title: Permanent draft genome ofThiobacillus thioparusDSM 505T, an obligately chemolithoautotrophic member of theBetaproteobacteria.
abstract: Thiobacillus thioparusDSM 505Tis one of first two isolated strains of inorganic sulfur-oxidisingBacteria. The original strain ofT. thioparuswas lost almost 100 years ago and the working type strain is Culture CT(=DSM 505T= ATCC 8158T) 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 horseshoein lieuof Krebs' cyclesensu stricto. Terminal oxidases were identified,viz. cytochromecoxidase (cbb3, EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). There is a partialsoxoperon of the Kelly-Friedrich pathway of inorganic sulfur-oxidation that containssoxXYZABgenes but lackingsoxCDEF, there is also a lack of the DUF302 gene previously noted in thesoxoperon of other members of the 'Proteobacteria' that can use trithionate as an energy source. In spite of apparently not growing anaerobically with denitrification, thenar,nir,norandnosoperons encoding enzymes of denitrification are found in theT. thioparusgenome, in the same arrangements as in the true denitrifierT. denitrificans.
authors.affiliation: School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, PL4 8AA UK.|Sustainable Earth Institute, University of Plymouth, Drake Circus, Plymouth, PL4 8AA UK.
authors.forename: Lee P
authors.initials: LP
authors.lastname: Hutt
authors.affiliation: DOE Joint Genome Institute, 94598 Walnut Creek, CA USA.
authors.forename: Marcel
authors.initials: M
authors.lastname: Huntemann
authors.affiliation: DOE Joint Genome Institute, 94598 Walnut Creek, CA USA.
authors.forename: Alicia
authors.initials: A
authors.lastname: Clum
authors.affiliation: DOE Joint Genome Institute, 94598 Walnut Creek, CA USA.
authors.forename: Manoj
authors.initials: M
authors.lastname: Pillay
authors.affiliation: DOE Joint Genome Institute, 94598 Walnut Creek, CA USA.
authors.forename: Krishnaveni
authors.initials: K
authors.lastname: Palaniappan
authors.affiliation: DOE Joint Genome Institute, 94598 Walnut Creek, CA USA.
authors.forename: Neha
authors.initials: N
authors.lastname: Varghese
authors.affiliation: DOE Joint Genome Institute, 94598 Walnut Creek, CA USA.
authors.forename: Natalia
authors.initials: N
authors.lastname: Mikhailova
authors.affiliation: DOE Joint Genome Institute, 94598 Walnut Creek, CA USA.
authors.forename: Dimitrios
authors.initials: D
authors.lastname: Stamatis
authors.affiliation: DOE Joint Genome Institute, 94598 Walnut Creek, CA USA.
authors.forename: Tatiparthi
authors.initials: T
authors.lastname: Reddy
authors.affiliation: DOE Joint Genome Institute, 94598 Walnut Creek, CA USA.
authors.forename: Chris
authors.initials: C
authors.lastname: Daum
authors.affiliation: DOE Joint Genome Institute, 94598 Walnut Creek, CA USA.
authors.forename: Nicole
authors.initials: N
authors.lastname: Shapiro
authors.affiliation: DOE Joint Genome Institute, 94598 Walnut Creek, CA USA.
authors.forename: Natalia
authors.initials: N
authors.lastname: Ivanova
authors.affiliation: DOE Joint Genome Institute, 94598 Walnut Creek, CA USA.
authors.forename: Nikos
authors.initials: N
authors.lastname: Kyrpides
authors.affiliation: DOE Joint Genome Institute, 94598 Walnut Creek, CA USA.
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.affiliation: School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, PL4 8AA UK.|Sustainable Earth Institute, University of Plymouth, Drake Circus, Plymouth, PL4 8AA UK.
authors.forename: Rich
authors.identifier: 0000-0002-4496-152X
authors.initials: R
authors.lastname: Boden
keywords: Betaproteobacteria; Carboxysome; Chemolithoautotroph; Denitrification; Sulfur oxidation; Thiobacillus thioparus