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Title: Permanent draft genome of Thiobacillus thioparus DSM 505T, an obligately chemolithoautotrophic member of the Betaproteobacteria

Abstract

Thiobacillus thioparus DSM 505 T is one of first two isolated strains of inorganic sulfur-oxidising Bacteria. The original strain of T. thioparus was lost almost 100 years ago and the working type strain is Culture C T (=DSM 505 T = ATCC 8158 T ) isolated by Starkey in 1934 from agricultural soil at Rutgers University, New Jersey, USA. It is an obligate chemolithoautotroph that conserves energy from the oxidation of reduced inorganic sulfur compounds using the Kelly-Trudinger pathway and uses it to fix carbon dioxide It is not capable of heterotrophic or mixotrophic growth. The strain has a genome size of 3,201,518 bp. Here we report the genome sequence, annotation and characteristics. The genome contains 3,135 protein coding and 62 RNA coding genes. Genes encoding the transaldolase variant of the Calvin-Benson-Bassham cycle were also identified and an operon encoding carboxysomes, along with Smith's 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). There is a partial sox operon of the Kelly-Friedrich pathway of inorganic sulfur-oxidation that contains soxXYZAB genes but lacking soxCDEF, there is also a lack of the DUF302 gene previouslymore » noted in the sox operon of other members of the 'Proteobacteria' that can use trithionate as an energy source. In spite of apparently not growing anaerobically with denitrification, the nar, nir, nor and nos operons encoding enzymes of denitrification are found in the T. thioparus genome, in the same arrangements as in the true denitrifier T. denitrificans.« less

Authors:
 [1];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2]; ORCiD logo [1]
  1. Univ. of Plymouth (United Kingdom). School of Biological and Marine Sciences and Sustainable Earth Inst.
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1379686
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; thiobacillus thioparus; betaproteobacteria; sulfur oxidation; chemolithoautotroph; carboxysome; denitrification

Citation Formats

Hutt, Lee P., Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, Tatiparthi, Daum, Chris, Shapiro, Nicole, Ivanova, Natalia, Kyrpides, Nikos, Woyke, Tanja, and Boden, Rich. Permanent draft genome of Thiobacillus thioparus DSM 505T, an obligately chemolithoautotrophic member of the Betaproteobacteria. United States: N. p., 2017. Web. doi:10.1186/s40793-017-0229-3.
Hutt, Lee P., Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, Tatiparthi, Daum, Chris, Shapiro, Nicole, Ivanova, Natalia, Kyrpides, Nikos, Woyke, Tanja, & Boden, Rich. Permanent draft genome of Thiobacillus thioparus DSM 505T, an obligately chemolithoautotrophic member of the Betaproteobacteria. United States. doi:10.1186/s40793-017-0229-3.
Hutt, Lee P., Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, Tatiparthi, Daum, Chris, Shapiro, Nicole, Ivanova, Natalia, Kyrpides, Nikos, Woyke, Tanja, and Boden, Rich. Thu . "Permanent draft genome of Thiobacillus thioparus DSM 505T, an obligately chemolithoautotrophic member of the Betaproteobacteria". United States. doi:10.1186/s40793-017-0229-3. https://www.osti.gov/servlets/purl/1379686.
@article{osti_1379686,
title = {Permanent draft genome of Thiobacillus thioparus DSM 505T, an obligately chemolithoautotrophic member of the Betaproteobacteria},
author = {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 Daum, Chris and Shapiro, Nicole and Ivanova, Natalia and Kyrpides, Nikos and Woyke, Tanja and Boden, Rich},
abstractNote = {Thiobacillus thioparus DSM 505 T is one of first two isolated strains of inorganic sulfur-oxidising Bacteria. The original strain of T. thioparus was lost almost 100 years ago and the working type strain is Culture C T (=DSM 505 T = ATCC 8158 T ) isolated by Starkey in 1934 from agricultural soil at Rutgers University, New Jersey, USA. It is an obligate chemolithoautotroph that conserves energy from the oxidation of reduced inorganic sulfur compounds using the Kelly-Trudinger pathway and uses it to fix carbon dioxide It is not capable of heterotrophic or mixotrophic growth. The strain has a genome size of 3,201,518 bp. Here we report the genome sequence, annotation and characteristics. The genome contains 3,135 protein coding and 62 RNA coding genes. Genes encoding the transaldolase variant of the Calvin-Benson-Bassham cycle were also identified and an operon encoding carboxysomes, along with Smith's 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). There is a partial sox operon of the Kelly-Friedrich pathway of inorganic sulfur-oxidation that contains soxXYZAB genes but lacking soxCDEF, there is also a lack of the DUF302 gene previously noted in the sox operon of other members of the 'Proteobacteria' that can use trithionate as an energy source. In spite of apparently not growing anaerobically with denitrification, the nar, nir, nor and nos operons encoding enzymes of denitrification are found in the T. thioparus genome, in the same arrangements as in the true denitrifier T. denitrificans.},
doi = {10.1186/s40793-017-0229-3},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 12,
place = {United States},
year = {Thu Jan 19 00:00:00 EST 2017},
month = {Thu Jan 19 00:00:00 EST 2017}
}

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