1887

Abstract

The ubiquitous bacterial second messenger bis-(3′-5′)-cyclic dimeric GMP (c-di-GMP) is involved in the regulation of numerous processes including biofilm formation, motility, virulence, cell cycle and differentiation. In this study, we searched the genome of the ecologically important marine alphaproteobacterium Dinoroseobacter shibae DFL12 for genes encoding putative c-di-GMP-modulating enzymes. Overall, D. shibae was found to possess two diguanylate cyclases (Dshi_2814 and Dshi_2820) as well as two c-di-GMP-specific phosphodiesterases (Dhi_0329 and Dshi_3065). Recombinant expression and purification followed by enzymatic analysis revealed that all four proteins exhibit their proposed activity. Furthermore, adjacent to Dshi_2814 we identified a gene encoding a heme nitric oxide/oxygen binding (H-NOX) protein. These proteins are often found in association with c-di-GMP signal transduction pathways and modulate their function through binding of diatomic gases such as nitric oxide. Here, we demonstrate that H-NOX constitutes a functional unit together with the diguanylate cyclase Dshi_2814. NO-bound H-NOX strongly inhibits DGC activity. Based on these results, and with respect to previously published data including micro-array analysis, we propose an interlinkage of c-di-GMP signalling with cell–cell communication and differentiation in D. shibae.

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2018-09-17
2024-04-26
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References

