Journal of Biotechnology 188 (2014) 110–111
Contents lists available at ScienceDirect
Journal of Biotechnology journal homepage: www.elsevier.com/locate/jbiotec
Genome Announcement
Complete genome sequence of Bacillus methanolicus MGA3, a thermotolerant amino acid producing methylotroph夽 Marta Irla a,b , Armin Neshat c , Anika Winkler c , Andreas Albersmeier c , Tonje M.B. Heggeset d , Trygve Brautaset d , Jörn Kalinowski c , Volker F. Wendisch a,b , Christian Rückert c,∗ a
Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany c Technology Platform Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany d Department of Molecular Biology, SINTEF Materials and Chemistry, N-7465 Trondheim, Norway b
a r t i c l e
i n f o
Article history: Received 5 August 2014 Accepted 12 August 2014 Available online 22 August 2014 Keywords: Bacillus methanolicus Genome Methylotrophy Amino acid production
a b s t r a c t Bacillus methanolicus MGA3 was isolated from freshwater marsh soil and characterised as a thermotolerant and methylotrophic l-glutamate producer. The complete genome consists of a circular chromosome and the two plasmids pBM19 and pBM69. It includes genomic information about C1 metabolism and amino acid biosynthetic pathways. © 2014 Elsevier B.V. All rights reserved.
Bacillus methanolicus MGA3 (=ATCC 53907) is a Gram-positive bacterium of the class Bacilli, order Bacillales, family Bacillaceae. Members of the genus Bacillus live in a wide variety of habitats and possess a wide variety of capabilities. Therefore, the number of available sequences for Bacillus species is growing quickly, including those of medical importance, e.g., B. anthracis (Rückert et al., 2012), as well as those of biotechnological interest, e.g., B. amyloliqefaciens, involved in plant growth promotion (Cai et al., 2014; He et al., 2012; Rückert et al., 2011), B. thuringiensis, usable for plant protection (Wang et al., 2014), and B. firmus, a candidate for environmental bioremediation (Geng et al., 2014). B. methanolicus was isolated from freshwater marsh soil (Schendel et al., 1990) and classified as B. methanolicus in 1992 (Arfman et al., 1992). It is a rod shaped, endospore-forming bacterium with strictly respiratory metabolism and shows the capability to grow between 37 ◦ C and 65 ◦ C with optimum at 50–53 ◦ C (Schendel et al., 1990).
夽 Nucleotide sequence accession numbers: The complete genome sequences have been deposited in DDBJ/EMBL/GenBank under accession nos. CP007739 (chromosome), CP007740 (pBM69), and CP007741 (pBM19). ∗ Corresponding author. Tel.: +49 521 106 12252. E-mail address: [email protected] (C. Rückert). http://dx.doi.org/10.1016/j.jbiotec.2014.08.013 0168-1656/© 2014 Elsevier B.V. All rights reserved.
B. methanolicus MGA3 is a facultative methylotroph which can also grow on mannitol and glucose as the sole carbon and energy sources. It utilises an NAD-dependent methanol dehydrogenase for methanol oxidation and subsequently assimilates the created formaldehyde via the ribulose monophosphate pathway (Arfman et al., 1992; Schendel et al., 1990). B. methanolicus is an industrially relevant organism not only because of its methylotrophy and thermotolerance but also because it is able to overproduce l-glutamate during fed-batch fermentations up to 59 g/L (Brautaset et al., 2010). Moreover, mutants overproducing l-lysine up to 65 g/L in fed-batch fermentations were obtained both by classical mutagenesis and selection as well as by metabolic engineering (Brautaset et al., 2010, 2003; Hanson et al., 1996). The genome of B. methanolicus MGA3 was sequenced using a mixed strategy. Sequencing of a whole-genome shotgun library, prepared with the Nextera DNA Sample Prep Kit, and a 8K mate pair library, prepared with the Nextera Mate Pair Sample Preparation Kit (both Illumina, San Diego, CA, USA) was performed on a MiSeq sequencer (Illumina). Using Newbler v. 2.8 for assembly, 2,699,120 reads were assembled into 3 scaffolds (one for each replicon) consisting of 42 contigs. In total, the assembly consisted of 51 contigs larger than 500 bp, the average coverage was 182-fold. The genome sequence was finished in silico using the CONSED software package (Gordon, 2003; Gordon et al., 1998) to close gaps caused by repeats and to resolve SNPs in those repeats based on MatePair data.
