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Jakobs M, Meinhardt F. What renders Bacilli genetically competent? A gaze beyond the model organism. Appl Microbiol Biotechnol 2014; 99:1557-70. [DOI: 10.1007/s00253-014-6316-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 12/08/2014] [Accepted: 12/09/2014] [Indexed: 12/20/2022]
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Abstract
ABSTRACT
The family
Bacillaceae
constitutes a phenotypically diverse and globally ubiquitous assemblage of bacteria. Investigation into how evolution has shaped, and continues to shape, this family has relied on several widely ranging approaches from classical taxonomy, ecological field studies, and evolution in soil microcosms to genomic-scale phylogenetics, laboratory, and directed evolution experiments. One unifying characteristic of the
Bacillaceae
, the endospore, poses unique challenges to answering questions regarding both the calculation of evolutionary rates and claims of extreme longevity in ancient environmental samples.
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Abstract
The complete annotated genome sequence of Bacillus megaterium bacteriophage Slash is described here. Several key features related to morphogenesis, replication/recombination, DNA metabolism, and lysis are described. Slash also encodes a homolog of SleB, a germination-specific cell wall amidase.
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4
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Eppinger M, Bunk B, Johns MA, Edirisinghe JN, Kutumbaka KK, Koenig SSK, Huot Creasy H, Rosovitz MJ, Riley DR, Daugherty S, Martin M, Elbourne LDH, Paulsen I, Biedendieck R, Braun C, Grayburn S, Dhingra S, Lukyanchuk V, Ball B, Ul-Qamar R, Seibel J, Bremer E, Jahn D, Ravel J, Vary PS. Genome sequences of the biotechnologically important Bacillus megaterium strains QM B1551 and DSM319. J Bacteriol 2011; 193:4199-213. [PMID: 21705586 PMCID: PMC3147683 DOI: 10.1128/jb.00449-11] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2011] [Accepted: 06/10/2011] [Indexed: 11/20/2022] Open
Abstract
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 B(12), 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 B(12) 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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Affiliation(s)
- Mark Eppinger
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201
| | - Boyke Bunk
- German Collection for Microorganisms and Cell Cultures, Braunschweig 38124, Germany
| | - Mitrick A. Johns
- Northern Illinois University, Department of Biological Sciences, DeKalb, Illinois 60115
| | - Janaka N. Edirisinghe
- Northern Illinois University, Department of Biological Sciences, DeKalb, Illinois 60115
| | - Kirthi K. Kutumbaka
- Northern Illinois University, Department of Biological Sciences, DeKalb, Illinois 60115
| | - Sara S. K. Koenig
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201
| | - Heather Huot Creasy
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201
| | | | - David R. Riley
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201
| | - Sean Daugherty
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201
| | - Madeleine Martin
- Technische Universität Braunschweig, Institute of Microbiology, Braunschweig 38106, Germany
| | - Liam D. H. Elbourne
- Macquarie University, Department of Chemistry and Biomolecular Sciences, Sydney 2109, Australia
| | - Ian Paulsen
- Macquarie University, Department of Chemistry and Biomolecular Sciences, Sydney 2109, Australia
| | - Rebekka Biedendieck
- Technische Universität Braunschweig, Institute of Microbiology, Braunschweig 38106, Germany
| | - Christopher Braun
- Northern Illinois University, Department of Biological Sciences, DeKalb, Illinois 60115
| | - Scott Grayburn
- Northern Illinois University, Department of Biological Sciences, DeKalb, Illinois 60115
| | - Sourabh Dhingra
- Northern Illinois University, Department of Biological Sciences, DeKalb, Illinois 60115
| | - Vitaliy Lukyanchuk
- Northern Illinois University, Department of Biological Sciences, DeKalb, Illinois 60115
| | - Barbara Ball
- Northern Illinois University, Department of Biological Sciences, DeKalb, Illinois 60115
| | - Riaz Ul-Qamar
- Technische Universität Braunschweig, Institute of Microbiology, Braunschweig 38106, Germany
| | - Jürgen Seibel
- Julius-Maximilians-Universität Würzburg, Institute of Organic Chemistry, Würzburg 97074, Germany
| | - Erhard Bremer
- Philipps-Universität Marburg, Laboratory for Molecular Microbiology, Marburg 35043, Germany
| | - Dieter Jahn
- Technische Universität Braunschweig, Institute of Microbiology, Braunschweig 38106, Germany
| | - Jacques Ravel
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201
| | - Patricia S. Vary
- Northern Illinois University, Department of Biological Sciences, DeKalb, Illinois 60115
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Bunk B, Schulz A, Stammen S, Münch R, Warren MJ, Rohde M, Jahn D, Biedendieck R. A short story about a big magic bug. Bioeng Bugs 2010; 1:85-91. [PMID: 21326933 PMCID: PMC3026448 DOI: 10.4161/bbug.1.2.11101] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 01/04/2010] [Indexed: 11/19/2022] Open
