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4 - Evaluation of stress response in sulphate-reducing bacteria through genome analysis

Published online by Cambridge University Press:  22 August 2009

By
J. D. Wall ,
H. C. Bill Yen  and
E. C. Drury
Edited by
Larry L. Barton  and
W. Allan Hamilton
Larry L. Barton
Affiliation:
University of New Mexico
W. Allan Hamilton
Affiliation:
University of Aberdeen
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Summary

INTRODUCTION

The unique ability of the anaerobic sulphate-reducing bacteria (SRB) to respire sulphate provides access to niches that may be restricted from other bacteria. However, environmental niches are by definition constantly in flux. Thus, for scientists to reach a level of understanding that will allow prediction and/or control of the activities of the SRB, it is necessary to learn how the bacteria respond to changes in environmental parameters; such as, nutrient availability, presence of toxic substances, altered salt concentrations, temperature fluctuations, and a myriad of other variables. With the recent sequencing of a number of SRB (Klenk et al., 1997; Heidelberg et al., 2004; Rabus et al., 2004), the available proteins and regulatory sites of the bacteria have been revealed. Nevertheless, a significant percentage of the predicted open reading frames (ORFs) encode hypothetical or conserved hypothetical proteins for which functions remain obscure. Much work is yet to be done to elucidate the interplay of functions that allow the SRB to survive or even flourish in the changing conditions prevailing in their environment. Here we discuss preliminary transcriptional analyses of the responses of Desulfovibrio vulgaris Hildenborough to a number of environmental stressors.

A description of optimal growth conditions for D. vulgaris Hildenborough is derived from its early characterization. This strain is a mesophilic Gram-negative anaerobe which was isolated in 1946 from Wealden Clay near Hildenborough, Kent, in the United Kingdom (Postgate, 1984).

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Sulphate-Reducing Bacteria
Environmental and Engineered Systems
 , pp. 141 - 166
Publisher: Cambridge University Press
Print publication year: 2007

