A peptide profile of the Bacillus subtilis genome

Akbar, 1999, Two genes from Bacillus subtilis under the sole control of the general stress transcription factor sigma(B), Microbiol, 145, 1069, 10.1099/13500872-145-5-1069 Altschul, 1997, Gapped BLAST and PSI-BLAST, Nucleic Acids Res, 25, 3389, 10.1093/nar/25.17.3389 Babasaki, 1985, Subtilosin A, a new antibiotic peptide produced by Bacillus subtilis 168, J Biochem, 98, 583, 10.1093/oxfordjournals.jbchem.a135315 Bai, 1993, SinI modulates the activity of SinR, a developmental switch protein of Bacillus subtilis, by protein-protein interaction, Genes Dev, 7, 139, 10.1101/gad.7.1.139 Bateman, 2000, The Pfam protein families database, Nucleic Acids Res, 28, 263, 10.1093/nar/28.1.263 Behravan, 2000, Mutations in the gerP locus of Bacillus subtilis and Bacillus cereus affect access of germinants to their targets in spores, J Bacteriol, 182, 1987, 10.1128/JB.182.7.1987-1994.2000 Blattner, 1997, The complete genome sequence of Escherichia coli K-12, Science, 277, 1453, 10.1126/science.277.5331.1453 Boylan, 1993, Stress-induced activation of the σB transcription factor of Bacillus subtilis, J Bacteriol, 175, 7931, 10.1128/jb.175.24.7931-7937.1993 Boylan, 1991, Genetic method to identify regulons controlled by nonessential elements, J Bacteriol, 173, 7856, 10.1128/jb.173.24.7856-7866.1991 Burbulys, 1991, Initiation of sporulation in B. subtilis is controlled by a multicomponent phosphorelay, Cell, 64, 545, 10.1016/0092-8674(91)90238-T Burkholder, 2001, Replication initiation proteins regulate a developmental checkpoint in Bacillus subtilis, Cell, 104, 269, 10.1016/S0092-8674(01)00211-2 Cabrera-Hernandez, 1999, Regulation of four genes encoding small, acid-soluble spore proteins in Bacillus subtilis, Gene, 232, 1, 10.1016/S0378-1119(99)00124-9 Chen, 1992, 4-Oxalocrotonate tautomerase, an enzyme composed of 62 amino acid residues per monomer, J Biol Chem, 267, 17716, 10.1016/S0021-9258(19)37101-7 Chen, 1987, Nucleotide sequence of the overlapping genes for the subunits of Bacillus subtilis aspartokinase II and their control regions, J Biol Chem, 262, 8787, 10.1016/S0021-9258(18)47484-4 Chung, 1998, All seven comG open reading frames are required for DNA binding during transformation of competent Bacillus subtilis, J Bacteriol, 180, 41, 10.1128/JB.180.1.41-45.1998 Cole, 1998, Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence, Nature, 393, 537, 10.1038/31159 Cutting, 1997, SpoVM, a small protein essential to development in Bacillus subtilis, interacts with the ATP-dependent protease FtsH, J Bacteriol, 179, 5534, 10.1128/jb.179.17.5534-5542.1997 D’Souza, 1994, Identification of comS, a gene of the srfA operon that regulates the establishment of genetic competence in Bacillus subtilis, Proc Natl Acad Sci USA, 91, 9397, 10.1073/pnas.91.20.9397 Decatur, 1997, Translation of the mRNA for the sporulation gene spoIIID of Bacillus subtilis is dependent upon translation of a small upstream open reading frame, J Bacteriol, 179, 1324, 10.1128/jb.179.4.1324-1328.1997 Driks, 1999, Bacillus subtilis spore coat, Microbiol Mol Biol Rev, 63, 1, 10.1128/MMBR.63.1.1-20.1999 Dubnau, 1994, Two-component regulators and genetic competence in Bacillus subtilis, Res Microbiol, 145, 403, 10.1016/0923-2508(94)90088-4 Ebbole, 1987, Cloning and characterization of a 12-gene cluster from Bacillus subtilis encoding nine enzymes for de novo purine nucleotide synthesis, J Biol Chem, 262, 8274, 10.1016/S0021-9258(18)47560-6 Estruch, 1996, Vip3A, a novel Bacillus thuringiensis vegetative insecticidal protein with a wide spectrum of activities against lepidopteran insects, Proc Natl Acad Sci USA, 93, 5389, 10.1073/pnas.93.11.5389 Fajardo-Cavazos, 2000, The TRAP-like SplA protein is a trans-acting negative regulator of spore photoproduct lyase synthesis during Bacillus subtilis sporulation, J Bacteriol, 182, 555, 10.1128/JB.182.2.555-560.2000 Gollnick, 1990, The mtr locus is a two-gene operon required for transcription attenuation in the trp operon of Bacillus