Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125

Abstract

A considerable fraction of life develops in the sea at temperatures lower than 15 degrees C. Little is known about the adaptive features selected under those conditions. We present the analysis of the genome sequence of the fast growing Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. We find that it copes with the increased solubility of oxygen at low temperature by multiplying dioxygen scavenging while deleting whole pathways producing reactive oxygen species. Dioxygen-consuming lipid desaturases achieve both protection against oxygen and synthesis of lipids making the membrane fluid. A remarkable strategy for avoidance of reactive oxygen species generation is developed by P. haloplanktis, with elimination of the ubiquitous molybdopterin-dependent metabolism. The P. haloplanktis proteome reveals a concerted amino acid usage bias specific to psychrophiles, consistently appearing apt to accommodate asparagine, a residue prone to make proteins age. Adding to its originality, P. haloplanktis further differs from its marine counterparts with recruitment of a plasmid origin of replication for its second chromosome.

Figure 1.

Circular representation of the Pseudoalteromonas haloplanktis genome. Circles display (from the outside): (1) predicted coding regions transcribed in the clockwise direction; (2) predicted coding regions transcribed in the counterclockwise direction. Genes displayed in 1 and 2 are color-coded according to different functional categories: salmon indicates amino acid biosynthesis; orange indicates purines, pyrimidines, nucleosides, and nucleotides; purple indicates fatty acid and phospholipid metabolism; light blue indicates biosynthesis of cofactors, prosthetic groups, and carriers; light green indicates cell envelope; red indicates cellular processes; brown indicates central intermediary metabolism; yellow indicates DNA metabolism; green indicates energy metabolism; pink indicates protein fate/synthesis; blue indicates regulatory functions; grey indicates transcription; teal indicates transport and binding proteins; and black indicates hypothetical and conserved hypothetical proteins. (3) tRNAs (green) and rRNA (pink) on chrI/genes similar to phage proteins (red) on chrII; (4) and tonB and tonB-like genes in grey. Chromosome II gene names similar to that of the R1 plasmid replication apparatus (unidirectional) are colored in green.

Figure 2.

Putative orthologs and syntenies between the genome of P. haloplanktis and the genome of related bacteria. The alphabetic letters A to F refer to the Supplemental Table 4 (T4, A to F). (A) The percentage of P. haloplanktis genes homologs to a selection of 34 complete bacterial proteomes (i.e., 30% identity and a ratio of 0.8 of the length of the smaller protein to that of the larger one) is represented by red bars for chrI and by yellow bars for chrII. The percentage of P. haloplanktis genes in synteny groups with a selection of 34 complete bacterial genomes is represented by green bars for chrI and by blue bars for chrII. The closest organism is S. oneidensis. (B) Comparison of the gene content of Pseudoalteromonas haloplanktis, Shewanella oneidensis, Vibrio vulnificus, Photobacterium profundum, and Idiomarina ioihiensis. Putative orthologs are defined as genes showing a minimum of 30% identity and a ratio of 0.8 of the length of the smaller protein to that of the larger one, or as two genes included in a synteny group. The intersections between the three circles give the number of genes found in the two or three compared species. Genes outside these areas are specific to the corresponding organism. The total number of annotated genes is also given under each species name.

Figure 3.

Distribution of the protein sequences on the CA space determined by the three first factors. The first one discriminates proteins by their hydrophobicity; the second one, by the GC content of genes coding for them; and the third one, by their asparagine content. Five classes of proteins are found by clustering method (see “General Features of Proteome”) and are represented: (1) IIMP by pink triangles, (2) proteins involved in the metabolism of small molecules by blue diamonds, (3) proteins associated to information transfer pathways by red circles, (4) proteins associated to the outer membrane or secreted by green stars, and (5) proteins with unknown functions, or likely to be of phage origin, by yellow squares. Amino acids are represented by black pluses.

Figure 4.

hns complementation in E. coli with P. haloplanktis csrA. A DNA fragment encompassing P. haloplanktis gene csrA with 140 bp of its upstream region was cloned into plasmid pcDNA2.1 (pDIA616) and the phenotypes of the resulting E. coli hns transformants were compared to the hns mutant (BE1410) and to the wild-type FB8 parental strain. (A) Motility assay: Partial motility is restored with the csrA gene of P. haloplanktis. Other phenotypes such as serine sensitivity of the hns mutant are restored by the csrA gene as well. (B) Growth at 25°C: overnight cultures were diluted to 0.05 OD₆₀₀ in LB medium with ampicillin 100 μg/mL, and growth was monitored (as in Dersch et al. 1994). Significant improvement of growth is witnessed with the csrA gene of P. haloplanktis. (C) CsrA-dependent storage of glycogen in E. coli MG1655. Expression of P. haloplanktis csrA inhibits glycogen storage (light iodine color, right panel).