains from **Natronomonas pharaonis** (1)	Type strain
5897	N. pharaonis SP1, DSM 3395, ATCC 43100, CCM 3737, NCMB ...

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
121792	negative	rod-shaped
125438				92

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
985	NATRONOBACTERIA MEDIUM (DSMZ Medium 371)	Medium recipe at MediaDive	Name: NATRONOBACTERIA MEDIUM (DSMZ Medium 371) Composition: NaCl 200.0 g/l Agar 20.0 g/l Casamino acids 5.0 g/l Yeast extract 5.0 g/l Na2CO3 5.0 g/l Na2-glutamate 1.0 g/l KH2PO4 1.0 g/l KCl 1.0 g/l NH4Cl 1.0 g/l MgSO4 x 7 H2O 0.24 g/l CaSO4 x 2 H2O 0.17 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l H3BO3 6e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water
40918	MEDIUM 47 - for Natronomonas pharaonis		Sodium carbonate decahydrate (5.000 g);Distilled water make up to (1000.000ml);Sodium chloride (250.000 g);Potassium chloride (1.000 g);Magnesium sulphate heptahydrate (0.240 g);Agar (20.000 g);Yeast extract (5.000 g);Potassium di-hydrogen phosphate (1.00
121792	CIP Medium 47	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
985	positive	growth	37
40918	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic
121792	positive	growth	30-37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	90.4

Spore formation

@ref	Spore formation	Confidence
125439		90.6

Halophily

@ref	Salt	Growth	Tested relation	Concentration
121792	NaCl	positive	growth	0-6 %
121792	NaCl		growth	8 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
121792	17632 ChEBI	nitrate	-	reduction
121792	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
121792	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
121792	alcohol dehydrogenase	-	1.1.1.1
121792	beta-galactosidase	+	3.2.1.23
121792	catalase	+	1.11.1.6
121792	gelatinase	+
121792	lysine decarboxylase	-	4.1.1.18
121792	ornithine decarboxylase	-	4.1.1.17
121792	urease	-	3.5.1.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	denitrification	100	2 of 2
66794	factor 420 biosynthesis	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	ethanol fermentation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	propionate fermentation	90	9 of 10
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	palmitate biosynthesis	86.36	19 of 22
66794	propanol degradation	85.71	6 of 7
66794	citric acid cycle	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	vitamin B1 metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	pantothenate biosynthesis	83.33	5 of 6
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	vitamin K metabolism	80	4 of 5
66794	lipoate biosynthesis	80	4 of 5
66794	valine metabolism	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	biotin biosynthesis	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	lipid metabolism	74.19	23 of 31
66794	vitamin B12 metabolism	73.53	25 of 34
66794	alanine metabolism	72.41	21 of 29
66794	NAD metabolism	72.22	13 of 18
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	arginine metabolism	70.83	17 of 24
66794	threonine metabolism	70	7 of 10
66794	pyrimidine metabolism	68.89	31 of 45
66794	octane oxidation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	nitrate assimilation	66.67	6 of 9
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	enterobactin biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	purine metabolism	65.96	62 of 94
66794	glycolysis	64.71	11 of 17
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	photosynthesis	64.29	9 of 14
66794	carotenoid biosynthesis	63.64	14 of 22
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	phosphatidylethanolamine bioynthesis	61.54	8 of 13
66794	methionine metabolism	61.54	16 of 26
66794	Entner Doudoroff pathway	60	6 of 10
66794	3-chlorocatechol degradation	60	3 of 5
66794	creatinine degradation	60	3 of 5
66794	histidine metabolism	58.62	17 of 29
66794	non-pathway related	57.89	22 of 38
66794	tryptophan metabolism	57.89	22 of 38
66794	glutathione metabolism	57.14	8 of 14
66794	heme metabolism	57.14	8 of 14
66794	lipid A biosynthesis	55.56	5 of 9
66794	d-mannose degradation	55.56	5 of 9
66794	serine metabolism	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	proline metabolism	54.55	6 of 11
66794	pentose phosphate pathway	54.55	6 of 11
66794	oxidative phosphorylation	53.85	49 of 91
66794	sulfate reduction	53.85	7 of 13
66794	lysine metabolism	52.38	22 of 42
66794	glycine metabolism	50	5 of 10
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	quinate degradation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	gluconeogenesis	50	4 of 8
66794	butanoate fermentation	50	2 of 4
66794	CDP-diacylglycerol biosynthesis	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	tyrosine metabolism	50	7 of 14
66794	urea cycle	46.15	6 of 13
66794	isoprenoid biosynthesis	46.15	12 of 26
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	arachidonic acid metabolism	44.44	8 of 18
66794	mevalonate metabolism	42.86	3 of 7
66794	methanogenesis from CO2	41.67	5 of 12
66794	D-cycloserine biosynthesis	40	2 of 5
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	glycine betaine biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	degradation of sugar acids	40	10 of 25
66794	gallate degradation	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	chlorophyll metabolism	33.33	6 of 18
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	degradation of pentoses	32.14	9 of 28
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	myo-inositol biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	degradation of hexoses	27.78	5 of 18
66794	vitamin B6 metabolism	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	alginate biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	vitamin E metabolism	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	toluene degradation	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	phenylpropanoid biosynthesis	23.08	3 of 13

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Environmental	#Aquatic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
985	water sample	Wadi Natrun	Egypt	EGY	Africa
67770	Alkaline brines of eutrophic desert lakes of Wadi Natrun		Egypt	EGY	Africa
121792	Environment, Alkaline brine in lakes of Wadi Natrum		Egypt	EGY	Africa

Taxonmaps

69479

Global distribution of 16S sequence NR_074179 (>99% sequence identity) for Natronomonas pharaonis subclade from Microbeatlas

Aquatic Samples	25
Soil Samples	8
Animal Samples
Plant Samples
Total Samples	33

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
985	1	Risk group (German classification) According to TRBA 466
121792	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2604v1 assembly for Natronomonas pharaonis DSM 2160 Gabara	complete	GCA_000026045	348780.14	637000187	348780	98.57

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
985	Natronomonas pharaonis strain Gabara 16S ribosomal RNA, complete sequence	NR_074179	1466	2257
67770	Natronobacterium pharaonis DNA for 16S rRNA	D87971	1465	348780
124043	Natronomonas pharaonis gene for 16S rRNA, complete sequence, strain: JCM 8858.	AB663432	1467	348780

GC content

@ref	GC-content (mol%)	Method
67770	62.6	thermal denaturation, midpoint method (Tm)
67770	64.3	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Natronomonas pharaonis Gabara, DSM 2160
IMG: 637000187