Abstract
Bacillus megaterium, the "big beast," is a Gram-positive bacterium with a size of 4 × 1.5 µm. During the last years, it became more and more popular in the field of biotechnology for its recombinant protein production capacity. For the purpose of intra- as well as extracellular protein synthesis several vectors were constructed and commercialized (MoBiTec GmbH, Germany). On the basis of two compatible vectors, a T7 RNA polymerase driven protein production system was established. Vectors for chromosomal integration enable the direct manipulation of the genome. The vitamin B(12) biosynthesis of B. megaterium served as a model for the systematic development of a production strain using these tools. For this purpose, the overexpression of chromosomal and plasmid encoded genes and operons, the synthesis of anti-sense RNA for gene silencing, the removal of inhibitory regulatory elements in combination with the utilization of strong promoters, directed protein design, and the recombinant production of B(12) binding proteins to overcome feedback inhibition were successfully employed. For further system biotechnology based optimization strategies the genome sequence will provide a closer look into genomic capacities of B. megaterium. DNA arrays are available. Proteome, fluxome and metabolome analyses are possible. All data can be integrated by using a novel bioinformatics platform. Finally, the size of the "big beast" B. megaterium invites for cell biology research projects. All these features provide a solid basis for challenging biotechnological approaches.
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Affiliation(s)
- Boyke Bunk
- Institute of Microbiology; Technische Universität Braunschweig; Braunschweig, Germany
| | | | - Simon Stammen
- Institute of Microbiology; Technische Universität Braunschweig; Braunschweig, Germany
| | - Richard Münch
- Institute of Microbiology; Technische Universität Braunschweig; Braunschweig, Germany
| | - Martin J Warren
- Protein Science Group; Department of Biosciences; University of Kent; Canterbury, Kent UK
| | - Manfred Rohde
- Department of Microbial Pathogenesis; HZ1-Helmholtz Ceter for Infection Research; Braunschweig, Germany
| | - Dieter Jahn
- Institute of Microbiology; Technische Universität Braunschweig; Braunschweig, Germany
| | - Rebekka Biedendieck
- Protein Science Group; Department of Biosciences; University of Kent; Canterbury, Kent UK
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Abstract
Transduction is the process in which bacterial DNA is transferred from one bacterial cell to another by means of a phage particle. There are two types of transduction, generalized transduction and specialized transduction. In this chapter two of the best-studied systems - Escherichia coli-phage P1, and Salmonella enterica-phage P22 - are discussed from theoretical and practical perspectives.
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Affiliation(s)
- Anne Thierauf
- Department of Microbiology, University of Illinois, Urbana, IL, USA
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Vary PS, Biedendieck R, Fuerch T, Meinhardt F, Rohde M, Deckwer WD, Jahn D. Bacillus megaterium—from simple soil bacterium to industrial protein production host. Appl Microbiol Biotechnol 2007; 76:957-67. [PMID: 17657486 DOI: 10.1007/s00253-007-1089-3] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Revised: 06/11/2007] [Accepted: 06/12/2007] [Indexed: 10/23/2022]
Abstract
Bacillus megaterium has been industrially employed for more than 50 years, as it possesses some very useful and unusual enzymes and a high capacity for the production of exoenzymes. It is also a desirable cloning host for the production of intact proteins, as it does not possess external alkaline proteases and can stably maintain a variety of plasmid vectors. Genetic tools for this species include transducing phages and several hundred mutants covering the processes of biosynthesis, catabolism, division, sporulation, germination, antibiotic resistance, and recombination. The seven plasmids of B. megaterium strain QM B1551 contain several unusual metabolic genes that may be useful in bioremediation. Recently, several recombinant shuttle vectors carrying different strong inducible promoters and various combinations of affinity tags for simple protein purification have been constructed. Leader sequences-mediated export of affinity-tagged proteins into the growth medium was made possible. These plasmids are commercially available. For a broader application of B. megaterium in industry, sporulation and protease-deficient as well as UV-sensitive mutants were constructed. The genome sequence of two different strains, plasmidless DSM319 and QM B1551 carrying seven natural plasmids, is now available. These sequences allow for a systems biotechnology optimization of the production host B. megaterium. Altogether, a "toolbox" of hundreds of genetically characterized strains, genetic methods, vectors, hosts, and genomic sequences make B. megaterium an ideal organism for industrial, environmental, and experimental applications.
