Abstract
BackgroundOceans 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°C; 16°C) conditions was analyzed taking into consideration the differentially expressed genes belonging to the flexible gene pool.ResultsThese 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.ConclusionThese 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.
Highlights
Oceans cover approximately 70% of the Earth's surface with an average depth of 3800 m and a pressure of 38 MPa, a large part of the biosphere is occupied by high pressure environments
Genomic comparison between different P. profundum strains The first question that arises from the genomic comparison between SS9 and the other two strains is: "how many SS9 genes are missing or highly divergent in the 3TCK and DSJ4 genomes?". 544 open reading frames (ORFs) were determined to be absent in 3TCK strain genome, 313 (9.1% of the ORFs located on chr1) belong to the SS9 chr1 and 231 (11.5% of the ORFs located on chr2) to chr2
This indicates that chr2 (Figure 2) contains a proportionally larger flexible gene pool and that it has been the target of more gene transfer events for its size (~2.2 Mbp) than chr1 (~4.1 Mbp) that contains the most
Summary
Oceans cover approximately 70% of the Earth's surface with an average depth of 3800 m and a pressure of 38 MPa, 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. Gamma-proteobacterial isolate, Photobacterium profundum strain SS9, has been the subject of a number of studies addressing the nature and regulation of genes important for pressure-sensing and high pressure adaptation, owing to the relative ease of its cultivation as well as its genetic tractability [1]. P. profundum strain DSJ4 was recovered from a sediment sample obtained from the Ryukyu Trench (Japan) at a depth of 5110 m and displays its optimum growth at 10 MPa (with little change in growth at pressures up to 50 MPa) and a temperature optimum of 10°C [3]. A.) and exhibits optimal growth at atmospheric pressure and a broad temperature span for growth from below 0°C to above 20°C
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