A comprehensive genomic, transcriptomic and proteomic analysis of a hyperosmotic stress sensitive α-proteobacterium

BMC Microbiology

Suely L Gomes³  Michael Hecker¹  Julia Schüler¹  Dirk Albrecht¹  Jörg Bernhardt¹  Rogério F Lourenço³  Christian Kohler² 

[1] Institut for Microbiology, Ernst-Moritz-Arndt Universität, Greifswald, Germany;Present address: Friedrich Loeffler Institut for Medical Microbiology, Greifswald, Germany;Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, 05508-000, SP, Brazil

关键词: Caulobacter crescentus;    Integrative omic analysis;    Compatible solute;    Osmotic stress adaptation;   

Others  :  1212080
DOI  :  10.1186/s12866-015-0404-x

 received in 2014-12-04, accepted in 2015-03-11,  发布年份 2015

【 摘 要 】

Background

With the aim of remaining viable, bacteria must deal with changes in environmental conditions, including increases in external osmolarity. While studies concerning bacterial response to this stress condition have focused on soil, marine and enteric species, this report is about Caulobacter crescentus, a species inhabiting freshwater oligotrophic habitats.

Results

A genomic analysis reported in this study shows that most of the classical genes known to be involved in intracellular solute accumulation under osmotic adaptation are missing in C. crescentus. Consistent with this observation, growth assays revealed a restricted capability of the bacterium to propagate under hyperosmotic stress, and addition of the compatible solute glycine betaine did not improve bacterial resistance. A combination of transcriptomic and proteomic analyses indicated quite similar changes triggered by the presence of either salt or sucrose, including down-regulation of many housekeeping processes and up-regulation of functions related to environmental adaptation. Furthermore, a GC-MS analysis revealed some metabolites at slightly increased levels in stressed cells, but none of them corresponding to well-established compatible solutes.

Conclusion

Despite a clear response to hyperosmotic stress, it seems that the restricted capability of C. crescentus to tolerate this unfavorable condition is probably a consequence of the inability to accumulate intracellular solutes. This finding is consistent with the ecology of the bacterium, which inhabits aquatic environments with low nutrient concentration.