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	90.60	no
125439	motility	BacteriaNetⓘ	yes	61.80	no
125439	gram_stain	BacteriaNetⓘ	negative	84.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	90.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Natronomonas pharaonis DSM 2160 Gabara
NCBI: GCA_000026045.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	78.60	no
125438	anaerobic	anaerobicⓘ	no	80.39	no
125438	aerobic	aerobicⓘ	yes	73.32	no
125438	spore-forming	spore-formingⓘ	no	86.56	no
125438	thermophilic	thermophileⓘ	no	79.84	yes
125438	flagellated	motile2+ⓘ	no	92.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Halophilic archaea produce wax esters and use an alternative fatty acyl-coenzyme A reductase for precursor synthesis.	Grossi V, Cuny P, Militon C, Witwinowski J, Eddhif B, Sylvi L, Nowakowski M, Kosta A, Antheaume I, Cornil J, Dubrac S, Kende J, Gribaldo S, Borrel G.	ISME J	10.1093/ismejo/wraf035	2025
Genetics	Metagenomic assembled genomes indicated the potential application of hypersaline microbiome for plant growth promotion and stress alleviation in salinized soils.	Dindhoria K, Kumar R, Bhargava B, Kumar R.	mSystems	10.1128/msystems.01050-23	2024
	Differences in archaeal diversity and potential ecological functions between saline and hypersaline lakes on Qinghai-Tibet Plateau were driven by multiple environmental and non-environmental factors beyond the salinity.	Wang Y, Li W, Bao G, Bai M, Ye H.	BMC Microbiol	10.1186/s12866-024-03307-3	2024
Enzymology	Bacterial-like nitric oxide synthase in the haloalkaliphilic archaeon Natronomonas pharaonis.	Orsini SS, James KL, Reyes DJ, Couto-Rodriguez RL, Gulko MK, Witte A, Carroll RK, Rice KC.	Microbiologyopen	10.1002/mbo3.1124	2020
	Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes.	Bold BM, Sokolov M, Maity S, Wanko M, Dohmen PM, Kranz JJ, Kleinekathofer U, Hofener S, Elstner M.	Phys Chem Chem Phys	10.1039/c9cp05753f	2020
	Membrane Independence of Ultrafast Photochemistry in Pharaonis Halorhodopsin: Testing the Role of Bacterioruberin.	Gdor I, Mani-Hazan M, Friedman N, Sheves M, Ruhman S.	J Phys Chem B	10.1021/acs.jpcb.6b12698	2017
	Crystal Structure of the 11-cis Isomer of Pharaonis Halorhodopsin: Structural Constraints on Interconversions among Different Isomeric States.	Chan SK, Kawaguchi H, Kubo H, Murakami M, Ihara K, Maki K, Kouyama T.	Biochemistry	10.1021/acs.biochem.6b00277	2016
Genetics	Deciphering the microbial communities of alkaline hot spring in Panamik, Ladakh, India using a high-throughput sequencing approach.	Choudhary G, Kumari S, Anu K, Devi S.	Braz J Microbiol	10.1007/s42770-024-01346-6	2024
	Dual color optogenetic tool enables heart arrest, bradycardic, and tachycardic pacing in Drosophila melanogaster.	Gracheva E, Wang Y, Zhu J, Wang F, Matt A, Fishman M, Liang H, Zhou C.	Commun Biol	10.1038/s42003-024-06703-7	2024
Metabolism	Probing the Cl--pumping photocycle of pharaonis halorhodopsin: Examinations with bacterioruberin, an intrinsic dye, and membrane potential-induced modulation of the photocycle.	Kikukawa T, Kusakabe C, Kokubo A, Tsukamoto T, Kamiya M, Aizawa T, Ihara K, Kamo N, Demura M.	Biochim Biophys Acta	10.1016/j.bbabio.2015.05.002	2015
	Halocin H4 is activated through cleavage by halolysin HlyR4.	Chen S, Dai Y, Ke J, Luo Y, Wang C, Hao Y, Zhang A, Han J, Xiang H.	Appl Environ Microbiol	10.1128/aem.02284-23	2024
	Crystal structures of an O-like blue form and an anion-free yellow form of pharaonis halorhodopsin.	Kanada S, Takeguchi Y, Murakami M, Ihara K, Kouyama T.	J Mol Biol	10.1016/j.jmb.2011.08.021	2011
Metabolism	An amino acid residue (S201) in the retinal binding pocket regulates the photoreaction pathway of phoborhodopsin.	Dai G, Zhang Y, Tamogami J, Demura M, Kamo N, Kandori H, Iwasa T.	Biochemistry	10.1021/bi200598r	2011
	Hydrogen-bonding changes of internal water molecules upon the actions of microbial rhodopsins studied by FTIR spectroscopy.	Furutani Y, Kandori H.	Biochim Biophys Acta	10.1016/j.bbabio.2013.09.004	2014
	Draft Genome Sequence of the Polyextremophilic Halorubrum sp. Strain AJ67, Isolated from Hyperarsenic Lakes in the Argentinian Puna.	Burguener GF, Maldonado MJ, Revale S, Fernandez Do Porto D, Rascovan N, Vazquez M, Farias ME, Marti MA, Turjanski AG.	Genome Announc	10.1128/genomea.01096-13	2014
	Dynamics of Dangling Bonds of Water Molecules in pharaonis Halorhodopsin during Chloride Ion Transportation.	Furutani Y, Fujiwara K, Kimura T, Kikukawa T, Demura M, Kandori H.	J Phys Chem Lett	10.1021/jz301287n	2012
Metabolism	Retinal-protein interactions in halorhodopsin from Natronomonas pharaonis: binding and retinal thermal isomerization catalysis.	Maiti TK, Engelhard M, Sheves M.	J Mol Biol	10.1016/j.jmb.2009.09.024	2009
Metabolism	A Large and Phylogenetically Diverse Class of Type 1 Opsins Lacking a Canonical Retinal Binding Site.	Becker EA, Yao AI, Seitzer PM, Kind T, Wang T, Eigenheer R, Shao KS, Yarov-Yarovoy V, Facciotti MT.	PLoS One	10.1371/journal.pone.0156543	2016
	Monomorium sahlbergi Emery, 1898 (Formicidae, Hymenoptera): a cryptic globally introduced species.	Boer P, Loss AC, Bakker F, Beentjes K, Fisher BL.	Zookeys	10.3897/zookeys.979.55342	2020
	Characterization of growth and metabolism of the haloalkaliphile Natronomonas pharaonis.	Gonzalez O, Oberwinkler T, Mansueto L, Pfeiffer F, Mendoza E, Zimmer R, Oesterhelt D.	PLoS Comput Biol	10.1371/journal.pcbi.1000799	2010
Metabolism	Role of Arg123 in light-driven anion pump mechanisms of pharaonis halorhodopsin.	Kubo M, Kikukawa T, Miyauchi S, Seki A, Kamiya M, Aizawa T, Kawano K, Kamo N, Demura M.	Photochem Photobiol	10.1111/j.1751-1097.2009.00538.x	2009
Metabolism	Proton release group of pharaonis phoborhodopsin revealed by ATR-FTIR spectroscopy.	Kitade Y, Furutani Y, Kamo N, Kandori H.	Biochemistry	10.1021/bi801984u	2009
Metabolism	Sucrose Metabolism in Haloarchaea: Reassessment Using Genomics, Proteomics, and Metagenomics.	Williams TJ, Allen MA, Liao Y, Raftery MJ, Cavicchioli R.	Appl Environ Microbiol	10.1128/aem.02935-18	2019
	Deciphering excited state evolution in halorhodopsin with stimulated emission pumping.	Bismuth O, Komm P, Friedman N, Eliash T, Sheves M, Ruhman S.	J Phys Chem B	10.1021/jp910853n	2010
	Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints.	Christoffer C, Harini K, Archit G, Kihara D.	J Mol Biol	10.1016/j.jmb.2024.168486	2024
	Dynamics change of phoborhodopsin and transducer by activation: study using D75N mutant of the receptor by site-directed solid-state 13C NMR.	Kawamura I, Yoshida H, Ikeda Y, Yamaguchi S, Tuzi S, Saito H, Kamo N, Naito A.	Photochem Photobiol	10.1111/j.1751-1097.2008.00326.x	2008
	Ultrafast pump-probe study of the primary photoreaction process in pharaonis halorhodopsin: halide ion dependence and isomerization dynamics.	Nakamura T, Takeuchi S, Shibata M, Demura M, Kandori H, Tahara T.	J Phys Chem B	10.1021/jp803282s	2008
Enzymology	Pro219 is an electrostatic color determinant in the light-driven sodium pump KR2.	Nakajima Y, Pedraza-Gonzalez L, Barneschi L, Inoue K, Olivucci M, Kandori H.	Commun Biol	10.1038/s42003-021-02684-z	2021
Metabolism	Structural changes in the O-decay accelerated mutants of pharaonis phoborhodopsin.	Sudo Y, Furutani Y, Iwamoto M, Kamo N, Kandori H.	Biochemistry	10.1021/bi701885k	2008
	Tryptophan 171 in Pharaonis phoborhodopsin (sensory rhodopsin II) interacts with the chromophore retinal and its substitution with alanine or threonine slowed down the decay of M- and O-intermediate.	Iwasa T, Abe E, Yakura Y, Yoshida H, Kamo N.	Photochem Photobiol	10.1562/2006-06-15-ra-928	2007
	Effect of polarization on the opsin shift in rhodopsins. 1. A combined QM/QM/MM model for bacteriorhodopsin and pharaonis sensory rhodopsin II.	Wanko M, Hoffmann M, Hoffmann M, Frauenheim T, Elstner M.	J Phys Chem B	10.1021/jp802408g	2008
	Properties of the anion-binding site of pharaonis Halorhodopsin studied by ultrafast pump-probe spectroscopy and low-temperature FTIR spectroscopy.	Nakashima K, Nakamura T, Takeuchi S, Shibata M, Demura M, Tahara T, Kandori H.	J Phys Chem B	10.1021/jp902596k	2009
Stress	HtrAs are essential for the survival of the haloarchaeon Natrinema gari J7-2 in response to heat, high salinity, and toxic substances.	Luo H, Qu X, Deng X, He L, Wu Y, Liu Y, He D, Yin J, Wang B, Gan F, Tang B, Tang X-F.	Appl Environ Microbiol	10.1128/aem.02048-23	2024
	Effect of polarization on the opsin shift in rhodopsins. 2. Empirical polarization models for proteins.	Wanko M, Hoffmann M, Frahmcke J, Frauenheim T, Elstner M.	J Phys Chem B	10.1021/jp802409k	2008
	FTIR study of primate color visual pigments.	Katayama K, Kandori H.	Biophysics (Nagoya-shi)	10.2142/biophysics.11.61	2015
	Assignment of the hydrogen-out-of-plane and -in-plane vibrations of the retinal chromophore in the K intermediate of pharaonis phoborhodopsin.	Furutani Y, Sudo Y, Wada A, Ito M, Shimono K, Kamo N, Kandori H.	Biochemistry	10.1021/bi0610597	2006
Metabolism	Role of putative anion-binding sites in cytoplasmic and extracellular channels of Natronomonas pharaonis halorhodopsin.	Sato M, Kubo M, Aizawa T, Kamo N, Kikukawa T, Nitta K, Demura M.	Biochemistry	10.1021/bi047500f	2005
	Temperature-dependent interactions between photoactivated pharaonis phoborhodopsin and its transducer.	Kamada K, Furutani Y, Sudo Y, Kamo N, Kandori H.	Biochemistry	10.1021/bi060047i	2006
	Protein-protein interaction of a Pharaonis halorhodopsin mutant forming a complex with Pharaonis halobacterial transducer protein II detected by Fourier-transform infrared spectroscopy.	Furutani Y, Ito M, Sudo Y, Kamo N, Kandori H.	Photochem Photobiol	10.1111/j.1751-1097.2008.00317.x	2008
Genetics	Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea.	Pfeiffer F, Dyall-Smith M.	Genes (Basel)	10.3390/genes12070963	2021
Genetics	A manual curation strategy to improve genome annotation: application to a set of haloarchael genomes.	Pfeiffer F, Oesterhelt D.	Life (Basel)	10.3390/life5021427	2015
	Lipid membrane mimetics and oligomerization tune functional properties of proteorhodopsin.	Han CT, Nguyen KDQ, Berkow MW, Hussain S, Kiani A, Kinnebrew M, Idso MN, Baxter N, Chang E, Aye E, Winslow E, Rahman M, Seppala S, O'Malley MA, Chmelka BF, Mertz B, Han S.	Biophys J	10.1016/j.bpj.2022.11.012	2023
Metabolism	Retinal Configuration of ppR Intermediates Revealed by Photoirradiation Solid-State NMR and DFT.	Makino Y, Kawamura I, Okitsu T, Wada A, Kamo N, Sudo Y, Ueda K, Naito A.	Biophys J	10.1016/j.bpj.2018.05.030	2018
	All-optical switching in Pharaonis phoborhodopsin protein molecules.	Roy S, Kikukawa T, Sharma P, Kamo N.	IEEE Trans Nanobioscience	10.1109/tnb.2006.880828	2006
Metabolism	The core and unique proteins of haloarchaea.	Capes MD, DasSarma P, DasSarma S.	BMC Genomics	10.1186/1471-2164-13-39	2012
Enzymology	Sequence analysis of an Archaeal virus isolated from a hypersaline lake in Inner Mongolia, China.	Pagaling E, Haigh RD, Grant WD, Cowan DA, Jones BE, Ma Y, Ventosa A, Heaphy S.	BMC Genomics	10.1186/1471-2164-8-410	2007
Metabolism	Steric constraint in the primary photoproduct of an archaeal rhodopsin from regiospecific perturbation of C-D stretching vibration of the retinyl chromophore.	Sudo Y, Furutani Y, Wada A, Ito M, Kamo N, Kandori H.	J Am Chem Soc	10.1021/ja056203a	2005
Metabolism	Large deformation of helix F during the photoreaction cycle of Pharaonis halorhodopsin in complex with azide.	Nakanishi T, Kanada S, Murakami M, Ihara K, Kouyama T.	Biophys J	10.1016/j.bpj.2012.12.018	2013
	Participation of the surface structure of Pharaonis phoborhodopsin, ppR and its A149S and A149V mutants, consisting of the C-terminal alpha-helix and E-F loop, in the complex-formation with the cognate transducer pHtrII, as revealed by site-directed 13C solid-state NMR.	Kawamura I, Ikeda Y, Sudo Y, Iwamoto M, Shimono K, Yamaguchi S, Tuzi S, Saito H, Kamo N, Naito A.	Photochem Photobiol	10.1562/2006-06-20-ra-940	2007
Metabolism	Ant cuticular hydrocarbons are heritable and associated with variation in colony productivity.	Walsh J, Pontieri L, d'Ettorre P, Linksvayer TA.	Proc Biol Sci	10.1098/rspb.2020.1029	2020
Metabolism	The influence of the halide ions on the photochemical reaction cycle of pharaonis halorhodopsin.	Magyari K, Simon V, Varo G.	J Photochem Photobiol B	10.1016/j.jphotobiol.2005.08.005	2006
Metabolism	The Halophile protein database.	Sharma N, Farooqi MS, Chaturvedi KK, Lal SB, Grover M, Rai A, Pandey P.	Database (Oxford)	10.1093/database/bau114	2014
	Crystal structures of the L1, L2, N, and O states of pharaonis halorhodopsin.	Kouyama T, Kawaguchi H, Nakanishi T, Kubo H, Murakami M.	Biophys J	10.1016/j.bpj.2015.04.027	2015
	Dynamic pictures of membrane proteins in two-dimensional crystal, lipid bilayer and detergent as revealed by site-directed solid-state 13C NMR.	Saito H.	Chem Phys Lipids	10.1016/j.chemphyslip.2004.09.009	2004
	Disassembling and bleaching of chloride-free pharaonis halorhodopsin by octyl-beta-glucoside.	Kubo M, Sato M, Aizawa T, Kojima C, Kamo N, Mizuguchi M, Kawano K, Demura M.	Biochemistry	10.1021/bi0511235	2005
Metabolism	Kinetic isotope effects in the photochemical reaction cycle of ion transporting retinal proteins.	Szakacs J, Lakatos M, Ganea C, Varo G.	J Photochem Photobiol B	10.1016/j.jphotobiol.2005.01.001	2005
Metabolism	Structural changes of the complex between pharaonis phoborhodopsin and its cognate transducer upon formation of the M photointermediate.	Furutani Y, Kamada K, Sudo Y, Shimono K, Kamo N, Kandori H.	Biochemistry	10.1021/bi047893i	2005
Metabolism	An active photoreceptor intermediate revealed by in situ photoirradiated solid-state NMR spectroscopy.	Tomonaga Y, Hidaka T, Kawamura I, Nishio T, Ohsawa K, Okitsu T, Wada A, Sudo Y, Kamo N, Ramamoorthy A, Naito A.	Biophys J	10.1016/j.bpj.2011.10.022	2011
	Linker region of a halobacterial transducer protein interacts directly with its sensor retinal protein.	Sudo Y, Okuda H, Yamabi M, Fukuzaki Y, Mishima M, Kamo N, Kojima C.	Biochemistry	10.1021/bi047573z	2005
	An evolutionarily conserved pathway mediated by neuroparsin-A regulates reproductive plasticity in ants.	Zhang X, Xie N, Ding G, Ning D, Dai W, Xiong Z, Zhong W, Zuo D, Zhao J, Zhang P, Liu C, Li Q, Ran H, Liu W, Zhang G.	PLoS Biol	10.1371/journal.pbio.3002763	2024
Metabolism	Role of charged residues of pharaonis phoborhodopsin (sensory rhodopsin II) in its interaction with the transducer protein.	Sudo Y, Iwamoto M, Shimono K, Kamo N.	Biochemistry	10.1021/bi048803c	2004
	Complete genome sequence of 'Halanaeroarchaeum sulfurireducens' M27-SA2, a sulfur-reducing and acetate-oxidizing haloarchaeon from the deep-sea hypersaline anoxic lake Medee.	Messina E, Sorokin DY, Kublanov IV, Toshchakov S, Lopatina A, Arcadi E, Smedile F, La Spada G, La Cono V, Yakimov MM.	Stand Genomic Sci	10.1186/s40793-016-0155-9	2016
Metabolism	Amino acid substitutions in cold-adapted proteins from Halorubrum lacusprofundi, an extremely halophilic microbe from antarctica.	DasSarma S, Capes MD, Karan R, DasSarma P.	PLoS One	10.1371/journal.pone.0058587	2013
	Transient movement of helix F revealed by photo-induced inactivation by reaction of a bulky SH-reagent to cysteine-introduced pharaonis phoborhodopsin (sensory rhodopsin II).	Yoshida H, Sudo Y, Shimono K, Iwamoto M, Kamo N.	Photochem Photobiol Sci	10.1039/b315454h	2004
Metabolism	Interaction of Natronobacterium pharaonis phoborhodopsin (sensory rhodopsin II) with its cognate transducer probed by increase in the thermal stability.	Sudo Y, Yamabi M, Iwamoto M, Shimono K, Kamo N.	Photochem Photobiol	10.1562/0031-8655(2003)078<0511:ionpps>2.0.co;2	2003
Metabolism	Deciphering Pathways for Carotenogenesis in Haloarchaea.	Giani M, Miralles-Robledillo JM, Peiro G, Pire C, Martinez-Espinosa RM.	Molecules	10.3390/molecules25051197	2020
	Characterizing the DNA Methyltransferases of Haloferax volcanii via Bioinformatics, Gene Deletion, and SMRT Sequencing.	Ouellette M, Gogarten JP, Lajoie J, Makkay AM, Papke RT.	Genes (Basel)	10.3390/genes9030129	2018
	Proton release and uptake of pharaonis phoborhodopsin (sensory rhodopsin II) reconstituted into phospholipids.	Iwamoto M, Hasegawa C, Sudo Y, Shimono K, Araiso T, Kamo N.	Biochemistry	10.1021/bi035960n	2004
Metabolism	Chimeric microbial rhodopsins containing the third cytoplasmic loop of bovine rhodopsin.	Nakatsuma A, Yamashita T, Sasaki K, Kawanabe A, Inoue K, Furutani Y, Shichida Y, Kandori H.	Biophys J	10.1016/j.bpj.2011.02.054	2011
Metabolism	Ser-130 of Natronobacterium pharaonis halorhodopsin is important for the chloride binding.	Sato M, Kikukawa T, Araiso T, Okita H, Shimono K, Kamo N, Demura M, Nitta K.	Biophys Chem	10.1016/s0301-4622(02)00368-x	2003
	FTIR spectroscopy of the O photointermediate in pharaonis phoborhodopsin.	Furutani Y, Iwamoto M, Shimono K, Wada A, Ito M, Kamo N, Kandori H.	Biochemistry	10.1021/bi036316b	2004
