Intragenomic diversity of the V1 regions of 16S rRNA genes in high-alkaline protease-producing Bacillus clausii spp

Acinas SG, Marcelino LA, Klepac-Ceraj V, Polz MF (2004) Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol 186:2629–2635 Betzel C, Klupsch S, Papendorf G, Hastrup S, Branner S, Wilson KS (1992) Crystal structure of the alkaline proteinase Savinase from Bacillus lentus at 1.4 Å resolution. J Mol Biol 223:427–445 Borin S, Daffonchio D, Sorlini C (1997) Single strand conformation polymorphism analysis of PCR-tDNA fingerprinting to address the identification of Bacillus species. FEMS Microbiol Lett 157:87–93 Coenye T, Vandamme P (2003) Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes. FEMS Microbiol Lett 228:45–49 Daffonchio D, Borin S, Frova G, Manachini PL, Sorlini C (1998) PCR fingerprinting of whole genomes: the spacers between the 16S and 23S rRNA genes and of intergenic tRNA gene regions reveal a different intraspecific genomic variability of Bacillus cereus and Bacillus licheniformis. Int J Syst Bacteriol 48:107–116 Denizci AA, Kazan D, Abeln ECA, Erarslan A (2004) Newly isolated Bacillus clausii GMBAE 42: an alkaline protease producer capable to grow under higly alkaline conditions. J Appl Microbiol 96:320–327 Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229 Ghosh S, Joseph S (2005) Nonbridging phosphate oxygens in 16S rRNA important for 30S subunit assembly and association with the 50S ribosomal subunit. RNA 11:657–667 Gray MW, Sankoff D, Cedergren RJ (1984) On the evolutionary descent of organisms and organelles: a global phylogeny based on a highly conserved structural core in small subunit ribosomal RNA. Nucleic Acids Res 12:5837–5852 Hakamada Y, Kobayashi T, Hitomi J, Kawai S, Ito S (1994) Molecular cloning and nucleotide sequence of the gene for an alkaline protease from the alkalophilic Bacillus sp. KSM-K16. J Ferment Bioeng 78:105–108 Horikoshi K (1971) Production of alkaline enzymes by alkalophilic microorganisms. I. Alkaline protease produced by Bacillus no. 221. Agric Biol Chem 35:1407–1414 Horikoshi K (1991) Isolation and classification of alkalophilic microorganisms. In: Microorganisms in alkaline environments. Kodansha, Tokyo, pp 5–24 Ito S, Kobayashi T, Ara K, Ozaki K, Kawai S, Hatada Y (1998) Alkaline detergent enzymes from alkaliphiles: enzymatic properties, genetics, and structures. Extremophiles 2:185–190 Ivanova N, Sorokin A, Anderson I, Galleron N, Candelon B, Kapatral V, Bhattacharyya A, Reznik G, Mikhailova N, Lapidus A et al (2003) Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature 423:87–91 Jones BE, Grant WD, Duckworth AW, Owenson GG (1998) Microbial diversity of soda lakes. Extremophiles 2:191–200 Kobayashi T, Hakamada Y, Adachi S, Hitomi J, Yoshimatsu T, Koike K, Kawai S, Ito S (1995) Purification and properties of an alkaline protease from alkalophilic Bacillus sp. KSM-K16. Appl Microbiol Biotechnol 43:473–481 Kobayashi T, Hakamada Y, Hitomi J, Koike K, Ito S (1996) Purification of alkaline proteases from a Bacillus strain and their possible interrelationship. Appl Microbiol Biotechnol 45:63–71 Kobayashi T, Kageyama Y, Sumitomo N, Saeki K, Shirai T, Ito S (2005) Contribution of a salt bridge triad to the thermostability of a highly alkaline protease from an alkaliphilic Bacillus strain. World J Microbiol Biotechnol 21:961–967 Komagata K, Suzuki K (1987) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–207 Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessieres P, Bolotin A, Borchert S et al (1997) The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390:249–256 Liu SL, Hessel A, Sanderson KE (1993) Genomic mapping with I-CeuI, an intron-encoded endonuclease specific for genes for ribosomal RNA, in Salmonella spp., Escherichia coli, and other bacteria. Proc Natl Acad Sci USA 90:6874–6878 Moreno C, Romero J, Espejo RT (2002) Polymorphism in repeated 16S rRNA genes is a common property of type strains and environmental isolates of the genus Vibrio. Microbiology 148:1233–1239 Nielsen P, Rainey FA, Outtrup H, Priest FG, Fritze D (1994) Comparative 16S rDNA sequence analysis of some alkaliphilic bacilli and the establishment of a sixth rRNA group