M. Irla et al. / Journal of Biotechnology 188 (2014) 110–111 Table 1 Genome features of B. methanolicus MGA3.
111
References
Features
Chromosome
Plasmid pBM19
Plasmid pBM69
Length (bp) DNA-coding regions (bp) G + C content (%) CDS rRNA genes (operons) tRNA genes
3,337,035 2,726,049 38.66 3218 27 (9) 92
19,174 13,725 36.69 22 0 (0) 0
68,999 48,960 35.80 82 0 (0) 0
Altogether, the genome of B. methanolicus MGA3 consists of one circular chromosome (3,337,035 bp, 38.66% G + C) and two plasmids pBM19 (19,174 bp, 36.69% G + C) and pBM69 (68,999 bp, 35.80% G + C). The finished genome was analysed with GenDB (Meyer et al., 2003) which enabled the prediction of 3322 protein-coding genes, 27 ribosomal RNA genes in 9 operons, and 92 tRNA genes (Table 1). Analysis of the draft genome sequence of B. methanolics MGA3 published in 2012 (Heggeset et al., 2012) enabled the characterisation of several metabolic pathways particularly interesting with regards to production of industrially relevant compounds such as amino acids from methanol. The special emphasis was put on description of central carbon metabolism pathways including methanol oxidation and subsequent formaldehyde assimilation, as well as l-lysine and l-glutamate biosynthesis pathways (Heggeset et al., 2012). Interestingly, most of the enzymes of the ribulose monophosphate (RuMP) pathway are encoded both by a chromosomal gene and by a gene on the plasmid pBM19. Methylotrophy of B. methanolicus MGA3 was shown to depend on plasmid pBM19 since a pBM19-cured mutant could not grow with methanol as sole carbon source (Brautaset et al., 2004). Expression of the RuMP cycle genes encoded on pBM19 were shown to be methanol-induced (Heggeset et al., 2012). In some instances, biochemical characterisation of purified enzymes revealed different kinetic properties of the plasmid- and the chromosomally encoded enzyme. For example, the chromosomally encoded bisphosphatase GlpXC is the major fructose 1,6-bisphosphatase of B. methanolicus whereas the pBM19-encoded enzyme GlpXP is active as a sedoheptulose 1,7bisphosphatase (Stolzenberger et al., 2013). B. methanolicus MGA3 is auxotrophic for biotin (Schendel et al., 1990). Its genome encodes putative homologs of the biotin synthesis genes bioF, bioA, bioD and bioB, but lacks an intact bioI homolog and only a remnant is present on plasmid pBM69. In B. subtilis, the cytochrome P450 hydroxylase BioI oxidatively cleaves a carbon-carbon bond of an acyl-ACP intermediate of fatty acid biosynthesis to generate pimeloyl-ACP (Lin and Cronan, 2011), the precursor metabolite of the biotin biosynthetic enzymes BioF, BioA, BioD and BioB. Complementation of biotin auxotrophy by heterologous gene expression is an important target in strain development (Peters-Wendisch et al., 2014) in order to decrease costs for media components in large-scale fermentations. Acknowledgements MI and AN are a fellows of the CLIB2021 graduate cluster at Bielefeld University. VFW and MI acknowledge support by the FP7 EU project PROMYSE (289540).