	FTIR spectroscopy of the K photointermediate of Neurospora rhodopsin: structural changes of the retinal, protein, and water molecules after photoisomerization.	Furutani Y, Bezerra AG, Waschuk S, Sumii M, Brown LS, Kandori H.	Biochemistry	10.1021/bi049158c	2004
Metabolism	Illumination accelerates the decay of the O-intermediate of pharaonis phoborhodopsin (sensory rhodopsin II).	Iwamoto M, Sudo Y, Shimono K, Kamo N.	Photochem Photobiol	10.1562/0031-8655(2002)076<0462:iatdot>2.0.co;2	2002
Metabolism	Roles of Ser130 and Thr126 in chloride binding and photocycle of pharaonis halorhodopsin.	Sato M, Kikukawa T, Araiso T, Okita H, Shimono K, Kamo N, Demura M, Nitta K.	J Biochem	10.1093/jb/mvg123	2003
Transcriptome	Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux.	Lynch EA, Langille MG, Darling A, Wilbanks EG, Haltiner C, Shao KS, Starr MO, Teiling C, Harkins TT, Edwards RA, Eisen JA, Facciotti MT.	PLoS One	10.1371/journal.pone.0041389	2012
Metabolism	Arg-72 of pharaonis phoborhodopsin (sensory rhodopsin II) is important for the maintenance of the protein structure in the solubilized states.	Ikeura Y, Shimono K, Iwamoto M, Sudo Y, Kamo N.	Photochem Photobiol	10.1562/0031-8655(2003)077<0096:aoppsr>2.0.co;2	2003
	Vibrational modes of the protonated Schiff base in pharaonis phoborhodopsin.	Shimono K, Furutani Y, Kamo N, Kandori H.	Biochemistry	10.1021/bi034284m	2003
	Red-shifting mutation of light-driven sodium-pump rhodopsin.	Inoue K, Del Carmen Marin M, Tomida S, Nakamura R, Nakajima Y, Olivucci M, Kandori H.	Nat Commun	10.1038/s41467-019-10000-x	2019
Metabolism	FTIR spectroscopy of the complex between pharaonis phoborhodopsin and its transducer protein.	Furutani Y, Sudo Y, Kamo N, Kandori H.	Biochemistry	10.1021/bi034317y	2003
	Hydrogen bonding alteration of Thr-204 in the complex between pharaonis phoborhodopsin and its transducer protein.	Sudo Y, Furutani Y, Shimono K, Kamo N, Kandori H.	Biochemistry	10.1021/bi035678g	2003
Genetics	Bipyrimidine Signatures as a Photoprotective Genome Strategy in G + C-rich Halophilic Archaea.	Jones DL, Baxter BK.	Life (Basel)	10.3390/life6030037	2016
Metabolism	Dynamic structure of pharaonis phoborhodopsin (sensory rhodopsin II) and complex with a cognate truncated transducer as revealed by site-directed 13C solid-state NMR.	Arakawa T, Shimono K, Yamaguchi S, Tuzi S, Sudo Y, Kamo N, Saito H.	FEBS Lett	10.1016/s0014-5793(03)00065-6	2003
	Association between a photo-intermediate of a M-lacking mutant D75N of pharaonis phoborhodopsin and its cognate transducer.	Sudo Y, Iwamoto M, Shimono K, Kamo N.	J Photochem Photobiol B	10.1016/s1011-1344(02)00322-6	2002
	Internal water molecules of pharaonis phoborhodopsin studied by low-temperature infrared spectroscopy.	Kandori H, Furutani Y, Shimono K, Shichida Y, Kamo N.	Biochemistry	10.1021/bi011621n	2001
Metabolism	Pharaonis phoborhodopsin binds to its cognate truncated transducer even in the presence of a detergent with a 1:1 stoichiometry.	Sudo Y, Iwamoto M, Shimono K, Kamo N.	Photochem Photobiol	10.1562/0031-8655(2001)074<0489:ppbtic>2.0.co;2	2001
	Comprehensive analysis of male-free reproduction in Monomorium triviale (Formicidae: Myrmicinae).	Idogawa N, Sasaki T, Tsuji K, Dobata S.	PLoS One	10.1371/journal.pone.0246710	2021
Metabolism	Ribonucleotide reduction - horizontal transfer of a required function spans all three domains.	Lundin D, Gribaldo S, Torrents E, Sjoberg BM, Poole AM.	BMC Evol Biol	10.1186/1471-2148-10-383	2010
	Proton transfer reactions in the F86D and F86E mutants of pharaonis phoborhodopsin (sensory rhodopsin II).	Iwamoto M, Furutani Y, Kamo N, Kandori H.	Biochemistry	10.1021/bi0270283	2003
Metabolism	Interaction of Asn105 with the retinal chromophore during photoisomerization of pharaonis phoborhodopsin.	Kandori H, Shimono K, Shichida Y, Kamo N.	Biochemistry	10.1021/bi0120749	2002
	Photochemistry and photoinduced proton-transfer by pharaonis phoborhodopsin.	Kamo N, Shimono K, Iwamoto M, Sudo Y.	Biochemistry (Mosc)	10.1023/a:1013187403599	2001
	Selective reaction of hydroxylamine with chromophore during the photocycle of pharaonis phoborhodopsin.	Iwamoto M, Sudo Y, Shimono K, Kamo N.	Biochim Biophys Acta	10.1016/s0005-2736(01)00380-7	2001
	Functional expression of a two-transmembrane HtrII protein using cell-free synthesis.	Sudo Y, Tanaka R, Kobayashi T, Kamo N, Kohno T, Kojima C.	Biophysics (Nagoya-shi)	10.2142/biophysics.7.51	2011
Metabolism	Association of pharaonis phoborhodopsin with its cognate transducer decreases the photo-dependent reactivity by water-soluble reagents of azide and hydroxylamine.	Sudo Y, Iwamoto M, Shimono K, Kamo N.	Biochim Biophys Acta	10.1016/s0005-2736(01)00423-0	2002
	A pharaonis phoborhodopsin mutant with the same retinal binding site residues as in bacteriorhodopsin.	Shimono K, Furutani Y, Kandori H, Kamo N.	Biochemistry	10.1021/bi025636c	2002
	Environment around the chromophore in pharaonis phoborhodopsin: mutation analysis of the retinal binding site.	Shimono K, Ikeura Y, Sudo Y, Iwamoto M, Kamo N.	Biochim Biophys Acta	10.1016/s0005-2736(01)00394-7	2001
Metabolism	Dihydroxyacetone metabolism in Haloferax volcanii.	Ouellette M, Makkay AM, Papke RT.	Front Microbiol	10.3389/fmicb.2013.00376	2013
Pathogenicity	Homotrimer formation and dissociation of pharaonis halorhodopsin in detergent system.	Tsukamoto T, Sasaki T, Fujimoto KJ, Kikukawa T, Kamiya M, Aizawa T, Kawano K, Kamo N, Demura M.	Biophys J	10.1016/j.bpj.2012.05.008	2012
Metabolism	Stopped-flow analysis on anion binding to blue-form halorhodopsin from Natronobacterium pharaonis: comparison with the anion-uptake process during the photocycle.	Sato M, Kanamori T, Kamo N, Demura M, Nitta K.	Biochemistry	10.1021/bi011788g	2002
Metabolism	Time-resolved detection of transient movement of helix F in spin-labelled pharaonis sensory rhodopsin II.	Wegener AA, Chizhov I, Engelhard M, Steinhoff HJ.	J Mol Biol	10.1006/jmbi.2000.4008	2000
	Structural changes of pharaonis phoborhodopsin upon photoisomerization of the retinal chromophore: infrared spectral comparison with bacteriorhodopsin.	Kandori H, Shimono K, Sudo Y, Iwamoto M, Shichida Y, Kamo N.	Biochemistry	10.1021/bi0103819	2001
	Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis.	Zuo G, Xu Z, Hao B.	Life (Basel)	10.3390/life5010949	2015
	Effects of three characteristic amino acid residues of pharaonis phoborhodopsin on the absorption maximum.	Shimono K, Iwamoto M, Sumi M, Kamo N.	Photochem Photobiol	10.1562/0031-8655(2000)072<0141:eotcaa>2.0.co;2	2000
	Involvement of two groups in reversal of the bathochromic shift of pharaonis phoborhodopsin by chloride at low pH.	Shimono K, Kitami M, Iwamoto M, Kamo N.	Biophys Chem	10.1016/s0301-4622(00)00195-2	2000
	Halophiles and Their Biomolecules: Recent Advances and Future Applications in Biomedicine.	Corral P, Amoozegar MA, Ventosa A.	Mar Drugs	10.3390/md18010033	2019
Metabolism	Purification of histidine tagged bacteriorhodopsin, pharaonis halorhodopsin and pharaonis sensory rhodopsin II functionally expressed in Escherichia coli.	Hohenfeld IP, Wegener AA, Engelhard M.	FEBS Lett	10.1016/s0014-5793(98)01659-7	1999
	Azide accelerates the decay of M-intermediate of pharaonis phoborhodopsin.	Takao K, Kikukawa T, Araiso T, Kamo N.	Biophys Chem	10.1016/s0301-4622(98)00156-2	1998
	V108M mutant of pharaonis phoborhodopsin: substitution caused no absorption change but affected its M-state.	Shimono K, Iwamoto M, Sumi M, Kamo N.	J Biochem	10.1093/oxfordjournals.jbchem.a022126	1998
Genetics	Living with two extremes: conclusions from the genome sequence of Natronomonas pharaonis.	Falb M, Pfeiffer F, Palm P, Rodewald K, Hickmann V, Tittor J, Oesterhelt D.	Genome Res	10.1101/gr.3952905	2005
	Functional expression of pharaonis phoborhodopsin in Escherichia coli.	Shimono K, Iwamoto M, Sumi M, Kamo N.	FEBS Lett	10.1016/s0014-5793(97)01487-7	1997
Metabolism	Positioning proton-donating residues to the Schiff-base accelerates the M-decay of pharaonis phoborhodopsin expressed in Escherichia coli.	Iwamoto M, Shimono K, Sumi M, Kamo N.	Biophys Chem	10.1016/s0301-4622(99)00054-x	1999
	Heterologous coexpression of the blue light receptor psRII and its transducer pHtrII from Natronobacterium pharaonis in the Halobacterium salinarium strain Pho81/w restores negative phototaxis.	Luttenberg B, Wolff EK, Engelhard M.	FEBS Lett	10.1016/s0014-5793(98)00322-6	1998
Genetics	Sequence evidence in the archaeal genomes that tRNAs emerged through the combination of ancestral genes as 5' and 3' tRNA halves.	Fujishima K, Sugahara J, Tomita M, Kanai A.	PLoS One	10.1371/journal.pone.0001622	2008
	The complete genome sequence of Natrinema sp. J7-2, a haloarchaeon capable of growth on synthetic media without amino acid supplements.	Feng J, Liu B, Zhang Z, Ren Y, Li Y, Gan F, Huang Y, Chen X, Shen P, Wang L, Tang B, Tang XF.	PLoS One	10.1371/journal.pone.0041621	2012
	Understanding Colour Tuning Rules and Predicting Absorption Wavelengths of Microbial Rhodopsins by Data-Driven Machine-Learning Approach.	Karasuyama M, Inoue K, Nakamura R, Kandori H, Takeuchi I.	Sci Rep	10.1038/s41598-018-33984-w	2018
	Detection of a protein-bound water vibration of halorhodopsin in aqueous solution.	Fukuda T, Muroda K, Kandori H.	Biophysics (Nagoya-shi)	10.2142/biophysics.9.167	2013
	Using nutritional geometry to define the fundamental macronutrient niche of the widespread invasive ant Monomorium pharaonis.	Krabbe BA, Arnan X, Lannes P, Bergstedt CE, Larsen RS, Pedersen JS, Shik JZ.	PLoS One	10.1371/journal.pone.0218764	2019
Metabolism	Steric constraint in the primary photoproduct of sensory rhodopsin II is a prerequisite for light-signal transfer to HtrII.	Ito M, Sudo Y, Furutani Y, Okitsu T, Wada A, Homma M, Spudich JL, Kandori H.	Biochemistry	10.1021/bi8003507	2008
	Reason for the lack of light-dark adaptation in pharaonis phoborhodopsin: reconstitution with 13-cis-retinal.	Hirayma J, Kamo N, Imamoto Y, Shichida Y, Yoshizawa T.	FEBS Lett	10.1016/0014-5793(95)00381-i	1995
Metabolism	Isolation of photochemically active archaebacterial photoreceptor, pharaonis phoborhodopsin from Natronobacterium pharaonis.	Tomioka H, Sasabe H.	Biochim Biophys Acta	10.1016/0005-2736(94)00292-w	1995
	Identification of polyhydroxyalkanoates in Halococcus and other haloarchaeal species.	Legat A, Gruber C, Zangger K, Wanner G, Stan-Lotter H.	Appl Microbiol Biotechnol	10.1007/s00253-010-2611-6	2010
	Insights into dynamics of mobile genetic elements in hyperthermophilic environments from five new Thermococcus plasmids.	Krupovic M, Gonnet M, Hania WB, Forterre P, Erauso G.	PLoS One	10.1371/journal.pone.0049044	2013
	The novel ion pump rhodopsins from Haloarcula form a family independent from both the bacteriorhodopsin and archaerhodopsin families/tribes.	Tateno M, Ihara K, Mukohata Y.	Arch Biochem Biophys	10.1006/abbi.1994.1480	1994
	The lifetimes of Pharaonis phoborhodopsin signaling states depend on the rates of proton transfers--effects of hydrostatic pressure and stopped flow experiments.	Kikukawa T, Saha CK, Balashov SP, Imasheva ES, Zaslavsky D, Gennis RB, Abe T, Kamo N.	Photochem Photobiol	10.1111/j.1751-1097.2008.00318.x	2008
Genetics	Genome-scale metabolic model analysis indicates low energy production efficiency in marine ammonia-oxidizing archaea.	Li F, Xie W, Yuan Q, Luo H, Li P, Chen T, Zhao X, Wang Z, Ma H.	AMB Express	10.1186/s13568-018-0635-y	2018
Metabolism	Shape of the chromophore binding site in pharaonis phoborhodopsin from a study using retinal analogs.	Hirayama J, Imamoto Y, Shichida Y, Yoshizawa T, Asato AE, Liu RS, Kamo N.	Photochem Photobiol	10.1111/j.1751-1097.1994.tb05121.x	1994
Enzymology	Wide distribution among halophilic archaea of a novel polyhydroxyalkanoate synthase subtype with homology to bacterial type III synthases.	Han J, Hou J, Liu H, Cai S, Feng B, Zhou J, Xiang H.	Appl Environ Microbiol	10.1128/aem.01117-10	2010
	Blue halorhodopsin from Natronobacterium pharaonis: wavelength regulation by anions.	Scharf B, Engelhard M.	Biochemistry	10.1021/bi00187a002	1994
Metabolism	The Streptomyces NrdR transcriptional regulator is a Zn ribbon/ATP cone protein that binds to the promoter regions of class Ia and class II ribonucleotide reductase operons.	Grinberg I, Shteinberg T, Gorovitz B, Aharonowitz Y, Cohen G, Borovok I.	J Bacteriol	10.1128/jb.00903-06	2006
	Transcriptomic basis and evolution of the ant nurse-larval social interactome.	Warner MR, Mikheyev AS, Linksvayer TA.	PLoS Genet	10.1371/journal.pgen.1008156	2019
	Functional Promiscuity of Homologues of the Bacterial ArsA ATPases.	Castillo R, Saier MH.	Int J Microbiol	10.1155/2010/187373	2010
Metabolism	Phylogenomic reconstruction of archaeal fatty acid metabolism.	Dibrova DV, Galperin MY, Mulkidjanian AY.	Environ Microbiol	10.1111/1462-2920.12359	2014
	Properties and the primary structure of a new halorhodopsin from halobacterial strain mex.	Otomo J, Tomioka H, Sasabe H.	Biochim Biophys Acta	10.1016/0005-2736(92)90246-i	1992
Metabolism	The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism.	Hove-Jensen B, Brodersen DE, Manav MC.	Microbiol Mol Biol Rev	10.1128/mmbr.00040-18	2019
	Gene cloning and heterologous synthesis of a haloalkaliphilic extracellular protease of Natrialba magadii (Nep).	De Castro RE, Ruiz DM, Gimenez MI, Silveyra MX, Paggi RA, Maupin-Furlow JA.	Extremophiles	10.1007/s00792-008-0174-6	2008
Metabolism	Photocycle of phoborhodopsin from haloalkaliphilic bacterium (Natronobacterium pharaonis) studied by low-temperature spectrophotometry.	Hirayama J, Imamoto Y, Shichida Y, Kamo N, Tomioka H, Yoshizawa T.	Biochemistry	10.1021/bi00122a029	1992
	Chromophore configuration of pharaonis phoborhodopsin and its isomerization on photon absorption.	Imamoto Y, Shichida Y, Hirayama J, Tomioka H, Kamo N, Yoshizawa T.	Biochemistry	10.1021/bi00124a012	1992
Phylogeny	Quantifying homologous replacement of loci between haloarchaeal species.	Williams D, Gogarten JP, Papke RT.	Genome Biol Evol	10.1093/gbe/evs098	2012
	Novel archaeal adhesion pilins with a conserved N terminus.	Esquivel RN, Xu R, Pohlschroder M.	J Bacteriol	10.1128/jb.00572-13	2013
Phylogeny	The dispersed archaeal eukaryome and the complex archaeal ancestor of eukaryotes.	Koonin EV, Yutin N.	Cold Spring Harb Perspect Biol	10.1101/cshperspect.a016188	2014
Metabolism	Heterologous expression of Pharaonis halorhodopsin in Xenopus laevis oocytes and electrophysiological characterization of its light-driven Cl- pump activity.	Seki A, Miyauchi S, Hayashi S, Kikukawa T, Kubo M, Demura M, Ganapathy V, Kamo N.	Biophys J	10.1529/biophysj.106.093153	2007
Genetics	Identification and genomic analysis of transcription factors in archaeal genomes exemplifies their functional architecture and evolutionary origin.	Perez-Rueda E, Janga SC.	Mol Biol Evol	10.1093/molbev/msq033	2010
Enzymology	Diversity of Haloquadratum and other haloarchaea in three, geographically distant, Australian saltern crystallizer ponds.	Oh D, Porter K, Russ B, Burns D, Dyall-Smith M.	Extremophiles	10.1007/s00792-009-0295-6	2010
Metabolism	Protein-protein interaction changes in an archaeal light-signal transduction.	Kandori H, Sudo Y, Furutani Y.	J Biomed Biotechnol	10.1155/2010/424760	2010
	Chemoreceptor Evolution in Hymenoptera and Its Implications for the Evolution of Eusociality.	Zhou X, Rokas A, Berger SL, Liebig J, Ray A, Zwiebel LJ.	Genome Biol Evol	10.1093/gbe/evv149	2015
Transcriptome	The effect of sequencing errors on metagenomic gene prediction.	Hoff KJ.	BMC Genomics	10.1186/1471-2164-10-520	2009
Metabolism	Asymmetric Functional Conversion of Eubacterial Light-driven Ion Pumps.	Inoue K, Nomura Y, Kandori H.	J Biol Chem	10.1074/jbc.m116.716498	2016
Metabolism	Properties and photochemistry of a halorhodopsin from the haloalkalophile, Natronobacterium pharaonis.	Duschl A, Lanyi JK, Zimanyi L.	J Biol Chem	10.1016/s0021-9258(19)40007-0	1990
	The primary structure of a halorhodopsin from Natronobacterium pharaonis. Structural, functional and evolutionary implications for bacterial rhodopsins and halorhodopsins.	Lanyi JK, Duschl A, Hatfield GW, May K, Oesterhelt D.	J Biol Chem	10.1016/s0021-9258(19)40006-9	1990
Enzymology	Glycerate kinase of the hyperthermophilic archaeon Thermoproteus tenax: new insights into the phylogenetic distribution and physiological role of members of the three different glycerate kinase classes.	Kehrer D, Ahmed H, Brinkmann H, Siebers B.	BMC Genomics	10.1186/1471-2164-8-301	2007
Phylogeny	Whole-genome based Archaea phylogeny and taxonomy: A composition vector approach.	Sun J, Xu Z, Hao B.	Chin Sci Bull	10.1007/s11434-010-3008-8	2010
	General transcription factor specified global gene regulation in archaea.	Facciotti MT, Reiss DJ, Pan M, Kaur A, Vuthoori M, Bonneau R, Shannon P, Srivastava A, Donohoe SM, Hood LE, Baliga NS.	Proc Natl Acad Sci U S A	10.1073/pnas.0611663104	2007
Genetics	Genome information management and integrated data analysis with HaloLex.	Pfeiffer F, Broicher A, Gillich T, Klee K, Mejia J, Rampp M, Oesterhelt D.	Arch Microbiol	10.1007/s00203-008-0389-z	2008