【 授权许可】

   
2015 Kohler et al.; licensee BioMed Central.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

【 参考文献 】

• [1]Yancey P. Compatible and counteracting solutes. In: Cellular and molecular physiology of cell volume regulation. Strange K, editor. CRC Press, Boca Raton; 1994: p.81-109.
• [2]Record MT, Courtenay ES, Cayley DS, Guttman HJ. Responses of E. coli to osmotic stress: large changes in amounts of cytoplasmic solutes and water. Trends Biochem Sci. 1998; 23(4):143-8.
• [3]Galinski E, Trüper HG. Microbial behaviour in salt-stressed ecosystems. FEMS Microbiol Rev. 1994; 15:95-108.
• [4]Ventosa A, Nieto JJ, Oren A. Biology of moderately halophilic aerobic bacteria. Microbiol Mol Biol Rev. 1998; 62(2):504-44.
• [5]Kempf B, Bremer E. Uptake and synthesis of compatible solutes as microbial stress responses to high-osmolality environments. Arch Microbiol. 1998; 170(5):319-30.
• [6]Empadinhas N, da Costa MS. Osmoadaptation mechanisms in prokaryotes: distribution of compatible solutes. Int Microbiol. 2008; 11(3):151-61.
• [7]Csonka LNEW et al.. Osmoregulation. In: Escherichia coli and Salmonella . Neidhardt FC, editor. Cellular and molecular biology. ASM Press, Washington, DC; 1996: p.1210-23.
• [8]Stumpe SSA, Schleyer M, Bakker EP. K+ circulation across the prokaryotic cell membrane: K+-uptake systems. In: Transport processes in eukaryotic and prokaryotic organisms. Konings WN, Kaback HR, Lolkema JS, editors. Elsevier, Amsterdam; 1996: p.473-99.
• [9]Higgins CFCJ, Stirling DA, Sutherland L, Booth IR. Osmotic regulation of gene expression: ionic strength as an intracellular signal? Trends Biochem Sci. 1987; 12:339-44.
• [10]Epstein W. Osmoregulation by potassium transport in Escherichia coli. FEMS Microbiol Rev. 1986; 39:73-8.
• [11]Sleator RD, Hill C. Bacterial osmoadaptation: the role of osmolytes in bacterial stress and virulence. FEMS Microbiol Rev. 2002; 26(1):49-71.
• [12]Giaever HM, Styrvold OB, Kaasen I, Strom AR. Biochemical and genetic characterization of osmoregulatory trehalose synthesis in Escherichia coli. J Bacteriol. 1988; 170(6):2841-9.
• [13]Strom AR, Kaasen I. Trehalose metabolism in Escherichia coli: stress protection and stress regulation of gene expression. Mol Microbiol. 1993; 8(2):205-10.
• [14]Empadinhas N, da Costa MS. Diversity and biosynthesis of compatible solutes in hyper/thermophiles. Int Microbiol. 2006; 9(3):199-206.
• [15]Lapteva NA. Ecological features of distribution of bacteria of the genus Caulobacter in freshwater bodies. Mikrobiologiya. 1987; 56:537-43.
• [16]Poindexter JS. The caulobacters: ubiquitous unusual bacteria. Microbiol Rev. 1981; 45(1):123-79.
• [17]Nierman WC, Feldblyum TV, Laub MT, Paulsen IT, Nelson KE, Eisen JA et al.. Complete genome sequence of Caulobacter crescentus. Proc Natl Acad Sci U S A. 2001; 98(7):4136-41.
• [18]Zuleta LF, Italiani VC, Marques MV. Isolation and characterization of NaCl-sensitive mutants of Caulobacter crescentus. Appl Environ Microbiol. 2003; 69(6):3029-35.
• [19]Lourenco RF, Kohler C, Gomes SL. A two-component system, an anti-sigma factor and two paralogous ECF sigma factors are involved in the control of general stress response in Caulobacter crescentus. Mol Microbiol. 2011; 80(6):1598-612.
• [20]Alvarez-Martinez CE, Lourenco RF, Baldini RL, Laub MT, Gomes SL. The ECF sigma factor sigma(T) is involved in osmotic and oxidative stress responses in Caulobacter crescentus. Mol Microbiol. 2007; 66(5):1240-55.
• [21]Polikanov YS, Blaha GM, Steitz TA. How hibernation factors RMF, HPF, and YfiA turn off protein synthesis. Science. 2012; 336(6083):915-8.
• [22]Rehm BH, Kruger N, Steinbuchel A. A new metabolic link between fatty acid de novo synthesis and polyhydroxyalkanoic acid synthesis. The PHAG gene from Pseudomonas putida KT2440 encodes a 3-hydroxyacyl-acyl carrier protein-coenzyme a transferase. J Biol Chem. 1998; 273(37):24044-51.
• [23]Fiedler S, Steinbuchel A, Rehm BH. PhaG-mediated synthesis of Poly(3-hydroxyalkanoates) consisting of medium-chain-length constituents from nonrelated carbon sources in recombinant Pseudomonas fragi. Appl Environ Microbiol. 2000; 66(5):2117-24.
• [24]Fujita M, Tanaka K, Takahashi H, Amemura A. Transcription of the principal sigma-factor genes, rpoD and rpoS, in Pseudomonas aeruginosa is controlled according to the growth phase. Mol Microbiol. 1994; 13(6):1071-7.
• [25]Sootsuwan K, Thanonkeo P, Keeratirakha N, Thanonkeo S, Jaisil P, Yamada M. Sorbitol required for cell growth and ethanol production by Zymomonas mobilis under heat, ethanol, and osmotic stresses. Biotechnol Biofuels. 2013; 6(1):180. BioMed Central Full Text
