Archive BacDiveID:10.13145/bacdive16857.20230509.8.1

Strain identifier

BacDive ID: 16857

Type strain:

Species: Pyrococcus horikoshii

Strain Designation: OT-3

Strain history: C. Kato <-- F. Robb OT-3.

NCBI tax ID(s): 53953 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 4716

BacDive-ID: 16857

DSM-Number: 12428

keywords: genome sequence, 16S sequence, Archaea, anaerobe, hyperthermophilic

description: Pyrococcus horikoshii OT-3 is an anaerobe, hyperthermophilic archaeon that was isolated from marine hydrothermal vent at 1395 m depth.

NCBI tax id

NCBI tax id: 53953
Matching level: species

strain history

@ref	history
4716	<- JCM <- C. Kato, Japan Marine Science and Technology Center, Yokosuka, Japan <- F. T. Robb, University of Maryland Biotechnology Institute, Baltimore MD, USA; OT-3 {1992}
67770	C. Kato <-- F. Robb OT-3.

doi: 10.13145/bacdive16857.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/archaea
keyword: phylum/methanobacteriota
domain: Archaea
phylum: Methanobacteriota
class: Thermococci
order: Thermococcales
family: Thermococcaceae
genus: Pyrococcus
species: Pyrococcus horikoshii
full scientific name: Pyrococcus horikoshii González et al. 1999

@ref: 4716

domain: Archaea

phylum: Euryarchaeota

class: Thermococci

order: Thermococcales

family: Thermococcaceae

genus: Pyrococcus

species: Pyrococcus horikoshii

full scientific name: Pyrococcus horikoshii González et al. 1999

strain designation: OT-3

type strain: yes

Culture and growth conditions

culture medium

@ref: 4716
name: PYROCOCCUS MEDIUM (DSMZ Medium 377)
growth: yes
link: https://mediadive.dsmz.de/medium/377
composition: Name: PYROCOCCUS MEDIUM (DSMZ Medium 377) Composition: Sulfur 30.0 g/l Peptone 5.0 g/l MgCl2 x 6 H2O 2.75 g/l Yeast extract 1.0 g/l KH2PO4 0.5 g/l Na2S x 9 H2O 0.5 g/l KCl 0.33 g/l NaBr 0.05 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l (NH4)2SO4 0.01 g/l SrCl2 x 6 H2O 0.007 g/l Citric acid 0.005 g/l MnSO4 x H2O 0.005 g/l CoSO4 x 7 H2O 0.0018 g/l ZnSO4 x 7 H2O 0.0018 g/l CaCl2 x 2 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Sodium resazurin 0.0005 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l CuSO4 x 5 H2O 0.0001 g/l Na2MoO4 x 2 H2O 0.0001 g/l H3BO3 0.0001 g/l KI 5e-05 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
4716	positive	growth	95	hyperthermophilic
67770	positive	growth	95	hyperthermophilic

Physiology and metabolism

oxygen tolerance

@ref: 4716
oxygen tolerance: anaerobe

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent	latitude	longitude
4716	marine hydrothermal vent at 1395 m depth	Pacific Ocean, Okinawa Trough	Japan	JPN	Asia	27.55	126.933
67770	Hydrothermal vent at the Okinawa Trough

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Aquatic	#Marine
#Condition	#Thermophilic (>45°C)

Safety information

risk assessment

@ref: 4716
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	Pyrococcus horikoshii strain DSM 12428 16S ribosomal RNA gene, partial sequence	AY099169	1454	ena	53953
20218	Pyrococcus horikoshii strain DSM 12428 16S-23S ribosomal RNA intergenic spacer region, complete sequence	AY099205	190	ena	53953

Genome sequences

@ref: 67770
description: Pyrococcus horikoshii OT3
accession: GCA_000011105
assembly level: complete
database: ncbi
NCBI tax ID: 70601

