1. Genome sequence of the deep-sea [gamma]-proteobacterium Idiomarina Ioihiensis reveals amino acid fermentation as a source of carbon and energy
- Author
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Hou, Shaobin, Saw, Jimmy H., Lee, Kit Shan, Freitas, Tracey A., Belisle, Claude, Kawarabayasi, Yutaka, Donachie, Stuart P., Pikina, Alla, Galperin, Michael Y., Koonin, Eugene V., Makarova, Kira S., Omelchenko, Marina V., Sorokin, Alexander, Wolf, Yuri I., Li, Qing X., Keum, Young Soo, Campbell, Sonia, Denery, Judith, Aizawa, Shin-Ichi, Shibata, Satoshi, Malahoff, Alexander, and Alam, Maqsudul
- Subjects
Genomes -- Research ,Science and technology - Abstract
We report the complete genome sequence of the deep-sea [gamma]-proteobacterium, Idiomarina Ioihiensis, isolated recently from a hydrothermal vent at 1,300-m depth on the Loihi submarine volcano, Hawaii. The I. Ioihiensis 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. Ioihiensis 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. Ioihiensis 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, lle, Val, Thr, and Met are incomplete. Auxotrophy for Val and Thr was confirmed by in vivo experiments. The I. Ioihiensis 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. Ioihiensis growth are the proteinaceous particles present in the deep sea hydrothermal vent waters. I. Ioihiensis would colonize these particles by using the secreted exopolysaccharide, digest these proteins, and metabolize the resulting peptides and amino acids. In summary, the I. Ioihiensis genome reveals an integrated mechanism of metabolic adaptation to the constantly changing deep-sea hydrothermal ecosystem.
- Published
- 2004