Chapter 35 : A Gene Odyssey: Exploring the Genomes of Endospore-Forming Bacteria

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This chapter provides hints about how much of the sporulation process and its regulation is conserved. The recent release of the complete bacterial genome of has provided data that are in general agreement with the conclusions of the chapter. It is noteworthy that this complex operon is fully conserved in , , , and , whereas it is absent from all other genomes sequenced so far. The current sequence data indicate that all the genes involved in the phosphorelay are present in and , with the possible exception of . It was reasonable to expect that many genes involved in the sporulation process would be highly specific to endospore formers. The most significant variations are seen when the interface between the bacterium and its environment is involved. The various and species inhabit a wide range of ecological niches, and it seems logical that environmental signals would be differentially relayed to SpoOA depending on their chemical nature, that hostile signals threatening spore viability would be countered with an adequate coat shell, and that germination signals would be detected by a specialized, niche-appropriate array of receptors. The conclusions suggested in this chapter are obviously tentative and doomed to be contradicted by the endless flow of incoming genomic data.

Citation: Stragier P. 2002. A Gene Odyssey: Exploring the Genomes of Endospore-Forming Bacteria, p 519-525. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch35
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Image of FIGURE 1

Gene organization around the locus of various endospore formers. Genes are shown as rectangles, and intergenic regions are shown as thin lines. Transcription goes from top to bottom. To emphasize the local synteny between (), (), (), and (), longer thin lines join two adjacent genes when additional genes are present in another species. For the sake of clarity, clusters of genes specific to one species are shown as a single larger rectangle. No inference should be drawn about the size of the genes and their operon structure. Genes are named from their orthologue (including those of unknown function with a y nomenclature), whereas genes with no orthologue are labeled . The genes discussed in the text are highlighted by a bold rectangle. The synteny between and spp. stops upstream of the gene and downstream of . The operon is located in another region of the chromosome.

