Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete Genome Sequences of Thermus thermophilus Strains AA2-20 and AA2-29, Isolated from Arima Onsen in Japan.

ABSTRACT: We isolated halophilic and thermophilic Thermus thermophilus strains AA2-20 and AA2-29 from nonvolcanic, oceanic Arima Onsen (hot spring) in Japan. Here, we report the complete genome sequences of these organisms to gain insights into halophilicity.

SUBMITTER: Miyazaki K

PROVIDER: S-EPMC6675998 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Complete Genome Sequences of Thermus thermophilus Strains AA2-20 and AA2-29, Isolated from Arima Onsen in Japan.

Miyazaki Kentaro K Tomariguchi Natsuki N

Microbiology resource announcements 20190801 31

We isolated halophilic and thermophilic <i>Thermus thermophilus</i> strains AA2-20 and AA2-29 from nonvolcanic, oceanic Arima Onsen (hot spring) in Japan. Here, we report the complete genome sequences of these organisms to gain insights into halophilicity. ...[more]

PMID: 31371550

Similar Datasets

Complete Genome Sequences of Rhodothermus marinus Strains AA2-13 and AA3-38, Isolated from Arima Onsen Hot Spring in Japan.

Project description:We isolated Rhodothermus marinus strains AA2-13 and AA3-38 from Arima Onsen, a hot spring in Japan, and sequenced their genomes. The average nucleotide identity between their genomes was 99.2%, and that with the genome of R. marinus strain DSM 4252T (isolated from Iceland) was ∼95.2%, suggesting close relationships among these strains.

| S-EPMC6952675 | biostudies-literature

Complete Genome Sequences of Four Halophilic Thermus thermophilus Strains Isolated from Arima Hot Spring in Japan.

Project description:We isolated four Thermus thermophilus strains from Arima Hot Spring in Japan. Complete genome sequencing revealed that they showed average nucleotide identities of ≥99.21% to each other and to strains previously isolated from the same spot, but of ≤97.86% to strains from geographically different spots in Japan, reflecting habitat-specific genomic conservation.

| S-EPMC8496358 | biostudies-literature

Complete Genome Sequences of Thermus thermophilus Strains HB5002 and HB5008, Isolated from Mine Hot Spring in Japan.

Project description:We isolated Thermus thermophilus strains HB5002 and HB5008 from Mine Hot Spring in Japan. Whole-genome sequencing revealed that they showed ∼100% average nucleotide identity to each other, ≥98.53% to the T. thermophilus strains originating from the same spot but ≤97.64% to the T. thermophilus strains from geographically different places in Japan.

| S-EPMC8063650 | biostudies-literature

Complete Genome Sequence of Rubrobacter xylanophilus Strain AA3-22, Isolated from Arima Onsen in Japan.

Project description:Rubrobacter xylanophilus strain AA3-22, belonging to the phylum Actinobacteria, was isolated from nonvolcanic Arima Onsen (hot spring) in Japan. Here, we report the complete genome sequence of this organism, which was obtained by combining Oxford Nanopore long-read and Illumina short-read sequencing data.

| S-EPMC6706694 | biostudies-literature

Complete Genome Sequences of <i>Thermus</i> Strains Isolated from Senami Hot Spring in Japan.

Project description:Extremely thermophilic strains belonging to the genus Thermus were isolated from Senami Hot Spring in Japan. Here, I report the complete genome sequences of five Thermus thermophilus strains and one Thermus brockianus strain, which were obtained by combining Oxford Nanopore long-read and DNBSEQ or Illumina short-read sequencing data.

| S-EPMC9302132 | biostudies-literature

Lateral transfer of the denitrification pathway genes among Thermus thermophilus strains.

