Document Detail

Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy.
MedLine Citation:
PMID:  15596722     Owner:  NLM     Status:  MEDLINE    
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.
Shaobin Hou; Jimmy H Saw; Kit Shan Lee; Tracey A Freitas; Claude Belisle; Yutaka Kawarabayasi; Stuart P Donachie; Alla Pikina; Michael Y Galperin; Eugene V Koonin; Kira S Makarova; Marina V Omelchenko; Alexander Sorokin; Yuri I Wolf; Qing X Li; Young Soo Keum; Sonia Campbell; Judith Denery; Shin-Ichi Aizawa; Satoshi Shibata; Alexander Malahoff; Maqsudul Alam
Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.     Date:  2004-12-13
Journal Detail:
Title:  Proceedings of the National Academy of Sciences of the United States of America     Volume:  101     ISSN:  0027-8424     ISO Abbreviation:  Proc. Natl. Acad. Sci. U.S.A.     Publication Date:  2004 Dec 
Date Detail:
Created Date:  2004-12-29     Completed Date:  2005-02-28     Revised Date:  2012-12-20    
Medline Journal Info:
Nlm Unique ID:  7505876     Medline TA:  Proc Natl Acad Sci U S A     Country:  United States    
Other Details:
Languages:  eng     Pagination:  18036-41     Citation Subset:  IM    
Department of Microbiology, University of Hawaii, Snyder Hall 111, 2538 The Mall, Honolulu, HI 96822, USA.
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MeSH Terms
Amino Acids / metabolism*
Carbon / metabolism*
Gammaproteobacteria / genetics*
Genome, Bacterial*
Models, Biological
Molecular Sequence Data
Multigene Family
RNA, Ribosomal / genetics
RNA, Transfer / genetics
Signal Transduction
Grant Support
Reg. No./Substance:
0/Amino Acids; 0/RNA, Ribosomal; 7440-44-0/Carbon; 9014-25-9/RNA, Transfer

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