	MetaGene: prokaryotic gene finding from environmental genome shotgun sequences.	Noguchi H, Park J, Takagi T.	Nucleic Acids Res	10.1093/nar/gkl723	2006
Metabolism	LccA, an archaeal laccase secreted as a highly stable glycoprotein into the extracellular medium by Haloferax volcanii.	Uthandi S, Saad B, Humbard MA, Maupin-Furlow JA.	Appl Environ Microbiol	10.1128/aem.01757-09	2010
Enzymology	Modelling the evolution of the archeal tryptophan synthase.	Merkl R.	BMC Evol Biol	10.1186/1471-2148-7-59	2007
Metabolism	The evolutionary relationship between microbial rhodopsins and metazoan rhodopsins.	Shen L, Chen C, Zheng H, Jin L.	ScientificWorldJournal	10.1155/2013/435651	2013
Genetics	Genome analysis of DNA repair genes in the alpha proteobacterium Caulobacter crescentus.	Martins-Pinheiro M, Marques RC, Menck CF.	BMC Microbiol	10.1186/1471-2180-7-17	2007
Enzymology	Evolution of DNA ligases of nucleo-cytoplasmic large DNA viruses of eukaryotes: a case of hidden complexity.	Yutin N, Koonin EV.	Biol Direct	10.1186/1745-6150-4-51	2009
	Crystal structure of Cruxrhodopsin-3 from Haloarcula vallismortis.	Chan SK, Kitajima-Ihara T, Fujii R, Gotoh T, Murakami M, Ihara K, Kouyama T.	PLoS One	10.1371/journal.pone.0108362	2014
Genetics	A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T.	Siddaramappa S, Challacombe JF, Decastro RE, Pfeiffer F, Sastre DE, Gimenez MI, Paggi RA, Detter JC, Davenport KW, Goodwin LA, Kyrpides N, Tapia R, Pitluck S, Lucas S, Woyke T, Maupin-Furlow JA.	BMC Genomics	10.1186/1471-2164-13-165	2012
Genetics	The GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection.	Arakawa K, Tomita M.	Evol Bioinform Online		2007
Metabolism	The photochemical reaction cycle and photoinduced proton transfer of sensory rhodopsin II (Phoborhodopsin) from Halobacterium salinarum.	Tamogami J, Kikukawa T, Ikeda Y, Takemura A, Demura M, Kamo N.	Biophys J	10.1016/j.bpj.2009.12.4288	2010
	Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes.	Paul S, Bag SK, Das S, Harvill ET, Dutta C.	Genome Biol	10.1186/gb-2008-9-4-r70	2008
	Photoreaction pathways and photointermediates of retinal-binding photoreceptor proteins as revealed by in situ photoirradiation solid-state NMR spectroscopy.	Naito A, Makino Y, Shigeta A, Kawamura I.	Biophys Rev	10.1007/s12551-019-00501-w	2019
Enzymology	Crystal structures of a halophilic archaeal malate synthase from Haloferax volcanii and comparisons with isoforms A and G.	Bracken CD, Neighbor AM, Lamlenn KK, Thomas GC, Schubert HL, Whitby FG, Howard BR.	BMC Struct Biol	10.1186/1472-6807-11-23	2011
Biotechnology	Synthesis, production, and biotechnological applications of exopolysaccharides and polyhydroxyalkanoates by archaea.	Poli A, Di Donato P, Abbamondi GR, Nicolaus B.	Archaea	10.1155/2011/693253	2011
Phylogeny	The relationships between the isoelectric point and: length of proteins, taxonomy and ecology of organisms.	Kiraga J, Mackiewicz P, Mackiewicz D, Kowalczuk M, Biecek P, Polak N, Smolarczyk K, Dudek MR, Cebrat S.	BMC Genomics	10.1186/1471-2164-8-163	2007
Enzymology	The UlaG protein family defines novel structural and functional motifs grafted on an ancient RNase fold.	Fernandez FJ, Garces F, Lopez-Estepa M, Aguilar J, Baldoma L, Coll M, Badia J, Vega MC.	BMC Evol Biol	10.1186/1471-2148-11-273	2011
	An economical and highly adaptable optogenetics system for individual and population-level manipulation of Caenorhabditis elegans.	Koopman M, Janssen L, Nollen EAA.	BMC Biol	10.1186/s12915-021-01085-2	2021
Genetics	Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber.	Pasic L, Rodriguez-Mueller B, Martin-Cuadrado AB, Mira A, Rohwer F, Rodriguez-Valera F.	BMC Genomics	10.1186/1471-2164-10-570	2009
	Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes.	Kastenmuller G, Schenk ME, Gasteiger J, Mewes HW.	Genome Biol	10.1186/gb-2009-10-3-r28	2009
	Characterization of the photochemical reaction cycle of proteorhodopsin.	Varo G, Brown LS, Lakatos M, Lanyi JK.	Biophys J	10.1016/s0006-3495(03)74934-0	2003
	A long-lived M-like state of phoborhodopsin that mimics the active state.	Sudo Y, Nishihori T, Iwamoto M, Shimono K, Kojima C, Kamo N.	Biophys J	10.1529/biophysj.107.125294	2008
Metabolism	Autocatalytic maturation of the Tat-dependent halophilic subtilase Nep produced by the archaeon Natrialba magadii.	Ruiz DM, Paggi RA, Gimenez MI, De Castro RE.	J Bacteriol	10.1128/jb.06792-11	2012
Metabolism	Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis.	Gao B, Gupta RS.	BMC Genomics	10.1186/1471-2164-8-86	2007
Metabolism	Tyr-199 and charged residues of pharaonis Phoborhodopsin are important for the interaction with its transducer.	Sudo Y, Iwamoto M, Shimono K, Kamo N.	Biophys J	10.1016/s0006-3495(02)75180-1	2002
Genetics	The haloarchaeal MCM proteins: bioinformatic analysis and targeted mutagenesis of the beta7-beta8 and beta9-beta10 hairpin loops and conserved zinc binding domain cysteines.	Kristensen TP, Maria Cherian R, Gray FC, MacNeill SA.	Front Microbiol	10.3389/fmicb.2014.00123	2014
Metabolism	A novel pathway for the biosynthesis of heme in Archaea: genome-based bioinformatic predictions and experimental evidence.	Storbeck S, Rolfes S, Raux-Deery E, Warren MJ, Jahn D, Layer G.	Archaea	10.1155/2010/175050	2010
Genetics	Information theoretic perspective on genome clustering.	Veluchamy A, Mehta P, Srividhya KV, Vikram H, Govind MK, Gupta R, Aziz Bin Dukhyil A, Abdullah Alharbi R, Abdullah Aloyuni S, Hassan MM, Krishnaswamy S.	Saudi J Biol Sci	10.1016/j.sjbs.2020.12.039	2021
	Correlation of the O-intermediate rate with the pKa of Asp-75 in the dark, the counterion of the Schiff base of Pharaonis phoborhodopsin (sensory rhodopsin II).	Iwamoto M, Sudo Y, Shimono K, Araiso T, Kamo N.	Biophys J	10.1529/biophysj.104.045583	2005
	Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms.	Nasir A, Naeem A, Khan MJ, Nicora HD, Caetano-Anolles G.	Genes (Basel)	10.3390/genes2040869	2011
	Estimating the fraction of non-coding RNAs in mammalian transcriptomes.	Xin Y, Quarta G, Gan HH, Schlick T.	Bioinform Biol Insights	10.4137/bbi.s443	2008
	Photo-induced proton transport of pharaonis phoborhodopsin (sensory rhodopsin II) is ceased by association with the transducer.	Sudo Y, Iwamoto M, Shimono K, Sumi M, Kamo N.	Biophys J	10.1016/s0006-3495(01)76070-5	2001
Metabolism	The nitrate transporting photochemical reaction cycle of the pharaonis halorhodopsin.	Balint Z, Lakatos M, Ganea C, Lanyi JK, Varo G.	Biophys J	10.1016/s0006-3495(04)74234-4	2004
	Role of Asp193 in chromophore-protein interaction of pharaonis phoborhodopsin (sensory rhodopsin II).	Iwamoto M, Furutani Y, Sudo Y, Shimono K, Kandori H, Kamo N.	Biophys J	10.1016/s0006-3495(02)75236-3	2002
Metabolism	Characterization of the azide-dependent bacteriorhodopsin-like photocycle of salinarum halorhodopsin.	Lakatos M, Groma GI, Ganea C, Lanyi JK, Varo G.	Biophys J	10.1016/s0006-3495(02)75521-5	2002
	Low-temperature FTIR study of multiple K intermediates in the photocycles of bacteriorhodopsin and xanthorhodopsin.	Dioumaev AK, Wang JM, Lanyi JK.	J Phys Chem B	10.1021/jp908698f	2010
Metabolism	Ectopic expression of multiple microbial rhodopsins restores ON and OFF light responses in retinas with photoreceptor degeneration.	Zhang Y, Ivanova E, Bi A, Pan ZH.	J Neurosci	10.1523/jneurosci.0184-09.2009	2009
Metabolism	Role of Arg-72 of pharaonis Phoborhodopsin (sensory rhodopsin II) on its photochemistry.	Ikeura Y, Shimono K, Iwamoto M, Sudo Y, Kamo N.	Biophys J	10.1016/s0006-3495(04)74359-3	2004
Metabolism	Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification.	Haft DH, Payne SH, Selengut JD.	J Bacteriol	10.1128/jb.06026-11	2012
	Characterization of the proton-transporting photocycle of pharaonis halorhodopsin.	Kulcsar A, Groma GI, Lanyi JK, Varo G.	Biophys J	10.1016/s0006-3495(00)76508-8	2000
	Electric-field dependent decays of two spectroscopically different M-states of photosensory rhodopsin II from Natronobacterium pharaonis.	Rivas L, Hippler-Mreyen S, Engelhard M, Hildebrandt P.	Biophys J	10.1016/s0006-3495(03)75114-5	2003
	Charge motions during the photocycle of pharaonis halorhodopsin.	Ludmann K, Ibron G, Lanyi JK, Varo G.	Biophys J	10.1016/s0006-3495(00)76653-7	2000
Metabolism	The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate- specific aldolase.	Reher M, Fuhrer T, Bott M, Schonheit P.	J Bacteriol	10.1128/jb.01281-09	2010
Metabolism	A Saccharomyces cerevisiae assay system to investigate ligand/AdipoR1 interactions that lead to cellular signaling.	Aouida M, Kim K, Shaikh AR, Pardo JM, Eppinger J, Yun DJ, Bressan RA, Narasimhan ML.	PLoS One	10.1371/journal.pone.0065454	2013
	Time-resolved detection of sensory rhodopsin II-transducer interaction.	Inoue K, Sasaki J, Morisaki M, Tokunaga F, Terazima M.	Biophys J	10.1529/biophysj.104.043521	2004
	Conformation and dynamics of the [3-(13)C]Ala, [1-(13)C]Val-labeled truncated pharaonis transducer, pHtrII(1-159), as revealed by site-directed (13)C solid-state NMR: changes due to association with phoborhodopsin (sensory rhodopsin II).	Yamaguchi S, Shimono K, Sudo Y, Tuzi S, Naito A, Kamo N, Saito H.	Biophys J	10.1016/s0006-3495(04)74361-1	2004
	FTIR spectroscopy of the M photointermediate in pharaonis rhoborhodopsin.	Furutani Y, Iwamoto M, Shimono K, Kamo N, Kandori H.	Biophys J	10.1016/s0006-3495(02)75347-2	2002
	A study in entire chromosomes of violations of the intra-strand parity of complementary nucleotides (Chargaff's second parity rule).	Powdel BR, Satapathy SS, Kumar A, Jha PK, Buragohain AK, Borah M, Ray SK.	DNA Res	10.1093/dnares/dsp021	2009
	Noncellulosomal cohesin- and dockerin-like modules in the three domains of life.	Peer A, Smith SP, Bayer EA, Lamed R, Borovok I.	FEMS Microbiol Lett	10.1111/j.1574-6968.2008.01420.x	2009
Metabolism	The M intermediate of Pharaonis phoborhodopsin is photoactive.	Balashov SP, Sumi M, Kamo N.	Biophys J	10.1016/s0006-3495(00)76851-2	2000
	Optical Techniques in Optogenetics.	Mohanty SK, Lakshminarayananan V.	J Mod Opt	10.1080/09500340.2015.1010620	2015
	Synthesis and use of stable isotope enriched retinals in the field of vitamin A.	Dawadi PB, Lugtenburg J.	Molecules	10.3390/molecules15031825	2010
	Photoreactions and structural changes of anabaena sensory rhodopsin.	Kawanabe A, Kandori H.	Sensors (Basel)	10.3390/s91209741	2009
	Chemical shift tensor - the heart of NMR: Insights into biological aspects of proteins.	Saito H, Ando I, Ramamoorthy A.	Prog Nucl Magn Reson Spectrosc	10.1016/j.pnmrs.2010.04.005	2010
Metabolism	Role of alcohols in growth, lipid composition, and membrane fluidity of yeasts, bacteria, and archaea.	Huffer S, Clark ME, Ning JC, Blanch HW, Clark DS.	Appl Environ Microbiol	10.1128/aem.00694-11	2011
	Retinal Chromophore Configuration in the O Intermediate of Sensory Rhodopsin II from Natronomonas pharaonis.	Fujisawa T, Tanaka N, Tamogami J, Unno M.	Biochemistry	10.1021/acs.biochem.4c00420	2024
	Important amino acid residues in the chloride pump halorhodopsin that accelerate ion transport despite no direct interaction with the substrate.	Zhai Y, Shimosaka A, Tsukamoto T, Kikukawa T.	J Biol Chem	10.1016/j.jbc.2025.110703	2025
	Structural changes of Natronomonas pharaonis halorhodopsin in its late photocycle revealed by solid-state NMR spectroscopy.	Zhang X, Tamaki H, Kikukawa T, Fujiwara T, Matsuki Y.	Biophys Chem	10.1016/j.bpc.2024.107329	2024
	Key determinants for signaling in the sensory rhodopsin II/transducer complex are different between Halobacterium salinarum and Natronomonas pharaonis.	Matsunami-Nakamura R, Tamogami J, Takeguchi M, Ishikawa J, Kikukawa T, Kamo N, Nara T.	FEBS Lett	10.1002/1873-3468.14711	2023
	Unique Vibrational Characteristics and Structures of the Photoexcited Retinal Chromophore in Ion-Pumping Rhodopsins.	Li Z, Mizuno M, Ejiri T, Hayashi S, Kandori H, Mizutani Y.	J Phys Chem B	10.1021/acs.jpcb.3c02146	2023
	Optogenetics in oral and craniofacial research.	Zhang Q, Song L, Fu M, He J, Yang G, Jiang Z.	J Zhejiang Univ Sci B	10.1631/jzus.b2300322	2024
	Direct detection of the chloride release and uptake reactions of Natronomonas pharaonis halorhodopsin.	Hamada C, Murabe K, Tsukamoto T, Kikukawa T.	J Biol Chem	10.1016/j.jbc.2024.107712	2024
	Rhodopsin from Haloquadratum walsbyi is a light-driven magnesium transporter.	Ko LN, Lim GZ, Chen JC, Ko T, Li GY, Yang CS.	Nat Commun	10.1038/s41467-025-59795-y	2025
	Ambiguities in and completeness of SAS data analysis of membrane proteins: the case of the sensory rhodopsin II-transducer complex.	Ryzhykau YL, Vlasov AV, Orekhov PS, Rulev MI, Rulev MI, Rogachev AV, Vlasova AD, Kazantsev AS, Verteletskiy DP, Skoi VV, Brennich ME, Pernot P, Murugova TN, Gordeliy VI, Kuklin AI.	Acta Crystallogr D Struct Biol	10.1107/s2059798321009542	2021
Genetics	Genomic language models (gLMs) decode bacterial genomes for improved gene prediction and translation initiation site identification.	Akotenou G, El Allali A.	Brief Bioinform	10.1093/bib/bbaf311	2025
	Light-driven anion-pumping rhodopsin with unique cytoplasmic anion-release mechanism.	Ishizuka T, Suzuki K, Konno M, Shibata K, Kawasaki Y, Akiyama H, Murata T, Inoue K.	J Biol Chem	10.1016/j.jbc.2024.107797	2024
	Structural basis for the prolonged photocycle of sensory rhodopsin II revealed by serial synchrotron crystallography.	Bosman R, Ortolani G, Ghosh S, James D, Norder P, Hammarin G, Ulfarsdottir TB, Ostojic L, Weinert T, Dworkowski F, Tomizaki T, Standfuss J, Branden G, Neutze R.	Nat Commun	10.1038/s41467-025-58263-x	2025
	Elucidation of Expression Patterns and Functional Properties of Archaerhodopsin Derived from Halorubrum sp. Ejinoor.	Chao L, Yang Y.	Biology (Basel)	10.3390/biology14040360	2025
	Low-Temperature Raman Spectroscopy of Halorhodopsin from Natronomonas pharaonis: Structural Discrimination of Blue-Shifted and Red-Shifted Photoproducts.	Fujisawa T, Kiyota H, Kikukawa T, Unno M.	Biochemistry	10.1021/acs.biochem.9b00643	2019
Genetics	Comprehensive whole metagenomics analysis uncovers microbial community and resistome variability across anthropogenically contaminated soils in urban and suburban areas of Tamil Nadu, India.	Vasanthrao R, Nidhin IK, Taj Z, Chattopadhyay I.	Front Microbiol	10.3389/fmicb.2025.1649872	2025
Genetics	Metagenomic insights into the microbial community of the Buhera soda pans, Zimbabwe.	Mangoma N, Zhou N, Ncube T.	BMC Microbiol	10.1186/s12866-024-03655-0	2024
	Emergent biotechnology applications in urology: a mini review.	Liu C, Rivera Ruiz A, Zhang Y, Zimmern P, Li Z.	Front Bioeng Biotechnol	10.3389/fbioe.2025.1539126	2025
Metabolism	Liposome-based measurement of light-driven chloride transport kinetics of halorhodopsin.	Feroz H, Ferlez B, Oh H, Mohammadiarani H, Ren T, Baker CS, Gajewski JP, Lugar DJ, Gaudana SB, Butler P, Huhn J, Lamping M, Parak WJ, Blatt MR, Kerfeld CA, Smirnoff N, Vashisth H, Golbeck JH, Kumar M.	Biochim Biophys Acta Biomembr	10.1016/j.bbamem.2021.183637	2021
	Solid-state NMR for the characterization of retinal chromophore and Schiff base in TAT rhodopsin embedded in membranes under weakly acidic conditions.	Arikawa S, Sugimoto T, Okitsu T, Wada A, Katayama K, Kandori H, Kawamura I.	Biophys Physicobiol	10.2142/biophysico.bppb-v20.s017	2023
Phylogeny	Metataxonomic analysis of halophilic archaea community in two geothermal oases in the southern Tunisian Sahara.	Najjari A, Elmnasri K, Cherif H, Burleigh S, Guesmi A, Mahjoubi M, Linares-Pasten JA, Cherif A, Ouzari HI.	FEMS Microbiol Lett	10.1093/femsle/fnae106	2025
	Natronomonas pharaonis halorhodopsin Ser81 plays a role in maintaining chloride ions near the Schiff base.	Sakajiri Y, Sugano E, Watanabe Y, Sakajiri T, Tabata K, Kikuchi T, Tomita H.	Biochem Biophys Res Commun	10.1016/j.bbrc.2018.06.156	2018
Metabolism	Characterisation of denatured states of sensory rhodopsin II by solution-state NMR.	Tan YL, Mitchell J, Klein-Seetharaman J, Nietlispach D.	J Mol Biol	10.1016/j.jmb.2019.04.039	2019
	Conformational Dynamics of Sensory Rhodopsin II in Nanolipoprotein and Styrene-Maleic Acid Lipid Particles.	Mosslehy W, Voskoboynikova N, Colbasevici A, Ricke A, Klose D, Klare JP, Mulkidjanian AY, Steinhoff HJ.	Photochem Photobiol	10.1111/php.13096	2019
	3D-printed optogenetic neural probe integrated with microfluidic tube for opsin/drug delivery.	Sukesan R, Mohammed M, Oh K, Sharma M, Chaudhury D, Ha S.	Sci Rep	10.1038/s41598-025-13654-4	2025
	Near-Infrared Activation of Sensory Rhodopsin II Mediated by NIR-to-Blue Upconversion Nanoparticles.	Yaguchi M, Jia X, Schlesinger R, Jiang X, Ataka K, Heberle J.	Front Mol Biosci	10.3389/fmolb.2021.782688	2021
	Three-Step Isomerization of the Retinal Chromophore during the Anion Pumping Cycle of Halorhodopsin.	Kouyama T, Ihara K, Maki K, Chan SK.	Biochemistry	10.1021/acs.biochem.8b00631	2018
Metabolism	Microbial Halorhodopsins: Light-Driven Chloride Pumps.	Engelhard C, Chizhov I, Siebert F, Engelhard M.	Chem Rev	10.1021/acs.chemrev.7b00715	2018
