Genomics, evolution, and crystal structure of a new family of bacterial spore kinases

Bacterial spore formation is a complex process of fundamental relevance to biology and human disease. The spore coat structure is complex and poorly understood, and the roles of many of the protein components remain unclear. We describe a new family of spore coat proteins, the bacterial spore kinases (BSKs), and the first crystal structure of a BSK, YtaA (CotI) from Bacillus subtilis. BSKs are widely distributed in spore‐forming Bacillus and Clostridium species, and have a dynamic evolutionary history. Sequence and structure analyses indicate that the BSKs are CAKs, a prevalent group of small molecule kinases in bacteria that is distantly related to the eukaryotic protein kinases. YtaA has substantial structural similarity to CAKs, but also displays distinctive features that broaden our understanding of the CAK group. Evolutionary constraint analysis of the protein surfaces indicates that members of the BSK family have distinct clade‐conserved patterns in the substrate binding region, and probably bind and phosphorylate distinct targets. Several classes of BSKs have apparently independently lost catalytic activity to become pseudokinases, indicating that the family also has a major noncatalytic function. Proteins 2010. © 2009 Wiley‐Liss, Inc.

[1]  D. V. van Aalten,et al.  ATP and MO25α Regulate the Conformational State of the STRADα Pseudokinase and Activation of the LKB1 Tumour Suppressor , 2009, PLoS Biology.

[2]  Stefan Knapp,et al.  Structure of the Pseudokinase VRK3 Reveals a Degraded Catalytic Site, a Highly Conserved Kinase Fold, and a Putative Regulatory Binding Site , 2009, Structure.

[3]  G. Labesse,et al.  ROP2 from Toxoplasma gondii: a virulence factor with a protein-kinase fold and no enzymatic activity. , 2008, Structure.

[4]  Robert D. Finn,et al.  InterPro: the integrative protein signature database , 2008, Nucleic Acids Res..

[5]  E. Papoutsakis,et al.  The transcriptional program underlying the physiology of clostridial sporulation , 2008, Genome Biology.

[6]  G. Petsko,et al.  How Enzymes Work , 2008, Science.

[7]  Lawrence E. Page,et al.  The Genome of Heliobacterium modesticaldum, a Phototrophic Representative of the Firmicutes Containing the Simplest Photosynthetic Apparatus , 2008, Journal of bacteriology.

[8]  T. Südhof,et al.  CASK Functions as a Mg2+-Independent Neurexin Kinase , 2008, Cell.

[9]  A. Henriques,et al.  Structure, assembly, and function of the spore surface layers. , 2007, Annual review of microbiology.

[10]  I-Min A. Chen,et al.  The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions , 2007, Nucleic Acids Res..

[11]  Vincent B. Chen,et al.  MolProbity: all-atom contacts and structure validation for proteins and nucleic acids , 2007, Nucleic Acids Res..

[12]  Gerard Manning,et al.  Structural and Functional Diversity of the Microbial Kinome , 2007, PLoS biology.

[13]  M. Konrad,et al.  Elucidation of human choline kinase crystal structures in complex with the products ADP or phosphocholine. , 2006, Journal of Molecular Biology.

[14]  G. Barton,et al.  Emerging roles of pseudokinases. , 2006, Trends in cell biology.

[15]  J. Sebolt-Leopold,et al.  Mechanisms of drug inhibition of signalling molecules , 2006, Nature.

[16]  L. Klobutcher,et al.  The Bacillus subtilis spore coat provides "eat resistance" during phagocytic predation by the protozoan Tetrahymena thermophila. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[17]  P. Eichenberger,et al.  The Bacillus subtilis spore coat protein interaction network , 2006, Molecular microbiology.

[18]  Philip E. Bourne,et al.  Structural Evolution of the Protein Kinase–Like Superfamily , 2005, PLoS Comput. Biol..

[19]  A. F. Neuwald,et al.  Did protein kinase regulatory mechanisms evolve through elaboration of a simple structural component? , 2005, Journal of molecular biology.

[20]  Adam R Farley,et al.  Establishing the principles of recognition in the adenine-binding region of an aminoglycoside antibiotic kinase [APH(3')-IIIa]. , 2005, Biochemistry.

[21]  Itay Mayrose,et al.  ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures , 2005, Nucleic Acids Res..

[22]  Zukang Feng,et al.  Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. , 2004, Acta crystallographica. Section D, Biological crystallography.

[23]  Shane T. Jensen,et al.  The Program of Gene Transcription for a Single Differentiating Cell Type during Sporulation in Bacillus subtilis , 2004, PLoS biology.

[24]  Susan S. Taylor,et al.  Regulation of protein kinases; controlling activity through activation segment conformation. , 2004, Molecular cell.

[25]  R. Losick,et al.  Dynamic Patterns of Subcellular Protein Localization during Spore Coat Morphogenesis in Bacillus subtilis , 2004, Journal of bacteriology.

[26]  E. Goldsmith,et al.  Crystal structure of the kinase domain of WNK1, a kinase that causes a hereditary form of hypertension. , 2004, Structure.

[27]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[28]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[29]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[30]  P. Bork,et al.  The KIND module: a putative signalling domain evolved from the C lobe of the protein kinase fold. , 2003, Trends in biochemical sciences.

[31]  T. Terwilliger.  Improving macromolecular atomic models at moderate resolution by automated iterative model building, statistical density modification and refinement , 2003, Acta crystallographica. Section D, Biological crystallography.

[32]  C. Kent,et al.  The crystal structure of choline kinase reveals a eukaryotic protein kinase fold. , 2003, Structure.

