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

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

doi:10.1186/s40793-017-0229-3

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

Journal Article · Thu Jan 19 00:00:00 EST 2017 · Standards in Genomic Sciences

DOI:https://doi.org/10.1186/s40793-017-0229-3· OSTI ID:1618960

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;

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 ( cbb 3, 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 .

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1618960

Alternate ID(s):: OSTI ID: 1379686

Journal Information:: Standards in Genomic Sciences, Journal Name: Standards in Genomic Sciences Journal Issue: 1 Vol. 12; ISSN 1944-3277

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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

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59 BASIC BIOLOGICAL SCIENCES
betaproteobacteria
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denitrification
sulfur oxidation
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Permanent draft genome of Thiobacillus thioparus DSM 505T, an obligately chemolithoautotrophic member of the Betaproteobacteria

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