Crystal structure of GerE, the ultimate transcriptional regulator of spore formation in Bacillus subtilis.

The small, DNA-binding protein GerE regulates gene transcription in the terminally differentiated mother-cell compartment during late stages of sporulation in Bacillus subtilis. This versatile transcription factor shares sequence homology with the LuxR/FixJ/UhpA family of activators and modulates the expression of a number of genes, in particular those encoding the components of the coat that surrounds the mature spore. GerE orchestrates the final stages of coat deposition and maturation that lead to a spore with remarkable resistance properties but that must be responsive to low levels of germination signals. As this germination process is largely passive and can occur in the absence of de novo protein synthesis, the correct assembly of germination machinery, including germinant receptors and energy storage compounds, is crucial to the survival of the cell. The crystal structure of GerE has been solved at 2.05 A resolution using multi-wavelength anomalous dispersion techniques and reveals the nature of the GerE dimer. Each monomer comprises four alpha-helices, of which the central pair forms a helix-turn-helix DNA-binding motif. Implications for DNA-binding and the structural organisation of the LuxR/FixJ/UhpA family of transcription activator domains are discussed.

[1]  L. Kroos,et al.  Regulation of the transcription of a cluster of Bacillus subtilis spore coat genes. , 1994, Journal of molecular biology.

[2]  D. Kahn,et al.  Conformational changes induced by phosphorylation of the FixJ receiver domain. , 1999, Structure.

[3]  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.

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

[5]  D. Crothers Upsetting the balance of forces in DNA. , 1994, Science.

[6]  G N Murshudov,et al.  Use of TLS parameters to model anisotropic displacements in macromolecular refinement. , 2001, Acta crystallographica. Section D, Biological crystallography.

[7]  J. Errington,et al.  Bacillus subtilis sporulation: regulation of gene expression and control of morphogenesis. , 1993, Microbiological reviews.

[8]  A. Wilkinson,et al.  Bacillus subtilis regulatory protein GerE. , 1998, Acta crystallographica. Section D, Biological crystallography.

[9]  A. Brunger Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. , 1992 .

[10]  Y. Nakamura,et al.  Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions (supplement). , 1996, DNA research : an international journal for rapid publication of reports on genes and genomes.

[11]  D. Kahn,et al.  Modular structure of Fix J: homology of the transcriptional activator domain with the ‐35 binding domain of sigma factors , 1991, Molecular microbiology.

[12]  A. Goffeau,et al.  The complete genome sequence of the Gram-positive bacterium Bacillus subtilis , 1997, Nature.

[13]  G. Murshudov,et al.  Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.

[14]  K. N. Trueblood,et al.  On the rigid-body motion of molecules in crystals , 1968 .

[15]  D. A. Smith,et al.  The genetics of bacterial spore germination. , 1990, Annual review of microbiology.

[16]  L. Beamer,et al.  Refined 1.8 p crystal structure of the ? repressor-operator complex*1 , 1992 .

[17]  R. Dickerson,et al.  Structure of the Escherichia coli response regulator NarL. , 1996, Biochemistry.

[18]  B. Matthews,et al.  The helix-turn-helix DNA binding motif. , 1989, The Journal of biological chemistry.

[19]  L. Kroos,et al.  Combined Action of Two Transcription Factors Regulates Genes Encoding Spore Coat Proteins of Bacillus subtilis * , 2000, The Journal of Biological Chemistry.

[20]  R. Losick,et al.  Adjacent and divergently oriented operons under the control of the sporulation regulatory protein GerE in Bacillus subtilis , 1995, Journal of bacteriology.

[21]  C. Sander,et al.  Protein structure comparison by alignment of distance matrices. , 1993, Journal of molecular biology.

[22]  A. Henriques,et al.  CotM of Bacillus subtilis, a member of the alpha-crystallin family of stress proteins, is induced during development and participates in spore outer coat formation , 1997, Journal of bacteriology.

[23]  J. Mandelstam,et al.  The possible DNA-binding nature of the regulatory proteins, encoded by spoIID and gerE, involved in the sporulation of Bacillus subtilis. , 1987, Journal of general microbiology.

[24]  H. Jenkinson,et al.  Protease Deficiency and Its Association with Defects in Spore Coat Structure, Germination and Resistance Properties in a Mutant of Bacillus subtilis , 1983 .

