Cyclic di-GMP acts as a cell cycle oscillator to drive chromosome replication

Fundamental to all living organisms is the capacity to coordinate cell division and cell differentiation to generate appropriate numbers of specialized cells. Whereas eukaryotes use cyclins and cyclin-dependent kinases to balance division with cell fate decisions, equivalent regulatory systems have not been described in bacteria. Moreover, the mechanisms used by bacteria to tune division in line with developmental programs are poorly understood. Here we show that Caulobacter crescentus, a bacterium with an asymmetric division cycle, uses oscillating levels of the second messenger cyclic diguanylate (c-di-GMP) to drive its cell cycle. We demonstrate that c-di-GMP directly binds to the essential cell cycle kinase CckA to inhibit kinase activity and stimulate phosphatase activity. An upshift of c-di-GMP during the G1–S transition switches CckA from the kinase to the phosphatase mode, thereby allowing replication initiation and cell cycle progression. Finally, we show that during division, c-di-GMP imposes spatial control on CckA to install the replication asymmetry of future daughter cells. These studies reveal c-di-GMP to be a cyclin-like molecule in bacteria that coordinates chromosome replication with cell morphogenesis in Caulobacter. The observation that c-di-GMP-mediated control is conserved in the plant pathogen Agrobacterium tumefaciens suggests a general mechanism through which this global regulator of bacterial virulence and persistence coordinates behaviour and cell proliferation.

[1]  Runjun D. Kumar,et al.  PoxA, yjeK, and elongation factor P coordinately modulate virulence and drug resistance in Salmonella enterica. , 2010, Molecular cell.

[2]  Franziska Zähringer,et al.  Structure and signaling mechanism of a zinc-sensory diguanylate cyclase. , 2013, Structure.

[3]  Johannes Söding,et al.  Fast and accurate automatic structure prediction with HHpred , 2009, Proteins.

[4]  Michael T Laub,et al.  Two-Component Signal Transduction Pathways Regulating Growth and Cell Cycle Progression in a Bacterium: A System-Level Analysis , 2005, PLoS biology.

[5]  A S Belmont,et al.  In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition , 1996, The Journal of cell biology.

[6]  Michael T Laub,et al.  Spatial gradient of protein phosphorylation underlies replicative asymmetry in a bacterium , 2010, Proceedings of the National Academy of Sciences.

[7]  A. Grossman,et al.  Control of development by altered localization of a transcription factor in B. subtilis. , 1999, Molecular cell.

[8]  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.

[9]  Michael T Laub,et al.  A dynamic complex of signaling proteins uses polar localization to regulate cell-fate asymmetry in Caulobacter crescentus. , 2011, Developmental cell.

[10]  S. Fesik,et al.  Heteronuclear three-dimensional NMR spectroscopy of the inflammatory protein C5a. , 1989, Biochemistry.

[11]  Lucy Shapiro,et al.  Cell Type-Specific Phosphorylation and Proteolysis of a Transcriptional Regulator Controls the G1-to-S Transition in a Bacterial Cell Cycle , 1997, Cell.

[12]  Benjamin D. Simons,et al.  Unravelling stem cell dynamics by lineage tracing , 2013, Nature Reviews Molecular Cell Biology.

[13]  M. Malumbres,et al.  Cyclin-dependent kinases , 2014, Genome Biology.

[14]  Patrick T. McGrath,et al.  Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[15]  T. Schwede,et al.  Second messenger-mediated spatiotemporal control of protein degradation regulates bacterial cell cycle progression. , 2009, Genes & development.

[16]  B. Ely.  Genetics of Caulobacter crescentus. , 1991, Methods in enzymology.

[17]  Joseph Chen,et al.  Identification of a Dehydrogenase Required for Lactose Metabolism in Caulobacter crescentus , 2010, Applied and Environmental Microbiology.

[18]  T. Blundell,et al.  Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.

[19]  R. Riek,et al.  Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Michael T. Laub,et al.  Regulation of the bacterial cell cycle by an integrated genetic circuit , 2006, Nature.

[21]  C. Fuqua,et al.  Coordination of Division and Development Influences Complex Multicellular Behavior in Agrobacterium tumefaciens , 2013, PloS one.