Arfman, N., Dijkhuizen, L., Kirchhof, G., Ludwig, W., Schleifer, K.H., Bulygina, E.S., Chumakov, K.M., Govorukhina, N.I., Trotsenko, Y.A., White, D., Sharp, R.J., 1992. Bacillus methanolicus sp. nov., a new species of thermotolerant, methanol-utilizing, endospore-forming bacteria. Int. J. Syst. Bacteriol. 42, 439–445. Brautaset, T., Jakobsen, O.M., Degnes, K.F., Netzer, R., Naerdal, I., Krog, A., Dillingham, R., Flickinger, M.C., Ellingsen, T.E., 2010. Bacillus methanolicus pyruvate carboxylase and homoserine dehydrogenase I and II and their roles for l-lysine production from methanol at 50 degrees C. Appl. Microbiol. Biotechnol. 87, 951–964. Brautaset, T., Jakobsen, Ø.M., Flickinger, M.C., Valla, S., Ellingsen, T.E., 2004. Plasmiddependent methylotrophy in thermotolerant Bacillus methanolicus. J. Bacteriol. 186, 1229–1238. Brautaset, T., Williams, M.D., Dillingham, R.D., Kaufmann, C., Bennaars, A., Crabbe, E., Flickinger, M.C., 2003. Role of the Bacillus methanolicus citrate synthase II gene, citY, in regulating the secretion of glutamate in l-lysine-secreting mutants. Appl. Environ. Microbiol. 69, 3986–3995. Cai, J., Liu, F., Liao, X., Zhang, R., 2014. Complete genome sequence of Bacillus amyloliquefaciens LFB112 isolated from Chinese herbs, a strain of a broad inhibitory spectrum against domestic animal pathogens. J. Biotechnol. 175, 63–64. Geng, C., Tang, Z., Peng, D., Shao, Z., Zhu, L., Zheng, J., Wang, H., Ruan, L., Sun, M., 2014. Draft genome sequence of Bacillus firmus DS1. J. Biotechnol. 177, 20–21. Gordon, D., 2003. Viewing and editing assembled sequences using Consed. Curr Protoc Bioinformatics, Chapter 11, Unit11 12. Gordon, D., Abajian, C., Green, P., 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8, 195–202. Hanson, R.S., Dillingham, R.L., Olson, P., Lee, G.H., Cue, D., Schendel, F.J., Bremmon, C., MC, F., 1996. Production of l-lysine and some other amino acids by mutants of B. methanolicus. In: Lidstrom, M.E., Tabita, F.R. (Eds.), Microbial Growth on C1 compounds. Kluwer Academic Publishers, Dordrecht/Boston, pp. 227– 234. He, P., Hao, K., Blom, J., Rückert, C., Vater, J., Mao, Z., Wu, Y., Hou, M., He, Y., Borriss, R., 2012. Genome sequence of the plant growth promoting strain Bacillus amyloliquefaciens subsp. plantarum B9601-Y2 and expression of mersacidin and other secondary metabolites. J. Biotechnol. 164, 281–291. Heggeset, T.M., Krog, A., Balzer, S., Wentzel, A., Ellingsen, T.E., Brautaset, T., 2012. Genome sequence of thermotolerant Bacillus methanolicus: features and regulation related to methylotrophy and production of l-lysine and l-glutamate from methanol. Appl. Environ. Microbiol. 78, 5170–5181. Lin, S., Cronan, J.E., 2011. Closing in on complete pathways of biotin biosynthesis. Mol Biosyst 7, 1811–1821. Meyer, F., Goesmann, A., McHardy, A.C., Bartels, D., Bekel, T., Clausen, J., Kalinowski, J., Linke, B., Rupp, O., Giegerich, R., Pühler, A., 2003. GenDB – an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 31, 2187–2195. Peters-Wendisch, P., Götker, S., Heider, S.A., Komati Reddy, G., Nguyen, A.Q., Stansen, K.C., Wendisch, V.F., 2014. Engineering biotin prototrophic Corynebacterium glutamicum strains for amino acid, diamine and carotenoid production. J Biotechnol, http://dx.doi.org/10.1016/j.jbiotec.2014.01.023. Rückert, C., Blom, J., Chen, X., Reva, O., Borriss, R., 2011. Genome sequence of B. amyloliquefaciens type strain DSM7T reveals differences to plant-associated B. amyloliquefaciens FZB42. J. Biotechnol. 155, 78–85. Rückert, C., Licht, K., Kalinowski, J., Espirito Santo, C., Antwerpen, M., Hanczaruk, M., Reischl, U., Holzmann, T., Gessner, A., Tiemann, C., Grass, G., 2012. Draft genome sequence of Bacillus anthracis UR-1, isolated from a German heroin user. J. Bacteriol. 194, 5997–5998. Schendel, F.J., Bremmon, C.E., Flickinger, M.C., Guettler, M., Hanson, R.S., 1990. l-Lysine production at 50 degrees C by mutants of a newly isolated and characterized methylotrophic Bacillus sp. Appl. Environ. Microbiol. 56, 963– 970. Stolzenberger, J., Lindner, S.N., Persicke, M., Brautaset, T., Wendisch, V.F., 2013. Characterization of fructose 1,6-bisphosphatase and sedoheptulose 1,7-bisphosphatase from the facultative ribulose monophosphate cycle methylotroph Bacillus methanolicus. J. Bacteriol. 195, 5112–5122. Wang, P., Zhang, C., Guo, M., Guo, S., Zhu, Y., Zheng, J., Zhu, L., Ruan, L., Peng, D., Sun, M., 2014. Complete genome sequence of Bacillus thuringiensis YBT-1518, a typical strain with high toxicity to nematodes. J. Biotechnol. 171, 1–2.