• [26]Loos H, Kramer R, Sahm H, Sprenger GA. Sorbitol promotes growth of Zymomonas mobilis in environments with high concentrations of sugar: evidence for a physiological function of glucose-fructose oxidoreductase in osmoprotection. J Bacteriol. 1994; 176(24):7688-93.
• [27]Kadouri D, Jurkevitch E, Okon Y. Poly beta-hydroxybutyrate depolymerase (PhaZ) in Azospirillum brasilense and characterization of a phaZ mutant. Arch Microbiol. 2003; 180(5):309-18.
• [28]Ayub ND, Pettinari MJ, Ruiz JA, Lopez NI. A polyhydroxybutyrate-producing Pseudomonas sp. isolated from Antarctic environments with high stress resistance. Curr Microbiol. 2004; 49(3):170-4.
• [29]Langenbach S, Rehm BH, Steinbuchel A. Functional expression of the PHA synthase gene phaC1 from Pseudomonas aeruginosa in Escherichia coli results in poly(3-hydroxyalkanoate) synthesis. FEMS Microbiol Lett. 1997; 150(2):303-9.
• [30]Britos L, Abeliuk E, Taverner T, Lipton M, McAdams H, Shapiro L. Regulatory response to carbon starvation in Caulobacter crescentus. PLoS One. 2011; 6(4):e18179.
• [31]Boncompagni E, Osteras M, Poggi MC, le Rudulier D. Occurrence of choline and glycine betaine uptake and metabolism in the family rhizobiaceae and their roles in osmoprotection. Appl Environ Microbiol. 1999; 65(5):2072-7.
• [32]Sugawara M, Cytryn EJ, Sadowsky MJ. Functional role of Bradyrhizobium japonicum trehalose biosynthesis and metabolism genes during physiological stress and nodulation. Appl Environ Microbiol. 2010; 76(4):1071-81.
• [33]Chang WS, Franck WL, Cytryn E, Jeong S, Joshi T, Emerich DW et al.. An oligonucleotide microarray resource for transcriptional profiling of Bradyrhizobium japonicum. Mol Plant Microbe Interact. 2007; 20(10):1298-307.
• [34]Fida TT, Breugelmans P, Lavigne R, Coronado E, Johnson DR, van der Meer JR et al.. Exposure to solute stress affects genome-wide expression but not the polycyclic aromatic hydrocarbon-degrading activity of Sphingomonas sp. strain LH128 in biofilms. Appl Environ Microbiol. 2012; 78(23):8311-20.
• [35]Tsuzuki M, Moskvin OV, Kuribayashi M, Sato K, Retamal S, Abo M et al.. Salt stress-induced changes in the transcriptome, compatible solutes, and membrane lipids in the facultatively phototrophic bacterium Rhodobacter sphaeroides. Appl Environ Microbiol. 2011; 77(21):7551-9.
• [36]Dominguez-Ferreras A, Perez-Arnedo R, Becker A, Olivares J, Soto MJ, Sanjuan J. Transcriptome profiling reveals the importance of plasmid pSymB for osmoadaptation of Sinorhizobium meliloti. J Bacteriol. 2006; 188(21):7617-25.
• [37]Ely B. Genetics of Caulobacter crescentus. Methods Enzymol. 1991; 204:372-84.
• [38]Kohler C, Lourenco RF, Avelar GM, Gomes SL. Extracytoplasmic function (ECF) sigma factor sigmaF is involved in Caulobacter crescentus response to heavy metal stress. BMC Microbiol. 2012; 12:210. BioMed Central Full Text
• [39]Bernhardt J, Buttner K, Scharf C, Hecker M. Dual channel imaging of two-dimensional electropherograms in Bacillus subtilis. Electrophoresis. 1999; 20(11):2225-40.
• [40]Berth M, Moser FM, Kolbe M, Bernhardt J. The state of the art in the analysis of two-dimensional gel electrophoresis images. Appl Microbiol Biotechnol. 2007; 76(6):1223-43.
• [41]Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA et al.. TM4 microarray software suite. Methods Enzymol. 2006; 411:134-93.
• [42]Eymann C, Dreisbach A, Albrecht D, Bernhardt J, Becher D, Gentner S et al.. A comprehensive proteome map of growing Bacillus subtilis cells. Proteomics. 2004; 4(10):2849-76.
• [43]Haft DH, Selengut JD, White O. The TIGRFAMs database of protein families. Nucleic Acids Res. 2003; 31(1):371-3.
• [44]Bernhardt J, Funke S, Hecker M, Siebourg J. Visualizing gene expression data via voronoi treemaps, Proceedings of the 2009 Sixth International Symposium on Voronoi Diagrams. IEEE Comput Soc. 2009:233–241.
• [45]Strelkov S, von Elstermann M, Schomburg D. Comprehensive analysis of metabolites in Corynebacterium glutamicum by gas chromatography/mass spectrometry. Biol Chem. 2004; 385(9):853-61.
• [46]Gierok P, Harms M, Richter E, Hildebrandt JP, Lalk M, Mostertz J et al.. Staphylococcus aureus alpha-toxin mediates general and cell type-specific changes in metabolite concentrations of immortalized human airway epithelial cells. PLoS One. 2014; 9(4):e94818.
• [47]Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR et al.. Pfam: the protein families database. Nucleic Acids Res. 2014; 42(Database issue):D222-30.