Sequence analysis of GerM and SpoVS, uncharacterized bacterial 'sporulation' proteins with widespread phylogenetic distribution

Bioinformatics

Volumn 24, Issue 16, 2008, Pages 1793-1797

  Rigden, Daniel J ^a   Galperin, Michael Y ^b  

^a UNIVERSITY OF LIVERPOOL   (United Kingdom)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; CELL PROTEIN; DNA BINDING PROTEIN; FIBRONECTIN; GERM PROTEIN; GMAD1 PROTEIN; GMAD2 PROTEIN; PEPTIDOGLYCAN; SPOVS PROTEIN;

AB INITIO CALCULATION; AMINO ACID SEQUENCE; BACILLUS SUBTILIS; BACTERIAL MEMBRANE; CELL DIVISION; CELL SEPARATION; CONFERENCE PAPER; CONTROLLED STUDY; GENE EXPRESSION; GENE IDENTIFICATION; MOLECULAR PHYLOGENY; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; SPORE GERMINATION; SPOROGENESIS; TRANSCRIPTION REGULATION;

ARCHAEA; BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); CYANOBACTERIA; FIRMICUTES; PROTEOBACTERIA; SPIROCHAETES;

EID: 49549088390     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn314     Document Type: Conference Paper

References (47)

1. Aanensen,D.M. et al. (2007) Predicted functions and linkage specificities of the products of the Streptococcus pneumoniae capsular biosynthetic loci. J. Bacteriol., 189, 7856-7876.
2. Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST - a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
3. Andreeva,A. et al. (2008) Data growth and its impact on the SCOP database: New developments. Nucleic Acids Res., 36, D419-D425.
4. Aravind,L. et al. (2003) The two faces of Alba: The evolutionary connection between proteins participating in chromatin structure and RNA metabolism. Genome Biol., 4, R64.
5. Baker,N.A. et al. (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl Acad. Sci. USA, 98, 10037-10041.
6. Bork,P. and Doolittle,R.F. (1992) Proposed acquisition of an animal protein domain by bacteria. Proc. Natl Acad. Sci. USA, 89, 8990-8994.
7. Bujnicki,J.M. et al. (2001) Structure prediction meta server. Bioinformatics, 17, 750-751.
8. Canutescu,A.A. et al. (2003) A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci., 12, 2001-2014.
9. Etchenberger,P. et al. (2004) The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis. PLoS Biol., 2, e328.
10. Errington,J. (2003) Regulation of endospore formation in Bacillus subtilis. Nat. Rev. Microbiol., 1, 117-126.
11. Finn,R.D. et al. (2008) The Pfam protein families database. Nucleic Acids Res., 36, D281-D288.
12. Ginalski,K. et al. (2003) 3D-Jury: A simple approach to improve protein structure predictions. Bioinformatics, 19, 1015-1018.
13. Holm,L. and Sander,C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
14. Hoskisson,P.A. and Hutchings,M.I. (2006) MtrAB-LpqB: A conserved three-component system in actinobacteria? Trends Microbiol., 14 444-449.
15. Hulo,N. et al. (2008) The 20 years of PROSITE. Nucleic Acids Res., 36, D245-D249.
16. Jee,J.G et al. (2002) Solution structure of the fibronectin type III domain from Bacillus circulans WL-12 chitinase A1. J. Biol. Chem., 277, 1388-1397.
17. Jones,D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
18. Koonin,E.V. and Galperin,M.Y (2003) Sequence-Evolution-Function. Kluwer Academic, Boston, MA.
19. Laskowski,R.A. et al. (1993) Main-chain bond lengths and bond angles in protein structures. J. Mol. Biol., 231, 1049-1067.
20. Lee,S.Y and Skolnick,J. (2007) Development and berchmarking of TASSER(iter) for the iterative improvement of protein structure predictions. Proteins, 68, 39-47.
21. Little,E. et al. (1994) Tracing the spread of fibronectin type III domains in bacterial glycohydrolases. J. Mol. Evol., 39, 631-4643.
22. Lüthy,R. et al. (1992) Assessment of protein models with three-dimensional profiles. Nature, 356, 83-85.