Enzymology	Characterization of Denatured States and Reversible Unfolding of Sensory Rhodopsin II.	Tan YL, Mitchell J, Klein-Seetharaman J, Nietlispach D.	J Mol Biol	10.1016/j.jmb.2018.07.031	2018
Pathogenicity	Lipoprotein N-terminal modification in Bacillus: a new paradigm for extracellular acetylation and species-dependent Toll-like receptor 2 immunomodulation.	Komazin G, Wigmore RM, Ranade AM, Rizk AA, Gardiner JH, Meredith TC.	mBio	10.1128/mbio.00996-25	2025
Metabolism	Dcf1 Improves Behavior Deficit in Drosophila and Mice Caused by Optogenetic Suppression.	Liu Q, Gan L, Ni J, Chen Y, Chen Y, Huang Z, Huang X, Wen T.	J Cell Biochem	10.1002/jcb.26048	2017
Enzymology	Protein folding: Funnel model revised.	Roterman I, Slupina M, Konieczny L.	Comput Struct Biotechnol J	10.1016/j.csbj.2024.10.030	2024
	Uncovering the prevalence, key biogenesis enzymes, and biological significance of archaeal lipoproteins.	Hong Y, Makarova KS, Garcia AA, Xu R, Pfeiffer F, Welander PV, Pohlschroder M.	Nat Commun	10.1038/s41467-025-63625-6	2025
Genetics	Microbial diversity analysis of Chumathang geothermal spring, Ladakh, India.	Anu K, Kumari S, Choudhary G, Devi S.	Braz J Microbiol	10.1007/s42770-024-01284-3	2024
	Microbial Proteins as Novel Industrial Biotechnology Hosts to Treat Epilepsy.	Amtul Z, Aziz AA.	Mol Neurobiol	10.1007/s12035-016-0279-3	2017
	Conformational states of HAMP domains interacting with sensory rhodopsin membrane systems: an integrated all-atom and coarse-grained molecular dynamics simulation approach.	Sahoo BR, Fujiwara T.	Mol Biosyst	10.1039/c6mb00730a	2016
Genetics	Metagenomics insight into Puga geothermal geyser located in Himalayan Geothermal Belt (Trans-Himalayan Plateau) Ladakh, India.	Kumari S, Choudhary G, Anu K, Devi S.	Braz J Microbiol	10.1007/s42770-024-01408-9	2024
	The lateral habenula contributes to regulation of body temperature.	Wang X, Chen X, Zhang Z, Liu X, Lv Q, Song M, Zhao D, Su J, Su Y, Zhao G, Sun J, Lin W, Zhao H.	iScience	10.1016/j.isci.2025.112923	2025
	Genetic identification of acetyl-CoA synthetases involved in acetate activation in Haloferax mediterranei.	Mitra R, Xu Y, Lin L, Guo J, Xu T, Zhou M, Guo F, Li H, Xiang H, Han J.	Appl Environ Microbiol	10.1128/aem.01843-24	2025
Metabolism	The effects of chloride ion binding on the photochemical properties of sensory rhodopsin II from Natronomonas pharaonis.	Tamogami J, Iwano K, Matsuyama A, Kikukawa T, Demura M, Nara T, Kamo N.	J Photochem Photobiol B	10.1016/j.jphotobiol.2014.10.010	2014
	Transient Conformational Changes of Sensory Rhodopsin II Investigated by Vibrational Stark Effect Probes.	Mohrmann H, Kube I, Lorenz-Fonfria VA, Engelhard M, Heberle J.	J Phys Chem B	10.1021/acs.jpcb.6b01900	2016
Metabolism	The role of retinal light induced dipole in halorhodopsin structural alteration.	Dutta S, Hirshfeld A, Sheves M.	FEBS Lett	10.1016/j.febslet.2015.10.005	2015
	Perspective on the Effect of Membrane Mimetics on Dynamic Properties of Integral Membrane Proteins.	Sahu ID, Lorigan GA.	J Phys Chem B	10.1021/acs.jpcb.2c07324	2023
	Tools and methods for cell ablation and cell inhibition in Caenorhabditis elegans.	Rentsch D, Bergs A, Shao J, Elvers N, Ruse C, Seidenthal M, Aoki I, Gottschalk A.	Genetics	10.1093/genetics/iyae119	2025
Metabolism	Role of Thr218 in the light-driven anion pump halorhodopsin from Natronomonas pharaonis.	Shibasaki K, Shigemura H, Kikukawa T, Kamiya M, Aizawa T, Kawano K, Kamo N, Demura M.	Biochemistry	10.1021/bi401295e	2013
	Effect of a bound anion on the structure and dynamics of halorhodopsin from Natronomonas pharaonis.	Mizuno M, Shimoo Y, Kandori H, Mizutani Y.	Struct Dyn	10.1063/1.5125621	2019
	A bibliometric profile of optogenetics: quantitative and qualitative analyses.	Zhou Z, Wang X, Li X, Liao L.	Front Neurosci	10.3389/fnins.2023.1221316	2023
	Diversity and Potential Multifunctionality of Archaeal CetZ Tubulin-like Cytoskeletal Proteins.	Brown HJ, Duggin IG.	Biomolecules	10.3390/biom13010134	2023
	Lipid Dynamics in Diisobutylene-Maleic Acid (DIBMA) Lipid Particles in Presence of Sensory Rhodopsin II.	Voskoboynikova N, Orekhov P, Bozdaganyan M, Kodde F, Rademacher M, Schowe M, Budke-Gieseking A, Brickwedde B, Psathaki OE, Mulkidjanian AY, Cosentino K, Shaitan KV, Steinhoff HJ.	Int J Mol Sci	10.3390/ijms22052548	2021
Metabolism	Thermodynamic parameters of anion binding to halorhodopsin from Natronomonas pharaonis by isothermal titration calorimetry.	Hayashi S, Tamogami J, Kikukawa T, Okamoto H, Shimono K, Miyauchi S, Demura M, Nara T, Kamo N.	Biophys Chem	10.1016/j.bpc.2013.01.001	2013
Genetics	The biosynthesis mechanism of bacterioruberin in halophilic archaea revealed by genome and transcriptome analysis.	Ma Y, Sun Z, Yang H, Xie W, Song M, Zhang B, Sui L.	Appl Environ Microbiol	10.1128/aem.00540-24	2024
	Cation binding to halorhodopsin.	Dutta S, Weiner L, Sheves M.	Biochemistry	10.1021/acs.biochem.5b00039	2015
Enzymology	Engineered-membranes and engineered-micelles as efficient tools for purification of halorhodopsin and bacteriorhodopsin.	Dutta S, Nair DK, Namboothiri IN, Wachtel E, Friedman N, Sheves M, Patchornik G.	Analyst	10.1039/c4an01423e	2015
	A Comprehensive Narrative Review of Neuropathic Pain: From Pathophysiology to Surgical Treatment.	Lima Pessoa B, Hauwanga WN, Thomas A, Valentim G, McBenedict B.	Cureus	10.7759/cureus.58025	2024
	Characteristics of halorhodopsin-bacterioruberin complex from Natronomonas pharaonis membrane in the solubilized system.	Sasaki T, Razak NW, Kato N, Mukai Y.	Biochemistry	10.1021/bi201876p	2012
Metabolism	Biochemical properties of glycerol kinase from the hypersaline-adapted archaeon Haloferax volcanii.	Sanchez KM, Maupin-Furlow JA.	Appl Environ Microbiol	10.1128/aem.00886-25	2025
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	Spectroscopic Characterization of Halorhodopsin Reconstituted into Nanodisks Using Native Lipids.	Yamamoto A, Tsukamoto T, Suzuki K, Hashimoto E, Kobashigawa Y, Shibasaki K, Uchida T, Inagaki F, Demura M, Ishimori K.	Biophys J	10.1016/j.bpj.2020.04.021	2020
	Challenges and opportunities in next-generation LED therapeutic devices.	Wang C, Yu Q, Li M, Chen H, Fan H, Ma Y, Zhang Z, Wu MX, Lu M.	Light Sci Appl	10.1038/s41377-025-01990-z	2025
Metabolism	Light-induced silencing of neural activity in Rosa26 knock-in and BAC transgenic mice conditionally expressing the microbial halorhodopsin eNpHR3.	Imayoshi I, Tabuchi S, Matsumoto M, Kitano S, Miyachi H, Kageyama R, Yamanaka A.	Sci Rep	10.1038/s41598-020-59984-3	2020
	Ground state structure of D75N mutant of sensory rhodopsin II in complex with its cognate transducer.	Ishchenko A, Round E, Borshchevskiy V, Grudinin S, Gushchin I, Klare JP, Balandin T, Remeeva A, Engelhard M, Buldt G, Gordeliy V.	J Photochem Photobiol B	10.1016/j.jphotobiol.2013.03.008	2013
	Thalamo-hippocampal pathway determines aggression and self-harm.	Jung J, You IJ, Shin S.	Sci Adv	10.1126/sciadv.ady5540	2025
	UV photoreactions of the extremely haloalkaliphilic euryarchaeon Natronomonas pharaonis.	Moeller R, Reitz G, Douki T, Cadet J, Horneck G, Stan-Lotter H.	FEMS Microbiol Ecol	10.1111/j.1574-6941.2010.00893.x	2010
Metabolism	Degradation of channelopsin-2 in the absence of retinal and degradation resistance in certain mutants.	Ullrich S, Gueta R, Nagel G.	Biol Chem	10.1515/hsz-2012-0256	2013
	Involvement of ArlI, ArlJ, and CirA in archaeal type IV pilin-mediated motility regulation.	Chatterjee P, Garcia MA, Cote JA, Yun K, Legerme GP, Habib R, Tripepi M, Young C, Kulp D, Dyall-Smith M, Pohlschroder M.	J Bacteriol	10.1128/jb.00089-24	2024
	Distinct septo-hippocampal cholinergic projections separately mediate stress-induced emotional and cognitive deficits.	Wu JL, Li ZM, Chen H, Chen WJ, Hu NY, Jin SY, Li XW, Chen YH, Yang JM, Gao TM.	Sci Adv	10.1126/sciadv.ado1508	2024
Metabolism	A Unique Light-Driven Proton Transportation Signal in Halorhodopsin from Natronomonas pharaonis.	Chen XR, Huang YC, Yi HP, Yang CS.	Biophys J	10.1016/j.bpj.2016.11.003	2016
	Optogenetic approaches to therapy for inherited retinal degenerations.	De Silva SR, Moore AT.	J Physiol	10.1113/jp282076	2022
	Comparative simulations of the ground state and the M-intermediate state of the sensory rhodopsin II-transducer complex with a HAMP domain model.	Nishikata K, Ikeguchi M, Kidera A.	Biochemistry	10.1021/bi300696b	2012
	Retinal-Carotenoid Interactions in a Sodium-Ion-Pumping Rhodopsin: Implications on Oligomerization and Thermal Stability.	Ghosh M, Misra R, Bhattacharya S, Majhi K, Jung KH, Sheves M.	J Phys Chem B	10.1021/acs.jpcb.2c07502	2023
	Chimeric microbial rhodopsins for optical activation of Gs-proteins.	Yoshida K, Yamashita T, Sasaki K, Inoue K, Shichida Y, Kandori H.	Biophys Physicobiol	10.2142/biophysico.14.0_183	2017
	Application of a sensitive near-field microwave microprobe to the nondestructive characterization of microbial rhodopsin.	Kim S, Yoon Y, Lee H, Choi AR, Jung KH, Babajanyan A, Abrahamyan T, Yoo H, Lee JH, Cha D, Berthiau G, Friedman B, Lee K.	J Biophotonics	10.1002/jbio.201100143	2013
	Solution NMR studies of integral polytopic alpha-helical membrane proteins: the structure determination of the seven-helix transmembrane receptor sensory rhodopsin II, pSRII.	Gautier A, Nietlispach D.	Methods Mol Biol	10.1007/978-1-62703-023-6_3	2012
	Crystal structure of the light-driven chloride pump halorhodopsin from Natronomonas pharaonis.	Kouyama T, Kanada S, Takeguchi Y, Narusawa A, Murakami M, Ihara K.	J Mol Biol	10.1016/j.jmb.2009.11.061	2010
	Optogenetic inhibition of Purkinje cell activity reveals cerebellar control of blood pressure during postural alterations in anesthetized rats.	Tsubota T, Ohashi Y, Tamura K, Miyashita Y.	Neuroscience	10.1016/j.neuroscience.2012.03.014	2012
	Optogenetics: Therapeutic spark in neuropathic pain.	Liu K, Wang L.	Bosn J Basic Med Sci	10.17305/bjbms.2019.4114	2019
	Optogenetic Suppression of Lateral Septum Somatostatin Neurons Enhances Hippocampus Cholinergic Theta Oscillations and Local Synchrony.	Espinosa N, Alonso A, Caneo M, Moran C, Fuentealba P.	Brain Sci	10.3390/brainsci13010001	2022
Metabolism	Photo-induced bleaching of sensory rhodopsin II (phoborhodopsin) from Halobacterium salinarum by hydroxylamine: identification of the responsible intermediates.	Tamogami J, Kikukawa T, Ikeda Y, Demura M, Nara T, Kamo N.	J Photochem Photobiol B	10.1016/j.jphotobiol.2011.10.009	2012
Metabolism	Aldehyde dehydrogenase of the haloalkaliphilic archaeon Natronomonas pharaonis and its function in ethanol metabolism.	Cao Y, Liao L, Xu XW, Oren A, Wu M.	Extremophiles	10.1007/s00792-008-0187-1	2008
	Halorhodopsin from natronomonas pharaonis forms a trimer even in the presence of a detergent, dodecyl-beta-D-maltoside.	Sasaki T, Kubo M, Kikukawa T, Kamiya M, Aizawa T, Kawano K, Kamo N, Demura M.	Photochem Photobiol	10.1111/j.1751-1097.2008.00406.x	2009
Metabolism	Active state of sensory rhodopsin II: structural determinants for signal transfer and proton pumping.	Gushchin I, Reshetnyak A, Borshchevskiy V, Ishchenko A, Round E, Grudinin S, Engelhard M, Buldt G, Gordeliy V.	J Mol Biol	10.1016/j.jmb.2011.07.022	2011
	Optical inactivation of the anterior cingulate cortex modulate descending pain pathway in a rat model of trigeminal neuropathic pain created via chronic constriction injury of the infraorbital nerve.	Moon HC, Heo WI, Kim YJ, Lee D, Won SY, Kim HR, Ha SM, Lee YJ, Park YS.	J Pain Res	10.2147/jpr.s138626	2017
Metabolism	Transmembrane signal transduction in archaeal phototaxis: the sensory rhodopsin II-transducer complex studied by electron paramagnetic resonance spectroscopy.	Klare JP, Bordignon E, Engelhard M, Steinhoff HJ.	Eur J Cell Biol	10.1016/j.ejcb.2011.04.013	2011
Metabolism	Direct auditory cortical input to the lateral periaqueductal gray controls sound-driven defensive behavior.	Wang H, Chen J, Xu X, Sun WJ, Chen X, Zhao F, Luo MH, Liu C, Guo Y, Xie W, Zhong H, Bai T, Tian Y, Mao Y, Ye C, Tao W, Li J, Farzinpour Z, Li J, Zhou JN, Wang K, He J, Chen L, Zhang Z.	PLoS Biol	10.1371/journal.pbio.3000417	2019
	Structure of a retinal chromophore of dark-adapted middle rhodopsin as studied by solid-state nuclear magnetic resonance spectroscopy.	Kawamura I, Seki H, Tajima S, Makino Y, Shigeta A, Okitsu T, Wada A, Naito A, Sudo Y.	Biophys Physicobiol	10.2142/biophysico.bppb-v18.019	2021
Metabolism	Oligomeric states of microbial rhodopsins determined by high-speed atomic force microscopy and circular dichroic spectroscopy.	Shibata M, Inoue K, Ikeda K, Konno M, Singh M, Kataoka C, Abe-Yoshizumi R, Kandori H, Uchihashi T.	Sci Rep	10.1038/s41598-018-26606-y	2018
	Structural characteristics around the beta-ionone ring of the retinal chromophore in Salinibacter sensory rhodopsin I.	Irieda H, Reissig L, Kawanabe A, Homma M, Kandori H, Sudo Y.	Biochemistry	10.1021/bi200284s	2011
Metabolism	Characterization of alcohol dehydrogenase from the haloalkaliphilic archaeon Natronomonas pharaonis.	Cao Y, Liao L, Xu XW, Oren A, Wang C, Zhu XF, Wu M.	Extremophiles	10.1007/s00792-007-0133-7	2008
	Major Contribution of Somatostatin-Expressing Interneurons and Cannabinoid Receptors to Increased GABA Synaptic Activity in the Striatum of Huntington's Disease Mice.	Holley SM, Galvan L, Kamdjou T, Dong A, Levine MS, Cepeda C.	Front Synaptic Neurosci	10.3389/fnsyn.2019.00014	2019
	Spin labeling EPR.	Klare JP, Steinhoff HJ.	Photosynth Res	10.1007/s11120-009-9490-7	2009
Metabolism	Spectroscopic evidence for the formation of an N intermediate during the photocycle of sensory rhodopsin II (phoborhodopsin) from Natronobacterium pharaonis.	Tateishi Y, Abe T, Tamogami J, Nakao Y, Kikukawa T, Kamo N, Unno M.	Biochemistry	10.1021/bi1019572	2011
Metabolism	Structural analysis of the phototactic transducer protein HtrII linker region from Natronomonas pharaonis.	Hayashi K, Sudo Y, Jee J, Mishima M, Hara H, Kamo N, Kojima C.	Biochemistry	10.1021/bi701837n	2007
Metabolism	Role of the HAMP domain region of sensory rhodopsin transducers in signal transduction.	Gushchin IY, Gordeliy VI, Grudinin S.	Biochemistry	10.1021/bi101032a	2011
Metabolism	Overexpression of Different Types of Microbial Rhodopsins with a Highly Expressible Bacteriorhodopsin from Haloarcula marismortui as a Single Protein in E. coli.	Tu CH, Yi HP, Hsieh SY, Lin HS, Yang CS.	Sci Rep	10.1038/s41598-018-32399-x	2018
	The photocycle of channelrhodopsin-2: ultrafast reaction dynamics and subsequent reaction steps.	Verhoefen MK, Bamann C, Blocher R, Forster U, Bamberg E, Wachtveitl J.	Chemphyschem	10.1002/cphc.201000181	2010
	Optogenetic Manipulations of Amygdala Neurons Modulate Spinal Nociceptive Processing and Behavior Under Normal Conditions and in an Arthritis Pain Model.	Mazzitelli M, Marshall K, Pham A, Ji G, Neugebauer V.	Front Pharmacol	10.3389/fphar.2021.668337	2021
	Complex formation and light activation in membrane-embedded sensory rhodopsin II as seen by solid-state NMR spectroscopy.	Etzkorn M, Seidel K, Li L, Martell S, Geyer M, Engelhard M, Baldus M.	Structure	10.1016/j.str.2010.01.011	2010
	Expression of the halobacterial transducer protein HtrII from Natronomonas pharaonis in Escherichia coli.	Mennes N, Klare JP, Chizhov I, Seidel R, Schlesinger R, Engelhard M.	FEBS Lett	10.1016/j.febslet.2007.03.005	2007
Metabolism	Genome-wide proteomics of Natronomonas pharaonis.	Konstantinidis K, Tebbe A, Klein C, Scheffer B, Aivaliotis M, Bisle B, Falb M, Pfeiffer F, Siedler F, Oesterhelt D.	J Proteome Res	10.1021/pr060352q	2007
	Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis.	Aivaliotis M, Gevaert K, Falb M, Tebbe A, Konstantinidis K, Bisle B, Klein C, Martens L, Staes A, Timmerman E, Van Damme J, Siedler F, Pfeiffer F, Vandekerckhove J, Oesterhelt D.	J Proteome Res	10.1021/pr0700347	2007
	Molecular impact of the membrane potential on the regulatory mechanism of proton transfer in sensory rhodopsin II.	Jiang X, Engelhard M, Ataka K, Heberle J.	J Am Chem Soc	10.1021/ja102295g	2010
	Spin labeling of Natronomonas pharaonis halorhodopsin: probing the cysteine residues environment.	Mevorat-Kaplan K, Weiner L, Sheves M.	J Phys Chem B	10.1021/jp054750c	2006
	Analysis of light-induced conformational changes of Natronomonas pharaonis sensory rhodopsin II by time resolved electron paramagnetic resonance spectroscopy.	Bordignon E, Klare JP, Holterhues J, Martell S, Krasnaberski A, Engelhard M, Steinhoff HJ.	Photochem Photobiol	10.1562/2006-07-05-ra-960	2007
	Effect of chloride binding on the thermal trimer-monomer conversion of halorhodopsin in the solubilized system.	Sasaki T, Aizawa T, Kamiya M, Kikukawa T, Kawano K, Kamo N, Demura M.	Biochemistry	10.1021/bi901380c	2009
	Optogenetics in Understanding Mechanisms of Acute Kidney Injury.	Tanaka S, Okusa MD.	Nephron	10.1159/000491498	2018
	Signaling and Adaptation Modulate the Dynamics of the Photosensoric Complex of Natronomonas pharaonis.	Orekhov PS, Klose D, Mulkidjanian AY, Shaitan KV, Engelhard M, Klare JP, Steinhoff HJ.	PLoS Comput Biol	10.1371/journal.pcbi.1004561	2015