Contents lists available at ScienceDirect
Journal of Biotechnology journal homepage: www.elsevier.com/locate/jbiotec
Genome Announcement
Complete genome sequence of Bacillus methanolicus MGA3, a thermotolerant amino acid producing methylotroph夽 Marta Irla a,b , Armin Neshat c , Anika Winkler c , Andreas Albersmeier c , Tonje M.B. Heggeset d , Trygve Brautaset d , Jörn Kalinowski c , Volker F. Wendisch a,b , Christian Rückert c,∗ a
Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany c Technology Platform Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany d Department of Molecular Biology, SINTEF Materials and Chemistry, N-7465 Trondheim, Norway b
a r t i c l e
i n f o
Article history: Received 5 August 2014 Accepted 12 August 2014 Available online 22 August 2014 Keywords: Bacillus methanolicus Genome Methylotrophy Amino acid production
a b s t r a c t Bacillus methanolicus MGA3 was isolated from freshwater marsh soil and characterised as a thermotolerant and methylotrophic l-glutamate producer. The complete genome consists of a circular chromosome and the two plasmids pBM19 and pBM69. It includes genomic information about C1 metabolism and amino acid biosynthetic pathways. © 2014 Elsevier B.V. All rights reserved.
Bacillus methanolicus MGA3 (=ATCC 53907) is a Gram-positive bacterium of the class Bacilli, order Bacillales, family Bacillaceae. Members of the genus Bacillus live in a wide variety of habitats and possess a wide variety of capabilities. Therefore, the number of available sequences for Bacillus species is growing quickly, including those of medical importance, e.g., B. anthracis (Rückert et al., 2012), as well as those of biotechnological interest, e.g., B. amyloliqefaciens, involved in plant growth promotion (Cai et al., 2014; He et al., 2012; Rückert et al., 2011), B. thuringiensis, usable for plant protection (Wang et al., 2014), and B. firmus, a candidate for environmental bioremediation (Geng et al., 2014). B. methanolicus was isolated from freshwater marsh soil (Schendel et al., 1990) and classified as B. methanolicus in 1992 (Arfman et al., 1992). It is a rod shaped, endospore-forming bacterium with strictly respiratory metabolism and shows the capability to grow between 37 ◦ C and 65 ◦ C with optimum at 50–53 ◦ C (Schendel et al., 1990).
夽 Nucleotide sequence accession numbers: The complete genome sequences have been deposited in DDBJ/EMBL/GenBank under accession nos. CP007739 (chromosome), CP007740 (pBM69), and CP007741 (pBM19). ∗ Corresponding author. Tel.: +49 521 106 12252. E-mail address: [email protected] (C. Rückert). http://dx.doi.org/10.1016/j.jbiotec.2014.08.013 0168-1656/© 2014 Elsevier B.V. All rights reserved.
B. methanolicus MGA3 is a facultative methylotroph which can also grow on mannitol and glucose as the sole carbon and energy sources. It utilises an NAD-dependent methanol dehydrogenase for methanol oxidation and subsequently assimilates the created formaldehyde via the ribulose monophosphate pathway (Arfman et al., 1992; Schendel et al., 1990). B. methanolicus is an industrially relevant organism not only because of its methylotrophy and thermotolerance but also because it is able to overproduce l-glutamate during fed-batch fermentations up to 59 g/L (Brautaset et al., 2010). Moreover, mutants overproducing l-lysine up to 65 g/L in fed-batch fermentations were obtained both by classical mutagenesis and selection as well as by metabolic engineering (Brautaset et al., 2010, 2003; Hanson et al., 1996). The genome of B. methanolicus MGA3 was sequenced using a mixed strategy. Sequencing of a whole-genome shotgun library, prepared with the Nextera DNA Sample Prep Kit, and a 8K mate pair library, prepared with the Nextera Mate Pair Sample Preparation Kit (both Illumina, San Diego, CA, USA) was performed on a MiSeq sequencer (Illumina). Using Newbler v. 2.8 for assembly, 2,699,120 reads were assembled into 3 scaffolds (one for each replicon) consisting of 42 contigs. In total, the assembly consisted of 51 contigs larger than 500 bp, the average coverage was 182-fold. The genome sequence was finished in silico using the CONSED software package (Gordon, 2003; Gordon et al., 1998) to close gaps caused by repeats and to resolve SNPs in those repeats based on MatePair data.
