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

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in

A Gene Odyssey: Exploring the Genomes of Endospore-Forming Bacteria, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817992/9781555812058_Chap35-1.gif /docserver/preview/fulltext/10.1128/9781555817992/9781555812058_Chap35-2.gif


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

Key Concept Ranking

Gene Expression and Regulation
Cell Wall Biosynthesis
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


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
Permissions and Reprints Request Permissions
Download as Powerpoint


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 100:551560.
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 35:1105311061.
3. Bilwes, A. M.,, L. A. Alex,, B. R. Crane, and M. I. Simon. 1999. Structure of CheA, a signal-transducing histidine kinase. Cell 96:131141.
4. Blatch, G. L.,, and M. Lassie. 1999. The tetratricopeptide repeat: a structural motif mediating protein-protein interactions. BioEssays 21:932939.
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. 14:411426.
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. 26:10971108.
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. 181:19751983.
9. Groves, M. R.,, and D. Barford. 1999. Topological characteristics of helical repeat proteins. Curr. Opin. Struct. Biol. 9:383389.
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 53:7987.
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. 182:303310.
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: 717723.
15. Kunst, F.,, and K. Devine. 1991. The project of sequencing the entire Bacillus subtilis genome. Res. Microbiol. 142: 905912.
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 237:223234.
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: 917925.
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. 178:27492756.
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. 181:36663673.
20. Martinez-Hackert, E.,, and A. M. Stock. 1997. The DNA-binding domain of OmpR: crystal structure of a winged helix transcription factor. Structure 5:109124.
21. Mizuno, T. 1997. Compilation of all genes encoding two-component phosphotransfer signal transducers in the genome of Escherichia coli. DNARes. 4:161168.
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: 43614373.
23. Mutoh, N.,, and M. I. Simon. 1986. Nucleotide sequence corresponding to five chemotaxis genes in Escherichia coli. J. Bacteriol. 165:161166.
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. 172:48614869.
25. Novick, R. P., 1999. Regulation of pathogenicity in Staphylococcus aureus by a peptide-based density-sensing system, p. 129146. 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 91:17561760.
27. Perego, M. 1997. A peptide export-import control circuit modulating bacterial development regulates protein phosphatases of the phosphorelay. Proc. Natl. Acad. Sci. USA 94:86128617.
28. Perego, M. 1998. Kinase-phosphatase competition regulates Bacillus subtilis development. Trends Microbiol. 6: 366370.
29. Perego, M., 1999. Self-signaling by Phr peptides modulates Bacillus subtilis development, p. 243258. 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. 19:11511157.
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. 1:125132.
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 93:15491553.
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 101:199210.
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 60:307317.
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. 28:43174331.
39. Thomason, P.,, and R. Kay. 2000. Eukaryotic signal transduction via histidine-aspartate phosphorelay. J. Cell Sci. 113:31413150.
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. 35:566576.
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. Nat. Struct. Biol. 6: 729734.
42. Uhl, M. A.,, and J. F. Miller,. 1995. Bordetella pertussis Bv-gAS virulence control system, p. 333349. 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 2:485493.
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. 17:275285.
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 91:961971.
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: 851862.
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 34:1385813870.


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

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error