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References

Birrell, G. W., Brown, J. A., Wu, H. I.et al. (2002). Transcription response of Saccharomyces cerevisiae to DNA-damaging agents does not identify the genes that protect against these agents. PNAS, 99, 8778–83.CrossRefGoogle Scholar
Blankenhorn, D., Phillips, J. and Slonczowski, J. L. (1999). Acid- and base-induced proteins during aerobic and anaerobic growth of Escherichia coli revealed by two-dimensional gel electrophoresis. J. Bacteriol., 181, 2209–16.Google ScholarPubMed
Bremer, E. and Kramer, R. (2000). Coping with osmotic challenges: osmoregulation through accumulation and release of compatible solutes in bacteria. In Storz, G. and Hengge-Aronis, R. (eds.), Bacterial stress reponses. Washington, DC: ASM Press. pp. 79–97.Google Scholar
Cases, I., Ussery, D. W. and Lorenzo, V. (2003). The sigma54 regulon (sigmulon) of Pseudomonas putida. Environ. Microbiol., 5, 1281–93.CrossRefGoogle ScholarPubMed
Cheung, K. J., Badarinarayana, V., Selinger, D. W., Janse, D. and Church, G. M. (2003). A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli. Genome Res., 13, 206–15.CrossRefGoogle ScholarPubMed
Chhabra, S. R., He, Q., Huang, K. H.et al. (2006). Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough. J. Bacteriol., 188, 1817–28.CrossRefGoogle ScholarPubMed
Colantuoni, C., Henry, G., Zeger, S. and Pevsner, J. (2002). Local mean normalization of microarray element signal intensities across an array surface: quality control and correction of spatially systematic artifacts. Biotechniques, 32, 1316–20.Google ScholarPubMed
Csonka, L. N. and Epstein, W. (1996). Osmoregulation. In Neidhardt, F. C., Curtiss, R. III, Ingraham, J. L.et al. (eds.), Escherichia coli and Salmonella: cellular and molecular biology, 2nd edn. Washington, DC: ASM Press. pp. 1210–23.Google Scholar
Cypionka, H. (1995). Solute transport and cell energetics. In Barton, L. L. (ed.), Sulphate-reducing bacteria. New York: Plenum Press. pp. 151–84.CrossRefGoogle Scholar
Foster, J. W. (2004). Escherichia coli acid resistance: tales of an amateur acidophile. Nat. Rev. Microbiol., 11, 898–907.CrossRefGoogle Scholar
Giaever, G., Chu, A. M., Ni, L.et al. (2002). Functional profiling of the Saccharomyces cerevisiae genome. Nature, 418, 387–91.CrossRefGoogle ScholarPubMed
Gorby, Y. A. and Lovley, D. R. (1992). Enzymatic uranium precipitation. Environ. Sci. Technol., 26, 205–7.CrossRefGoogle Scholar
Graumann, P. L. and Marahiel, M. A. (1998). A superfamily of proteins that contain the cold-shock domain. Trends Biochem. Sci., 23, 286–90.CrossRefGoogle ScholarPubMed
Greene, E. A., Hubert, C., Nemati, M., Jenneman, G. E. and Voordouw, G. (2003). Nitrite reductase activity of sulphate-reducing bacteria prevents their inhibition by nitrate-reducing sulfide-oxidizing bacteria. Environ. Microbiol., 5, 607–17.CrossRefGoogle Scholar
Gross, C. A. (1996). Function and regulation of the heat shock proteins. In Neidhardt, F. C., Curtiss, R. III, Ingraham, E. C.C J. L.. et al. (eds.), Escherichia coli and Salmonella: cellular and molecular biology, 2nd edn. Washington, D.C.: ASM Press. pp. 1382–99.Google Scholar
Hantke, K. and Braun, V. (2000). The art of keeping low and high iron concentrations in balance. In Storz, G. and Hengge-Aronis, R. (eds.), Bacterial stress reponses. Washington, DC: ASM Press. pp. 275–88.Google Scholar
Haveman, S. A., Greene, E. A., Stilwell, C. P., Voordouw, J. K. and Voordouw, G. (2004). Physiological and gene expression analysis of inhibition of Desulfovibrio vulgaris Hildenborough by nitrite. J. Bacteriol., 186, 7944–50.CrossRefGoogle ScholarPubMed
He, Q., Huang, K. H., He, Z. et al. (2006). Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol., 72, 4370–81.CrossRefGoogle ScholarPubMed
Heidelberg, J. F., Seshadri, R., Haveman, S. A.et al. (2004). The genomic sequence of the anaerobic, sulphate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nat. Biotechnol., 22, 554–9.CrossRefGoogle Scholar
Hengge-Aronis, R. (2000). The general stress response in Escherichia coli. In Storz, G. and Hengge-Aronis, R. (eds.), Bacterial stress reponses. Washington, DC: ASM Press. pp. 161–78.Google Scholar
Jones, P. G. and Inouye, M. (1996). RbfA, a 30S ribosomal binding factor, is a cold-shock protein whose absence triggers the cold-shock response. Mol. Microbiol., 21, 1207–18.CrossRefGoogle ScholarPubMed