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Affiliation(s)
- Patricia S Vary
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA
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López NI, Floccari ME, Steinbüchel A, GarcÃa AF, Méndez BS. Effect of poly(3-hydroxybutyrate) (PHB) content on the starvation-survival of bacteria in natural waters. FEMS Microbiol Ecol 1995. [DOI: 10.1111/j.1574-6941.1995.tb00273.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Abstract
Temperate and virulent bacteriophages isolated from soil were shown to carry out generalized transduction of Bacillus stearothermophilus NUB36. A transducing frequency of 1 X 10(-5) to 7 X 10(-4) was obtained for temperate phages TP-42 and TP-56. The transducing frequency for virulent phage TP-68 was two to three orders of magnitude lower. Cotransfer analysis with the three phages showed that hom-1 is linked to thr-1 and that gly-1 is linked to his-1.
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Affiliation(s)
- N E Welker
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois 60208
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Brey RN, Banner CD, Wolf JB. Cloning of multiple genes involved with cobalamin (Vitamin B12) biosynthesis in Bacillus megaterium. J Bacteriol 1986; 167:623-30. [PMID: 3015883 PMCID: PMC212935 DOI: 10.1128/jb.167.2.623-630.1986] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
An effective shotgun cloning procedure was developed for Bacillus megaterium by amplifying gene libraries in Bacillus subtilis. This technique was useful in isolating at least 11 genes from B. megaterium which are involved with cobalamin (vitamin B12) biosynthesis. Amplified plasmid banks were transformed into protoplasts of both a series of Cob mutants blocked before the biosynthesis of cobinamide and Cbl mutants blocked in the conversion of cobinamide into cobalamin. Amplification of gene libraries overcame the cloning barriers inherent in the relatively low protoplast transformation frequency of B. megaterium. A family of plasmids was isolated by complementation of seven different Cob and Cbl mutants. Each plasmid capable of complementing a Cob or Cbl mutant was transformed into each one of the series of Cob and Cbl mutants; many of the plasmids isolated by complementation of one mutation carried genetic activity for complementation of other mutations. By these criteria, four different complementation groups were resolved. At least six genes involved in the biosynthesis of cobinamide are carried on a fragment of DNA approximately 2.7 kilobase pairs in length; other genes involved in the biosynthesis of cobinamide were located in two other complementation groups. The physical and genetic data permitted an ordering of genes within several of the complementation groups. The presence of complementing plasmids in mutants blocked in cobalamin synthesis resulted in restoration of cobalamin biosynthesis.
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Wolf JB, Brey RN. Isolation and genetic characterizations of Bacillus megaterium cobalamin biosynthesis-deficient mutants. J Bacteriol 1986; 166:51-8. [PMID: 3082859 PMCID: PMC214555 DOI: 10.1128/jb.166.1.51-58.1986] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Ethanolamine is deaminated by the action of ethanolamine ammonia-lyase (EC 4.3.1.7), an adenosylcobalamin-dependent enzyme. Consequently, to grow on ethanolamine as a sole nitrogen source, Bacillus megaterium requires vitamin B12. Identification of B. megaterium mutants deficient for growth on ethanolamine as the sole nitrogen source yielded a total of 34 vitamin B12 auxotrophs. The vitamin B12 auxotrophs were divided into two major phenotypic groups: Cob mutants, which could use cobinamide or vitamin B12 to grow on ethanolamine, and Cbl mutants, which could be supplemented only by vitamin B12. The Cob mutants were resolved into six classes and the Cbl mutants were resolved into three, based on the spectrum of cobalt-labeled corrinoid compounds which they accumulated. Although some radiolabeled cobalamin was detected in the wild type, little or none was evident in the auxotrophs. The results indicate that Cob mutants contain lesions in biosynthetic steps before the synthesis of combinamide, while Cbl mutants are defective in the conversion of cobinamide to cobalamin. Analysis of phage-mediated transduction experiments revealed tight genetic linkage within the Cob class and within the Cbl class. Similar transduction analysis indicated the Cob and Cbl classes are weakly linked. In addition, cross-feeding experiments in which extracts prepared from mutants were examined for their effect on growth of various other mutants allowed a partial ordering of mutations within the cobalamin biosynthetic pathway.