  1. Biebl H, Allgaier M, Tindall BJ, Koblizek M, Lünsdorf H et al. Dinoroseobacter shibae gen. nov., sp. nov., a new aerobic phototrophic bacterium isolated from dinoflagellates. Int J Syst Evol Microbiol 2005; 55:1089–1096 [View Article][PubMed]
    [Google Scholar]
  2. Wagner-Döbler I, Ballhausen B, Berger M, Brinkhoff T, Buchholz I et al. The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea. ISME J 2010; 4:61–77 [View Article][PubMed]
    [Google Scholar]
  3. Ebert M, Laaß S, Burghartz M, Petersen J, Koßmehl S et al. Transposon mutagenesis identified chromosomal and plasmid genes essential for adaptation of the marine bacterium Dinoroseobacter shibae to anaerobic conditions. J Bacteriol 2013; 195:4769–4777 [View Article][PubMed]
    [Google Scholar]
  4. Laass S, Kleist S, Bill N, Drüppel K, Kossmehl S et al. Gene regulatory and metabolic adaptation processes of Dinoroseobacter shibae DFL12T during oxygen depletion. J Biol Chem 2014; 289:13219–13231 [View Article][PubMed]
    [Google Scholar]
  5. Bill N, Tomasch J, Riemer A, Müller K, Kleist S et al. Fixation of CO2 using the ethylmalonyl-CoA pathway in the photoheterotrophic marine bacterium Dinoroseobacter shibae. Environ Microbiol 2017; 19:2645–2660 [View Article][PubMed]
    [Google Scholar]
  6. Allgaier M, Uphoff H, Felske A, Wagner-Döbler I. Aerobic anoxygenic photosynthesis in Roseobacter clade bacteria from diverse marine habitats. Appl Environ Microbiol 2003; 69:5051–5059 [View Article][PubMed]
    [Google Scholar]
  7. Patzelt D, Wang H, Buchholz I, Rohde M, Gröbe L et al. You are what you talk: quorum sensing induces individual morphologies and cell division modes in Dinoroseobacter shibae. ISME J 2013; 7:2274–2286 [View Article][PubMed]
    [Google Scholar]
  8. Wang H, Ziesche L, Frank O, Michael V, Martin M et al. The CtrA phosphorelay integrates differentiation and communication in the marine alphaproteobacterium Dinoroseobacter shibae. BMC Genomics 2014; 15:130 [View Article][PubMed]
    [Google Scholar]
  9. Laub MT, Chen SL, Shapiro L, McAdams HH. Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle. Proc Natl Acad Sci USA 2002; 99:4632–4637 [View Article][PubMed]
    [Google Scholar]
  10. Lori C, Ozaki S, Steiner S, Böhm R, Abel S et al. Cyclic di-GMP acts as a cell cycle oscillator to drive chromosome replication. Nature 2015; 523:236–239 [View Article][PubMed]
    [Google Scholar]
  11. Hengge R. Principles of c-di-GMP signalling in bacteria. Nat Rev Microbiol 2009; 7:263–273 [View Article][PubMed]
    [Google Scholar]
  12. Römling U, Galperin MY, Gomelsky M. Cyclic di-GMP: the first 25 years of a universal bacterial second messenger. Microbiol Mol Biol Rev 2013; 77:1–52 [View Article][PubMed]
    [Google Scholar]
  13. Galperin MY, Nikolskaya AN, Koonin EV. Novel domains of the prokaryotic two-component signal transduction systems. FEMS Microbiol Lett 2001; 203:11–21[PubMed]
    [Google Scholar]
  14. Kulasakara H, Lee V, Brencic A, Liberati N, Urbach J et al. Analysis of Pseudomonas aeruginosa diguanylate cyclases and phosphodiesterases reveals a role for bis-(3'-5')-cyclic-GMP in virulence. Proc Natl Acad Sci USA 2006; 103:2839–2844 [View Article][PubMed]
    [Google Scholar]
  15. Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 1970; 227:680–685 [View Article][PubMed]
    [Google Scholar]
  16. Gill SC, von Hippel PH. Calculation of protein extinction coefficients from amino acid sequence data. Anal Biochem 1989; 182:319–326[PubMed]
    [Google Scholar]
  17. Christen M, Christen B, Folcher M, Schauerte A, Jenal U. Identification and characterization of a cyclic di-GMP-specific phosphodiesterase and its allosteric control by GTP. J Biol Chem 2005; 280:30829–30837 [View Article][PubMed]
    [Google Scholar]
  18. Paul R, Weiser S, Amiot NC, Chan C, Schirmer T et al. Cell cycle-dependent dynamic localization of a bacterial response regulator with a novel di-guanylate cyclase output domain. Genes Dev 2004; 18:715–727 [View Article][PubMed]
    [Google Scholar]
  19. Li Y, Heine S, Entian M, Sauer K, Frankenberg-Dinkel N. NO-induced biofilm dispersion in Pseudomonas aeruginosa is mediated by an MHYT domain-coupled phosphodiesterase. J Bacteriol 2013; 195:3531–3542 [View Article][PubMed]
    [Google Scholar]
  20. Kyhse-Andersen J. Electroblotting of multiple gels: a simple apparatus without buffer tank for rapid transfer of proteins from polyacrylamide to nitrocellulose. J Biochem Biophys Methods 1984; 10:203–209 [View Article][PubMed]
    [Google Scholar]
  21. Boehm A, Kaiser M, Li H, Spangler C, Kasper CA et al. Second messenger-mediated adjustment of bacterial swimming velocity. Cell 2010; 141:107–116 [View Article][PubMed]
    [Google Scholar]
  22. Plate L, Marletta MA. Nitric oxide-sensing H-NOX proteins govern bacterial communal behavior. Trends Biochem Sci 2013; 38:566–575 [View Article][PubMed]
    [Google Scholar]
  23. Boon EM, Marletta MA. Ligand discrimination in soluble guanylate cyclase and the H-NOX family of heme sensor proteins. Curr Opin Chem Biol 2005; 9:441–446 [View Article][PubMed]
    [Google Scholar]
  24. Karow DS, Pan D, Tran R, Pellicena P, Presley A et al. Spectroscopic characterization of the soluble guanylate cyclase-like heme domains from Vibrio cholerae and Thermoanaerobacter tengcongensis. Biochemistry 2004; 43:10203–10211 [View Article][PubMed]
    [Google Scholar]
  25. Carlson HK, Vance RE, Marletta MA. H-NOX regulation of c-di-GMP metabolism and biofilm formation in Legionella pneumophila. Mol Microbiol 2010; 77:930–942 [View Article][PubMed]
    [Google Scholar]
  26. Price MS, Chao LY, Marletta MA. Shewanella oneidensis MR-1 H-NOX regulation of a histidine kinase by nitric oxide. Biochemistry 2007; 46:13677–13683 [View Article][PubMed]
    [Google Scholar]
  27. Plate L, Marletta MA. Nitric oxide modulates bacterial biofilm formation through a multicomponent cyclic-di-GMP signaling network. Mol Cell 2012; 46:449–460 [View Article][PubMed]
    [Google Scholar]
  28. Liu N, Xu Y, Hossain S, Huang N, Coursolle D et al. Nitric oxide regulation of cyclic di-GMP synthesis and hydrolysis in Shewanella woodyi. Biochemistry 2012; 51:2087–2099 [View Article][PubMed]
    [Google Scholar]
  29. Ebert M, Laaß S, Thürmer A, Roselius L, Eckweiler D et al. FnrL and three Dnr regulators are used for the metabolic adaptation to low oxygen tension in Dinoroseobacter shibae. Front Microbiol 2017; 8: [View Article][PubMed]
    [Google Scholar]
  30. Rao M, Smith BC, Marletta MA. Nitric oxide mediates biofilm formation and symbiosis in Silicibacter sp. strain TrichCH4B. MBio 2015; 6:e00206-15 [View Article][PubMed]
    [Google Scholar]
  31. Brown PJ, Hardy GG, Trimble MJ, Brun YV. Complex regulatory pathways coordinate cell-cycle progression and development in Caulobacter crescentus. Adv Microb Physiol 2009; 54:1–101 [View Article][PubMed]
    [Google Scholar]
  32. Studier FW, Rosenberg AH, Dunn JJ, Dubendorff JW. Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol 1990; 185:60–89[PubMed]
    [Google Scholar]
  33. Yanisch-Perron C, Vieira J, Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 1985; 33:103–119 [View Article][PubMed]
    [Google Scholar]
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