within the genus Bacillus. FEMS Microbiol Lett 117:61–65 Nielsen P, Fritze D, Priest G. (1995) Phenitic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Microbiology 141:1745–1761 Nogi Y, Takami H, Horikoshi K (2005) Characterization of alkaliphilic Bacillus strains used in industry: proposal of five novel species. Int J Syst Evol Microbiol 55:2309–2315 Ogawa A, Sumitomo N, Okuda M, Saeki K, Kawai S, Kobayashi T, Ito S (2003) Nucleotide and deduced amino acid sequences of a high-molecular-mass subtilisin from an alkaliphilic Bacillus isolate. Biochim Biophys Acta 1624:109–114 Okuda M, Sumitomo N, Takimura Y, Ogawa A, Saeki K, Kawai S, Kobayashi T, Ito S (2004) A new subtilisin family: nucleotide and deduced amino acid sequences of new highmolecular-mass alkaline proteases from Bacillus spp. Extremophiles 8:229–235 Pettersson B, Lembke F, Hammer P, Stackebrandt E, Priest FG (1996) Bacillus sporothermodurans, a new species producing highly heat-resistant endospores. Int J Syst Bacteriol 46:759–764 Pruss BM, Francis KP, von Stetten F, Scherer S (1999) Correlation of 16S ribosomal DNA signature sequences with temperature-dependent growth rates of mesophilic and psychrotolerant strains of the Bacillus cereus group. J Bacteriol 181:2624–2630 Rasko DA, Ravel J, Okstad OA, Helgason E, Cer RZ, Jiang L, Shores KA, Fouts DE, Tourasse NJ, Angiuoli SV et al (2004) The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1. Nucleic Acids Res 32:977–988 Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR et al (2003) The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423:81–86 Rey MW, Ramaiya P, Nelson BA, Brody-Karpin SD, Zaretsky EJ, Tang M, Lopez de Leon A, Xiang H, Gusti V, Clausen IG et al. (2004) Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species. Genome Biol 5:R77 Saeki K, Okuda M, Hatada Y, Kobayashi T, Ito S, Takami H, Horikoshi K (2000) Novel oxidatively stable subtilisin-like serine proteases from alkaliphilic Bacillus spp.: enzymatic properties, sequences, and evolutionary relationships. Biochem Biophys Res Commun 279:313–319 Saeki K, Hitomi J, Okuda M, Hatada Y, Kageyama Y, Takaiwa M, Kubota H, Hagihara H, Kobayashi T, Kawai S, Ito S (2002) A novel species of alkaliphilic Bacillus that produces an oxidatively stable alkaline serine protease. Extremophiles 6:65–72 Saito H, Miura K (1963) Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 72:619–629 Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425 Sapag A, Vartikar JV, Draper DE (1990) Dissection of the 16S rRNA binding site for ribosomal protein S4. Biochim Biophys Acta 1050:34–37 Senesi S, Celandroni F, Tavanti A, Ghelardi E (2001) Molecular characterization and identification of Bacillus clausii strains marketed for use in oral bacteriotherapy. Appl Environ Microbiol 67:834–839 Shirai T, Suzuki A, Yamane T, Ashida T, Kobayashi T, Hitomi J, Ito S (1997) High-resolution crystal structure of M-protease: phylogeny aided analysis of the high-alkaline adaptation mechanism. Protein Eng 10:627–634 Siezen RJ, Leunissen JA (1997) Subtilases: The superfamily of subtilisin-like serine proteases. Protein Sci 6:501–523 Takami H, Nakasone K, Hirama C, TakakiY, Masui N, Fuji F, Nakamura Y, Inoue A (1999) An improved physical and genetic map of the genome of alkaliphilic Bacillus sp. C-125. Extremophiles 3:21–28 Takami H, Nakasone K, Takaki Y, Maeno G, Sasaki R, Masui N, Fuji F, Hirama C, Nakamura Y, Ogasawara N et al (2000) Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis. Nucleic Acids Res 28:4317–4331 Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876–4882 Ueda K, Seki T, Kudo T, Yoshida T, Kataoka M (1999) Two distinct mechanisms cause heterogeneity of 16S rRNA. J Bacteriol 181:249–255 van der Laan JM, Teplyakov AV, Kelders H, Kalk KH, Misset O, Mulleners LJ,Dijkstra BW (1992) Crystal structure of the high-alkaline serine protease PB92 from Bacillus alcalophilus. Protein Eng 5:405–411 Veith B, Herzberg C, Steckel S, Feesche J, Maurer KH, Ehrenreich P, Baumer S, Henne A, Liesegang H, Merkl R et al (2004) The complete genome sequence of Bacillus licheniformis DSM13, an organism with great industrial potential. J Mol Microbiol Biotechnol 7:204–211