Thermus oshimai JL-2 and T. thermophilus JL-18 genome analysis illuminates pathways for carbon, nitrogen, and sulfur cycling | Zendy

Senthil K. Murugapiran | Zendy; Marcel Huntemann | Zendy; ChiaLin Wei | Zendy; James Han | Zendy; John C. Detter | Zendy; Cliff Han | Zendy; Tracy Erkkila | Zendy; Hazuki Teshima | Zendy; Amy Chen | Zendy; Nikos C. Kyrpides | Zendy; Konstantinos Mavrommatis | Zendy; Victor Markowitz | Zendy; Ernest Szeto | Zendy; Natalia Ivanova | Zendy; Ioanna Pagani | Zendy; Amrita Pati | Zendy; Lynne Goodwin | Zendy; Lin Peters | Zendy; Sam Pitluck | Zendy; Jenny Lam | Zendy; Austin I. McDonald | Zendy; Jeremy A. Dodsworth | Zendy; Tanja Woyke | Zendy; Brian P. Hedlund | Zendy

Open Access

Thermus oshimai JL-2 and T. thermophilus JL-18 genome analysis illuminates pathways for carbon, nitrogen, and sulfur cycling

Author(s) -

Senthil K. Murugapiran,

Marcel Huntemann,

ChiaLin Wei,

James Han,

John C. Detter,

Cliff Han,

Tracy Erkkila,

Hazuki Teshima,

Amy Chen,

Nikos C. Kyrpides,

Konstantinos Mavrommatis,

Victor Markowitz,

Ernest Szeto,

Natalia Ivanova,

Ioanna Pagani,

Amrita Pati,

Lynne Goodwin,

Lin Peters,

Sam Pitluck,

Jenny Lam,

Austin I. McDonald,

Jeremy A. Dodsworth,

Tanja Woyke,

Brian P. Hedlund

Publication year - 2013

Publication title -

standards in genomic sciences

Language(s) - English

Resource type - Journals

ISSN - 1944-3277

DOI - 10.4056/sigs.3667269

Subject(s) - thermus thermophilus , biology , synteny , genetics , nitrite reductase , biochemistry , nitrous oxide reductase , gene , gene cluster , genome , escherichia coli , nitrate reductase , enzyme

The complete genomes of Thermus oshimai JL-2 and T. thermophilus JL-18 each consist of a circular chromosome, 2.07 Mb and 1.9 Mb, respectively, and two plasmids ranging from 0.27 Mb to 57.2 kb. Comparison of the T. thermophilus JL-18 chromosome with those from other strains of T. thermophilus revealed a high degree of synteny, whereas the megaplasmids from the same strains were highly plastic. The T. oshimai JL-2 chromosome and megaplasmids shared little or no synteny with other sequenced Thermus strains. Phylogenomic analyses using a concatenated set of conserved proteins confirmed the phylogenetic and taxonomic assignments based on 16S rRNA phylogenetics. Both chromosomes encode a complete glycolysis, tricarboxylic acid (TCA) cycle, and pentose phosphate pathway plus glucosidases, glycosidases, proteases, and peptidases, highlighting highly versatile heterotrophic capabilities. Megaplasmids of both strains contained a gene cluster encoding enzymes predicted to catalyze the sequential reduction of nitrate to nitrous oxide; however, the nitrous oxide reductase required for the terminal step in denitrification was absent, consistent with their incomplete denitrification phenotypes. A sox gene cluster was identified in both chromosomes, suggesting a mode of chemolithotrophy. In addition, nrf and psr gene clusters in T. oshmai JL-2 suggest respiratory nitrite ammonification and polysulfide reduction as possible modes of anaerobic respiration.

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