Metabolism	Sensory rhodopsin II/transducer complex formation in detergent and in lipid bilayers studied with FRET.	Kriegsmann J, Brehs M, Klare JP, Engelhard M, Fitter J.	Biochim Biophys Acta	10.1016/j.bbamem.2008.11.011	2009
	Crystal structure of Halobacterium salinarum halorhodopsin with a partially depopulated primary chloride-binding site.	Schreiner M, Schlesinger R, Heberle J, Niemann HH.	Acta Crystallogr F Struct Biol Commun	10.1107/s2053230x16012796	2016
	Transducer binding establishes localized interactions to tune sensory rhodopsin II.	Cisneros DA, Oberbarnscheidt L, Pannier A, Klare JP, Helenius J, Engelhard M, Oesterhelt F, Muller DJ.	Structure	10.1016/j.str.2008.04.014	2008
	Signal transfer in haloarchaeal sensory rhodopsin- transducer complexes.	Sasaki J, Spudich JL.	Photochem Photobiol	10.1111/j.1751-1097.2008.00314.x	2008
	The hidden simplicity of metabolic networks is revealed by multireaction dependencies.	Kuken A, Langary D, Nikoloski Z.	Sci Adv	10.1126/sciadv.abl6962	2022
	Molecular modeling of the HAMP domain of sensory rhodopsin II transducer from Natronomonas pharaonis.	Nishikata K, Fuchigami S, Ikeguchi M, Kidera A.	Biophysics (Nagoya-shi)	10.2142/biophysics.6.27	2010
	HwMR is a novel magnesium-associated protein.	Ko LN, Lim GZ, Chen XR, Cai CJ, Liu KT, Yang CS.	Biophys J	10.1016/j.bpj.2022.06.010	2022
Metabolism	The distinct signaling mechanisms of microbial sensory rhodopsins in Archaea, Eubacteria and Eukarya.	Jung KH.	Photochem Photobiol	10.1562/2006-03-20-ir-853	2007
Phylogeny	Lipid biomarker and phylogenetic analyses to reveal archaeal biodiversity and distribution in hypersaline microbial mat and underlying sediment.	Jahnke LL, Orphan VJ, Embaye T, Turk KA, Kubo MD, Summons RE, DES Marais DJ.	Geobiology	10.1111/j.1472-4669.2008.00165.x	2008
Enzymology	Extraction and reconstitution of membrane proteins into lipid nanodiscs encased by zwitterionic styrene-maleic amide copolymers.	Fiori MC, Zheng W, Kamilar E, Simiyu G, Altenberg GA, Liang H.	Sci Rep	10.1038/s41598-020-66852-7	2020
Metabolism	Constitutive activity in chimeras and deletions localize sensory rhodopsin II/HtrII signal relay to the membrane-inserted domain.	Sasaki J, Nara T, Spudich EN, Spudich JL.	Mol Microbiol	10.1111/j.1365-2958.2007.05983.x	2007
Metabolism	Multimodal fast optical interrogation of neural circuitry.	Zhang F, Wang LP, Brauner M, Liewald JF, Kay K, Watzke N, Wood PG, Bamberg E, Nagel G, Gottschalk A, Deisseroth K.	Nature	10.1038/nature05744	2007
	Development of a rapid Buffer-exchange system for time-resolved ATR-FTIR spectroscopy with the step-scan mode.	Furutani Y, Kimura T, Okamoto K.	Biophysics (Nagoya-shi)	10.2142/biophysics.9.123	2013
	The trans-cis isomerization reaction dynamics in sensory rhodopsin II by femtosecond time-resolved midinfrared spectroscopy: chromophore and protein dynamics.	Diller R, Jakober R, Schumann C, Peters F, Klare JP, Engelhard M.	Biopolymers	10.1002/bip.20475	2006
Metabolism	The cytoplasmic membrane-proximal domain of the HtrII transducer interacts with the E-F loop of photoactivated Natronomonas pharaonis sensory rhodopsin II.	Yang CS, Sineshchekov O, Spudich EN, Spudich JL.	J Biol Chem	10.1074/jbc.m406504200	2004
	Optimized photo-stimulation of halorhodopsin for long-term neuronal inhibition.	Zhang C, Yang S, Flossmann T, Gao S, Witte OW, Nagel G, Holthoff K, Kirmse K.	BMC Biol	10.1186/s12915-019-0717-6	2019
Metabolism	Interaction of the halobacterial transducer to a halorhodopsin mutant engineered so as to bind the transducer: Cl- circulation within the extracellular channel.	Hasegawa C, Kikukawa T, Miyauchi S, Seki A, Sudo Y, Kubo M, Demura M, Kamo N.	Photochem Photobiol	10.1562/2006-06-09-ra-916	2007
	The Prospects for Retinal Organoids in Treatment of Retinal Diseases.	Xue Y, Lin B, Chen JT, Tang WC, Browne AW, Seiler MJ.	Asia Pac J Ophthalmol (Phila)	10.1097/apo.0000000000000538	2022
Metabolism	Dynamics of light-induced conformational changes of the phoborhodopsin/transducer complex formed in the n-dodecyl beta-D-maltoside micelle.	Taniguchi Y, Ikehara T, Kamo N, Yamasaki H, Toyoshima Y.	Biochemistry	10.1021/bi602482s	2007
	Blue-shifted ancyromonad channelrhodopsins for multiplex optogenetics.	Govorunova EG, Sineshchekov OA, Li H, Gou Y, Chen H, Yang S, Wang Y, Mitchell S, Palmateer A, Brown LS, St-Pierre F, Xue M, Spudich JL.	Elife	10.7554/elife.106508	2025
	Membrane Protein Activity Induces Specific Molecular Changes in Nanodiscs Monitored by FTIR Difference Spectroscopy.	Baserga F, Vorkas A, Crea F, Schubert L, Chen JL, Redlich A, La Greca M, Storm J, Oldemeyer S, Hoffmann K, Schlesinger R, Heberle J.	Front Mol Biosci	10.3389/fmolb.2022.915328	2022
	Application of fluorescence resonance energy transfer (FRET) to investigation of light-induced conformational changes of the phoborhodopsin/transducer complex.	Taniguchi Y, Ikehara T, Kamo N, Watanabe Y, Yamasaki H, Toyoshima Y.	Photochem Photobiol	10.1562/2006-06-15-ra-922	2007
	Molecular mechanisms and evolutionary robustness of a color switch in proteorhodopsins.	Mao J, Jin X, Shi M, Heidenreich D, Brown LJ, Brown RCD, Lelli M, He X, Glaubitz C.	Sci Adv	10.1126/sciadv.adj0384	2024
	The Basolateral Amygdala to Ventral Hippocampus Circuit Controls Anxiety-Like Behaviors Induced by Morphine Withdrawal.	Deji C, Yan P, Ji Y, Yan X, Feng Y, Liu J, Liu Y, Wei S, Zhu Y, Lai J.	Front Cell Neurosci	10.3389/fncel.2022.894886	2022
	Electrostatic interactions and hydrogen bond dynamics in chloride pumping by halorhodopsin.	Jardon-Valadez E, Bondar AN, Tobias DJ.	Biochim Biophys Acta	10.1016/j.bbabio.2014.09.006	2014
Pathogenicity	Effect of anions on the photocycle of halorhodopsin. Substitution of chloride with formate anion.	Mevorat-Kaplan K, Brumfeld V, Engelhard M, Sheves M.	Biochemistry	10.1021/bi051323g	2005
	Optogenetic Control of Neural Circuits in the Mongolian Gerbil.	Keplinger S, Beiderbeck B, Michalakis S, Biel M, Grothe B, Kunz L.	Front Cell Neurosci	10.3389/fncel.2018.00111	2018
	Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling.	Ahrendt SR, Medina EM, Chang CA, Stajich JE.	PeerJ	10.7717/peerj.3206	2017
	Effects of solubilization on the structure and function of the sensory rhodopsin II/transducer complex.	Klare JP, Bordignon E, Doebber M, Fitter J, Kriegsmann J, Chizhov I, Steinhoff HJ, Engelhard M.	J Mol Biol	10.1016/j.jmb.2005.12.015	2006
Metabolism	Archaeal N-terminal protein maturation commonly involves N-terminal acetylation: a large-scale proteomics survey.	Falb M, Aivaliotis M, Garcia-Rizo C, Bisle B, Tebbe A, Klein C, Konstantinidis K, Siedler F, Pfeiffer F, Oesterhelt D.	J Mol Biol	10.1016/j.jmb.2006.07.086	2006
Metabolism	Development of the signal in sensory rhodopsin and its transfer to the cognate transducer.	Moukhametzianov R, Klare JP, Efremov R, Baeken C, Goppner A, Labahn J, Engelhard M, Buldt G, Gordeliy VI.	Nature	10.1038/nature04520	2006
Metabolism	Ser(262) determines the chloride-dependent colour tuning of a new halorhodopsin from Haloquadratum walsbyi.	Fu HY, Chang YN, Jheng MJ, Yang CS.	Biosci Rep	10.1042/bsr20120054	2012
	Regulatory Elements for Gene Therapy of Epilepsy.	Chesnokova E, Bal N, Alhalabi G, Balaban P.	Cells	10.3390/cells14030236	2025
	Rhizosphere-dwelling halophilic archaea: a potential candidate for alleviating salinity-associated stress in agriculture.	Naitam MG, Ramakrishnan B, Grover M, Kaushik R.	Front Microbiol	10.3389/fmicb.2023.1212349	2023
	Structural analysis of a HAMP domain: the linker region of the phototransducer in complex with sensory rhodopsin II.	Bordignon E, Klare JP, Doebber M, Wegener AA, Martell S, Engelhard M, Steinhoff HJ.	J Biol Chem	10.1074/jbc.m509391200	2005
	Photoactivation perturbs the membrane-embedded contacts between sensory rhodopsin II and its transducer.	Bergo VB, Spudich EN, Rothschild KJ, Spudich JL.	J Biol Chem	10.1074/jbc.m505555200	2005
	The archaeal sensory rhodopsin II/transducer complex: a model for transmembrane signal transfer.	Klare JP, Gordeliy VI, Labahn J, Buldt G, Steinhoff HJ, Engelhard M.	FEBS Lett	10.1016/s0014-5793(04)00193-0	2004
Metabolism	Light-Driven Chloride Transport Kinetics of Halorhodopsin.	Feroz H, Ferlez B, Lefoulon C, Ren T, Baker CS, Gajewski JP, Lugar DJ, Gaudana SB, Butler PJ, Huhn J, Lamping M, Parak WJ, Hibberd JM, Kerfeld CA, Smirnoff N, Blatt MR, Golbeck JH, Kumar M.	Biophys J	10.1016/j.bpj.2018.06.009	2018
	Light-induced intramolecular charge movements in microbial rhodopsins in intact E. coli cells.	Sineshchekov OA, Spudich JL.	Photochem Photobiol Sci	10.1039/b316207a	2004
	Flexibility of the cytoplasmic domain of the phototaxis transducer II from Natronomonas pharaonis.	Budyak IL, Mironova OS, Yanamala N, Manoharan V, Buldt G, Schlesinger R, Klein-Seetharaman J.	J Biophys	10.1155/2008/267912	2008
	Thalamocortical Circuit Controls Neuropathic Pain via Up-regulation of HCN2 in the Ventral Posterolateral Thalamus.	Yan Y, Zhu M, Cao X, Xu G, Shen W, Li F, Zhang J, Luo L, Zhang X, Zhang D, Liu T.	Neurosci Bull	10.1007/s12264-022-00989-5	2023
Metabolism	Photostimulation of a sensory rhodopsin II/HtrII/Tsr fusion chimera activates CheA-autophosphorylation and CheY-phosphotransfer in vitro.	Trivedi VD, Spudich JL.	Biochemistry	10.1021/bi034399q	2003
Phylogeny	A Combined Digital PCR and Next Generation DNA-Sequencing Based Approach for Tracking Nearshore Pollutant Dynamics Along the Southwest United States/Mexico Border.	Zimmer-Faust AG, Steele JA, Xiong X, Staley C, Griffith M, Sadowsky MJ, Diaz M, Griffith JF.	Front Microbiol	10.3389/fmicb.2021.674214	2021
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Metabolism	Functional expression of the eukaryotic proton pump rhodopsin OmR2 in Escherichia coli and its photochemical characterization.	Kikuchi M, Kojima K, Nakao S, Yoshizawa S, Kawanishi S, Shibukawa A, Kikukawa T, Sudo Y.	Sci Rep	10.1038/s41598-021-94181-w	2021
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	The anterior cingulate cortex projection to the dorsomedial striatum modulates hyperalgesia in a chronic constriction injury mouse model.	Zhuang X, Huang L, Gu Y, Wang L, Zhang R, Zhang M, Li F, Shi Y, Mo Y, Dai Q, Wei C, Wang J.	Arch Med Sci	10.5114/aoms.2019.85202	2021
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Enzymology	Isolation of a chymotrypsinogen B-like enzyme from the archaeon Natronomonas pharaonis and other halobacteria.	Stan-Lotter H, Doppler E, Jarosch M, Radax C, Gruber C, Inatomi KI.	Extremophiles	10.1007/s007920050111	1999
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Enzymology	Non-host class II ribonucleotide reductase in Thermus viruses: sequence adaptation and host interaction.	Loderer C, Holmfeldt K, Lundin D.	PeerJ	10.7717/peerj.6700	2019
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Metabolism	The signal transfer from the receptor NpSRII to the transducer NpHtrII is not hampered by the D75N mutation.	Holterhues J, Bordignon E, Klose D, Rickert C, Klare JP, Martell S, Li L, Engelhard M, Steinhoff HJ.	Biophys J	10.1016/j.bpj.2011.03.017	2011
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Metabolism	Salt-driven equilibrium between two conformations in the HAMP domain from Natronomonas pharaonis: the language of signal transfer?	Doebber M, Bordignon E, Klare JP, Holterhues J, Martell S, Mennes N, Li L, Engelhard M, Steinhoff HJ.	J Biol Chem	10.1074/jbc.m801931200	2008
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	Structure determination of the seven-helix transmembrane receptor sensory rhodopsin II by solution NMR spectroscopy.	Gautier A, Mott HR, Bostock MJ, Kirkpatrick JP, Nietlispach D.	Nat Struct Mol Biol	10.1038/nsmb.1807	2010
	Applicability of Styrene-Maleic Acid Copolymer for Two Microbial Rhodopsins, RxR and HsSRI.	Ueta T, Kojima K, Hino T, Shibata M, Nagano S, Sudo Y.	Biophys J	10.1016/j.bpj.2020.09.026	2020
	Olfactory Optogenetics: Light Illuminates the Chemical Sensing Mechanisms of Biological Olfactory Systems.	Zhu P, Tian Y, Chen Y, Chen W, Wang P, Du L, Wu C.	Biosensors (Basel)	10.3390/bios11090309	2021
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Biotechnology	Biotechnology and Biomaterial-Based Therapeutic Strategies for Age-Related Macular Degeneration. Part II: Cell and Tissue Engineering Therapies.	Jemni-Damer N, Guedan-Duran A, Fuentes-Andion M, Serrano-Bengoechea N, Alfageme-Lopez N, Armada-Maresca F, Guinea GV, Perez-Rigueiro J, Rojo F, Gonzalez-Nieto D, Kaplan DL, Panetsos F.	Front Bioeng Biotechnol	10.3389/fbioe.2020.588014	2020
Genetics	The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment.	Alcaraz LD, Olmedo G, Bonilla G, Cerritos R, Hernandez G, Cruz A, Ramirez E, Putonti C, Jimenez B, Martinez E, Lopez V, Arvizu JL, Ayala F, Razo F, Caballero J, Siefert J, Eguiarte L, Vielle JP, Martinez O, Souza V, Herrera-Estrella A, Herrera-Estrella L.	Proc Natl Acad Sci U S A	10.1073/pnas.0800981105	2008
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	Sec-Dependent Secretion of Subtilase SptE in Haloarchaea Facilitates Its Proper Folding and Heterocatalytic Processing by Halolysin SptA Extracellularly.	Mei S, Li M, Sun Y, Deng X, Chen N, Liu Y, Yin J, Luo H, Wu Y, He D, Gan F, Tang B, Tang XF.	Appl Environ Microbiol	10.1128/aem.00246-22	2022
Genetics	The Exploration of Novel Regulatory Relationships Drives Haloarchaeal Operon-Like Structural Dynamics over Short Evolutionary Distances.	Seitzer P, Yao AI, Cisneros A, Facciotti MT.	Microorganisms	10.3390/microorganisms8121900	2020
Metabolism	Implications for the impairment of the rapid channel closing of Proteomonas sulcata anion channelrhodopsin 1 at high Cl^- concentrations.	Tsukamoto T, Kikuchi C, Suzuki H, Aizawa T, Kikukawa T, Demura M.	Sci Rep	10.1038/s41598-018-31742-6	2018
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Metabolism	Quantitation of the neural silencing activity of anion channelrhodopsins in Caenorhabditis elegans and their applicability for long-term illumination.	Yamanashi T, Maki M, Kojima K, Shibukawa A, Tsukamoto T, Chowdhury S, Yamanaka A, Takagi S, Sudo Y.	Sci Rep	10.1038/s41598-019-44308-x	2019
Metabolism	Light-Activated Dynamic Clamp Using iPSC-Derived Cardiomyocytes.	Quach B, Krogh-Madsen T, Entcheva E, Christini DJ.	Biophys J	10.1016/j.bpj.2018.10.018	2018
	The crystal structures of a chloride-pumping microbial rhodopsin and its proton-pumping mutant illuminate proton transfer determinants.	Besaw JE, Ou WL, Morizumi T, Eger BT, Sanchez Vasquez JD, Chu JHY, Harris A, Brown LS, Miller RJD, Ernst OP.	J Biol Chem	10.1074/jbc.ra120.014118	2020
Metabolism	Basal forebrain somatostatin cells differentially regulate local gamma oscillations and functionally segregate motor and cognitive circuits.	Espinosa N, Alonso A, Lara-Vasquez A, Fuentealba P.	Sci Rep	10.1038/s41598-019-39203-4	2019
	Two distinct states of the HAMP domain from sensory rhodopsin transducer observed in unbiased molecular dynamics simulations.	Gushchin I, Gordeliy V, Grudinin S.	PLoS One	10.1371/journal.pone.0066917	2013
	Microbial light-activatable proton pumps as neuronal inhibitors to functionally dissect neuronal networks in C. elegans.	Husson SJ, Liewald JF, Schultheis C, Stirman JN, Lu H, Gottschalk A.	PLoS One	10.1371/journal.pone.0040937	2012
Metabolism	Dopamine receptor D2, but not D1, mediates descending dopaminergic pathway-produced analgesic effect in a trigeminal neuropathic pain mouse model.	Liu S, Tang Y, Shu H, Tatum D, Bai Q, Crawford J, Xing Y, Lobo MK, Bellinger L, Kramer P, Tao F.	Pain	10.1097/j.pain.0000000000001414	2019
Pathogenicity	Exposure to 1-Butanol Exemplifies the Response of the Thermoacidophilic Archaeon Sulfolobus acidocaldarius to Solvent Stress.	Benninghoff JC, Kuschmierz L, Zhou X, Albersmeier A, Pham TK, Busche T, Wright PC, Kalinowski J, Makarova KS, Brasen C, Flemming HC, Wingender J, Siebers B.	Appl Environ Microbiol	10.1128/aem.02988-20	2021
Metabolism	Complete genome sequence of Halorhodospira halophila SL1.	Challacombe JF, Majid S, Deole R, Brettin TS, Bruce D, Delano SF, Detter JC, Gleasner CD, Han CS, Misra M, Reitenga KG, Mikhailova N, Woyke T, Pitluck S, Nolan M, Land ML, Saunders E, Tapia R, Lapidus A, Ivanova N, Hoff WD.	Stand Genomic Sci	10.4056/sigs.3677284	2013
Metabolism	A novel DNA-binding protein, PhaR, plays a central role in the regulation of polyhydroxyalkanoate accumulation and granule formation in the haloarchaeon Haloferax mediterranei.	Cai S, Cai L, Zhao D, Liu G, Han J, Zhou J, Xiang H.	Appl Environ Microbiol	10.1128/aem.02878-14	2015
Metabolism	Altered Chloride Homeostasis Decreases the Action Potential Threshold and Increases Hyperexcitability in Hippocampal Neurons.	Sorensen AT, Ledri M, Melis M, Nikitidou Ledri L, Andersson M, Kokaia M.	eNeuro	10.1523/eneuro.0172-17.2017	2017
Metabolism	Presence of a Haloarchaeal Halorhodopsin-Like Cl^- Pump in Marine Bacteria.	Nakajima Y, Tsukamoto T, Kumagai Y, Ogura Y, Hayashi T, Song J, Kikukawa T, Demura M, Kogure K, Sudo Y, Yoshizawa S.	Microbes Environ	10.1264/jsme2.me17197	2018