M. Irla et al. / Journal of Biotechnology 188 (2014) 110–111 Table 1 Genome features of B. methanolicus MGA3.
111
References
Features
Chromosome
Plasmid pBM19
Plasmid pBM69
Length (bp) DNA-coding regions (bp) G + C content (%) CDS rRNA genes (operons) tRNA genes
3,337,035 2,726,049 38.66 3218 27 (9) 92
19,174 13,725 36.69 22 0 (0) 0
68,999 48,960 35.80 82 0 (0) 0
Altogether, the genome of B. methanolicus MGA3 consists of one circular chromosome (3,337,035 bp, 38.66% G + C) and two plasmids pBM19 (19,174 bp, 36.69% G + C) and pBM69 (68,999 bp, 35.80% G + C). The finished genome was analysed with GenDB (Meyer et al., 2003) which enabled the prediction of 3322 protein-coding genes, 27 ribosomal RNA genes in 9 operons, and 92 tRNA genes (Table 1). Analysis of the draft genome sequence of B. methanolics MGA3 published in 2012 (Heggeset et al., 2012) enabled the characterisation of several metabolic pathways particularly interesting with regards to production of industrially relevant compounds such as amino acids from methanol. The special emphasis was put on description of central carbon metabolism pathways including methanol oxidation and subsequent formaldehyde assimilation, as well as l-lysine and l-glutamate biosynthesis pathways (Heggeset et al., 2012). Interestingly, most of the enzymes of the ribulose monophosphate (RuMP) pathway are encoded both by a chromosomal gene and by a gene on the plasmid pBM19. Methylotrophy of B. methanolicus MGA3 was shown to depend on plasmid pBM19 since a pBM19-cured mutant could not grow with methanol as sole carbon source (Brautaset et al., 2004). Expression of the RuMP cycle genes encoded on pBM19 were shown to be methanol-induced (Heggeset et al., 2012). In some instances, biochemical characterisation of purified enzymes revealed different kinetic properties of the plasmid- and the chromosomally encoded enzyme. For example, the chromosomally encoded bisphosphatase GlpXC is the major fructose 1,6-bisphosphatase of B. methanolicus whereas the pBM19-encoded enzyme GlpXP is active as a sedoheptulose 1,7bisphosphatase (Stolzenberger et al., 2013). B. methanolicus MGA3 is auxotrophic for biotin (Schendel et al., 1990). Its genome encodes putative homologs of the biotin synthesis genes bioF, bioA, bioD and bioB, but lacks an intact bioI homolog and only a remnant is present on plasmid pBM69. In B. subtilis, the cytochrome P450 hydroxylase BioI oxidatively cleaves a carbon-carbon bond of an acyl-ACP intermediate of fatty acid biosynthesis to generate pimeloyl-ACP (Lin and Cronan, 2011), the precursor metabolite of the biotin biosynthetic enzymes BioF, BioA, BioD and BioB. Complementation of biotin auxotrophy by heterologous gene expression is an important target in strain development (Peters-Wendisch et al., 2014) in order to decrease costs for media components in large-scale fermentations. Acknowledgements MI and AN are a fellows of the CLIB2021 graduate cluster at Bielefeld University. VFW and MI acknowledge support by the FP7 EU project PROMYSE (289540).
Arfman, N., Dijkhuizen, L., Kirchhof, G., Ludwig, W., Schleifer, K.H., Bulygina, E.S., Chumakov, K.M., Govorukhina, N.I., Trotsenko, Y.A., White, D., Sharp, R.J., 1992. Bacillus methanolicus sp. nov., a new species of thermotolerant, methanol-utilizing, endospore-forming bacteria. Int. J. Syst. Bacteriol. 42, 439–445. Brautaset, T., Jakobsen, O.M., Degnes, K.F., Netzer, R., Naerdal, I., Krog, A., Dillingham, R., Flickinger, M.C., Ellingsen, T.E., 2010. Bacillus methanolicus pyruvate carboxylase and homoserine dehydrogenase I and II and their roles for l-lysine production from methanol at 50 degrees C. Appl. Microbiol. Biotechnol. 87, 951–964. Brautaset, T., Jakobsen, Ø.M., Flickinger, M.C., Valla, S., Ellingsen, T.E., 2004. Plasmiddependent methylotrophy in thermotolerant Bacillus methanolicus. J. Bacteriol. 186, 1229–1238. Brautaset, T., Williams, M.D., Dillingham, R.D., Kaufmann, C., Bennaars, A., Crabbe, E., Flickinger, M.C., 2003. Role of the Bacillus methanolicus citrate synthase II gene, citY, in regulating the secretion of glutamate in l-lysine-secreting mutants. Appl. Environ. Microbiol. 69, 3986–3995. Cai, J., Liu, F., Liao, X., Zhang, R., 2014. Complete genome sequence of Bacillus amyloliquefaciens LFB112 isolated from Chinese herbs, a strain of a broad inhibitory spectrum against domestic animal pathogens. J. Biotechnol. 175, 63–64. Geng, C., Tang, Z., Peng, D., Shao, Z., Zhu, L., Zheng, J., Wang, H., Ruan, L., Sun, M., 2014. Draft genome sequence of Bacillus firmus DS1. J. Biotechnol. 177, 20–21. Gordon, D., 2003. Viewing and editing assembled sequences using Consed. Curr Protoc Bioinformatics, Chapter 11, Unit11 12. Gordon, D., Abajian, C., Green, P., 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8, 195–202. Hanson, R.S., Dillingham, R.L., Olson, P., Lee, G.H., Cue, D., Schendel, F.J., Bremmon, C., MC, F., 1996. Production of l-lysine and some other amino acids by mutants of B. methanolicus. In: Lidstrom, M.E., Tabita, F.R. (Eds.), Microbial Growth on C1 compounds. Kluwer Academic Publishers, Dordrecht/Boston, pp. 227– 234. He, P., Hao, K., Blom, J., Rückert, C., Vater, J., Mao, Z., Wu, Y., Hou, M., He, Y., Borriss, R., 2012. Genome sequence of the plant growth promoting strain Bacillus amyloliquefaciens subsp. plantarum B9601-Y2 and expression of mersacidin and other secondary metabolites. J. Biotechnol. 164, 281–291. Heggeset, T.M., Krog, A., Balzer, S., Wentzel, A., Ellingsen, T.E., Brautaset, T., 2012. Genome sequence of thermotolerant Bacillus methanolicus: features and regulation related to methylotrophy and production of l-lysine and l-glutamate from methanol. Appl. Environ. Microbiol. 78, 5170–5181. Lin, S., Cronan, J.E., 2011. Closing in on complete pathways of biotin biosynthesis. Mol Biosyst 7, 1811–1821. Meyer, F., Goesmann, A., McHardy, A.C., Bartels, D., Bekel, T., Clausen, J., Kalinowski, J., Linke, B., Rupp, O., Giegerich, R., Pühler, A., 2003. GenDB – an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 31, 2187–2195. Peters-Wendisch, P., Götker, S., Heider, S.A., Komati Reddy, G., Nguyen, A.Q., Stansen, K.C., Wendisch, V.F., 2014. Engineering biotin prototrophic Corynebacterium glutamicum strains for amino acid, diamine and carotenoid production. J Biotechnol, http://dx.doi.org/10.1016/j.jbiotec.2014.01.023. Rückert, C., Blom, J., Chen, X., Reva, O., Borriss, R., 2011. Genome sequence of B. amyloliquefaciens type strain DSM7T reveals differences to plant-associated B. amyloliquefaciens FZB42. J. Biotechnol. 155, 78–85. Rückert, C., Licht, K., Kalinowski, J., Espirito Santo, C., Antwerpen, M., Hanczaruk, M., Reischl, U., Holzmann, T., Gessner, A., Tiemann, C., Grass, G., 2012. Draft genome sequence of Bacillus anthracis UR-1, isolated from a German heroin user. J. Bacteriol. 194, 5997–5998. Schendel, F.J., Bremmon, C.E., Flickinger, M.C., Guettler, M., Hanson, R.S., 1990. l-Lysine production at 50 degrees C by mutants of a newly isolated and characterized methylotrophic Bacillus sp. Appl. Environ. Microbiol. 56, 963– 970. Stolzenberger, J., Lindner, S.N., Persicke, M., Brautaset, T., Wendisch, V.F., 2013. Characterization of fructose 1,6-bisphosphatase and sedoheptulose 1,7-bisphosphatase from the facultative ribulose monophosphate cycle methylotroph Bacillus methanolicus. J. Bacteriol. 195, 5112–5122. Wang, P., Zhang, C., Guo, M., Guo, S., Zhu, Y., Zheng, J., Zhu, L., Ruan, L., Peng, D., Sun, M., 2014. Complete genome sequence of Bacillus thuringiensis YBT-1518, a typical strain with high toxicity to nematodes. J. Biotechnol. 171, 1–2.