subtilis, Proc Natl Acad Sci USA, 87, 8726, 10.1073/pnas.87.22.8726 Graumann, 1999, Cold shock proteins CspB and CspC are major stationary-phase-induced proteins in Bacillus subtilis, Arch Microbiol, 171, 135, 10.1007/s002030050690 Hamoen, 1995, A small gene, designated comS, located within the coding region of the fourth amino acid-activating domain of srfA, is required for competence development in Bacillus subtilis, Mol Microbiol, 15, 55, 10.1111/j.1365-2958.1995.tb02220.x Harris, 1998, Mismatch repair in Escherichia coli cells lacking single-strand exonucleases ExoI, ExoVII, and RecJ, J Bacteriol, 180, 989, 10.1128/JB.180.4.989-993.1998 Hecker, 1998, Non-specific, general and multiple stress resistance of growth-restricted Bacillus subtilis cells by the expression of the sigmaB regulon, Mol Microbiol, 29, 1129, 10.1046/j.1365-2958.1998.00977.x Helmann JD, Moran CP. RNA polymerase and sigma factors. In: Sonenshein AL, Losick R, Hoch JA, editors. Bacillus subtilis and its relatives: from genes to cells. Washington, DC: American Society for Microbiology, 2001. In press. Henkin, 1993, Ribosomal structure and genetics, 669 Henriques, 2000, Structure and assembly of the bacterial endospore coat, Methods, 20, 95, 10.1006/meth.1999.0909 Hirose, 2000, Proteome analysis of Bacillus subtilis extracellular proteins, Microbiol, 146, 65, 10.1099/00221287-146-1-65 Hoch, 2000, Two-component and phosphorelay signal transduction, Curr Opin Microbiol, 3, 165, 10.1016/S1369-5274(00)00070-9 Hofmann, 1998, A model of Cdc25 phosphatase catalytic domain and Cdk-interaction surface based on the presence of a rhodanese homology domain, J Mol Biol, 282, 195, 10.1006/jmbi.1998.1998 Huang, 1999, Identification of target promoters for the Bacillus subtilis extracytoplasmic function sigma factor, sigma W, Mol Microbiol, 31, 361, 10.1046/j.1365-2958.1999.01180.x Illing, 1991, The spoIIIA operon of Bacillus subtilis defines a new temporal class of mother-cell-specific sporulation genes under the control of the sigma E form of RNA polymerase, Mol Microbiol, 5, 1927, 10.1111/j.1365-2958.1991.tb00816.x Ireton, 1993, Integration of multiple developmental signals in Bacillus subtilis through the Spo0A transcription factor, Genes Dev, 7, 283, 10.1101/gad.7.2.283 Jack, 1995, Bacteriocins of Gram-positive bacteria, Microbiol Rev, 59, 171, 10.1128/MR.59.2.171-200.1995 Kajitani, 1994, Regulation of the Escherichia coli hfq gene encoding the host factor for phage Q beta, J Bacteriol, 176, 531, 10.1128/jb.176.2.531-534.1994 Klaenhammer, 1993, Genetics of bacteriocins produced by lactic acid bacteria, FEMS Microbiol Rev, 12, 39, 10.1111/j.1574-6976.1993.tb00012.x Koonin, 1994, A novel RNA-binding motif in omnipotent suppressors of translation termination, ribosomal proteins and a ribosome modification enzyme?, Nucleic Acids Res, 22, 2166, 10.1093/nar/22.11.2166 Krogh, 1996, The phage-like element PBSX and part of the skin element, which are resident at different locations on the Bacillus subtilis chromosome, are highly homologous, Microbiol, 142, 2031, 10.1099/13500872-142-8-2031 Kunst, 1997, The complete genome sequence of the gram-positive bacterium Bacillus subtilis, Nature, 390, 249, 10.1038/36786 Langer, 1992, Successive action of DnaK, DnaJ and GroEL along the pathway of chaperone-mediated protein folding, Nature, 356, 683, 10.1038/356683a0 Lazarevic, 1999, Nucleotide sequence of the Bacillus subtilis temperate bacteriophage SPβc2, Microbiol, 145, 1055, 10.1099/13500872-145-5-1055 Lazazzera, 1997, An exported peptide functions intracellularly to contribute to cell density signaling in B. subtilis, Cell, 89, 917, 10.1016/S0092-8674(00)80277-9 Lehmann, 1996, Rubrerythrin from Clostridium perfringens, J Bacteriol, 178, 7152, 10.1128/jb.178.24.7152-7158.1996 Lewis, 1998, An evolutionary link between sporulation and prophage induction in the structure of a repressor:anti-repressor complex, J Mol Biol, 283, 907, 10.1006/jmbi.1998.2163 Liu, 1999, Role of Lon and ClpX in the post-translational regulation of a