[33]  Shane T. Jensen,et al.  The sigmaE regulon and the identification of additional sporulation genes in Bacillus subtilis. , 2003, Journal of molecular biology.

[34]  J. Maddock,et al.  Proteomic Analysis of the Spore Coats of Bacillus subtilis and Bacillus anthracis , 2003, Journal of bacteriology.

[35]  Julie D Thompson,et al.  Multiple Sequence Alignment Using ClustalW and ClustalX , 2003, Current protocols in bioinformatics.

[36]  B. Kobe,et al.  Structural basis and prediction of substrate specificity in protein serine/threonine kinases , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[37]  K. Watabe,et al.  Proteomics characterization of novel spore proteins of Bacillus subtilis. , 2002, Microbiology.

[38]  Peter Kuhn,et al.  Blu-Ice and the Distributed Control System: software for data acquisition and instrument control at macromolecular crystallography beamlines. , 2002, Journal of synchrotron radiation.

[39]  George M Sheldrick,et al.  Substructure solution with SHELXD. , 2002, Acta crystallographica. Section D, Biological crystallography.

[40]  Adam Godzik,et al.  Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[41]  D. Fong,et al.  Substrate promiscuity of an aminoglycoside antibiotic resistance enzyme via target mimicry. , 2002, The EMBO journal.

[42]  A. Driks.  Maximum shields: the assembly and function of the bacterial spore coat. , 2002, Trends in microbiology.

[43]  Susan S. Taylor,et al.  Crystal structure of a transition state mimic of the catalytic subunit of cAMP-dependent protein kinase , 2002, Nature Structural Biology.

[44]  Earl W. Cornell,et al.  An approach to rapid protein crystallization using nanodroplets , 2002 .

[45]  A. Driks.  Overview: development in bacteria: spore formation in Bacillus subtilis , 2002, Cellular and Molecular Life Sciences CMLS.

[46]  P. Setlow,et al.  Localization of the Cortex Lytic Enzyme CwlJ in Spores of Bacillus subtilis , 2002, Journal of bacteriology.

[47]  A. Berghuis,et al.  Protein kinase inhibitors and antibiotic resistance. , 2002, Pharmacology & therapeutics.

[48]  A. Danchin,et al.  CotA of Bacillus subtilis Is a Copper-Dependent Laccase , 2001, Journal of bacteriology.

[49]  Liisa Holm,et al.  DaliLite workbench for protein structure comparison , 2000, Bioinform..

[50]  K. Watabe,et al.  Assembly of the CotSA coat protein into spores requires CotS in Bacillus subtilis. , 1999, FEMS microbiology letters.

[51]  Thomas C. Terwilliger,et al.  Automated MAD and MIR structure solution , 1999, Acta crystallographica. Section D, Biological crystallography.

[52]  K. Watabe,et al.  A Spore Coat Protein, CotS, of Bacillus subtilis Is Synthesized under the Regulation of ςKand GerE during Development and Is Located in the Inner Coat Layer of Spores , 1998, Journal of bacteriology.

[53]  David S. Moss,et al.  Error Estimates of Protein Structure Coordinates and Deviations from Standard Geometry by Full-Matrix Refinement of γB- and βB2-Crystallin , 1998 .

[54]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[55]  Robert M. Sweet,et al.  Structure of an Enzyme Required for Aminoglycoside Antibiotic Resistance Reveals Homology to Eukaryotic Protein Kinases , 1997, Cell.

[56]  C Sander,et al.  Mapping the Protein Universe , 1996, Science.

[57]  K. Watabe,et al.  A Bacillus subtilis spore coat polypeptide gene, cotS. , 1995, Microbiology.

[58]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[59]  Susan S. Taylor,et al.  Three protein kinase structures define a common motif. , 1994, Structure.

[60]  R. Huber,et al.  Phosphotransferase and substrate binding mechanism of the cAMP‐dependent protein kinase catalytic subunit from porcine heart as deduced from the 2.0 A structure of the complex with Mn2+ adenylyl imidodiphosphate and inhibitor peptide PKI(5‐24). , 1993, The EMBO journal.

[61]  C. Clépet,et al.  Isolation, organization and expression of the Pseudomonas aeruginosa threonine genes , 1992, Molecular microbiology.

[62]  D. Knighton,et al.  Crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase. , 1991, Science.

[63]  C. Gibbs,et al.  Rational scanning mutagenesis of a protein kinase identifies functional regions involved in catalysis and substrate interactions. , 1991, The Journal of biological chemistry.

[64]  G Vriend,et al.  WHAT IF: a molecular modeling and drug design program. , 1990, Journal of molecular graphics.

[65]  Martyn D Winn,et al.  Macromolecular TLS refinement in REFMAC at moderate resolutions. , 2003, Methods in enzymology.

[66]  Adam Godzik,et al.  Tolerating some redundancy significantly speeds up clustering of large protein databases , 2002, Bioinform..

[67]  A. Moir,et al.  Spore germination , 2002, Cellular and Molecular Life Sciences CMLS.

[68]  G. Garrity.  Bergey's Manual of systematic bacteriology , 2001 .

[69]  Michael Y. Galperin,et al.  The COG database: a tool for genome-scale analysis of protein functions and evolution , 2000, Nucleic Acids Res..

[70]  D S Moss,et al.  Error estimates of protein structure coordinates and deviations from standard geometry by full-matrix refinement of gammaB- and betaB2-crystallin. , 1998, Acta crystallographica. Section D, Biological crystallography.

[71]  H. Berman,et al.  Electronic Reprint Biological Crystallography the Protein Data Bank Biological Crystallography the Protein Data Bank , 2022 .