Phylogenetic relationship of the stringent response-related genes of marine bacteria

Bacteria living in marine environment encounter various challenges and limitations, thus in order to survive, they need to employ efficient stress-response mechanisms. One of these mechanisms is the stringent response, where unusual nucleotides, guanosine tetra- and pentaphosphates, herald starvation and physico-chemical stresses. All so far sequenced free-living bacteria contain the gene(s) responsible for (p)ppGpp synthesis - rsh (named after Escherichia coli genes, relA and spoT). Two similar genes were identified mostly in β- and γ-proteobacteria while other bacteria have only one gene coding the dual function of (p)ppGpp synthesis and degradation. Although the presence of (p)ppGpp-mediated response to the stress conditions has been shown for a few, and predicted for some other marine microorganisms, the (p)ppGpp effects may vary among different organisms. Thus, in this work we asked whether marine bacteria could have evolved a genetic adaptation specifically suited to adapt to environment with limited resources. The phylogenetic analyses of SpoT, RelA and RSH proteins from organisms associated with marine environment showed, however, that the evolutionary correlations obtained for these proteins are congruent with those constructed for 16S rRNA sequences and reflect taxonomical relationships of these organisms. Likewise, the similarity of specific amino acid residues indispensable for catalytic activity of these enzymes is very high, and any observed changes parallel with the taxonomical and evolutionary relationships. However, potential homologs of Mesh1 enzyme (metazoan SpoT homologs) that occur in both eukaryotic and prokaryotic organisms and contain the hydrolytic domain orthologous to SpoT were identified in Cellulophaga, Erythrobacter and Flavobacterium genera for the first time, as well as in soil bacterium Cytophaga hutchinsonii and freshwater Rhodothermus marinus.