TY - JOUR
T1 - Thermus oshimai JL-2 and T. thermophilus JL-18 genome analysis illuminates pathways for carbon, nitrogen, and sulfur cycling
AU - Murugapiran, Senthil K.
AU - Huntemann, Marcel
AU - Wei, Chia Lin
AU - Han, James
AU - Detter, J. C.
AU - Han, Cliff
AU - Erkkila, Tracy H.
AU - Teshima, Hazuki
AU - Chen, Amy
AU - Kyrpides, Nikos
AU - Mavrommatis, Konstantinos
AU - Markowitz, Victor
AU - Szeto, Ernest
AU - Ivanova, Natalia
AU - Pagani, Ioanna
AU - Pati, Amrita
AU - Goodwin, Lynne
AU - Peters, Lin
AU - Pitluck, Sam
AU - Lam, Jenny
AU - McDonald, Austin I.
AU - Dodsworth, Jeremy A.
AU - Woyke, Tanja
AU - Hedlund, Brian P.
N1 - Funding Information:
The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231. Additional support was sup-
PY - 2013
Y1 - 2013
N2 - 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.
AB - 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.
KW - Denitrification
KW - Great basin
KW - Hot springs
KW - Nitrous oxide
KW - Thermophiles
KW - Thermus
KW - Thermus oshimai
KW - Thermus thermophilus
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U2 - 10.4056/sigs.3667269
DO - 10.4056/sigs.3667269
M3 - Article
C2 - 24019992
AN - SCOPUS:84875396476
SN - 1944-3277
VL - 7
SP - 449
EP - 468
JO - Standards in Genomic Sciences
JF - Standards in Genomic Sciences
IS - 3
ER -