Cyclic‐di‐GMP‐mediated signalling within the σS network of Escherichia coli

Bis‐(3′−5′)‐cyclic‐di‐guanosine monophosphate (c‐di‐GMP) is a bacterial signalling molecule produced by diguanylate cyclases (DGC, carrying GGDEF domains) and degraded by specific phosphodiesterases (PDE, carrying EAL domains). Neither its full physiological impact nor its effector mechanisms are currently understood. Also, the existence of multiple GGDEF/EAL genes in the genomes of most species raises questions about output specificity and robustness of c‐di‐GMP signalling. Using microarray and gene fusion analyses, we demonstrate that at least five of the 29 GGDEF/EAL genes in Escherichia coli are not only stationary phase‐induced under the control of the general stress response master regulator σS (RpoS), but also exhibit differential control by additional environmental and temporal signals. Two of the corresponding proteins, YdaM (GGDEF only) and YciR (GGDEF + EAL), which in vitro show DGC and PDE activity, respectively, play an antagonistic role in the expression of the biofilm‐associated curli fimbriae. This control occurs at the level of transcription of the curli and cellulose regulator CsgD. Moreover, we show that H‐NS positively affects curli expression by inversely controlling the expression of ydaM and yciR. Furthermore, we demonstrate a temporally fine‐tuned GGDEF cascade in which YdaM controls the expression of another GGDEF protein, YaiC. By genome‐wide microarray analysis, evidence is provided that YdaM and YciR strongly and nearly exclusively control CsgD‐regulated genes. We conclude that specific GGDEF/EAL proteins have very distinct expression patterns, and when present in physiological amounts, can act in a highly precise, non‐global and perhaps microcompartmented manner on a few or even a single specific target(s).

[1]  M. Chapman,et al.  Secretion of curli fibre subunits is mediated by the outer membrane‐localized CsgG protein , 2006, Molecular microbiology.

[2]  J. Ghigo,et al.  Combined Inactivation and Expression Strategy To Study Gene Function under Physiological Conditions: Application to Identification of New Escherichia coli Adhesins , 2005, Journal of bacteriology.

[3]  J. Lazzaroni,et al.  CpxR/OmpR Interplay Regulates Curli Gene Expression in Response to Osmolarity in Escherichia coli , 2005, Journal of bacteriology.

[4]  David A. D'Argenio,et al.  Cyclic di-GMP as a bacterial second messenger. , 2004, Microbiology.

[5]  S. Normark,et al.  AgfD, the checkpoint of multicellular and aggregative behaviour in Salmonella typhimurium regulates at least two independent pathways , 2000, Molecular microbiology.

[6]  S. Mangan,et al.  Structure and function of the feed-forward loop network motif , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Michael Y. Galperin,et al.  Novel domains of the prokaryotic two-component signal transduction systems. , 2001, FEMS microbiology letters.

[8]  A. Camilli,et al.  Cyclic Diguanylate Regulates Vibrio cholerae Virulence Gene Expression , 2005, Infection and Immunity.

[9]  D. Amikam,et al.  c‐di‐GMP‐binding protein, a new factor regulating cellulose synthesis in Acetobacter xylinum , 1997, FEBS letters.

[10]  David A. D'Argenio,et al.  Autolysis and Autoaggregation in Pseudomonas aeruginosa Colony Morphology Mutants , 2002, Journal of bacteriology.

[11]  U. Römling,et al.  GGDEF and EAL domains inversely regulate cyclic di‐GMP levels and transition from sessility to motility , 2004, Molecular microbiology.

[12]  V. Wendisch,et al.  Genome-Wide Analysis of the General Stress Response Network in Escherichia coli: σS-Dependent Genes, Promoters, and Sigma Factor Selectivity , 2005, Journal of bacteriology.

[13]  S. McLeod,et al.  Coactivation of the RpoS-Dependent proPP2 Promoter by Fis and Cyclic AMP Receptor Protein , 2000, Journal of bacteriology.

[14]  Jeffrey H. Miller Experiments in molecular genetics , 1972 .

[15]  D. Karaolis,et al.  3′,5′-Cyclic Diguanylic Acid Reduces the Virulence of Biofilm-Forming Staphylococcus aureus Strains in a Mouse Model of Mastitis Infection , 2005, Antimicrobial Agents and Chemotherapy.

[16]  S. Shen-Orr,et al.  Network motifs: simple building blocks of complex networks. , 2002, Science.

[17]  B. Lazazzera Lessons from DNA microarray analysis: the gene expression profile of biofilms. , 2005, Current opinion in microbiology.

[18]  A. Camilli,et al.  Cyclic diguanylate (c‐di‐GMP) regulates Vibrio cholerae biofilm formation , 2004, Molecular microbiology.

[19]  A. Camilli,et al.  The EAL Domain Protein VieA Is a Cyclic Diguanylate Phosphodiesterase* , 2005, Journal of Biological Chemistry.

