Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy. Export

@article{citeulike:2755704, 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.}, address = {Department of Microbiology, University of Hawaii, Snyder Hall 111, 2538 The Mall, Honolulu, HI 96822, USA.}, author = {Hou, S. and Saw, J. H. and Lee, K. S. and Freitas, T. A. and Belisle, C. and Kawarabayasi, Y. and Donachie, S. P. and Pikina, A. and Galperin, M. Y. and Koonin, E. V. and Makarova, K. S. and Omelchenko, M. V. and Sorokin, A. and Wolf, Y. I. and Li, Q. X. and Keum, Y. S. and Campbell, S. and Denery, J. and Aizawa, S. and Shibata, S. and Malahoff, A. and Alam, M.}, citeulike-article-id = {2755704}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0407638102}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/15596722}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=15596722}, day = {28}, doi = {10.1073/pnas.0407638102}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, keywords = {bacteria, genome}, month = {December}, number = {52}, pages = {18036--18041}, posted-at = {2008-05-05 09:31:22}, priority = {2}, title = {Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy.}, url = {http://dx.doi.org/10.1073/pnas.0407638102}, volume = {101}, year = {2004} }

TY - JOUR ID - citeulike:2755704 L3 - citeulike-article-id:2755704 N2 - 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. IS - 52 JF - Proceedings of the National Academy of Sciences of the United States of America SN - 0027-8424 AD - Department of Microbiology, University of Hawaii, Snyder Hall 111, 2538 The Mall, Honolulu, HI 96822, USA. EP - 18041 TI - Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy. VL - 101 SP - 18036 KW - bacteria KW - genome AU - Hou, S AU - Saw, JH AU - Lee, KS AU - Freitas, TA AU - Belisle, C AU - Kawarabayasi, Y AU - Donachie, SP AU - Pikina, A AU - Galperin, MY AU - Koonin, EV AU - Makarova, KS AU - Omelchenko, MV AU - Sorokin, A AU - Wolf, YI AU - Li, QX AU - Keum, YS AU - Campbell, S AU - Denery, J AU - Aizawa, S AU - Shibata, S AU - Malahoff, A AU - Alam, M PY - 2004/12/28/ UR - http://dx.doi.org/10.1073/pnas.0407638102 ER -