Project description:Nitrate respiration is a common and strain-specific property in Thermus thermophilus encoded by the nitrate respiration conjugative element (NCE) that can be laterally transferred by conjugation. In contrast, nitrite respiration and further denitrification steps are restricted to a few isolates of this species. These later steps of the denitrification pathway are under the regulatory control of an NCE-encoded transcription factor, but nothing is known about their coding sequences or its putative genetic linkage to the NCE. In this study we examine the genetic linkage between nitrate and nitrite respiration through lateral gene transfer (LGT) assays and describe a cluster of genes encoding the nitrite-nitric oxide respiration in T. thermophilus PRQ25. We show that the whole denitrification pathway can be transferred from the denitrificant strain PRQ25 to an aerobic strain, HB27, and that the genes coding for nitrite and nitric oxide respiration are encoded near the NCE. Sequence data from the draft genome of PRQ25 confirmed these results and allowed us to describe the most compact nor-nir cluster known thus far and to demonstrate the expression and activities of the encoded enzymes in the HB27 denitrificant derivatives obtained by LGT. We conclude that this NCE nor-nir supercluster constitutes a whole denitrification island that can be spread by lateral transfer among Thermus thermophilus strains.

| S-EPMC3067210 | biostudies-literature

Complete Genome Sequencing of Thermus thermophilus Strain HC11, Isolated from Mine Geyser in Japan.

Project description:Thermus thermophilus strain HC11 was isolated from Mine Geyser in Japan, where type strain HB8 was isolated 50?years ago. In this article, the complete genome sequence of HC11 is presented. HC11 shares the highest average nucleotide identity with HB8 among known T. thermophilus genomes (93.1%) with no genetic rearrangements.

| S-EPMC6763646 | biostudies-literature

Complete Genome Sequence of Thermus thermophilus Strain HB5018, Isolated from Mine Hot Spring in Japan.

Project description:We isolated Thermus thermophilus strain HB5018 from Mine Hot Spring in Japan, where the type strain HB8 was isolated nearly half a century ago. The complete genome sequence of HB5018 showed 99.1% average nucleotide identity with HB8, suggesting strict species conservation in the habitat over the past 50 years.

| S-EPMC7953284 | biostudies-literature

Thiostrepton-resistant mutants of Thermus thermophilus.

Project description:Ribosomal protein L11 and its associated binding site on 23S rRNA together comprise one of the principle components that mediate interactions of translation factors with the ribosome. This site is also the target of the antibiotic thiostrepton, which has been proposed to act by preventing important structural transitions that occur in this region of the ribosome during protein synthesis. Here, we describe the isolation and characterization of spontaneous thiostrepton-resistant mutants of the extreme thermophile, Thermus thermophilus. All mutations were found at conserved positions in the flexible N-terminal domain of L11 or at conserved positions in the L11-binding site of 23S rRNA. A number of the mutant ribosomes were affected in in vitro EF-G-dependent GTP hydrolysis but all showed resistance to thiostrepton at levels ranging from high to moderate. Structure probing revealed that some of the mutations in L11 result in enhanced reactivity of adjacent rRNA bases to chemical probes, suggesting a more open conformation of this region. These data suggest that increased flexibility of the factor binding site results in resistance to thiostrepton by counteracting the conformation-stabilizing effect of the antibiotic.

| S-EPMC434449 | biostudies-literature

Transferable denitrification capability of Thermus thermophilus.

Project description:Laboratory-adapted strains of Thermus spp. have been shown to require oxygen for growth, including the model strains T. thermophilus HB27 and HB8. In contrast, many isolates of this species that have not been intensively grown under laboratory conditions keep the capability to grow anaerobically with one or more electron acceptors. The use of nitrogen oxides, especially nitrate, as electron acceptors is one of the most widespread capabilities among these facultative strains. In this process, nitrate is reduced to nitrite by a reductase (Nar) that also functions as electron transporter toward nitrite and nitric oxide reductases when nitrate is scarce, effectively replacing respiratory complex III. In many T. thermophilus denitrificant strains, most electrons for Nar are provided by a new class of NADH dehydrogenase (Nrc). The ability to reduce nitrite to NO and subsequently to N2O by the corresponding Nir and Nor reductases is also strain specific. The genes encoding the capabilities for nitrate (nar) and nitrite (nir and nor) respiration are easily transferred between T. thermophilus strains by natural competence or by a conjugation-like process and may be easily lost upon continuous growth under aerobic conditions. The reason for this instability is apparently related to the fact that these metabolic capabilities are encoded in gene cluster islands, which are delimited by insertion sequences and integrated within highly variable regions of easily transferable extrachromosomal elements. Together with the chromosomal genes, these plasmid-associated genetic islands constitute the extended pangenome of T. thermophilus that provides this species with an enhanced capability to adapt to changing environments.

| S-EPMC3911032 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data