sigma subunit of RNA polymerase required for cellular differentiation of Bacillus subtilis, Mol Microbiol, 33, 415, 10.1046/j.1365-2958.1999.01489.x Liu, 1997, The RNA molecule CsrB binds to the global regulatory protein CsrA and antagonizes its activity in Escherichia coli, J Biol Chem, 272, 17502, 10.1074/jbc.272.28.17502 Magnuson, 1994, Biochemical and genetic characterization of a competence pheromone from Bacillus subtilis, Cell, 77, 207, 10.1016/0092-8674(94)90313-1 Model, 1997, The Escherichia coli phage-shock-protein (psp) operon, Mol Microbiol, 24, 255, 10.1046/j.1365-2958.1997.3481712.x Morbidoni HR, D dM, Cronan JE. Bacillus subtilis acyl carrier protein is encoded in a cluster of lipid biosynthesis genes. J Bacteriol 1996;178:4794–800. Moszer, 1995, SubtiList, Microbiol, 141, 261, 10.1099/13500872-141-2-261 Mukai, 1992, Stabilization of phosphorylated Bacillus subtilis DegU by DegR, J Bacteriol, 174, 7954, 10.1128/jb.174.24.7954-7962.1992 Nielsen, 1981, The nucleotide sequence of the atp genes coding for the F0 subunits a, b, c and the F1 subunit delta of the membrane bound ATP synthase of Escherichia coli, Mol Gen Genet, 184, 33, 10.1007/BF00271191 Nogueira, 2000, Post-transcriptional control by global regulators of gene expression in bacteria, Curr Opin Microbiol, 3, 154, 10.1016/S1369-5274(00)00068-0 Ogura, 2000, Bacillus subtilis comZ (yjzA) negatively affects expression of comG but not comK, J Bacteriol, 182, 4992, 10.1128/JB.182.17.4992-4994.2000 Paik, 1998, Identification and characterization of the structural and transporter genes for, and the chemical and biological properties of, sublancin 168, a novel lantibiotic produced by Bacillus subtilis 168, J Biol Chem, 273, 23134, 10.1074/jbc.273.36.23134 Perego, 1999, Self-signaling by Phr peptides modulates Bacillus subtilis development, 243 Perego, 1996, Aspartyl-phosphate phosphatases deactivate the response regulator components of the sporulation signal transduction system in Bacillus subtilis, Mol Microbiol, 19, 1151, 10.1111/j.1365-2958.1996.tb02460.x Perego, 1995, Incorporation of D-alanine into lipoteichoic acid and wall teichoic acid in Bacillus subtilis. Identification of genes and regulation, J Biol Chem, 270, 15598, 10.1074/jbc.270.26.15598 Perego, 1994, Multiple protein-aspartate phosphatases provide a mechanism for the integration of diverse signals in the control of development in B. subtilis, Cell, 79, 1047, 10.1016/0092-8674(94)90035-3 Perego, 1991, The oligopeptide transport system of Bacillus subtilis plays a role in the initiation of sporulation, Mol Microbiol, 5, 173, 10.1111/j.1365-2958.1991.tb01838.x Phadtare, 1999, Cold-shock response and cold-shock proteins, Curr Opin Microbiol, 2, 175, 10.1016/S1369-5274(99)80031-9 Pitterle, 1993, The biosynthesis of molybdopterin. Purification and characterization of the converting factor, J Biol Chem, 268, 13506, 10.1016/S0021-9258(19)38678-8 Rivers, 1993, Molecular genetic analysis of the moa operon of Escherichia coli K-12 required for molybdenum cofactor biosynthesis, Mol Microbiol, 8, 1071, 10.1111/j.1365-2958.1993.tb01652.x Roggiani, 1993, ComA, a phosphorylated response regulator protein of Bacillus subtilis, binds to the promoter region of srfA, J Bacteriol, 175, 3182, 10.1128/jb.175.10.3182-3187.1993 Romeo, 1998, Global regulation by the small RNA-binding protein CsrA and the non-coding RNA molecule CsrB, Mol Microbiol, 29, 1321, 10.1046/j.1365-2958.1998.01021.x Rudner, 1991, The spo0K locus of Bacillus subtilis is homologous to the oligopeptide permease locus and is required for sporulation and competence, J Bacteriol, 173, 1388, 10.1128/jb.173.4.1388-1398.1991 Rutberg, 1997, Antitermination of transcription of catabolic operons, Mol Microbiol, 23, 413, 10.1046/j.1365-2958.1997.d01-1867.x Schindler, 1999, The family of cold shock proteins of Bacillus subtilis. Stability and dynamics in vitro and in vivo, J Biol Chem, 274, 3407, 10.1074/jbc.274.6.3407 Schultz, 1998, SMART, a simple modular architecture research tool, Proc Natl Acad Sci