GC content

@ref: 4716
GC-content: 41
method: sequence analysis

External links

@ref: 4716

culture collection no.: DSM 12428, JCM 9974, NBRC 100139

straininfo link

@ref: 85866
straininfo: 44181

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Enzymology	12215812	L-aspartate oxidase is present in the anaerobic hyperthermophilic archaeon Pyrococcus horikoshii OT-3: characteristics and role in the de novo biosynthesis of nicotinamide adenine dinucleotide proposed by genome sequencing.	Sakuraba H, Satomura T, Kawakami R, Yamamoto S, Kawarabayasi Y, Kikuchi H, Ohshima T	Extremophiles	10.1007/s00792-001-0254-3	2002	Amino Acid Oxidoreductases/chemistry/genetics/metabolism, Amino Acid Sequence, Cloning, Molecular, Enzyme Stability, Escherichia coli Proteins, Genome, Archaeal, Hydrogen-Ion Concentration, Kinetics, Molecular Sequence Data, NAD/biosynthesis, Pyrococcus/enzymology/genetics, Recombinant Proteins/genetics/metabolism, Substrate Specificity, Temperature	Genetics
Enzymology	15625325	Oxidative stress response in an anaerobic hyperthermophilic archaeon: presence of a functional peroxiredoxin in Pyrococcus horikoshii.	Kawakami R, Sakuraba H, Kamohara S, Goda S, Kawarabayasi Y, Ohshima T	J Biochem	10.1093/jb/mvh157	2004	Amino Acid Sequence, Archaeal Proteins/chemistry, Blotting, Northern, Cloning, Molecular, Culture Media/pharmacology, Databases, Genetic, Dithiothreitol/pharmacology, Electrons, Electrophoresis, Gel, Two-Dimensional, Electrophoresis, Polyacrylamide Gel, Escherichia coli/metabolism, Genome, Hot Temperature, Humans, Hydrogen-Ion Concentration, Models, Chemical, Molecular Sequence Data, Oxidative Stress, Oxygen/chemistry/metabolism, Peroxidases/chemistry/metabolism, Peroxiredoxins, Protein Structure, Tertiary, Pyrococcus horikoshii/metabolism, RNA/chemistry, Recombinant Proteins/chemistry, Sequence Homology, Amino Acid, Time Factors	Metabolism
Enzymology	16098188	A second novel dye-linked L-proline dehydrogenase complex is present in the hyperthermophilic archaeon Pyrococcus horikoshii OT-3.	Kawakami R, Sakuraba H, Tsuge H, Goda S, Katunuma N, Ohshima T	FEBS J	10.1111/j.1742-4658.2005.04810.x	2005	Amino Acid Sequence, Chromatography, High Pressure Liquid, Coloring Agents/metabolism, Genes, Archaeal, Molecular Sequence Data, Proline Oxidase/chemistry/genetics/isolation & purification/metabolism, Pyrococcus horikoshii/*enzymology, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Sequence Homology, Amino Acid	Metabolism
Enzymology	22752365	Comparative analysis of the catalytic components in the archaeal dye-linked L-proline dehydrogenase complexes.	Kawakami R, Noguchi C, Higashi M, Sakuraba H, Ohshima T	Appl Microbiol Biotechnol	10.1007/s00253-012-4201-2	2012	2,6-Dichloroindophenol/metabolism, Chromatography, Affinity, Cloning, Molecular, Enzyme Stability, Escherichia coli/genetics/metabolism, Ferricyanides/metabolism, Gene Expression, Hot Temperature, Kinetics, Proline/metabolism, Proline Oxidase/genetics/metabolism, Protein Stability, Pyrococcus/enzymology/genetics, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Thermococcus/enzymology/genetics, Time Factors	Metabolism
Metabolism	25963389	Identification of a novel amino acid racemase from a hyperthermophilic archaeon Pyrococcus horikoshii OT-3 induced by D-amino acids.	Kawakami R, Ohmori T, Sakuraba H, Ohshima T	Amino Acids	10.1007/s00726-015-2001-6	2015	Amino Acid Isomerases/analysis/metabolism, Amino Acids/administration & dosage/biosynthesis/metabolism, Genome, Archaeal, Pyrococcus horikoshii/enzymology/genetics/growth & development/metabolism	Genetics
Metabolism	28343923	First characterization of an archaeal amino acid racemase with broad substrate specificity from the hyperthermophile Pyrococcus horikoshii OT-3.	Kawakami R, Sakuraba H, Ohmori T, Ohshima T	J Biosci Bioeng	10.1016/j.jbiosc.2017.02.004	2017	Amino Acid Isomerases/metabolism, Amino Acid Sequence, Hydrophobic and Hydrophilic Interactions, Pyrococcus horikoshii/enzymology/physiology, Substrate Specificity, *Temperature	Enzymology
	30038603	A Novel PLP-Dependent Alanine/Serine Racemase From the Hyperthermophilic Archaeon Pyrococcus horikoshii OT-3.	Kawakami R, Ohshida T, Sakuraba H, Ohshima T	Front Microbiol	10.3389/fmicb.2018.01481	2018
Metabolism	35337912	Crystal structure of a novel type of ornithine delta-aminotransferase from the hyperthermophilic archaeon Pyrococcus horikoshii.	Kawakami R, Ohshida T, Hayashi J, Yoneda K, Furumoto T, Ohshima T, Sakuraba H	Int J Biol Macromol	10.1016/j.ijbiomac.2022.03.114	2022	Archaea/metabolism, Crystallography, X-Ray, Humans, Models, Molecular, Ornithine/chemistry, Pyridoxal Phosphate/chemistry, *Pyrococcus horikoshii/metabolism, Substrate Specificity, Transaminases/chemistry	Pathogenicity

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
4716	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12428)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-12428
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
85866	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID44181.1	StrainInfo: A central database for resolving microbial strain identifiers