Kammler, M., Schon, C. and Hantke, K. (1993). Characterization of the ferrous iron uptake system of Escherichia coli. J. Bacteriol., 175, 6212–9.CrossRefGoogle ScholarPubMed
Karatan, E., Duncan, T. R. and Watnick, P. I. (2005). NspS, a predicted polyamine sensor, mediates activation of Vibrio cholerae biofilm formation by norspermidine. J. Bacteriol., 187, 7434–43.CrossRefGoogle ScholarPubMed
Klenk, H. P., Clayton, R. A., Tomb, J. F.et al. (1997). The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature, 390, 364–70.CrossRefGoogle ScholarPubMed
Lovley, D. R., Phillips, E. J. P., Gorby, Y. A. and Landa, E. (1991). Microbial reduction of uranium. Nature, 350, 413–16.CrossRefGoogle Scholar
McFall, E. and Newman, E. B. (1996). Amino acids as carbon sources. In Neidhardt, F. C., Curtiss, R. III, Ingraham, J. L. (eds.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd edn. Washington, DC: ASM Press. pp. 358–79.Google Scholar
Minder, A. C., Fischer, H.-M., Hennecke, H. and Narberhaus, F. (2000). Role of HrcA and CIRCE in the heat shock regulatory network of Bradyrhizobium japonicum. J. Bacteriol., 182, 14–22.CrossRefGoogle ScholarPubMed
Moura, I., Bursakov, S., Costa, C. and Moura, J. J. G. (1997). Nitrate and nitrite utilization in sulphate-reducing bacteria. Anaerobe, 3, 279–90.CrossRefGoogle Scholar
Mukhopadhyay, A., He, Z., Yen, H.-C. (2006). Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach. J. Bacteriol., 188, 4068–78.CrossRefGoogle ScholarPubMed
Nies, D. H. (2004). Incidence and function of sigma factors in Ralstonia metallidurans and other bacteria. Arch. Microbiol., 181, 255–68.CrossRefGoogle ScholarPubMed
Pereira, I. A. C., LeGall, J., Zavier, A. V. and Teixeira, M. (2000). Characterization of heme c nitrite reductase from a non-ammonifying microorganism, Desulfovibrio vulgaris Hildenborough. Biochim. Biophys. Acta, 1481, 119–30.CrossRefGoogle ScholarPubMed
Phadtare, S., Yamanaka, K. and Inouye, M. (2000). The cold shock response. In Storz, G. and Hengge-Aronis, R. (eds.), Bacterial stress responses. Washington, DC: ASM Press. pp. 33–45.Google Scholar
Postgate, J. R. (1984). The sulphate reducing bacteria (2nd edn). Cambridge and London: Cambridge University Press.Google Scholar
Rabus, R., Ruepp, A., Frickey, T.et al. (2004). The genome Desulfotalea psychrophila, a sulphate-reducing bacterium from permanently cold Artic sediments. Environ. Microbiol., 6, 887–902.CrossRefGoogle Scholar
Raivio, T. L. and Silhavy, T. J. (2000). Sensing and responding to envelope stress. In Storz, G. and Hengge-Aronis, R. (eds.), Bacterial stress reponses. Washington, DC: ASM Press. pp. 19–32.Google Scholar
Roberts, R. C., Toochinda, C., Avedissian, M.et al. (1996). Identification of a Caulobacter crescentus operon encoding hrcA, involved in negatively regulating heat-inducible transcription and the chaperone gene grpE. J. Bacteriol., 178, 1829–41.CrossRefGoogle ScholarPubMed
Robey, M. and Cianciotto, N. P. (2002). Legionella pneumophila feoAB promotes ferrous iron uptake and intracellular infection. Infect. Immun., 70, 5659–69.CrossRefGoogle ScholarPubMed
Rodionov, D. A., Dubchak, I., Arkin, A. P., Alm, E. J. and Gelfand, M. S. (2004). Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria. Genome Biol., 5, R90.CrossRefGoogle ScholarPubMed
Stanik, L. M., Stanik, D. M., Schmid, B.et al. (2002). pH-Dependent expression of periplasmic proteins and amino acid catabolism in Escherichia coli. J. Bacteriol., 184, 4246–58.CrossRefGoogle Scholar
Vila-Sanjurjo, A., Schuwirth, B. S., Hau, C. W. and Cate, J. H.D. (2004). Structural basis for the control of translation initiation during stress. Nature Struc. Mol. Bio., 11, 1054–9.CrossRefGoogle ScholarPubMed
Wolfe, B. M., Lui, S. M. and Cowan, J. A. (1994). Desulfoviridin, a multimeric-dissimilatory sulfite reductase from Desulfovibrio vulgaris Hildenborough purification, characterization, kinetics and EPR studies. Eur. J. Biochem., 223, 79–89.CrossRefGoogle ScholarPubMed
Yura, T. K., Kanemori, M. and Morita, M. T. (2000). The heat shock response: regulation and function. In Storz, G. and Hengge-Aronis, R. (eds.), Bacterial stress reponses. Washington, DC: ASM Press. pp. 3–18.Google Scholar
Zuber, U. and Schumann, W. (1994). CIRCE, a novel heat shock element involved in regulation of heat shock operon dnaK ofBacillus subtilis. J. Bacteriol., 176, 1359–63.CrossRefGoogle Scholar

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