Citation: Stragier P. 2002. A Gene Odyssey: Exploring the Genomes of Endospore-Forming Bacteria, p 519-525. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch35
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1. Abe, Y.,, T. Shodai,, T. Muto,, K. Mihara,, H. Torii,, S.-C. Nishikawa,, T. Endo,, and D. Kohda. 2000. Structural basis of presequence recognition by the mitochondrial protein import receptor Tom20. Cell 100: 551 560.
2. Baikalov, I.,, I. Schroder,, M. Kaczor-Grzeskowiak,, K. Grzeskowiak,, R. P. Gunsalus,, and R. E. Dickerson. 1996. Structure of the Escherichia coli response regulator NarL. Biochemistry 35: 11053 11061.
3. Bilwes, A. M.,, L. A. Alex,, B. R. Crane, and M. I. Simon. 1999. Structure of CheA, a signal-transducing histidine kinase. Cell 96: 131 141.
4. Blatch, G. L.,, and M. Lassie. 1999. The tetratricopeptide repeat: a structural motif mediating protein-protein interactions. BioEssays 21: 932 939.
5. Brown, D. P.,, L. Ganova-Raeva,, B. D. Green,, S. R. Wilkinson,, M. Young,, and P. Youngman. 1994. Characterization of Spo0A homologues in diverse Bacillus and Clostridium species identifies a probable DNA-binding domain. Mol. Microbiol. 14: 411 426.
6. Core, L. J.,, S. Ishikawa,, and M. Perego. 2001. A free terminal carboxylate group is required for PhrA pentapeptide inhibition of RapA phosphatase. Peptides 22(10), in press.
7. Dartois, V.,, T. Djavakhishvili,, and J. A. Hoch. 1997. KapB is a lipoprotein required for KinB signal transduction and activation of the phosphorelay to sporulation in Bacillus subtilis. Mol. Microbiol. 26: 1097 1108.
8. Fabret, C.,, V. A. Feher,, and J. A. Hoch. 1999. Two-component signal transduction in Bacillus subtilis: how one organism sees its world. J. Bacteriol. 181: 1975 1983.
9. Groves, M. R.,, and D. Barford. 1999. Topological characteristics of helical repeat proteins. Curr. Opin. Struct. Biol. 9: 383 389.
10. Hess, J. F.,, K. Oosawa,, N. Kaplan, and M. I. Simon. 1988. Phosphorylation of three proteins in the signaling pathway of bacterial chemotaxis. Cell 53: 79 87.
11. Hoch, J. A. 2001. Unpublished data.
12. Hoch, J. A.,, and T. J. Silhavy (ed.). 1995. Two-Component Signal Transduction. American Society for Microbiology, Washington, D.C..
13. Jiang, M.,, R. Grau,, and M. Perego. 2000. Differential processing of propeptide inhibitors of Rap phosphatases in Bacillus subtilis. J. Bacteriol. 182: 303 310.
14. Kato, M.,, T. Mizuno,, T. Shimizu,, and T. Hakoshima. 1997. Insights into multistep phosphorelay from the crystal structure of the C-terminal HPt domain of ArcB. Cell 88: 717 723.
15. Kunst, F.,, and K. Devine. 1991. The project of sequencing the entire Bacillus subtilis genome. Res. Microbiol. 142: 905 912.
16. Lange, R.,, C. Wagner,, A. de Saizieu,, N. Flint,, J. Molnos,, M. Steiger,, P. Caspers,, M. Kamber,, W. Keck, and K. E. Amrein. 1999. Domain organization and molecular characterization of 13 two-component systems identified by genome sequencing of Streptococcus pneumoniae. Gene 237: 223 234.
17. Lazazzera, B. A.,, J. M. Solomon,, and A. D. Grossman. 1997. An exported peptide functions inttacellularly to contribute to cell density signaling in B. subtilis. Cell 89: 917 925.
18. Lereclus, D.,, H. Agaisse,, M. Gominet,, S. Salamitou,, and V. Sanchis. 1996. Identification of a Bacillus thuringiensis gene that positively regulates transcription of the phosphatidylinositol-specific phosphaolipase C gene at the onset of the stationary phase. J. Bacteriol. 178: 2749 2756.
19. Martin, P. K.,, T. Li,, D. Sun,, D. P. Biek,, and M. B. Schmid. 1999. Role in cell permeability of an essential two-component system in Staphylococcus aureus. J. Bacteriol. 181: 3666 3673.
20. Martinez-Hackert, E.,, and A. M. Stock. 1997. The DNA-binding domain of OmpR: crystal structure of a winged helix transcription factor. Structure 5: 109 124.
21. Mizuno, T. 1997. Compilation of all genes encoding two-component phosphotransfer signal transducers in the genome of Escherichia coli. DNARes. 4: 161 168.
22. Mueller, J. P.,, G. Bukusoglu,, and A. L. Sonenshein. 1992. Transcriptional regulation of Bacillus subtilis glucose starvation-inducible genes: control of gsiA by the ComP-ComA signal transduction system. J. Bacteriol. 174: 4361 4373.
23. Mutoh, N.,, and M. I. Simon. 1986. Nucleotide sequence corresponding to five chemotaxis genes in Escherichia coli. J. Bacteriol. 165: 161 166.
24. Nishiya, Y.,, and T. Imanaka. 1990. Cloning and nucleotide sequences of the Bacillus stearothermophilus neutral protease gene and its transcriptional activator gene. J. Bacteriol. 172: 4861 4869.
25. Novick, R. P., 1999. Regulation of pathogenicity in Staphylococcus aureus by a peptide-based density-sensing system, p. 129 146. In G. M. Dunny, and S. C. Winans (ed.), Cell-Cell Signaling in Bacteria. American Society for Microbiology, Washington, D.C..
