Strain identifier
BacDive ID: 5905
Type strain: 
Species: Haloarcula japonica
Strain Designation: TR-1
Strain history: T. Takashina TR-1.
NCBI tax ID(s): 1227453 (strain), 29282 (species)
version 9.3 (current version)
General
@ref: 2497
BacDive-ID: 5905
DSM-Number: 6131
keywords: genome sequence, 16S sequence, Archaea, mesophilic
description: Haloarcula japonica TR-1 is a mesophilic archaeon that was isolated from saltern soil.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1227453 | strain |
| 29282 | species |
strain history
| @ref | history |
|---|---|
| 2497 | <- JCM |
| 67770 | T. Takashina TR-1. |
doi: 10.13145/bacdive5905.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Halobacteria
- order: Halobacteriales
- family: Haloarculaceae
- genus: Haloarcula
- species: Haloarcula japonica
- full scientific name: Haloarcula japonica Takashina et al. 1991
@ref: 2497
domain: Archaea
phylum: Euryarchaeota
class: Halobacteria
order: Halobacteriales
family: Haloarculaceae
genus: Haloarcula
species: Haloarcula japonica
full scientific name: Haloarcula japonica Takashina et al. 1991
strain designation: TR-1
type strain: yes
Morphology
cell morphology
- @ref: 125439
- gram stain: negative
- confidence: 91.4
Culture and growth conditions
culture medium
- @ref: 2497
- name: HALOBACTERIA MEDIUM (DSMZ Medium 372)
- growth: yes
- link: https://mediadive.dsmz.de/medium/372
- composition: Name: HALOBACTERIA MEDIUM (DSMZ Medium 372) Composition: NaCl 200.0 g/l MgSO4 x 7 H2O 20.0 g/l Agar 20.0 g/l Yeast extract 5.0 g/l Casamino acids 5.0 g/l Na3-citrate 3.0 g/l KCl 2.0 g/l Na glutamate 1.0 g/l FeCl2 x 4 H2O 0.036 g/l MnCl2 x 4 H2O 0.00036 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 2497 | positive | growth | 37 |
| 67770 | positive | growth | 37 |
Physiology and metabolism
spore formation
- @ref: 125439
- spore formation: no
- confidence: 94.8
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 2497 | saltern soil | Nato Peninsula | Japan | JPN | Asia |
| 67770 | Saltern soil at Noto Peninsula | Japan | JPN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Condition | #Saline |
taxonmaps
- @ref: 69479
- File name: preview.99_187186.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17657;96_68837;97_89482;98_121762;99_187186&stattab=map
- Last taxonomy: Haloarcula
- 16S sequence: AB355986
- Sequence Identity:
- Total samples: 26
- soil counts: 13
- aquatic counts: 11
- animal counts: 2
Safety information
risk assessment
- @ref: 2497
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Haloarcula japonica gene for 16S ribosomal RNA, partial sequence, strain: JCM 7785 | AB355986 | 1472 | nuccore | 29282 |
| 20218 | Haloarcula japonica gene for 16S rRNA, complete sequence, strain: JCM 7785 | AB663353 | 1472 | nuccore | 29282 |
| 20218 | Haloarcula japonica strain JCM7785 16S ribosomal RNA (rrnA) gene, complete sequence | EF645684 | 1472 | nuccore | 29282 |
| 20218 | Haloarcula japonica strain JCM7785 16S ribosomal RNA (rrnB) gene, complete sequence | EF645685 | 1472 | nuccore | 29282 |
| 20218 | Haloarcula japonica strain JCM7785 16S ribosomal RNA (rrnC) gene, complete sequence | EF645686 | 1472 | nuccore | 29282 |
| 20218 | Haloarcula japonica gene for 16S ribosomal RNA, partial sequence | D28872 | 1424 | nuccore | 29282 |
| 124043 | Haloarcula japonica gene for 16S ribosomal RNA, partial sequence, strain: JCM7785, note: rrsA. | LC085248 | 1405 | nuccore | 29282 |
| 124043 | Haloarcula japonica gene for 16S ribosomal RNA, partial sequence, strain: JCM7785, note: rrsC. | LC085249 | 1405 | nuccore | 29282 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Haloarcula japonica DSM 6131 | 2534681902 | draft | img | 1227453 |
| 67770 | Haloarcula japonica DSM 6131 | GCA_000336635 | contig | ncbi | 1227453 |
| 66792 | Haloarcula japonica DSM 6131 | 1227453.3 | wgs | patric | 1227453 |
GC content
- @ref: 67770
- GC-content: 63.3
- method: Buoyant density centrifugation (BD)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence |
