title: Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy.
abstract: We report the complete genome sequence of the deep-sea gamma-proteobacterium, Idiomarina loihiensis, isolated recently from a hydrothermal vent at 1,300-m depth on the Loihi submarine volcano, Hawaii. The I. loihiensis genome comprises a single chromosome of 2,839,318 base pairs, encoding 2,640 proteins, four rRNA operons, and 56 tRNA genes. A comparison of I. loihiensis to the genomes of other gamma-proteobacteria reveals abundance of amino acid transport and degradation enzymes, but a loss of sugar transport systems and certain enzymes of sugar metabolism. This finding suggests that I. loihiensis relies primarily on amino acid catabolism, rather than on sugar fermentation, for carbon and energy. Enzymes for biosynthesis of purines, pyrimidines, the majority of amino acids, and coenzymes are encoded in the genome, but biosynthetic pathways for Leu, Ile, Val, Thr, and Met are incomplete. Auxotrophy for Val and Thr was confirmed by in vivo experiments. The I. loihiensis genome contains a cluster of 32 genes encoding enzymes for exopolysaccharide and capsular polysaccharide synthesis. It also encodes diverse peptidases, a variety of peptide and amino acid uptake systems, and versatile signal transduction machinery. We propose that the source of amino acids for I. loihiensis growth are the proteinaceous particles present in the deep sea hydrothermal vent waters. I. loihiensis would colonize these particles by using the secreted exopolysaccharide, digest these proteins, and metabolize the resulting peptides and amino acids. In summary, the I. loihiensis genome reveals an integrated mechanism of metabolic adaptation to the constantly changing deep-sea hydrothermal ecosystem.
authors.affiliation: Department of Microbiology, University of Hawaii, Snyder Hall 111, 2538 The Mall, Honolulu, HI 96822, USA.
authors.forename: Shaobin
authors.initials: S
authors.lastname: Hou
authors.forename: Jimmy H
authors.initials: JH
authors.lastname: Saw
authors.forename: Kit Shan
authors.initials: KS
authors.lastname: Lee
authors.forename: Tracey A
authors.initials: TA
authors.lastname: Freitas
authors.forename: Claude
authors.initials: C
authors.lastname: Belisle
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Kawarabayasi
authors.forename: Stuart P
authors.initials: SP
authors.lastname: Donachie
authors.forename: Alla
authors.initials: A
authors.lastname: Pikina
authors.forename: Michael Y
authors.initials: MY
authors.lastname: Galperin
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Koonin
authors.forename: Kira S
authors.initials: KS
authors.lastname: Makarova
authors.forename: Marina V
authors.initials: MV
authors.lastname: Omelchenko
authors.forename: Alexander
authors.initials: A
authors.lastname: Sorokin
authors.forename: Yuri I
authors.initials: YI
authors.lastname: Wolf
authors.forename: Qing X
authors.initials: QX
authors.lastname: Li
authors.forename: Young Soo
authors.initials: YS
authors.lastname: Keum
authors.forename: Sonia
authors.initials: S
authors.lastname: Campbell
authors.forename: Judith
authors.initials: J
authors.lastname: Denery
authors.forename: Shin-Ichi
authors.initials: S
authors.lastname: Aizawa
authors.forename: Satoshi
authors.initials: S
authors.lastname: Shibata
authors.forename: Alexander
authors.initials: A
authors.lastname: Malahoff
authors.forename: Maqsudul
authors.initials: M
authors.lastname: Alam
mesh_terms: D000596:Amino Acids / Q000378:metabolism*; D002244:Carbon / Q000378:metabolism*; D002633:Chemotaxis; D005285:Fermentation; D020563:Gammaproteobacteria / Q000235:genetics*; D016678:Genome; D016680:Genome, Bacterial; D008954:Models, Biological; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D015398:Signal Transduction
chemical_list: D000596:Amino Acids; D012335:RNA, Ribosomal; D002244:Carbon; D012343:RNA, Transfer