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

• Authors: Beata Guzow-Krzemińska , Tomasz Gąsior , Agnieszka Szalewska-Pałasz
• Languages of publication: EN

Abstracts

EN

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.

Keywords

EN

ppGpp; stringent response; marine bacteria

• Publisher: Polish Biochemical Society
• Journal: Acta Biochimica Polonica
• Year: 2015
• Volume: 62
• Issue: 4
• Pages: 773-783

Dates

published

2015

received

2015-07-30

revised

2015-09-18

accepted

2015-10-05

(unknown)

2015-12-07

Contributors

author

Beata Guzow-Krzemińska

• Department of Molecular Biology, University of Gdansk, Gdańsk, Poland

author

Tomasz Gąsior

• Department of Molecular Biology, University of Gdansk, Gdańsk, Poland

author

Agnieszka Szalewska-Pałasz

• Department of Molecular Biology, University of Gdansk, Gdańsk, Poland

References

• Amy PS, Pauling C, Morita RY (1983) Recovery from nutrient starvation by a marine Vibrio sp. Appl Environ Microbiol 45: 1685-1690. PMID: 6191662.
• Atkinson GC, Tenson T, Hauryliuk V (2011) The RelA/SpoT Homolog (RSH) Superfamily: Distribution and Functional Evolution of ppGpp Synthetases and Hydrolases across the Tree of Life. Stiller JW, ed. PLoS ONE 6: e23479.
• Battesti A, Bouveret E (2006) Acyl carrier protein/Spot interaction, the switch linking SpoT dependent stress response to fatty acid metabolism. Mol Microbiol 62: 1048-1063.
• Braeken K, Moris M, Daniels R, Vanderleyden J, Michiels J (2006) New horizons for (p)ppGpp in bacterial and plant physiology. Trends Microbiol 14: 45-54.
• Cabaj A, Palińska K, Kosakowska A, Kurlenda J (2006) Heterotrophic bacteria from brackish water of the southern Baltic Sea: biochemical and molecular identification and characterization. Oceanologia 48: 525-543.
• Dalebroux ZD, Svensson SL, Gaynor EC, Swanson MS (2010) ppGpp conjures bacterial virulence. Microbiol Mol Biol Rev 74: 171-99.
• Flärdh K, Cohen PS, Kjelleberg S (1992) Ribosomes exist in large excess over the apparent demand for protein synthesis during carbon starvation in marine Vibrio sp. strain CCUG 15956. J Bacteriol 174: 6780-6788. PMID: 1383195.
• Flärdh K, Axberg T, Albertson NH, Kjelleberg S (1994) Stringent control during carbon starvation of marine Vibrio sp. strain S14: molecular cloning, nucleotide sequence, and deletion of the relA gene. J Bacteriol 176: 5949-5957. PMID: 7928955.
• Hogg T, Mechold U, Malke H, Cashel M, Hilgenfeld R (2004) Conformational antagonism between opposing active sites in a bifunctional RelA/SpoT homolog modulates (p)ppGpp metabolism during the stringent response. Cell 117: 57-68.
• Kurath G, Morita RY (1983) Starvation-survival physiological studies of a marine Pseudomonas sp. Appl Environ Microbiol. 45: 1206-1211. PMID: 16346265.
• Miller MA, Pfeiffer W, Schwartz T (2010) Creating the CIPRES Science Gateway for inference of large phylogenetic trees in Proceedings of the Gateway Computing Environments Workshop (GCE), New Orleans, LA pp 1-8.
• Mudryk ZJ, Podgórska B (2005) Generic composition and respiratory activity of heterotrophic bacteria of marine sandy beach (Baltic Sea). Pol J Ecol 53: 97-103.
• Ostling J, Flärdh K, Kjelleberg S (1995) Isolation of a carbon starvation regulatory mutant in a marine Vibrio strain. J Bacteriol 177: 6978-6982. PMID: 7592494.
• Ostling J, Holmquist L, Kjelleberg S (1996) Global analysis of the carbon starvation response of a marine Vibrio species with disruptions in genes homologous to relA and spoT. J Bacteriol 178: 4901-4908. PMID 8759854.
• Page RD (1996) TreeView: an application to display phylogenetic trees on personal computers. Computer applications in the biosciences: CABIOS 12: 357-358.
• Potrykus K, Cashel M (2008) (p)ppGpp: still magical? Annu Rev Microbiol 62: 35-51.
• Riemann L, Leitet C, Pommier T, Simu K, Holmfeldt K, Larsson U, Hagström A (2008) The native bacterioplankton community in the central Baltic sea is influenced by freshwater bacterial species. Appl Environ Microbiol 74: 503-515.
• Sjöstedt J, Koch-Schmidt P, Pontarp M, Canbäck B, Tunlid A, Lundberg P, Hagström A, Riemann L (2012) Recruitment of members from the rare biosphere of marine bacterioplankton communities after an environmental disturbance. Appl Environ Microbiol 78: 1361-1369.
• Sogin ML, Morrison HG, Huber JA, Welch MD, Huse SM, Neal PR, Arrieta JM, Herndl GJ (2006) Microbial diversity in the deep sea and the underexplored 'rare biosphere'. Proc Natl Acad Sci USA 103: 12115-12120.
• Stolle C, Labrenz M, Meeske C, Jürgens K (2011) Bacterioneuston community structure in the southern Baltic sea and its dependence on meteorological conditions. Appl Environ Microbiol 77: 3726-3733.
• Sun D, Lee G, Lee JH, Kim HY, Rhee HW, Park SY, Kim KJ, Kim Y, Kim BY, Hong JI, Park C, Choy HE, Kim JH, Jeon YH, Chung J (2010) A metazoan ortholog of SpoT hydrolyzes ppGpp and functions in starvation responses. Nat Struct Mol Biol 17: 1188-1194.
• Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.

Identifiers

DOI

10.18388/abp.2015_1132