Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains.
BACKGROUND
Oceans cover approximately 70% of the Earth's surface with an average depth of 3800 m and a pressure of 38 MPa, thus a large part of the biosphere is occupied by high pressure environments. Piezophilic (pressure-loving) organisms are adapted to deep-sea life and grow optimally at pressures higher than 0.1 MPa. To better understand high pressure adaptation from a genomic point of view three different Photobacterium profundum strains were compared. Using the sequenced piezophile P. profundum strain SS9 as a reference, microarray technology was used to identify the genomic regions missing in two other strains: a pressure adapted strain (named DSJ4) and a pressure-sensitive strain (named 3TCK). Finally, the transcriptome of SS9 grown under different pressure (28 MPa; 45 MPa) and temperature (4 degrees C; 16 degrees C) conditions was analyzed taking into consideration the differentially expressed genes belonging to the flexible gene pool.


RESULTS
These studies indicated the presence of a large flexible gene pool in SS9 characterized by various horizontally acquired elements. This was verified by extensive analysis of GC content, codon usage and genomic signature of the SS9 genome. 171 open reading frames (ORFs) were found to be specifically absent or highly divergent in the piezosensitive strain, but present in the two piezophilic strains. Among these genes, six were found to also be up-regulated by high pressure.


CONCLUSIONS
These data provide information on horizontal gene flow in the deep sea, provide additional details of P. profundum genome expression patterns and suggest genes which could perform critical functions for abyssal survival, including perhaps high pressure growth.
Campanaro
Stefano
S
CRIBI Biotechnology Centre and Dept, of Biology, University of Padova, Via U, Bassi 58/B, 35131 Padova, Italy. stef@cribi.unipd.it
Vezzi
Alessandro
A
Vitulo
Nicola
N
Lauro
Federico M
FM
D'Angelo
Michela
M
Simonato
Francesca
F
Cestaro
Alessandro
A
Malacrida
Giorgio
G
Bertoloni
Giulio
G
Valle
Giorgio
G
Bartlett
Douglas H
DH
D001274:Atmospheric Pressure; D003062:Codon; D017931:DNA Primers / Q000737:chemistry; D005786:Gene Expression Regulation; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D016678:Genome; D016680:Genome, Bacterial; D007091:Image Processing, Computer-Assisted; D008954:Models, Biological; D009792:Oceans and Seas; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames; D010776:Photobacterium / Q000235:genetics*; D010802:Phylogeny; D011312:Pressure; D012333:RNA, Messenger / Q000378:metabolism; D012335:RNA, Ribosomal / Q000235:genetics; D012623:Seawater; D013696:Temperature; D014158:Transcription, Genetic
D003062:Codon; D017931:DNA Primers; D012333:RNA, Messenger; D012335:RNA, Ribosomal