[25]  H. Margalit,et al.  Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: in search of common principles. , 1995, Journal of molecular biology.

[26]  A. Ishihama,et al.  Protein-protein communication within the transcription apparatus , 1993, Journal of bacteriology.

[27]  R. Losick,et al.  Crisscross regulation of cell-type-specific gene expression during development in B. subtilis , 1992, Nature.

[28]  M. Billeter,et al.  Structural role of a buried salt bridge in the 434 repressor DNA-binding domain. , 1996, Journal of molecular biology.

[29]  S. Henikoff,et al.  Finding protein similarities with nucleotide sequence databases. , 1990, Methods in enzymology.

[30]  J. Mandelstam,et al.  The nucleotide sequence and the transcription during sporulation of the gerE gene of Bacillus subtilis. , 1986, Journal of general microbiology.

[31]  Richard H. Ebright,et al.  Promoter structure, promoter recognition, and transcription activation in prokaryotes , 1994, Cell.

[32]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[33]  A. Moir Germination properties of a spore coat-defective mutant of Bacillus subtilis , 1981, Journal of bacteriology.

[34]  Yasuo Kobayashi,et al.  Characterization of a New Sigma-K-Dependent Peptidoglycan Hydrolase Gene That Plays a Role in Bacillus subtilis Mother Cell Lysis , 1999, Journal of bacteriology.

[35]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[36]  A. Driks Bacillus subtilis Spore Coat , 1999, Microbiology and Molecular Biology Reviews.

[37]  S. Hanaoka,et al.  Structural comparison of the PhoB and OmpR DNA-binding/transactivation domains and the arrangement of PhoB molecules on the phosphate box. , 2000, Journal of molecular biology.

[38]  Sarah E. Ades,et al.  Engrailed (Gln50-->Lys) homeodomain-DNA complex at 1.9 A resolution: structural basis for enhanced affinity and altered specificity. , 1997, Structure.

[39]  R. Losick,et al.  Cascade regulation of spore coat gene expression in Bacillus subtilis. , 1990, Journal of molecular biology.

[40]  R. Losick,et al.  Molecular genetics of sporulation in Bacillus subtilis. , 1996, Annual review of genetics.

[41]  R. Sauer,et al.  Transcription factors: structural families and principles of DNA recognition. , 1992, Annual review of biochemistry.

[42]  A. Henriques,et al.  Structure and assembly of the bacterial endospore coat. , 2000, Methods.

[43]  L. Kroos,et al.  Negative Regulation by the Bacillus subtilis GerE Protein* , 1999, The Journal of Biological Chemistry.

[44]  H. Goldberg,et al.  The DNA binding arm of lambda repressor: critical contacts from a flexible region. , 1991, Science.

[45]  Victoria A. Feher,et al.  Two-Component Signal Transduction in Bacillus subtilis: How One Organism Sees Its World , 1999, Journal of bacteriology.

[46]  R. Losick,et al.  An additional GerE-controlled gene encoding an abundant spore coat protein from Bacillus subtilis , 1995, Journal of bacteriology.

[47]  R. Losick,et al.  Identification of the promoter for a spore coat protein gene in Bacillus subtilis and studies on the regulation of its induction at a late stage of sporulation. , 1988, Journal of molecular biology.

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

[49]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[50]  R. Losick,et al.  Sporulation regulatory protein GerE from Bacillus subtilis binds to and can activate or repress transcription from promoters for mother-cell-specific genes. , 1992, Journal of molecular biology.

[51]  S. Busby,et al.  Differential regulation by the homologous response regulators NarL and NarP of Escherichia coli K‐12 depends on DNA binding site arrangement , 1997, Molecular microbiology.

[52]  G. N. Ramachandran,et al.  Stereochemical criteria for polypeptide and protein chain conformations. II. Allowed conformations for a pair of peptide units. , 1965, Biophysical journal.

[53]  M. G. Oakley,et al.  GCN4 binds with high affinity to DNA sequences containing a single consensus half-site. , 2000, Biochemistry.

[54]  D. Kahn,et al.  Intramolecular signal transduction within the FixJ transcriptional activator: in vitro evidence for the inhibitory effect of the phosphorylatable regulatory domain. , 1994, Nucleic acids research.

[55]  B. Matthews Solvent content of protein crystals. , 1968, Journal of molecular biology.