|---|---|---|---|---|---|
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | aerobe | 86.1 |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 91.4 |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 50 |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 94.8 |
External links
@ref: 2497
culture collection no.: DSM 6131, ATCC 49778, JCM 7785, CGMCC 1.3717, CGMCC 1.6162, NBRC 101032, NCIMB 13157, VKM B-2009
straininfo link
| @ref | straininfo |
|---|---|
| 75385 | 45242 |
| 75386 | 312368 |
literature
| topic | Pubmed-ID | title | authors | journal | year | mesh | topic2 | DOI |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 8841572 | Structure and heterologous expression of the gene encoding the cell surface glycoprotein from Haloarcula japonica strain TR-1. | Wakai H, Takada K, Nakamura S, Horikoshi K | Nucleic Acids Symp Ser | 1995 | Amino Acid Sequence, Bacterial Proteins/*genetics, Base Sequence, Binding Sites/genetics, Cloning, Molecular, DNA, Bacterial/genetics, Gene Expression, *Genes, Bacterial, Glycosylation, Halobacterium/*genetics, Membrane Glycoproteins/*genetics, Molecular Sequence Data, Promoter Regions, Genetic | Genetics | |
| Enzymology | 9586023 | Molecular cloning of the gene encoding a 2Fe-2S ferredoxin from extremely halophilic archaeon Haloarcula japonica strain TR-1. | Ikeda A, Ichimata T, Sugimori D, Nakamura S | Nucleic Acids Symp Ser | 1997 | Amino Acid Sequence, Base Sequence, Cloning, Molecular, DNA Primers, Ferredoxins/*biosynthesis/chemistry/genetics, *Genes, Bacterial, Haloarcula/*genetics/metabolism, Molecular Sequence Data, Polymerase Chain Reaction, Recombinant Proteins/biosynthesis/chemistry/isolation & purification, Restriction Mapping | Genetics | |
| Enzymology | 9586024 | Primary structure of the novel bacterial rhodopsin from extremely halophilic archaeon Haloarcula japonica strain TR-1. | Yatsunami R, Kawakami T, Ohtani H, Nakamura S | Nucleic Acids Symp Ser | 1997 | Amino Acid Sequence, Bacteriorhodopsins/biosynthesis/*chemistry/genetics, Base Sequence, Cloning, Molecular, DNA Primers, Fluorescence, *Genes, Bacterial, Haloarcula/*genetics/metabolism, Molecular Sequence Data, Open Reading Frames, Polymerase Chain Reaction, Recombinant Proteins/biosynthesis/chemistry, Sequence Homology, Amino Acid | Genetics | |
| Enzymology | 9680334 | Cloning and sequencing of the gene encoding the cell surface glycoprotein of Haloarcula japonica strain TR-1. | Wakai H, Nakamura S, Kawasaki H, Takada K, Mizutani S, Aono R, Horikoshi K | Extremophiles | 1997 | Amino Acid Sequence, Archaeal Proteins/*genetics/metabolism, Base Sequence, Cell Membrane, Cloning, Molecular, DNA, Archaeal, Escherichia coli, *Genes, Archaeal, Haloarcula/*genetics, Membrane Glycoproteins/*genetics/metabolism, Molecular Sequence Data, Polymerase Chain Reaction, Sequence Analysis, DNA | Metabolism | 10.1007/s007920050012 |
| Cultivation | 10780385 | Transcriptional regulation of cruxrhodopsin gene from extremely halophilic archaeon Haloarcula japonica strain TR-1. | Yatsunami R, Kawakami T, Ohtani H, Nakamura S | Nucleic Acids Symp Ser | 1999 | *Archaeal Proteins, Bacteriorhodopsins/*genetics, Culture Media, Darkness, *Gene Expression Regulation, Archaeal/radiation effects, Genes, Archaeal, Genes, Regulator, Haloarcula/*genetics/growth & development/radiation effects, Light, Proton Pumps/*genetics, RNA, Messenger/genetics, *Transcription, Genetic/radiation effects | 10.1093/nass/42.1.73 | |
| Enzymology | 10780386 | Molecular cloning of A1-ATPase gene from extremely halophilic archaeon Haloarcula japonica strain TR-1. | Yatsunami R, Iwamoto M, Ihara K, Nakamura S | Nucleic Acids Symp Ser | 1999 | Adenosine Triphosphatases/chemistry/*genetics, Amino Acid Sequence, Base Sequence, Cloning, Molecular, Genes, Archaeal, Haloarcula/*enzymology/*genetics, Halobacterium salinarum/genetics, Haloferax volcanii/genetics, Hot Temperature, Macromolecular Substances, Molecular Sequence Data, Sequence Alignment | Stress | 10.1093/nass/42.1.75 |