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English JD, Vary PS. Isolation of recombination-defective and UV-sensitive mutants of Bacillus megaterium. J Bacteriol 1986; 165:155-60. [PMID: 3079746 PMCID: PMC214383 DOI: 10.1128/jb.165.1.155-160.1986] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Mutants of Bacillus megaterium QMB1551 sensitive to mitomycin C or methyl methanesulfonate were isolated and characterized phenotypically. Cell survival after UV-light and gamma-ray exposure was determined, as was transductional recombination. Of the mutants tested, three were sensitive to UV but remained recombination proficient. The UV-sensitive mutants were also reduced in host cell reactivation. At least three mutants had undetectable transduction frequencies, i.e., less than 0.3 to 1.3% of the parental strain frequencies, and so appear to be recombination deficient. Sensitivities of these mutant strains to UV light and gamma radiation were compared with those of parental B. megaterium as well as parental, recE4, recA1, uvrA19, and uvrB109 strains of Bacillus subtilis. In each case, the strains of B. megaterium, including the parental strains, showed a higher percentage of cell survival than B. subtilis.
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Cloning of a small, acid-soluble spore protein gene from Bacillus subtilis and determination of its complete nucleotide sequence. J Bacteriol 1985; 161:333-9. [PMID: 2981806 PMCID: PMC214876 DOI: 10.1128/jb.161.1.333-339.1985] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The first Bacillus subtilis small, acid-soluble spore protein (SASP) gene has been cloned by using previously cloned B. megaterium SASP genes as DNA-DNA hybridization probes. Determination of the DNA sequence of the B. subtilis SASP gene showed that it codes for a 72-residue protein (termed SASP-1) containing a single spore protease cleavage site as well as other sequences conserved in Bacillus megaterium SASPs A, C, C-1, C-2, and C-3. The B. subtilis SASP-1 genes's coding sequence is preceded by a potential Bacillus ribosome-binding site, and is followed by a sequence that could form a stem-and-loop structure characteristic of transcription termination sites. Upstream from the coding sequence there are no obvious homologies with other B. subtilis sporulation genes, but similarities with B. megaterium SASP genes are evident. SASP-1 mRNA (290 bases long) is absent from vegetative cells, but appears midway in sporulation and then disappears. The cloned SASP-1 gene hybridizes to three bands other than the SASP-1 gene itself in EcoRI or HindIII digests of B. subtilis DNA. Presumably these other bands represent SASP genes related to the SASP-1 gene, and we have been able to detect at least three such proteins in B. subtilis spores.
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Garbe JC, Hess GF, Franzen MA, Vary PS. Genetics of leucine biosynthesis in Bacillus megaterium QM B1551. J Bacteriol 1984; 157:454-9. [PMID: 6420390 PMCID: PMC215269 DOI: 10.1128/jb.157.2.454-459.1984] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Genes involved in the biosynthesis of leucine have been mapped in Bacillus megaterium QM B1551, using transducing phage MP13. Mutations were designated leuA, leuB, or leuC on the basis of enzyme assays. Two mutant strains were deficient in the enzyme activities of leuA (alpha-isopropylmalate synthase) and leuC (beta-isopropylmalate dehydrogenase) and so may contain polar mutations. Fine-structure transduction mapping established the gene order leuC-leuB-leuA-ilv-hem-phe. The orientation of the leu genes to the ilv gene is the same as in Bacillus subtilis, but the relationship in respect to two other linked markers, hem and phe, differs.
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Callahan JP, Crawford IP, Hess GF, Vary PS. Cotransductional mapping of the trp-his region of Bacillus megaterium. J Bacteriol 1983; 154:1455-8. [PMID: 6406433 PMCID: PMC217624 DOI: 10.1128/jb.154.3.1455-1458.1983] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Eight trp mutations (four trpE, two trpB, one trpC, and one trpD) have been mapped in Bacillus megaterium QM B1551 and were found to be linked to two hisH mutations and unlinked to several other his mutations.
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