[22]  Lucy Shapiro,et al.  A signal transduction protein cues proteolytic events critical to Caulobacter cell cycle progression , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Y. Choi,et al.  Signaling through cyclin D-dependent kinases , 2014, Oncogene.

[24]  Matteo Brilli,et al.  The diversity and evolution of cell cycle regulation in alpha-proteobacteria: a comparative genomic analysis , 2010, BMC Systems Biology.

[25]  X. Su,et al.  The structural basis for the sensing and binding of cyclic di-GMP by STING , 2012, Nature Structural &Molecular Biology.

[26]  O. Sliusarenko,et al.  Polar Localization of the CckA Histidine Kinase and Cell Cycle Periodicity of the Essential Master Regulator CtrA in Caulobacter crescentus , 2009, Journal of bacteriology.

[27]  F. Poulsen,et al.  Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution , 2011, Journal of biomolecular NMR.

[28]  C. Mello,et al.  Divide and differentiate , 2014, Cell cycle.

[29]  M. Laub,et al.  Allosteric Regulation of Histidine Kinases by Their Cognate Response Regulator Determines Cell Fate , 2008, Cell.

[30]  P. D. de Boer,et al.  Screening for synthetic lethal mutants in Escherichia coli and identification of EnvC (YibP) as a periplasmic septal ring factor with murein hydrolase activity , 2004, Molecular microbiology.

[31]  Shunichi Takeda,et al.  Cyclin-dependent kinases and cell-cycle transitions: does one fit all? , 2008, Nature Reviews Molecular Cell Biology.

[32]  A. Deacon,et al.  Cell Fate Regulation Governed by a Repurposed Bacterial Histidine Kinase , 2014, PLoS biology.

[33]  D O Morgan,et al.  Cyclin-dependent kinases: engines, clocks, and microprocessors. , 1997, Annual review of cell and developmental biology.

[34]  J. Mekalanos,et al.  Cyclic Dinucleotides and the Innate Immune Response , 2013, Cell.

[35]  James R. Brown,et al.  Evolution of two-component signal transduction. , 2000, Molecular biology and evolution.

[36]  Pia Abel zur Wiesch,et al.  Bi-modal Distribution of the Second Messenger c-di-GMP Controls Cell Fate and Asymmetry during the Caulobacter Cell Cycle , 2013, PLoS genetics.

[37]  L. Shapiro,et al.  Differential localization of two histidine kinases controlling bacterial cell differentiation. , 1999, Molecular cell.

[38]  K Wüthrich,et al.  TROSY in triple-resonance experiments: new perspectives for sequential NMR assignment of large proteins. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[39]  L. Shapiro,et al.  Negative control of bacterial DNA replication by a cell cycle regulatory protein that binds at the chromosome origin. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[40]  U. Jenal,et al.  Activation of the Diguanylate Cyclase PleD by Phosphorylation-mediated Dimerization* , 2007, Journal of Biological Chemistry.

[41]  L. Shapiro,et al.  A comprehensive set of plasmids for vanillate- and xylose-inducible gene expression in Caulobacter crescentus , 2007, Nucleic acids research.

[42]  James A. Taylor,et al.  The Caulobacter crescentus chromosome replication origin evolved two classes of weak DnaA binding sites , 2011, Molecular microbiology.

[43]  Lucy Shapiro,et al.  Cell Cycle–Dependent Polar Localization of an Essential Bacterial Histidine Kinase that Controls DNA Replication and Cell Division , 1999, Cell.

[44]  Michael Y. Galperin,et al.  Cyclic di-GMP: the First 25 Years of a Universal Bacterial Second Messenger , 2013, Microbiology and Molecular Reviews.

[45]  Michael T. Laub,et al.  Dynamics of Two Phosphorelays Controlling Cell Cycle Progression in Caulobacter crescentus , 2009, Journal of bacteriology.

[46]  S. Grzesiek,et al.  DgrA is a member of a new family of cyclic diguanosine monophosphate receptors and controls flagellar motor function in Caulobacter crescentus , 2007, Proceedings of the National Academy of Sciences.