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Title: Permanent draft genome of Thermithiobacillus tepidarius DSM 3134 T, a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia

Abstract

Thermithiobacillus tepidarius DSM 3134 T was originally isolated (1983) from the waters of a sulfidic spring entering the Roman Baths (Temple of Sulis-Minerva) at Bath, United Kingdom and is an obligate chemolithoautotroph growing at the expense of reduced sulfur species. This strain has a genome size of 2,958,498 bp. Here we report the genome sequence, annotation and characteristics. The genome comprises 2,902 protein coding and 66 RNA coding genes. Genes responsible for the transaldolase variant of the Calvin-Benson-Bassham cycle were identified along with a biosynthetic horseshoe in lieu of Krebs' cycle sensu stricto. Terminal oxidases were identified, viz. cytochrome c oxidase (cbb 3 , EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). Metalloresistance genes involved in pathways of arsenic and cadmium resistance were found. Evidence of horizontal gene transfer accounting for 5.9 % of the protein-coding genes was found, including transfer from Thiobacillus spp. and Methylococcus capsulatus Bath, isolated from the same spring. A sox gene cluster was found, similar in structure to those from other Acidithiobacillia - by comparison with Thiobacillus thioparus and Paracoccus denitrificans, an additional gene between soxA and soxB was found, annotated as a DUF302-family protein of unknown function. As the Kelly-Friedrich pathway of thiosulfate oxidationmore » (encoded by sox) is not used in Thermithiobacillus spp., the role of the operon (if any) in this species remains unknown. We speculate that DUF302 and sox genes may have a role in periplasmic trithionate oxidation.« less

Authors:
ORCiD logo [1];  [1];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2]
  1. Univ. of Plymouth (United Kingdom). School of Biological Sciences; Univ. of Plymouth (United Kingdom). Sustainable Earth Institute
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1377501
Grant/Contract Number:  
AC02-05CH11231; RG120444
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 11; Journal Issue: 1; Related Information: See also the Erratum: at doi: http://dx.doi.org/10.1186/s40793-016-0197-z; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Thermithiobacillus tepidarius; Acidithiobacillia; Sulfur oxidation; Chemolithoautotroph; Thiosulfate; DUF302

Citation Formats

Boden, Rich, Hutt, Lee P., Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, Tatiparthi, Ngan, Chew Yee, Daum, Chris, Shapiro, Nicole, Markowitz, Victor, Ivanova, Natalia, Woyke, Tanja, and Kyrpides, Nikos. Permanent draft genome of Thermithiobacillus tepidarius DSM 3134T, a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia. United States: N. p., 2016. Web. doi:10.1186/s40793-016-0188-0.
Boden, Rich, Hutt, Lee P., Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, Tatiparthi, Ngan, Chew Yee, Daum, Chris, Shapiro, Nicole, Markowitz, Victor, Ivanova, Natalia, Woyke, Tanja, & Kyrpides, Nikos. Permanent draft genome of Thermithiobacillus tepidarius DSM 3134T, a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia. United States. doi:10.1186/s40793-016-0188-0.
Boden, Rich, Hutt, Lee P., Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, Tatiparthi, Ngan, Chew Yee, Daum, Chris, Shapiro, Nicole, Markowitz, Victor, Ivanova, Natalia, Woyke, Tanja, and Kyrpides, Nikos. Mon . "Permanent draft genome of Thermithiobacillus tepidarius DSM 3134T, a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia". United States. doi:10.1186/s40793-016-0188-0. https://www.osti.gov/servlets/purl/1377501.
@article{osti_1377501,
title = {Permanent draft genome of Thermithiobacillus tepidarius DSM 3134T, a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia},
author = {Boden, Rich and Hutt, Lee P. and Huntemann, Marcel and Clum, Alicia and Pillay, Manoj and Palaniappan, Krishnaveni and Varghese, Neha and Mikhailova, Natalia and Stamatis, Dimitrios and Reddy, Tatiparthi and Ngan, Chew Yee and Daum, Chris and Shapiro, Nicole and Markowitz, Victor and Ivanova, Natalia and Woyke, Tanja and Kyrpides, Nikos},
abstractNote = {Thermithiobacillus tepidarius DSM 3134T was originally isolated (1983) from the waters of a sulfidic spring entering the Roman Baths (Temple of Sulis-Minerva) at Bath, United Kingdom and is an obligate chemolithoautotroph growing at the expense of reduced sulfur species. This strain has a genome size of 2,958,498 bp. Here we report the genome sequence, annotation and characteristics. The genome comprises 2,902 protein coding and 66 RNA coding genes. Genes responsible for the transaldolase variant of the Calvin-Benson-Bassham cycle were identified along with a biosynthetic horseshoe in lieu of Krebs' cycle sensu stricto. Terminal oxidases were identified, viz. cytochrome c oxidase (cbb3 , EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). Metalloresistance genes involved in pathways of arsenic and cadmium resistance were found. Evidence of horizontal gene transfer accounting for 5.9 % of the protein-coding genes was found, including transfer from Thiobacillus spp. and Methylococcus capsulatus Bath, isolated from the same spring. A sox gene cluster was found, similar in structure to those from other Acidithiobacillia - by comparison with Thiobacillus thioparus and Paracoccus denitrificans, an additional gene between soxA and soxB was found, annotated as a DUF302-family protein of unknown function. As the Kelly-Friedrich pathway of thiosulfate oxidation (encoded by sox) is not used in Thermithiobacillus spp., the role of the operon (if any) in this species remains unknown. We speculate that DUF302 and sox genes may have a role in periplasmic trithionate oxidation.},
doi = {10.1186/s40793-016-0188-0},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 11,
place = {United States},
year = {Mon Sep 26 00:00:00 EDT 2016},
month = {Mon Sep 26 00:00:00 EDT 2016}
}

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