23. Marchler-Bauer,A. et al. (2007) CDD: A conserved domain database for interactive domain family analysis. Nucleic Acids Res., 35 D237-D240.
24. Moker,N. et al. (2004) Deletion of the genes encoding the MtrA-MtrB two-component system of Corynebacterium glutamicum has a strong influence on cell morphology, antibiotics susceptibility and expression of genes involved in osmoprotection. Mol. Microbiol., 54, 420-438.
25. Neer,E.J. et al. (1994) The ancient regulatory-protein family of WD-repeat proteins. Nature, 371, 297-300.
26. Onaga,S. and Taira,T. (2008) A new ripe of plant chitinase containing LysM domains from a fern (Pteris ryukyuensis): Roles of LysM domains in chitin binding and anfifungal activity. Glycobiology, 18, 414-423.
27. Onyenwoke,R.U. et al. (2004) Sporulation genes in members of the low G+C Gram-type-positive phylogenetic branch (Firmicutes). Arch. Microbiol., 182, 182-192.
28. Perez,A.R. et al. (2006) Suppression of engulfment defects in Bacillus subtilis by elevated expression of the motility regulon. J. Bacteriol., 188, 1159-1164.
29. Piggot,P.J. and Losick,R. (2002) Sporulation genes and intercompartmental regulation. In Sonenshein,A.L. et al. (eds) Bacillus subtilis and its Closest Relatives: From Genes to Cells. ASM Press, Washington, D.C., pp. 483-518.
30. Resnekov,O. et al. (1995) Identification and characterization of sporulation gene spoVS from Bacillus subtilis. J. Bacteriol. 177, 5629-5635.
31. Sali,A. and Blundell,T.L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.
32. Sammons,R.L. et al. (1987) Genetical and molecular studies on gerM, a new developmental locus of Bacillus subtilis. J. Gen. Microbiol., 133, 3299-3312.
33. Sammut,S.J. et al. (2008) Pfam 10 years on: 10,000 families and still growing. Brief. Bioinform., 9, 210-219.
34. Sanchez,R. and Sali,A. (1998) Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc. Natl Acad Sci. USA, 95, 13597-13602.
35. Simons,K.T. et al. (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol., 268, 209-225.
36. Simons,K.T. et al. (1999) Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins, 34, 82-95.
37. Sippl,M.J. (1993) Recognition of errors in three-dimensional structures of proteins. Proteins, 17, 355-362.
38. Slynn,G.M. et al. (1994) Molecular genetical and phenotypical analysis of the gerM spore germination gene of Bacillus subtilis 168. FEMS Microbiol. Lett., 121, 315-320.
39. Soding,J. et al. (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res., 33, W244-W248.
40. Spaink,H.P. (2004) Specific recognition of bacteria by plant LysM domain receptor kinases. Trends Microbiol., 12, 201-204.
41. Steen,A. et al. (2003) Cell wall attachment of a widely distributed peptidoglycan binding domain is hindered by cell wall constituents. J. Biol. Chem., 278, 23874-23881.
42. Szilágyi,A and Skolnick,J. (2006) Efficient prediction of nucleic acid binding function from low-resolution protein structures. J. Mol. Biol., 358, 922-933.
43. Tatusov,R.L. et al. (2000) ThcCOG database: A tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res., 28, 33-36.
44. Toratani,T. et al. (2006) Structure of full-length bacterial chitinase containing two fibronectin type III domains revealed by small angle X-ray scattering. Biochem. Biophys. Res. Commun., 448, 814-818.
45. Wardleworth,B.N. et al. (2002) Structure of Alba: An archacal chromatin protein modulated by acetylation. EMBO J., 21, 4654-4662.
46. Winkler,M.E. and Hochm,J.A. (2009) Essentiality, bypass, and targeting of the YycFG (VicRK) two-component regulatory system in gram-positive bacteria. J. Bacteriol., 190, 2645-2648.
47. Wu,M. et al. (2005) Life in hot carbon monoxide: The complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. PLoS Genet., 1, e65.