26. Ohlsen, K. L.,, J. K. Grimsley,, and J. A. Hoch. 1994. Deactivation of the sporulation transcription factor Spo0A by the Spo0E protein phosphatase. Proc. Natl. Acad. Sci. USA 91: 1756 1760.
27. Perego, M. 1997. A peptide export-import control circuit modulating bacterial development regulates protein phosphatases of the phosphorelay. Proc. Natl. Acad. Sci. USA 94: 8612 8617.
28. Perego, M. 1998. Kinase-phosphatase competition regulates Bacillus subtilis development. Trends Microbiol. 6: 366 370.
29. Perego, M., 1999. Self-signaling by Phr peptides modulates Bacillus subtilis development, p. 243 258. In G. M. Dunny, and S. C. Winans (ed.), Cell-Cell Signaling in Bacteria. American Society for Microbiology, Washington, D.C..
30. Perego, M.,, and J. A. Brannigan. 2001. Pentapeptide regulation of aspartyl-phosphate phosphatases. Peptides 22(10), in press.
31. Perego, M.,, P. Glaser,, and J. A. Hoch. 1996. Aspartyl-phosphate phosphatases deactivate the response regulator components of the sporulation signal transduction system in Bacillus subtilis. Mol Microbiol. 19: 1151 1157.
32. Perego, M.,, and J. A. Hoch. 1987. Isolation and sequence of the Spo0E gene: its role in initiation of sporulation in Bacillus subtilis. Mol. Microbiol. 1: 125 132.
33. Perego, M.,, and J. A. Hoch. 1996. Cell-cell communication regulates the effects of protein aspartate phosphatases on the phosphorelay controlling development in Bacillus subtilis. Proc. Natl. Acad. Sci. USA 93: 1549 1553.
34. Perego, M. Unpublished results.
35. Scheufler, C.,, A. Brinker,, G. Bourenkov,, S. Pegoraro,, L. Moroder,, H. Bartunik,, F. U. Hard,, and I. Moarefi. 2000. Structure of TPR domain-peptide complexes: critical elements in the assembly of the Hsp70-Hsp90 multichaperone machine. Cell 101: 199 210.
36. Sikorski, R. S.,, M. S. Boguski,, M. Goebl,, and P. Hieter. 1990. A repeating amino acid motif in CDC23 defines a family of proteins and a new relationship among genes required for mitosis and RNA synthesis. Cell 60: 307 317.
37. Stephenson, S.,, and M. Perego. Unpublished results.
38. Takami, H.,, K. Nakasone,, Y. Takaki,, G. Maeno,, R. Sasaki,, N. Masui,, F. Fuji,, C. Hirama,, Y. Nakamura,, N. Ogasawara,, S. Kuhara,, and K. Horikoshi. 2000. Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis. Nucl. Acids Res. 28: 4317 4331.
39. Thomason, P.,, and R. Kay. 2000. Eukaryotic signal transduction via histidine-aspartate phosphorelay. J. Cell Sci. 113: 3141 3150.
40. Throup, J. P.,, K. K. Koretke,, A. P. Bryant,, K. A. Ingraham,, A. F. Chalker,, Y. Ge,, A. Marra,, N. G. Wallis,, J. R. Brown,, D. J. Holmes,, M. Rosenberg,, and M. K. Burn-ham. 2000. A genomic analysis of two-component signal transduction in Streptococcus pneumoniae. Mol. Microbiol. 35: 566 576.
41. Tomomori, C.,, T. Tanaka,, R. Dutta,, H. Park,, S. K. Saha,, Y. Zhu,, R. Ishima,, D. Liu,, K. I. Tong,, H. Kurokawa,, H. Qian,, K. Inouye,, and M. Ikura. 1999. Solution structure of the homodimeric core domain of Escherichia coli histidine kinase EnvZ. N at. Struct. Biol. 6: 729 734.
42. Uhl, M. A.,, and J. F. Miller,. 1995. Bordetella pertussis Bv-gAS virulence control system, p. 333 349. In J. A. Hoch, and T. J. Silhavy (ed.), Two-Component Signal Transduction. American Society for Microbiology, Washington, D.C..
43. Varughese, K., I. Madhusudan,, X. Z. Zhou,, J. M. Whiteley,, and J. A. Hoch. 1998. Formation of a novel four-helix bundle and molecular recognition sites by dimerization of a response regulator phosphotranserase. Mol. Cell 2: 485 493.
44. 44. Wilkinson, S. R.,, D. I. Young,, J. G. Morris,, and M. Young. 1995. Molecular genetics and the initiation of solventogenesis in Clostridium beijerinckii (formerly Clostridium acetobutylicum) NCIMB 8052. FEMS Microbiol. Rev. 17: 275 285.
45. Yaffe, M. B.,, K. Rittinger,, S. Volinia,, P. R. Caron,, A. Aitken,, H. Leffers,, S. J. Gamblin,, S. J. Smerdon,, and L. C. Cantley. 1997. The structural basis for 14-3-3:phospho-peptide binding specificity. Cell 91: 961 971.
46. Zapf, J. W.,, U. Sen, Madhusudan, J. A. Hoch, and K. 1. Varughese. 2000. A transient interaction between two phosphorelay proteins trapped in a crystal lattice reveals the mechanism of molecular recognition and phosphotransfer in signal transduction. Struct. Folding Design 8: 851 862.
47. Zhou, H.,, D. F. Lowry,, R. V. Swanson,, M. I. Simon,, and F. W. Dahlquist. 1995. NMR studies of the phosphotransfer domain of the histidine kinase CheA from Escherichia coli: assignments, secondary structure, general fold, and backbone dynamics. Biochemistry 34: 13858 13870.


Generic image for table

Conservation of developmental loci among endospore formers

Include , , , , , and .

Some genes conserved in Clostridium spp. and absent from Bacillus might be involved in sporulation but not yet identified.

Citation: Stragier P. 2002. A Gene Odyssey: Exploring the Genomes of Endospore-Forming Bacteria, p 519-525. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch35

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