This grant leverages considerable existing support to close, finish, annotate and perform comparative genomics analyses on the genomes of four deep-sea microbes. All of these organisms have been or are being sequenced as a result of the Gordon and Betty Moore Foundation Marine Microbiology Initiative. The goal is to develop a genome sequence platform, consisting of all five known genera of piezophilic (high pressure-adapted) bacteria, and to use this resource to locate genes and protein motifs that correlate with life in the depths of the oceans. The organisms to be examined are 1) Photobacterium profundum strain 3TCK, 2) Shewanella benthica strain KT99, 3) Psychromonas sp. strain CNPT3 and 4) Moritella sp. strain PE36. 3TCK is a pressure-sensitive member of the sames species as the piezophile P. profundum strain SS9. KT99 is the fastest growing extreme piezophile and is a member of the most commonly isolated piezophilic species. CNPT3 and PE36 are two of the best studied piezophiles. The available DNA sequences will be reassembled and areas of poor sequence coverage will be resequenced. Gaps will be closed by end sequencing BAC and fosmid libraries and by joining polymerase chain reactions. The resulting closed genomes will be annotated using a variety of software tools and algorithms to analyze genome and protein sequence data and managed by the MAGPIE genome annotation system. Eventually the genomes will be incorporated into a MySQL relational database along with the genomes of comparison piezophilic and related piezosensitive strains. Insertions/deletions and genome rearrangements among strains will be identified and possible differences in protein motifis, amino acid substitutions, codon usage and tRNA and rRNA structure will be explored. Genes under positive selection for variation in the deep sea will be identified, and the three-dimensional structure of selected piezophile-relevant deduced gene products of interest will be modeled. The result of these efforts will be an unprecedented view of the blue prints of life in the largest part of the biosphere: the deep ocean. The investigator is organizing a magazine and video description of marine genomics activities at Scripps Inst. Oceanography for the public.