| Enzymology | 10805565 | A novel bacteriorhodopsin-like protein from Haloarcula japonica strain TR-1: gene cloning, sequencing, and transcript analysis. | Yatsunami R, Kawakami T, Ohtani H, Nakamura S | Extremophiles | 2000 | Amino Acid Sequence, Archaeal Proteins/*genetics, Bacteriorhodopsins/*genetics, Base Sequence, Cloning, Molecular, Haloarcula/*genetics, Molecular Sequence Data, Proton Pumps/*genetics, RNA, Messenger/biosynthesis, Reverse Transcriptase Polymerase Chain Reaction, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Transcription, Genetic | Genetics | 10.1007/pl00010710 |
| Enzymology | 10831221 | Purification and characterization of a ferredoxin from Haloarcula japonica strain TR-1. | Sugimori D, Ichimata T, Ikeda A, Nakamura S | Biometals | 2000 | Amino Acid Sequence, Amino Acids/analysis, Archaeal Proteins/chemistry/genetics/*isolation & purification, Electron Spin Resonance Spectroscopy, Ferredoxins/chemistry/genetics/*isolation & purification, Haloarcula/*chemistry/genetics, Molecular Sequence Data, Molecular Weight, Sequence Homology, Amino Acid, Spectrophotometry | Phylogeny | 10.1023/a:1009260220682 |
| Enzymology | 12836259 | Gene clusters encoding ATP synthase of Haloarcula japonica strain TR-1. | Yatsunami R, Iwamoto M, Ihara K, Nakamura S | Nucleic Acids Res Suppl | 2001 | Adenosine Triphosphatases/*genetics, Cloning, Molecular, *Genes, Archaeal, Haloarcula/*enzymology, Halobacteriales/enzymology, *Multigene Family, Operon, Protein Subunits, Sequence Homology, Amino Acid | 10.1093/nass/1.1.51 | |
| Enzymology | 12903239 | The gene encoding a novel halorhodopsin-like protein of extremely halophilic archaeon Haloarcula japonica strain TR-1. | Yatsunami R, Aono S, Nakamura S | Nucleic Acids Symp Ser | 2000 | Amino Acid Sequence, Archaeal Proteins/*genetics, Base Sequence, Cloning, Molecular, DNA, Archaeal/genetics, Gene Expression Regulation, Archaeal/radiation effects, *Genes, Archaeal, Haloarcula/*genetics/radiation effects, Halorhodopsins/*genetics, Ion Pumps/genetics, Light, Molecular Sequence Data, Open Reading Frames | Genetics | 10.1093/nass/44.1.1 |
| Enzymology | 12903315 | Cloning and sequencing of ftsZ homolog from extremely halophilic archaeon Haloarcula japonica strain TR-1. | Kazumichi O, Yatsunami R, Nakamura S | Nucleic Acids Symp Ser | 2000 | Amino Acid Sequence, Archaeal Proteins/*genetics, Base Sequence, Cloning, Molecular, DNA, Archaeal/genetics, Genes, Archaeal, Haloarcula/*genetics, Molecular Sequence Data, Species Specificity | Genetics | 10.1093/nass/44.1.155 |
| Enzymology | 14510483 | A brp homolog of Haloarcula japonica: gene cloning and transcriptional analysis. | Yatsunami R, Iwamoto M, Ito S, Nakamura S | Nucleic Acids Res Suppl | 2003 | Amino Acid Sequence, Base Sequence, Cloning, Molecular, DNA, Bacterial, *Genes, Bacterial, Haloarcula/*genetics, Molecular Sequence Data, *Transcription, Genetic | Genetics | 10.1093/nass/3.1.267 |
| Enzymology | 14510506 | Gene cloning of ftsZ1 homolog from extremely halophilic archaeon Haloarcula japonica. | Ozawa K, Yatsunami R, Nakamura S | Nucleic Acids Res Suppl | 2003 | Amino Acid Sequence, Archaeal Proteins/*genetics, Base Sequence, Cloning, Molecular, DNA, Archaeal, Genes, Haloarcula/*genetics, Molecular Sequence Data, Open Reading Frames, Reverse Transcriptase Polymerase Chain Reaction, Transcription, Genetic | Genetics | 10.1093/nass/3.1.313 |
| Genetics | 15844012 | Gene cloning, expression and partial characterization of cell division protein FtsZ1 from extremely halophilic archaeon Haloarcula japonica strain TR-1. | Ozawa K, Harashina T, Yatsunami R, Nakamura S | Extremophiles | 2005 | Amino Acid Sequence, Archaeal Proteins/chemistry/*genetics/isolation & purification/*metabolism, Cell Division, Cloning, Molecular, GTP Phosphohydrolases/metabolism, *Gene Expression, Haloarcula/drug effects/*genetics, Histidine/genetics/metabolism, Molecular Sequence Data, Potassium Chloride/pharmacology, Sequence Alignment, Sequence Homology, Amino Acid, Sodium Chloride/pharmacology, Transcription, Genetic/genetics | Enzymology | 10.1007/s00792-005-0443-6 |