[20]  B. Giese,et al.  Cell cycle-dependent dynamic localization of a bacterial response regulator with a novel di-guanylate cyclase output domain. , 2004, Genes & development.

[21]  S. Normark,et al.  Expression of two csg operons is required for production of fibronectin‐ and Congo red‐binding curli polymers in Escherichia coli K‐12 , 1995, Molecular microbiology.

[22]  Markus Meuwly,et al.  Allosteric Control of Cyclic di-GMP Signaling* , 2006, Journal of Biological Chemistry.

[23]  M. Rohde,et al.  The multicellular morphotypes of Salmonella typhimurium and Escherichia coli produce cellulose as the second component of the extracellular matrix , 2001, Molecular microbiology.

[24]  W. Sierralta,et al.  Multicellular and aggregative behaviour of Salmonella typhimurium strains is controlled by mutations in the agfD promoter , 1998, Molecular microbiology.

[25]  Y. Hayakawa,et al.  Genome-wide Transcriptional Profile of Escherichia coli in Response to High Levels of the Second Messenger 3′,5′-Cyclic Diguanylic Acid* , 2006, Journal of Biological Chemistry.

[26]  B. Giese,et al.  Structural basis of activity and allosteric control of diguanylate cyclase. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[27]  Jeremy D. Glasner,et al.  Systematic Mutagenesis of the Escherichia coli Genome , 2004, Journal of bacteriology.

[28]  R. Hengge-aronis,et al.  Identification of a central regulator of stationary‐phase gene expression in Escherichia coli , 1991, Molecular microbiology.

[29]  B. Wanner,et al.  One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[30]  R. Hengge-aronis,et al.  The cellular concentration of the sigma S subunit of RNA polymerase in Escherichia coli is controlled at the levels of transcription, translation, and protein stability. , 1994, Genes & development.

[31]  Roger A. Jones,et al.  A glutamate‐alanine‐leucine (EAL) domain protein of Salmonella controls bacterial survival in mice, antioxidant defence and killing of macrophages: role of cyclic diGMP , 2005, Molecular microbiology.

[32]  U. Römling,et al.  Characterization of the rdar morphotype, a multicellular behaviour in Enterobacteriaceae , 2005, Cellular and Molecular Life Sciences CMLS.

[33]  R. Hengge-aronis,et al.  Role for the histone-like protein H-NS in growth phase-dependent and osmotic regulation of sigma S and many sigma S-dependent genes in Escherichia coli , 1995, Journal of bacteriology.

[34]  A. Zehnder,et al.  The curli biosynthesis regulator CsgD co-ordinates the expression of both positive and negative determinants for biofilm formation in Escherichia coli. , 2003, Microbiology.

[35]  Mark Gomelsky,et al.  Cyclic Diguanylate Is a Ubiquitous Signaling Molecule in Bacteria: Insights into Biochemistry of the GGDEF Protein Domain , 2005, Journal of bacteriology.

[36]  J. H. Boom,et al.  Regulation of cellulose synthesis in Acetobacter xylinum by cyclic diguanylic acid , 1987, Nature.

[37]  S. Normark,et al.  Fibronectin binding mediated by a novel class of surface organelles on Escherichia coll , 1989, Nature.

[38]  R. Hengge-aronis,et al.  Role of activator site position and a distal UP‐element half‐site for sigma factor selectivity at a CRP/H‐NS‐activated σS‐dependent promoter in Escherichia coli , 2001, Molecular microbiology.

[39]  A. Khodursky,et al.  Adaptation to famine: A family of stationary-phase genes revealed by microarray analysis , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[40]  S. Normark,et al.  The RpoS Sigma factor relieves H‐NS‐mediated transcriptional repression of csgA, the subunit gene of fibronectin‐binding curli in Escherichia coli , 1993, Molecular microbiology.

[41]  S. Shen-Orr,et al.  Networks Network Motifs : Simple Building Blocks of Complex , 2002 .

[42]  C. Dorel,et al.  Gene Expression Regulation by the Curli Activator CsgD Protein: Modulation of Cellulose Biosynthesis and Control of Negative Determinants for Microbial Adhesion , 2006, Journal of bacteriology.

[43]  R. Simons,et al.  Improved single and multicopy lac-based cloning vectors for protein and operon fusions. , 1987, Gene.

[44]  C. Dozois,et al.  MlrA, a novel regulator of curli (AgF) and extracellular matrix synthesis by Escherichia coli and Salmonella enterica serovar Typhimurium , 2001, Molecular microbiology.

[45]  S. Normark,et al.  σS‐dependent growth‐phase induction of the csgBA promoter in Escherichia coli can be achieved in vivo by σ70 in the absence of the nucleoid‐associated protein H‐NS , 1994, Molecular microbiology.

[46]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[47]  M. Casadaban,et al.  Transposition and fusion of the lac genes to selected promoters in Escherichia coli using bacteriophage lambda and Mu. , 1976, Journal of molecular biology.