USA, 95, 5857, 10.1073/pnas.95.11.5857 Setlow, 2000, Effects of major spore-specific DNA binding proteins on Bacillus subtilis sporulation and spore properties, J Bacteriol, 182, 6906, 10.1128/JB.182.24.6906-6912.2000 Shcheptov, 1997, Characterization of csgA, a new member of the forespore-expressed sigmaG-regulon from Bacillus subtilis, Gene, 184, 133, 10.1016/S0378-1119(96)00603-8 Siomi, 1994, Essential role for KH domains in RNA binding, Cell, 77, 33, 10.1016/0092-8674(94)90232-1 Solomon, 1996, Purification and characterization of an extracellular peptide factor that affects two different developmental pathways in Bacillus subtilis, Genes Dev, 10, 2014, 10.1101/gad.10.16.2014 Staker, 2000, Structure of Hsp15 reveals a novel RNA-binding motif, EMBO J, 19, 749, 10.1093/emboj/19.4.749 Stasinopoulos, 1998, Bacillus subtilis tetA(L) gene expression, Mol Microbiol, 30, 923, 10.1046/j.1365-2958.1998.01119.x Stragier, 1989, Chromosomal rearrangement generating a composite gene for a developmental transcription factor, Science, 243, 507, 10.1126/science.2536191 Takemaru, 1995, Complete nucleotide sequence of a skin element excised by DNA rearrangement during sporulation in Bacillus subtilis, Microbiol, 141, 323, 10.1099/13500872-141-2-323 Thomas, 2000, ClpB and HtpG facilitate de novo protein folding in stressed Escherichia coli cells, Mol Microbiol, 36, 1360, 10.1046/j.1365-2958.2000.01951.x Tjalsma, 2000, Signal peptide-dependent protein transport in Bacillus subtilis, Microbiol Mol Biol Rev, 64, 515, 10.1128/MMBR.64.3.515-547.2000 Turgay, 1997, Biochemical characterization of a molecular switch involving the heat shock protein ClpC, which controls the activity of ComK, the competence transcription factor of Bacillus subtilis, Genes Dev, 11, 119, 10.1101/gad.11.1.119 Vales, 1982, Subunit structure of Escherichia coli exonuclease VII, J Biol Chem, 257, 8799, 10.1016/S0021-9258(18)34201-7 van Sinderen, 1993, Characterization of the srfA locus of Bacillus subtilis, Mol Microbiol, 8, 833, 10.1111/j.1365-2958.1993.tb01630.x van Sinderen, 1995, comK encodes the competence transcription factor, the key regulatory protein for competence development in Bacillus subtilis, Mol Microbiol, 15, 455, 10.1111/j.1365-2958.1995.tb02259.x Wang, 1990, Complex character of senS, a novel gene regulating expression of extracellular-protein genes of Bacillus subtilis, J Bacteriol, 172, 1939, 10.1128/jb.172.4.1939-1947.1990 Weinrauch, 1990, A Bacillus subtilis regulatory gene product for genetic competence and sporulation resembles sensor protein members of the bacterial two-component signal-transduction systems, Genes Dev, 4, 860, 10.1101/gad.4.5.860 White, 1996, Phylogenetic distribution of the global regulatory gene csrA among eubacteria, Gene, 182, 221, 10.1016/S0378-1119(96)00547-1 Willins, 1991, Characterization of Lrp, and Escherichia coli regulatory protein that mediates a global response to leucine, J Biol Chem, 266, 10768, 10.1016/S0021-9258(18)99084-8 Wimmer, 1999, NMR structure and metal interactions of the CopZ copper chaperone, J Biol Chem, 274, 22597, 10.1074/jbc.274.32.22597 Wood, 1990, Characterization of PBSX, a defective prophage of Bacillus subtilis, J Bacteriol, 172, 2667, 10.1128/jb.172.5.2667-2674.1990 Wood, 1990, Characterisation of a repressor gene (xre) and a temperature-sensitive allele from the Bacillus subtilis prophage, PBSX, Gene, 96, 83, 10.1016/0378-1119(90)90344-Q Yang, 1986, Identification of the pleiotropic sacQ gene of Bacillus subtilis, J Bacteriol, 166, 113, 10.1128/jb.166.1.113-119.1986 Zeng, 1996, Repressor for the sn-glycerol 3-phosphate regulon of Escherichia coli K-12, J Bacteriol, 178, 7080, 10.1128/jb.178.24.7080-7089.1996 Zheng, 2000, Mutational analysis of the sbo-alb locus of Bacillus subtilis, J Bacteriol, 182, 3266, 10.1128/JB.182.11.3266-3273.2000 Zheng, 1999, The genes of the sbo-alb locus of Bacillus subtilis are required for the production of the anti-Listerial bacteriocin, subtilosin, J Bacteriol, 181, 7346, 10.1128/JB.181.23.7346-7355.1999