Metabolism	The elusive third subunit IIa of the bacterial B-type oxidases: the enzyme from the hyperthermophile Aquifex aeolicus.	Prunetti L, Brugna M, Lebrun R, Giudici-Orticoni MT, Guiral M.	PLoS One	10.1371/journal.pone.0021616	2011
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Metabolism	Restoration of the majority of the visual spectrum by using modified Volvox channelrhodopsin-1.	Tomita H, Sugano E, Murayama N, Ozaki T, Nishiyama F, Tabata K, Takahashi M, Saito T, Tamai M.	Mol Ther	10.1038/mt.2014.81	2014
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Metabolism	Reaction dynamics of halorhodopsin studied by time-resolved diffusion.	Inoue K, Kubo M, Demura M, Kamo N, Terazima M.	Biophys J	10.1016/j.bpj.2008.12.3932	2009
Metabolism	Unlocking conserved and diverged metabolic characteristics in cassava carbon assimilation via comparative genomics approach.	Siriwat W, Kalapanulak S, Suksangpanomrung M, Saithong T.	Sci Rep	10.1038/s41598-018-34730-y	2018
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Enzymology	A novel clade of unique eukaryotic ribonucleotide reductase R2 subunits is exclusive to apicomplexan parasites.	Munro JB, Jacob CG, Silva JC.	J Mol Evol	10.1007/s00239-013-9583-y	2013
Metabolism	Color Tuning in rhodopsins: the origin of the spectral shift between the chloride-bound and anion-free forms of halorhodopsin.	Ryazantsev MN, Altun A, Morokuma K.	J Am Chem Soc	10.1021/ja3009117	2012
	Auts2 deletion involves in DG hypoplasia and social recognition deficit: The developmental and neural circuit mechanisms.	Li J, Sun X, You Y, Li Q, Wei C, Zhao L, Sun M, Meng H, Zhang T, Yue W, Wang L, Zhang D.	Sci Adv	10.1126/sciadv.abk1238	2022
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	Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3.	Hosaka T, Yoshizawa S, Nakajima Y, Ohsawa N, Hato M, DeLong EF, Kogure K, Yokoyama S, Kimura-Someya T, Iwasaki W, Shirouzu M.	J Biol Chem	10.1074/jbc.m116.728220	2016
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	An optogenetic toolbox designed for primates.	Diester I, Kaufman MT, Mogri M, Pashaie R, Goo W, Yizhar O, Ramakrishnan C, Deisseroth K, Shenoy KV.	Nat Neurosci	10.1038/nn.2749	2011
Metabolism	Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes.	Lomsadze A, Gemayel K, Tang S, Borodovsky M.	Genome Res	10.1101/gr.230615.117	2018
Metabolism	A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators.	Needham DM, Yoshizawa S, Hosaka T, Poirier C, Choi CJ, Hehenberger E, Irwin NAT, Wilken S, Yung CM, Bachy C, Kurihara R, Nakajima Y, Kojima K, Kimura-Someya T, Leonard G, Malmstrom RR, Mende DR, Olson DK, Sudo Y, Sudek S, Richards TA, DeLong EF, Keeling PJ, Santoro AE, Shirouzu M, Iwasaki W, Worden AZ.	Proc Natl Acad Sci U S A	10.1073/pnas.1907517116	2019
	Multiple replication origins of Halobacterium sp. strain NRC-1: properties of the conserved orc7-dependent oriC1.	Coker JA, DasSarma P, Capes M, Wallace T, McGarrity K, Gessler R, Liu J, Xiang H, Tatusov R, Berquist BR, DasSarma S.	J Bacteriol	10.1128/jb.00210-09	2009
	Molecular evolution of troponin I and a role of its N-terminal extension in nematode locomotion.	Barnes DE, Hwang H, Ono K, Lu H, Ono S.	Cytoskeleton (Hoboken)	10.1002/cm.21281	2016
Metabolism	Three strategically placed hydrogen-bonding residues convert a proton pump into a sensory receptor.	Sudo Y, Spudich JL.	Proc Natl Acad Sci U S A	10.1073/pnas.0607467103	2006
Metabolism	eNpHR: a Natronomonas halorhodopsin enhanced for optogenetic applications.	Gradinaru V, Thompson KR, Deisseroth K.	Brain Cell Biol	10.1007/s11068-008-9027-6	2008
	Optogenetics: the new molecular approach to control functions of neural cells in epilepsy, depression and tumors of the central nervous system.	Camporeze B, Manica BA, Bonafe GA, Ferreira JJC, Diniz AL, de Oliveira CTP, Mathias Junior LR, de Aguiar PHP, Ortega MM.	Am J Cancer Res		2018
Metabolism	Thermophilic and halophilic beta-agarase from a halophilic archaeon Halococcus sp. 197A.	Minegishi H, Shimane Y, Echigo A, Ohta Y, Hatada Y, Kamekura M, Maruyama T, Usami R.	Extremophiles	10.1007/s00792-013-0575-z	2013
Metabolism	EvoMining reveals the origin and fate of natural product biosynthetic enzymes.	Selem-Mojica N, Aguilar C, Gutierrez-Garcia K, Martinez-Guerrero CE, Barona-Gomez F.	Microb Genom	10.1099/mgen.0.000260	2019
Metabolism	Crystal structure and functional characterization of a light-driven chloride pump having an NTQ motif.	Kim K, Kwon SK, Jun SH, Cha JS, Kim H, Lee W, Kim JF, Cho HS.	Nat Commun	10.1038/ncomms12677	2016
	Restoration of visual function by transplantation of optogenetically engineered photoreceptors.	Garita-Hernandez M, Lampic M, Chaffiol A, Guibbal L, Routet F, Santos-Ferreira T, Gasparini S, Borsch O, Gagliardi G, Reichman S, Picaud S, Sahel JA, Goureau O, Ader M, Dalkara D, Duebel J.	Nat Commun	10.1038/s41467-019-12330-2	2019
Metabolism	Retinoid production using metabolically engineered Escherichia coli with a two-phase culture system.	Jang HJ, Yoon SH, Ryu HK, Kim JH, Wang CL, Kim JY, Oh DK, Kim SW.	Microb Cell Fact	10.1186/1475-2859-10-59	2011
Metabolism	New approaches for the study of orexin function.	Yamanaka A, Tsunematsu T.	J Neuroendocrinol	10.1111/j.1365-2826.2010.02015.x	2010
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	Native-like membrane models of E. coli polar lipid extract shed light on the importance of lipid composition complexity.	Pluhackova K, Horner A.	BMC Biol	10.1186/s12915-020-00936-8	2021
	Crystallization, X-ray diffraction analysis and SIRAS/molecular-replacenent phasing of three crystal forms of Anabaena sensory rhodopsin transducer.	Vogeley L, Luecke H.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309106008359	2006
	Distribution, structure and diversity of "bacterial" genes encoding two-component proteins in the Euryarchaeota.	Ashby MK.	Archaea	10.1155/2006/562404	2006
Genetics	Molecular characterization of the minimal replicon and the unidirectional theta replication of pSCM201 in extremely halophilic archaea.	Sun C, Zhou M, Li Y, Xiang H.	J Bacteriol	10.1128/jb.00988-06	2006
Metabolism	A predictive computational model of the kinetic mechanism of stimulus-induced transducer methylation and feedback regulation through CheY in archaeal phototaxis and chemotaxis.	Streif S, Oesterhelt D, Marwan W.	BMC Syst Biol	10.1186/1752-0509-4-27	2010
	Distinct Contribution of Granular and Agranular Subdivisions of the Retrosplenial Cortex to Remote Contextual Fear Memory Retrieval.	Tsai TC, Yu TH, Hung YC, Fong LI, Hsu KS.	J Neurosci	10.1523/jneurosci.1303-21.2021	2022
Metabolism	Functional Insights Into Protein Acetylation in the Hyperthermophilic Archaeon Sulfolobus islandicus.	Cao J, Wang T, Wang Q, Zheng X, Huang L.	Mol Cell Proteomics	10.1074/mcp.ra119.001312	2019
	Integral membrane protein structure determination using pseudocontact shifts.	Crick DJ, Wang JX, Graham B, Swarbrick JD, Mott HR, Nietlispach D.	J Biomol NMR	10.1007/s10858-015-9899-6	2015
	Structural and functional similarities between osmotin from Nicotiana tabacum seeds and human adiponectin.	Miele M, Costantini S, Colonna G.	PLoS One	10.1371/journal.pone.0016690	2011
Metabolism	Mutational and bioinformatic analysis of haloarchaeal lipobox-containing proteins.	Storf S, Pfeiffer F, Dilks K, Chen ZQ, Imam S, Pohlschroder M.	Archaea	10.1155/2010/410975	2010
Metabolism	A Chimera Na+-Pump Rhodopsin as an Effective Optogenetic Silencer.	Hoque MR, Ishizuka T, Inoue K, Abe-Yoshizumi R, Igarashi H, Mishima T, Kandori H, Yawo H.	PLoS One	10.1371/journal.pone.0166820	2016
Metabolism	Activation of acid-sensing ion channels by localized proton transient reveals their role in proton signaling.	Zeng WZ, Liu DS, Liu L, She L, Wu LJ, Xu TL.	Sci Rep	10.1038/srep14125	2015
Metabolism	Rhodopsin-mediated photoreception in cryptophyte flagellates.	Sineshchekov OA, Govorunova EG, Jung KH, Zauner S, Maier UG, Spudich JL.	Biophys J	10.1529/biophysj.105.070920	2005
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Metabolism	An extremely halophilic proteobacterium combines a highly acidic proteome with a low cytoplasmic potassium content.	Deole R, Challacombe J, Raiford DW, Hoff WD.	J Biol Chem	10.1074/jbc.m112.420505	2013
	Bidirectional modulation of anxiety-related and social behaviors by amygdala projections to the medial prefrontal cortex.	Felix-Ortiz AC, Burgos-Robles A, Bhagat ND, Leppla CA, Tye KM.	Neuroscience	10.1016/j.neuroscience.2015.07.041	2016
	Role of a helix B lysine residue in the photoactive site in channelrhodopsins.	Li H, Govorunova EG, Sineshchekov OA, Spudich JL.	Biophys J	10.1016/j.bpj.2014.03.002	2014
	Optogenetic dissection reveals multiple rhythmogenic modules underlying locomotion.	Hagglund M, Dougherty KJ, Borgius L, Itohara S, Iwasato T, Kiehn O.	Proc Natl Acad Sci U S A	10.1073/pnas.1304365110	2013
Metabolism	An Approach to Heterologous Expression of Membrane Proteins. The Case of Bacteriorhodopsin.	Bratanov D, Balandin T, Round E, Shevchenko V, Gushchin I, Polovinkin V, Borshchevskiy V, Gordeliy V.	PLoS One	10.1371/journal.pone.0128390	2015
	Chloride dynamics alter the input-output properties of neurons.	Currin CB, Trevelyan AJ, Akerman CJ, Raimondo JV.	PLoS Comput Biol	10.1371/journal.pcbi.1007932	2020
Metabolism	Molecular analyses of a three-subunit euryarchaeal clamp loader complex from Methanosarcina acetivorans.	Chen YH, Lin Y, Yoshinaga A, Chhotani B, Lorenzini JL, Crofts AA, Mei S, Mackie RI, Ishino Y, Cann IK.	J Bacteriol	10.1128/jb.00414-09	2009
Metabolism	Identification of the haloarchaeal phasin (PhaP) that functions in polyhydroxyalkanoate accumulation and granule formation in Haloferax mediterranei.	Cai S, Cai L, Liu H, Liu X, Han J, Zhou J, Xiang H.	Appl Environ Microbiol	10.1128/aem.07114-11	2012
Metabolism	Purification and biochemical properties of a cytochrome bc complex from the aerobic hyperthermophilic archaeon Aeropyrum pernix.	Kabashima Y, Sakamoto J.	BMC Microbiol	10.1186/1471-2180-11-52	2011
	The Microbial Opsin Homolog Sop1 is involved in Sclerotinia sclerotiorum Development and Environmental Stress Response.	Lyu X, Shen C, Fu Y, Xie J, Jiang D, Li G, Cheng J.	Front Microbiol	10.3389/fmicb.2015.01504	2015
Metabolism	The Geoglobus acetivorans genome: Fe(III) reduction, acetate utilization, autotrophic growth, and degradation of aromatic compounds in a hyperthermophilic archaeon.	Mardanov AV, Slododkina GB, Slobodkin AI, Beletsky AV, Gavrilov SN, Kublanov IV, Bonch-Osmolovskaya EA, Skryabin KG, Ravin NV.	Appl Environ Microbiol	10.1128/aem.02705-14	2015
Enzymology	Comparative genomic analysis reveals 2-oxoacid dehydrogenase complex lipoylation correlation with aerobiosis in archaea.	Borziak K, Posner MG, Upadhyay A, Danson MJ, Bagby S, Dorus S.	PLoS One	10.1371/journal.pone.0087063	2014
Metabolism	Control of stress-induced persistent anxiety by an extra-amygdala septohypothalamic circuit.	Anthony TE, Dee N, Bernard A, Lerchner W, Heintz N, Anderson DJ.	Cell	10.1016/j.cell.2013.12.040	2014
	Specificity, Versatility, and Continual Development: The Power of Optogenetics for Epilepsy Research.	Christenson Wick Z, Krook-Magnuson E.	Front Cell Neurosci	10.3389/fncel.2018.00151	2018
	Using Haloarcula marismortui bacteriorhodopsin as a fusion tag for enhancing and visible expression of integral membrane proteins in Escherichia coli.	Hsu MF, Yu TF, Chou CC, Fu HY, Yang CS, Wang AH.	PLoS One	10.1371/journal.pone.0056363	2013
	Optical neural interfaces.	Warden MR, Cardin JA, Deisseroth K.	Annu Rev Biomed Eng	10.1146/annurev-bioeng-071813-104733	2014
	Seizing Control: From Current Treatments to Optogenetic Interventions in Epilepsy.	Bui AD, Alexander A, Soltesz I.	Neuroscientist	10.1177/1073858415619600	2017
	The role of hypocretin in driving arousal and goal-oriented behaviors.	Boutrel B, Cannella N, de Lecea L.	Brain Res	10.1016/j.brainres.2009.11.054	2010
	The uvrA, uvrB and uvrC genes are required for repair of ultraviolet light induced DNA photoproducts in Halobacterium sp. NRC-1.	Crowley DJ, Boubriak I, Berquist BR, Clark M, Richard E, Sullivan L, DasSarma S, McCready S.	Saline Syst	10.1186/1746-1448-2-11	2006
	A comprehensive history of motility and Archaellation in Archaea.	Jarrell KF, Albers SV, Machado JNS.	FEMS Microbes	10.1093/femsmc/xtab002	2021
	Haloquadratum walsbyi: limited diversity in a global pond.	Dyall-Smith ML, Pfeiffer F, Klee K, Palm P, Gross K, Schuster SC, Rampp M, Oesterhelt D.	PLoS One	10.1371/journal.pone.0020968	2011
	Photochemical reaction cycle transitions during anion channelrhodopsin gating.	Sineshchekov OA, Li H, Govorunova EG, Spudich JL.	Proc Natl Acad Sci U S A	10.1073/pnas.1525269113	2016
Phylogeny	The RelA/SpoT homolog (RSH) superfamily: distribution and functional evolution of ppGpp synthetases and hydrolases across the tree of life.	Atkinson GC, Tenson T, Hauryliuk V.	PLoS One	10.1371/journal.pone.0023479	2011
	A new class of marine Euryarchaeota group II from the Mediterranean deep chlorophyll maximum.	Martin-Cuadrado AB, Garcia-Heredia I, Molto AG, Lopez-Ubeda R, Kimes N, Lopez-Garcia P, Moreira D, Rodriguez-Valera F.	ISME J	10.1038/ismej.2014.249	2015
	Novel pili-like surface structures of Halobacterium salinarum strain R1 are crucial for surface adhesion.	Losensky G, Vidakovic L, Klingl A, Pfeifer F, Frols S.	Front Microbiol	10.3389/fmicb.2014.00755	2014
	Optogenetic and potassium channel gene therapy in a rodent model of focal neocortical epilepsy.	Wykes RC, Heeroma JH, Mantoan L, Zheng K, MacDonald DC, Deisseroth K, Hashemi KS, Walker MC, Schorge S, Kullmann DM.	Sci Transl Med	10.1126/scitranslmed.3004190	2012
Metabolism	Metabolism of halophilic archaea.	Falb M, Muller K, Konigsmaier L, Oberwinkler T, Horn P, von Gronau S, Gonzalez O, Pfeiffer F, Bornberg-Bauer E, Oesterhelt D.	Extremophiles	10.1007/s00792-008-0138-x	2008
	Smart Contact Lenses as Wearable Ophthalmic Devices for Disease Monitoring and Health Management.	Seo H, Chung WG, Kwon YW, Kim S, Hong YM, Park W, Kim E, Lee J, Lee S, Kim M, Lim K, Jeong I, Song H, Park JU.	Chem Rev	10.1021/acs.chemrev.3c00290	2023
Metabolism	Proteomic analysis of Haloferax volcanii reveals salinity-mediated regulation of the stress response protein PspA.	Bidle KA, Kirkland PA, Nannen JL, Maupin-Furlow JA.	Microbiology (Reading)	10.1099/mic.0.2007/015586-0	2008
Metabolism	Bioinformatic comparison of bacterial secretomes.	Song C, Kumar A, Saleh M.	Genomics Proteomics Bioinformatics	10.1016/s1672-0229(08)60031-5	2009
Metabolism	Color-tuned channelrhodopsins for multiwavelength optogenetics.	Prigge M, Schneider F, Tsunoda SP, Shilyansky C, Wietek J, Deisseroth K, Hegemann P.	J Biol Chem	10.1074/jbc.m112.391185	2012
Metabolism	Mutation of an Arabidopsis NatB N-alpha-terminal acetylation complex component causes pleiotropic developmental defects.	Ferrandez-Ayela A, Micol-Ponce R, Sanchez-Garcia AB, Alonso-Peral MM, Micol JL, Ponce MR.	PLoS One	10.1371/journal.pone.0080697	2013
Phylogeny	Essential and non-essential DNA replication genes in the model halophilic Archaeon, Halobacterium sp. NRC-1.	Berquist BR, DasSarma P, DasSarma S.	BMC Genet	10.1186/1471-2156-8-31	2007
	HAMP domain signal relay mechanism in a sensory rhodopsin-transducer complex.	Wang J, Sasaki J, Tsai AL, Spudich JL.	J Biol Chem	10.1074/jbc.m112.344622	2012
Enzymology	Metatranscriptomic analysis of extremely halophilic viral communities.	Santos F, Moreno-Paz M, Meseguer I, Lopez C, Rossello-Mora R, Parro V, Anton J.	ISME J	10.1038/ismej.2011.34	2011
Metabolism	Selective optical control of synaptic transmission in the subcortical visual pathway by activation of viral vector-expressed halorhodopsin.	Kaneda K, Kasahara H, Matsui R, Katoh T, Mizukami H, Ozawa K, Watanabe D, Isa T.	PLoS One	10.1371/journal.pone.0018452	2011
	Optical dissection of neural circuits responsible for Drosophila larval locomotion with halorhodopsin.	Inada K, Kohsaka H, Takasu E, Matsunaga T, Nose A.	PLoS One	10.1371/journal.pone.0029019	2011
Metabolism	Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea.	Walker CB, de la Torre JR, Klotz MG, Urakawa H, Pinel N, Arp DJ, Brochier-Armanet C, Chain PS, Chan PP, Gollabgir A, Hemp J, Hugler M, Karr EA, Konneke M, Shin M, Lawton TJ, Lowe T, Martens-Habbena W, Sayavedra-Soto LA, Lang D, Sievert SM, Rosenzweig AC, Manning G, Stahl DA.	Proc Natl Acad Sci U S A	10.1073/pnas.0913533107	2010
	The hydroxylamine reaction of sensory rhodopsin II: light-induced conformational alterations with C13=C14 nonisomerizable pigment.	Zadok U, Klare JP, Engelhard M, Sheves M.	Biophys J	10.1529/biophysj.105.065631	2005
	Optogenetic interrogation of neural circuits: technology for probing mammalian brain structures.	Zhang F, Gradinaru V, Adamantidis AR, Durand R, Airan RD, de Lecea L, Deisseroth K.	Nat Protoc	10.1038/nprot.2009.226	2010
Metabolism	Manual annotation, transcriptional analysis, and protein expression studies reveal novel genes in the agl cluster responsible for N glycosylation in the halophilic archaeon Haloferax volcanii.	Yurist-Doutsch S, Eichler J.	J Bacteriol	10.1128/jb.01838-08	2009