[48]  M. Gilles-Gonzalez,et al.  Phosphodiesterase A1, a regulator of cellulose synthesis in Acetobacter xylinum, is a heme-based sensor. , 2001, Biochemistry.

[49]  U. Römling,et al.  Expression of cellulose and curli fimbriae by Escherichia coli isolated from the gastrointestinal tract. , 2005, Journal of medical microbiology.

[50]  S. Gottesman Micros for microbes: non-coding regulatory RNAs in bacteria. , 2005, Trends in genetics : TIG.

[51]  Chankyu Park,et al.  Complex regulation of csgD promoter activity by global regulatory proteins , 2003, Molecular microbiology.

[52]  D. Belin,et al.  Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter , 1995, Journal of bacteriology.

[53]  C. Solano,et al.  Role of the GGDEF protein family in Salmonella cellulose biosynthesis and biofilm formation , 2004, Molecular microbiology.

[54]  G. May,et al.  The osmZ (bglY) gene encodes the DNA-binding protein H-NS (H1a), a component of the Escherichia coli K12 nucleoid , 1990, Molecular and General Genetics MGG.

[55]  R. Hengge-aronis,et al.  Signal Transduction and Regulatory Mechanisms Involved in Control of the σS (RpoS) Subunit of RNA Polymerase , 2002, Microbiology and Molecular Biology Reviews.

[56]  C. Dorman H-NS: a universal regulator for a dynamic genome , 2004, Nature Reviews Microbiology.

[57]  N. Ausmees,et al.  Structural and putative regulatory genes involved in cellulose synthesis in Rhizobium leguminosarum bv. trifolii. , 1999, Microbiology.

[58]  Regine Hengge,et al.  Multiple stress signal integration in the regulation of the complex σS‐dependent csiD‐ygaF‐gabDTP operon in Escherichia coli , 2003, Molecular microbiology.

[59]  Andrew J. Schmidt,et al.  The Ubiquitous Protein Domain EAL Is a Cyclic Diguanylate-Specific Phosphodiesterase: Enzymatically Active and Inactive EAL Domains , 2005, Journal of bacteriology.

[60]  Arkady B. Khodursky,et al.  Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[61]  Bentley Lim,et al.  Cyclic‐diGMP signal transduction systems in Vibrio cholerae: modulation of rugosity and biofilm formation , 2006, Molecular microbiology.

[62]  B. Kempf,et al.  Interactions of the nucleoid-associated DNA-binding protein H-NS with the regulatory region of the osmotically controlled proU operon of Escherichia coli. , 1994, The Journal of biological chemistry.

[63]  Matthias Christen,et al.  Identification and Characterization of a Cyclic di-GMP-specific Phosphodiesterase and Its Allosteric Control by GTP* , 2005, Journal of Biological Chemistry.

[64]  Michael Y. Galperin,et al.  C‐di‐GMP: the dawning of a novel bacterial signalling system , 2005, Molecular microbiology.

[65]  S. Rimsky Structure of the histone-like protein H-NS and its role in regulation and genome superstructure. , 2004, Current opinion in microbiology.

[66]  Patrick Goymer,et al.  Role of the GGDEF regulator PleD in polar development of Caulobacter crescentus , 2003, Molecular microbiology.

[67]  C. Prigent-Combaret,et al.  Complex Regulatory Network Controls Initial Adhesion and Biofilm Formation in Escherichia coli via Regulation of thecsgD Gene , 2001, Journal of bacteriology.

[68]  U. Römling,et al.  Hierarchical involvement of various GGDEF domain proteins in rdar morphotype development of Salmonella enterica serovar Typhimurium , 2006, Molecular microbiology.

[69]  Peter Ross,et al.  Three cdg Operons Control Cellular Turnover of Cyclic Di-GMP in Acetobacter xylinum: Genetic Organization and Occurrence of Conserved Domains in Isoenzymes , 1998, Journal of bacteriology.

[70]  T. Mizuno,et al.  Quantitative control of the stationary phase‐specific sigma factor, sigma S, in Escherichia coli: involvement of the nucleoid protein H‐NS. , 1995, The EMBO journal.

[71]  W. Sierralta,et al.  Curli Fibers Are Highly Conserved between Salmonella typhimurium and Escherichia coli with Respect to Operon Structure and Regulation , 1998, Journal of bacteriology.

[72]  U. Jenal Cyclic di-guanosine-monophosphate comes of age: a novel secondary messenger involved in modulating cell surface structures in bacteria? , 2004, Current opinion in microbiology.

[73]  Rapid confirmation of single copy lambda prophage integration by PCR. , 1994, Nucleic acids research.

[74]  A. G. Bobrov,et al.  HmsP, a putative phosphodiesterase, and HmsT, a putative diguanylate cyclase, control Hms‐dependent biofilm formation in Yersinia pestis , 2004, Molecular microbiology.