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Dutschei T, Zühlke MK, Welsch N, Eisenack T, