Genome Sequences of the Biotechnologically Important Bacillus megaterium Strains QM B1551 and DSM319

Institute for Genomic Sciences and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, MD 21201, USA.
Journal of bacteriology (Impact Factor: 2.81). 06/2011; 193(16):4199-213. DOI: 10.1128/JB.00449-11
Source: PubMed


Bacillus megaterium is deep-rooted in the Bacillus phylogeny, making it an evolutionarily key species and of particular importance in understanding genome evolution, dynamics,
and plasticity in the bacilli. B. megaterium is a commercially available, nonpathogenic host for the biotechnological production of several substances, including vitamin
B12, penicillin acylase, and amylases. Here, we report the analysis of the first complete genome sequences of two important B. megaterium strains, the plasmidless strain DSM319 and QM B1551, which harbors seven indigenous plasmids. The 5.1-Mbp chromosome carries
approximately 5,300 genes, while QM B1551 plasmids represent a combined 417 kb and 523 genes, one of the largest plasmid arrays
sequenced in a single bacterial strain. We have documented extensive gene transfer between the plasmids and the chromosome.
Each strain carries roughly 300 strain-specific chromosomal genes that account for differences in their experimentally confirmed
phenotypes. B. megaterium is able to synthesize vitamin B12 through an oxygen-independent adenosylcobalamin pathway, which together with other key energetic and metabolic pathways has
now been fully reconstructed. Other novel genes include a second ftsZ gene, which may be responsible for the large cell size of members of this species, as well as genes for gas vesicles, a second
β-galactosidase gene, and most but not all of the genes needed for genetic competence. Comprehensive analyses of the global
Bacillus gene pool showed that only an asymmetric region around the origin of replication was syntenic across the genus. This appears
to be a characteristic feature of the Bacillus spp. genome architecture and may be key to their sporulating lifestyle.

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Available from: Erhard Bremer, Oct 09, 2015
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    • "Comparing USB2103 16S rDNA sequence with sequences available in the NCBI Databases revealed high similarity (99 %) with strains DSM 319 and QMB 1551 (Eppinger et al. 2011) of Bacillus megaterium. B a c t e r i a l 1 6 S r D N A p a r t i a l s e q u e n c e s o f P. brassicacearum USB2101, USB2102 and USB2104, "
    European Journal of Plant Pathology 09/2015; DOI:10.1007/s10658-015-0767-8 · 1.49 Impact Factor
    • " be essential for competence development ( Chung and Dubnau 1998 ) . ComFB , playing an unknown role in competence , is encoded in B . subtilis , B . amyloliquefaciens , B . licheniformis and B . pumilus ( Kovacs et al . 2009 ) , but again missing in B . coagulans ( Kovacs et al . 2013 ) , B . cereus ( Mironczuk et al . 2008 ) and B . megaterium ( Eppinger et al . 2011 ) . Yet , ComFC that is encoded downstream of ComFB is ubiquitously pres - ent . B . coagulans further lacks the nuclease encoding nucA ( Kovacs et al . 2013 ) , which may detrimentally influence competence development as B . subtilis strains lacking NucA display largely reduced genetic competence ( Provvedi et al . 2001 ) . B . megater"
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    ABSTRACT: Natural genetic competence enables bacteria to take in and establish exogenously supplied DNA and thus constitutes a valuable tool for strain improvement. Extensively studied in the Gram-positive model organism Bacillus subtilis genetic competence has indeed proven successful for genetic manipulation aiming at enhancement of handling, yield, and biosafety. The majority of Bacilli, particularly those relevant for industrial application, do not or only poorly develop genetic competence, although rather homologous DNA-uptake machineries are routinely encoded. Establishing the competent state solely due to high cell densities (quorum sensing dependency) appears to be restricted to the model organism, in which the small signalling peptide ComS initiates the regulatory pathway that ultimately leads to the expression of all genes necessary for reaching the competent state. Agreeing with the lack of a functional ComS peptide, competence-mediated transformation of other Bacilli depends on nutrient exhaustion rather than cell density. Genetically, competent strains of the model organism B. subtilis, cultivated for a long time and selected for laboratory purposes, display probably not least to such selection a point mutation in the promoter of a regulatory gene that favors competence development whereas the wild-type progenitor only poorly displays genetic competence. Consistent with competence being a matter of deregulation, all strains of Bacillus licheniformis displaying efficient DNA uptake were found to carry mutations in regulator genes, which are responsible for their genetic competence. Thus, strain-specific genetic equipment and regulation as well as the proven role of domestication for the well-established laboratory strains ought to be considered when attempting to broaden the applicability of competence as a genetic tool for strains other than the model organism.
    Applied Microbiology and Biotechnology 12/2014; 99(4). DOI:10.1007/s00253-014-6316-0 · 3.34 Impact Factor
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    • "Expression of the genes for the membrane component (BLi03672) and ATPase subunit (BLi03671) was about 250- and 136-fold up-regulated in response to high salinity (Table S1 and S2). Homologs of this presumed multi-drug export system do not exist in B. subtilis but can be found in the genome sequences of B. megaterium [81] and Bacillus pumilus [95]. Wecke et al. [20] have shown that the expression of the structural genes for the BLi03671/BLi03672 ABC-type export system from B. licheniformis is up-regulated in response to the cell-wall damaging antibiotic vancomycin in a fashion that is independent of ECF-type sigma factors, indicating that its strong salt-stress-mediate induction might reflect cell-wall-damaging effects exerted by severe salt shocks. "
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    ABSTRACT: The Gram-positive endospore-forming bacterium Bacillus licheniformis can be found widely in nature and it is exploited in industrial processes for the manufacturing of antibiotics, specialty chemicals, and enzymes. Both in its varied natural habitats and in industrial settings, B. licheniformis cells will be exposed to increases in the external osmolarity, conditions that trigger water efflux, impair turgor, cause the cessation of growth, and negatively affect the productivity of cell factories in biotechnological processes. We have taken here both systems-wide and targeted physiological approaches to unravel the core of the osmostress responses of B. licheniformis. Cells were suddenly subjected to an osmotic upshift of considerable magnitude (with 1 M NaCl), and their transcriptional profile was then recorded in a time-resolved fashion on a genome-wide scale. A bioinformatics cluster analysis was used to group the osmotically up-regulated genes into categories that are functionally associated with the synthesis and import of osmostress-relieving compounds (compatible solutes), the SigB-controlled general stress response, and genes whose functional annotation suggests that salt stress triggers secondary oxidative stress responses in B. licheniformis. The data set focusing on the transcriptional profile of B. licheniformis was enriched by proteomics aimed at identifying those proteins that were accumulated by the cells through increased biosynthesis in response to osmotic stress. Furthermore, these global approaches were augmented by a set of experiments that addressed the synthesis of the compatible solutes proline and glycine betaine and assessed the growth-enhancing effects of various osmoprotectants. Combined, our data provide a blueprint of the cellular adjustment processes of B. licheniformis to both sudden and sustained osmotic stress.
    PLoS ONE 11/2013; 8(11):e80956. DOI:10.1371/journal.pone.0080956 · 3.23 Impact Factor
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