	Structure of a double transmembrane fragment of a G-protein-coupled receptor in micelles.	Neumoin A, Cohen LS, Arshava B, Tantry S, Becker JM, Zerbe O, Naider F.	Biophys J	10.1016/j.bpj.2009.01.012	2009
	Comparative proteomic analysis of pathogenic and non-pathogenic strains from the swine pathogen Mycoplasma hyopneumoniae.	Pinto PM, Klein CS, Zaha A, Ferreira HB.	Proteome Sci	10.1186/1477-5956-7-45	2009
Metabolism	Comparative genomic analyses of copper transporters and cuproproteomes reveal evolutionary dynamics of copper utilization and its link to oxygen.	Ridge PG, Zhang Y, Gladyshev VN.	PLoS One	10.1371/journal.pone.0001378	2008
Enzymology	Cloning and characterization of uronate dehydrogenases from two pseudomonads and Agrobacterium tumefaciens strain C58.	Yoon SH, Moon TS, Iranpour P, Lanza AM, Prather KJ.	J Bacteriol	10.1128/jb.00586-08	2009
	Mining proteomic data to expose protein modifications in Methanosarcina mazei strain Gö1.	Leon DR, Ytterberg AJ, Boontheung P, Kim U, Loo JA, Gunsalus RP, Ogorzalek Loo RR.	Front Microbiol	10.3389/fmicb.2015.00149	2015
Metabolism	Chimeric proton-pumping rhodopsins containing the cytoplasmic loop of bovine rhodopsin.	Sasaki K, Yamashita T, Yoshida K, Inoue K, Shichida Y, Kandori H.	PLoS One	10.1371/journal.pone.0091323	2014
	Low rates of lateral gene transfer among metabolic genes define the evolving biogeochemical niches of archaea through deep time.	Blank CE.	Archaea	10.1155/2012/843539	2012
Metabolism	Bimodal activation of different neuron classes with the spectrally red-shifted channelrhodopsin chimera C1V1 in Caenorhabditis elegans.	Erbguth K, Prigge M, Schneider F, Hegemann P, Gottschalk A.	PLoS One	10.1371/journal.pone.0046827	2012
Metabolism	Different conformations of the kinase-on and kinase-off signaling states in the Aer HAMP domain.	Watts KJ, Johnson MS, Taylor BL.	J Bacteriol	10.1128/jb.01069-10	2011
Metabolism	Abundant Lysine Methylation and N-Terminal Acetylation in Sulfolobus islandicus Revealed by Bottom-Up and Top-Down Proteomics.	Vorontsov EA, Rensen E, Prangishvili D, Krupovic M, Chamot-Rooke J.	Mol Cell Proteomics	10.1074/mcp.m116.058073	2016
	Attractant and repellent signaling conformers of sensory rhodopsin-transducer complexes.	Sineshchekov OA, Sasaki J, Wang J, Spudich JL.	Biochemistry	10.1021/bi100798w	2010
	Comparison of the structural changes occurring during the primary phototransition of two different channelrhodopsins from Chlamydomonas algae.	Ogren JI, Yi A, Mamaev S, Li H, Lugtenburg J, DeGrip WJ, Spudich JL, Rothschild KJ.	Biochemistry	10.1021/bi501243y	2015
	Microbial life at high salt concentrations: phylogenetic and metabolic diversity.	Oren A.	Saline Syst	10.1186/1746-1448-4-2	2008
	Genetic and Biochemical Identification of a Novel Single-Stranded DNA-Binding Complex in Haloferax volcanii.	Stroud A, Liddell S, Allers T.	Front Microbiol	10.3389/fmicb.2012.00224	2012
Metabolism	Glycerol-mediated repression of glucose metabolism and glycerol kinase as the sole route of glycerol catabolism in the haloarchaeon Haloferax volcanii.	Sherwood KE, Cano DJ, Maupin-Furlow JA.	J Bacteriol	10.1128/jb.00131-09	2009
	Voltage dependence of proton pumping by bacteriorhodopsin mutants with altered lifetime of the M intermediate.	Geibel S, Lorinczi E, Bamberg E, Friedrich T.	PLoS One	10.1371/journal.pone.0073338	2013
Metabolism	A small protein from the bop-brp intergenic region of Halobacterium salinarum contains a zinc finger motif and regulates bop and crtB1 transcription.	Tarasov VY, Besir H, Schwaiger R, Klee K, Furtwangler K, Pfeiffer F, Oesterhelt D.	Mol Microbiol	10.1111/j.1365-2958.2007.06081.x	2008
	A microbial rhodopsin with a unique retinal composition shows both sensory rhodopsin II and bacteriorhodopsin-like properties.	Sudo Y, Ihara K, Kobayashi S, Suzuki D, Irieda H, Kikukawa T, Kandori H, Homma M.	J Biol Chem	10.1074/jbc.m110.190058	2011
Genetics	The genome of the square archaeon Haloquadratum walsbyi : life at the limits of water activity.	Bolhuis H, Palm P, Wende A, Falb M, Rampp M, Rodriguez-Valera F, Pfeiffer F, Oesterhelt D.	BMC Genomics	10.1186/1471-2164-7-169	2006
Metabolism	GABAergic circuits mediate the reinforcement-related signals of striatal cholinergic interneurons.	English DF, Ibanez-Sandoval O, Stark E, Tecuapetla F, Buzsaki G, Deisseroth K, Tepper JM, Koos T.	Nat Neurosci	10.1038/nn.2984	2011
Metabolism	Disulfide bond formation in prokaryotes: history, diversity and design.	Hatahet F, Boyd D, Beckwith J.	Biochim Biophys Acta	10.1016/j.bbapap.2014.02.014	2014
	Many nonuniversal archaeal ribosomal proteins are found in conserved gene clusters.	Wang J, Dasgupta I, Fox GE.	Archaea	10.1155/2009/971494	2009
Metabolism	Targeting light-gated chloride channels to neuronal somatodendritic domain reduces their excitatory effect in the axon.	Messier JE, Chen H, Cai ZL, Xue M.	Elife	10.7554/elife.38506	2018
	Archaeal ApbC/Nbp35 homologs function as iron-sulfur cluster carrier proteins.	Boyd JM, Drevland RM, Downs DM, Graham DE.	J Bacteriol	10.1128/jb.01469-08	2009
Metabolism	Engineering of functional replication protein a homologs based on insights into the evolution of oligonucleotide/oligosaccharide-binding folds.	Lin Y, Lin LJ, Sriratana P, Coleman K, Ha T, Spies M, Cann IK.	J Bacteriol	10.1128/jb.01930-07	2008
Metabolism	Specific expression of channelrhodopsin-2 in single neurons of Caenorhabditis elegans.	Schmitt C, Schultheis C, Pokala N, Husson SJ, Liewald JF, Bargmann CI, Gottschalk A.	PLoS One	10.1371/journal.pone.0043164	2012
	Optical silencing of C. elegans cells with arch proton pump.	Okazaki A, Sudo Y, Takagi S.	PLoS One	10.1371/journal.pone.0035370	2012
	Faithful expression of multiple proteins via 2A-peptide self-processing: a versatile and reliable method for manipulating brain circuits.	Tang W, Ehrlich I, Wolff SB, Michalski AM, Wolfl S, Hasan MT, Luthi A, Sprengel R.	J Neurosci	10.1523/jneurosci.0359-09.2009	2009
	Unitary synaptic connections among substantia nigra pars reticulata neurons.	Higgs MH, Wilson CJ.	J Neurophysiol	10.1152/jn.00094.2016	2016
Metabolism	Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.	Helbig AO, Rosati S, Pijnappel PW, van Breukelen B, Timmers MH, Mohammed S, Slijper M, Heck AJ.	BMC Genomics	10.1186/1471-2164-11-685	2010
	Noninvasive optical inhibition with a red-shifted microbial rhodopsin.	Chuong AS, Miri ML, Busskamp V, Matthews GA, Acker LC, Sorensen AT, Young A, Klapoetke NC, Henninger MA, Kodandaramaiah SB, Ogawa M, Ramanlal SB, Bandler RC, Allen BD, Forest CR, Chow BY, Han X, Lin Y, Tye KM, Roska B, Cardin JA, Boyden ES.	Nat Neurosci	10.1038/nn.3752	2014
	Nitrogen metabolism in haloarchaea.	Bonete MJ, Martinez-Espinosa RM, Pire C, Zafrilla B, Richardson DJ.	Saline Syst	10.1186/1746-1448-4-9	2008
Metabolism	Systems analysis of bioenergetics and growth of the extreme halophile Halobacterium salinarum.	Gonzalez O, Gronau S, Pfeiffer F, Mendoza E, Zimmer R, Oesterhelt D.	PLoS Comput Biol	10.1371/journal.pcbi.1000332	2009
	Diminishing fear: Optogenetic approach toward understanding neural circuits of fear control.	Luchkina NV, Bolshakov VY.	Pharmacol Biochem Behav	10.1016/j.pbb.2017.05.005	2018
Metabolism	Transcriptional control by two leucine-responsive regulatory proteins in Halobacterium salinarum R1.	Schwaiger R, Schwarz C, Furtwangler K, Tarasov V, Wende A, Oesterhelt D.	BMC Mol Biol	10.1186/1471-2199-11-40	2010
	Saccade modulation by optical and electrical stimulation in the macaque frontal eye field.	Ohayon S, Grimaldi P, Schweers N, Tsao DY.	J Neurosci	10.1523/jneurosci.2675-13.2013	2013
Metabolism	Three putative cation/proton antiporters from the soda lake alkaliphile Alkalimonas amylolytica N10 complement an alkali-sensitive Escherichia coli mutant.	Wei Y, Liu J, Ma Y, Krulwich TA.	Microbiology (Reading)	10.1099/mic.0.2007/007450-0	2007
Metabolism	Rhomboid protease AarA mediates quorum-sensing in Providencia stuartii by activating TatA of the twin-arginine translocase.	Stevenson LG, Strisovsky K, Clemmer KM, Bhatt S, Freeman M, Rather PN.	Proc Natl Acad Sci U S A	10.1073/pnas.0608140104	2007
	Hexameric structures of the archaeal secretion ATPase GspE and implications for a universal secretion mechanism.	Yamagata A, Tainer JA.	EMBO J	10.1038/sj.emboj.7601544	2007
	Crystal structure of the Anabaena sensory rhodopsin transducer.	Vogeley L, Trivedi VD, Sineshchekov OA, Spudich EN, Spudich JL, Luecke H.	J Mol Biol	10.1016/j.jmb.2006.11.074	2007
	Laser-induced transient grating analysis of dynamics of interaction between sensory rhodopsin II D75N and the HtrII transducer.	Inoue K, Sasaki J, Spudich JL, Terazima M.	Biophys J	10.1529/biophysj.106.097493	2007
Metabolism	Structure of concatenated HAMP domains provides a mechanism for signal transduction.	Airola MV, Watts KJ, Bilwes AM, Crane BR.	Structure	10.1016/j.str.2010.01.013	2010
Metabolism	Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes.	Anderson I, Scheuner C, Goker M, Mavromatis K, Hooper SD, Porat I, Klenk HP, Ivanova N, Kyrpides N.	PLoS One	10.1371/journal.pone.0020237	2011
Metabolism	Dissection of the regulatory mechanism of a heat-shock responsive promoter in Haloarchaea: a new paradigm for general transcription factor directed archaeal gene regulation.	Lu Q, Han J, Zhou L, Coker JA, DasSarma P, DasSarma S, Xiang H.	Nucleic Acids Res	10.1093/nar/gkn152	2008
Metabolism	The C. elegans male exercises directional control during mating through cholinergic regulation of sex-shared command interneurons.	Sherlekar AL, Janssen A, Siehr MS, Koo PK, Caflisch L, Boggess M, Lints R.	PLoS One	10.1371/journal.pone.0060597	2013
Metabolism	IcmF is a fusion between the radical B12 enzyme isobutyryl-CoA mutase and its G-protein chaperone.	Cracan V, Padovani D, Banerjee R.	J Biol Chem	10.1074/jbc.m109.062182	2010
	Post-genomics of the model haloarchaeon Halobacterium sp. NRC-1.	DasSarma S, Berquist BR, Coker JA, DasSarma P, Muller JA.	Saline Syst	10.1186/1746-1448-2-3	2006
Pathogenicity	Optogenetic inhibition of dorsal medial prefrontal cortex attenuates stress-induced reinstatement of palatable food seeking in female rats.	Calu DJ, Kawa AB, Marchant NJ, Navarre BM, Henderson MJ, Chen B, Yau HJ, Bossert JM, Schoenbaum G, Deisseroth K, Harvey BK, Hope BT, Shaham Y.	J Neurosci	10.1523/jneurosci.2016-12.2013	2013
	Archaic chaos: intrinsically disordered proteins in Archaea.	Xue B, Williams RW, Oldfield CJ, Dunker AK, Uversky VN.	BMC Syst Biol	10.1186/1752-0509-4-s1-s1	2010
	Synthetic strategies for studying embryonic development.	Ouyang X, Chen JK.	Chem Biol	10.1016/j.chembiol.2010.04.013	2010
	Engineered G-protein Coupled Receptors are Powerful Tools to Investigate Biological Processes and Behaviors.	Nichols CD, Roth BL.	Front Mol Neurosci	10.3389/neuro.02.016.2009	2009
	Combined use of cultivation-dependent and cultivation-independent methods indicates that members of most haloarchaeal groups in an Australian crystallizer pond are cultivable.	Burns DG, Camakaris HM, Janssen PH, Dyall-Smith ML.	Appl Environ Microbiol	10.1128/aem.70.9.5258-5265.2004	2004
Metabolism	Mutational analyses of HAMP helices suggest a dynamic bundle model of input-output signalling in chemoreceptors.	Zhou Q, Ames P, Parkinson JS.	Mol Microbiol	10.1111/j.1365-2958.2009.06819.x	2009
Genetics	Genomic context analysis in Archaea suggests previously unrecognized links between DNA replication and translation.	Berthon J, Cortez D, Forterre P.	Genome Biol	10.1186/gb-2008-9-4-r71	2008
Metabolism	Protein adaptations in archaeal extremophiles.	Reed CJ, Lewis H, Trejo E, Winston V, Evilia C.	Archaea	10.1155/2013/373275	2013
Metabolism	Cloning, expression, and purification of functional Sec11a and Sec11b, type I signal peptidases of the archaeon Haloferax volcanii.	Fine A, Irihimovitch V, Dahan I, Konrad Z, Eichler J.	J Bacteriol	10.1128/jb.188.5.1911-1919.2006	2006
	Next-generation transgenic mice for optogenetic analysis of neural circuits.	Asrican B, Augustine GJ, Berglund K, Chen S, Chow N, Deisseroth K, Feng G, Gloss B, Hira R, Hoffmann C, Kasai H, Katarya M, Kim J, Kudolo J, Lee LM, Lo SQ, Mancuso J, Matsuzaki M, Nakajima R, Qiu L, Tan G, Tang Y, Ting JT, Tsuda S, Wen L, Zhang X, Zhao S.	Front Neural Circuits	10.3389/fncir.2013.00160	2013
	Ion channels to inactivate neurons in Drosophila.	Hodge JJ.	Front Mol Neurosci	10.3389/neuro.02.013.2009	2009
Metabolism	Gene duplications in prokaryotes can be associated with environmental adaptation.	Bratlie MS, Johansen J, Sherman BT, Huang da W, Lempicki RA, Drablos F.	BMC Genomics	10.1186/1471-2164-11-588	2010
	Multiple, non-allelic, intein-coding sequences in eukaryotic RNA polymerase genes.	Goodwin TJ, Butler MI, Poulter RT.	BMC Biol	10.1186/1741-7007-4-38	2006
Genetics	Whole-genome comparison between the type strain of Halobacterium salinarum (DSM 3754^T ) and the laboratory strains R1 and NRC-1.	Pfeiffer F, Losensky G, Marchfelder A, Habermann B, Dyall-Smith M.	Microbiologyopen	10.1002/mbo3.974	2020
Genetics	Genome-wide survey of prokaryotic serine proteases: analysis of distribution and domain architectures of five serine protease families in prokaryotes.	Tripathi LP, Sowdhamini R.	BMC Genomics	10.1186/1471-2164-9-549	2008
	Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea.	Zivanovic Y, Armengaud J, Lagorce A, Leplat C, Guerin P, Dutertre M, Anthouard V, Forterre P, Wincker P, Confalonieri F.	Genome Biol	10.1186/gb-2009-10-6-r70	2009
Enzymology	The biological functions of Naa10 - From amino-terminal acetylation to human disease.	Dorfel MJ, Lyon GJ.	Gene	10.1016/j.gene.2015.04.085	2015
	An evidence of laccases in archaea.	Sharma KK, Kuhad RC	Indian J Microbiol	10.1007/s12088-009-0039-4	2009
Metabolism	A halorhodopsin-overproducing mutant isolated from an extremely haloalkaliphilic archaeon Natronomonas pharaonis.	Ihara K, Narusawa A, Maruyama K, Takeguchi M, Kouyama T	FEBS Lett	10.1016/j.febslet.2008.07.030	2008
Phylogeny	Radiation sensitivity of N. pharaonis in comparison with E. coli K12 strains.	Quint RM, Solar S, Stan-Lotter H	Radiat Environ Biophys	10.1007/s00411-002-0146-7	2002
Metabolism	Genomic-based phylogenetic and metabolic analyses of the genus Natronomonas, and description of Natronomonas aquatica sp. nov.	Garcia-Roldan A, Duran-Viseras A, de la Haba RR, Corral P, Sanchez-Porro C, Ventosa A.	Front Microbiol	10.3389/fmicb.2023.1109549	2023
	Natronomonas salsuginis sp. nov., a New Inhabitant of a Marine Solar Saltern.	Duran-Viseras A, Sanchez-Porro C, Ventosa A.	Microorganisms	10.3390/microorganisms8040605	2020
	Haloglomus irregulare gen. nov., sp. nov., a New Halophilic Archaeon Isolated from a Marine Saltern.	Duran-Viseras A, Sanchez-Porro C, Ventosa A.	Microorganisms	10.3390/microorganisms8020206	2020
Phylogeny	Natrarchaeobius chitinivorans gen. nov., sp. nov., and Natrarchaeobius halalkaliphilus sp. nov., alkaliphilic, chitin-utilizing haloarchaea from hypersaline alkaline lakes.	Sorokin DY, Elcheninov AG, Toshchakov SV, Bale NJ, Sinninghe Damste JS, Khijniak TV, Kublanov IV.	Syst Appl Microbiol	10.1016/j.syapm.2019.01.001	2019
Genetics	Non-contiguous finished genome sequence and description of Halopiger goleamassiliensis sp. nov.	Ikram HI, Catherine R, Caroline M, Didier R, Hocine H, Christelle D.	Stand Genomic Sci	10.4056/sigs.4618288	2014
Genetics	Non-contiguous finished genome sequence and description of Halopiger djelfamassiliensis sp. nov.	Hassani II, Robert C, Michelle C, Raoult D, Hacene H, Desnues C.	Stand Genomic Sci	10.4056/sigs.4578289	2013
Phylogeny	Natronomonas gomsonensis sp. nov., isolated from a solar saltern.	Kim TY, Kim SJ, Park SJ, Kim JG, Cha IT, Jung MY, Lee SA, Roh SW, Yim KJ, Itoh T, Rhee SK	Antonie Van Leeuwenhoek	10.1007/s10482-013-9970-9	2013
Phylogeny	Halomarina oriensis gen. nov., sp. nov., a halophilic archaeon isolated from a seawater aquarium.	Inoue K, Itoh T, Ohkuma M, Kogure K	Int J Syst Evol Microbiol	10.1099/ijs.0.020677-0	2010
Phylogeny	Natronomonas moolapensis sp. nov., non-alkaliphilic isolates recovered from a solar saltern crystallizer pond, and emended description of the genus Natronomonas.	Burns DG, Janssen PH, Itoh T, Minegishi H, Usami R, Kamekura M, Dyall-Smith ML	Int J Syst Evol Microbiol	10.1099/ijs.0.010132-0	2009

References

#985	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 2160
#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#40918	; Curators of the CIP;
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#121792	Collection of Institut Pasteur ; Curators of the CIP; CIP 103997
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Natronomonas pharaonis (DSM 2160, ATCC 35678, Gabara)

Name and taxonomic classification

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Physiology and metabolism

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Genome browser: GCA_000026045

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