| Enzymology | 17150532 | Molecular cloning of transducer genes hjtA and hjtC from extremely halophilic archaeon Haloarcula japonica. | Kosaka T, Ozawa T, Yatsunami R, Nakamura S | Nucleic Acids Symp Ser (Oxf) | 2004 | Amino Acid Sequence, Archaeal Proteins/chemistry, Cloning, Molecular, *Genes, Archaeal, Haloarcula/*genetics, Hydrophobic and Hydrophilic Interactions, Molecular Sequence Data | Genetics | 10.1093/nass/48.1.169 |
| Phylogeny | 17150544 | Isolation of crtI homolog from extremely halophilic archaeon Haloarcula japonica strain TR-1. | Yatsunami R, Takaichi S, Nakamura S | Nucleic Acids Symp Ser (Oxf) | 2004 | Amino Acid Sequence, Archaeal Proteins/chemistry/genetics/*isolation & purification, Base Sequence, Haloarcula/*genetics, Molecular Sequence Data, *Sequence Homology, Amino Acid | Genetics | 10.1093/nass/48.1.193 |
| Enzymology | 25617115 | Effects of salt on the structure, stability, and function of a halophilic dihydrofolate reductase from a hyperhalophilic archaeon, Haloarcula japonica strain TR-1. | Miyashita Y, Ohmae E, Nakasone K, Katayanagi K | Extremophiles | 2015 | Amino Acid Sequence, Archaeal Proteins/*chemistry/metabolism, Enzyme Stability, Haloarcula/*enzymology, Molecular Sequence Data, NADP/metabolism, *Protein Denaturation, Sodium Chloride/chemistry, Tetrahydrofolate Dehydrogenase/*chemistry/metabolism, Urea/chemistry | Metabolism | 10.1007/s00792-015-0732-7 |
| Enzymology | 28349498 | Halophilic mechanism of the enzymatic function of a moderately halophilic dihydrofolate reductase from Haloarcula japonica strain TR-1. | Miyashita Y, Ohmae E, Ikura T, Nakasone K, Katayanagi K | Extremophiles | 2017 | Archaeal Proteins/chemistry/*metabolism, Haloarcula/*enzymology, Kinetics, Protein Binding, Salinity, Tetrahydrofolate Dehydrogenase/chemistry/*metabolism | Metabolism | 10.1007/s00792-017-0928-0 |
| Phylogeny | 33095133 | Haloarcula mannanilytica sp. nov., a galactomannan-degrading haloarchaeon isolated from commercial salt. | Enomoto S, Shimane Y, Ihara K, Kamekura M, Itoh T, Ohkuma M, Takahashi-Ando N, Fukushima Y, Yoshida Y, Usami R, Takai K, Minegishi H | Int J Syst Evol Microbiol | 2020 | Bacterial Typing Techniques, Base Composition, DNA, Archaeal/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Galactose/analogs & derivatives, Haloarcula/*classification/isolation & purification, Japan, Mannans/metabolism, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/*analysis | Transcriptome | 10.1099/ijsem.0.004535 |
| Enzymology | 34215877 | Characterization of 3-isopropylmalate dehydrogenase from extremely halophilic archaeon Haloarcula japonica. | Nagaoka S, Sugiyama N, Yatsunami R, Nakamura S | Biosci Biotechnol Biochem | 2021 | 3-Isopropylmalate Dehydrogenase/chemistry/*metabolism, Amino Acid Sequence, Archaeal Proteins/*metabolism, Biopolymers/chemistry, Genome, Archaeal, Halobacteriales/*enzymology/genetics, Hydrogen-Ion Concentration, Potassium Chloride/analysis, Temperature | Metabolism | 10.1093/bbb/zbab122 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 2497 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6131) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-6131 | |||
| 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 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 75385 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID45242.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 75386 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID312368.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 124043 | Isabel Schober, Julia Koblitz | Data extracted from sequence databases, automatically matched based on designation and taxonomy | ||||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |