Thermus oshimai JL-2 and T. thermophilus JL-18 genome analysis illuminates pathways for carbon, nitrogen, and sulfur cycling. Issue 3 (November 2013)

• Record Type: Journal Article
• Authors: Murugapiran, Senthil; Huntemann, Marcel; Wei, Chia-Lin; Han, James; Detter, J.; Han, Cliff; Erkkila, Tracy; Teshima, Hazuki; Chen, Amy; Kyrpides, Nikos; Mavrommatis, Konstantinos; Markowitz, Victor; Szeto, Ernest; Ivanova, Natalia; Pagani, Ioanna; Pati, Amrita; Goodwin, Lynne; Peters, Lin; Pitluck, Sam; Lam, Jenny; McDonald, Austin; Dodsworth, Jeremy; Woyke, Tanja; Hedlund, Brian
• Is Part Of: Standards in genomic sciences. Volume 7:Issue 3(2012)
• Page Start: 449
• Page End: 468
• Publication Date: 2013-11
• Subjects: Thermus -- Thermus oshimai -- Thermus thermophilus -- thermophiles -- hot springs -- denitrification -- nitrous oxide -- Great Basin; Genomics -- Periodicals; Genomics -- Periodicals; Genomics; Periodicals; 572.8605
• DOI: 10.4056/sigs.3667269
• Languages: English
• ISSNs: 1944-3277

Abstract

Abstract The complete genomes ofThermus oshimai JL-2 andT. 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 theT. thermophilus JL-18 chromosome with those from other strains ofT. thermophilus revealed a high degree of synteny, whereas the megaplasmids from the same strains were highly plastic. TheT. oshimai JL-2 chromosome and megaplasmids shared little or no synteny with other sequencedThermus 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. Asox gene cluster was identified in both chromosomes, suggesting a mode of chemolithotrophy. In addition, nrf andpsr gene clusters inT. oshmai JL-2 suggest respiratory nitrite ammonification and polysulfide reduction as possible modes of anaerobic respiration.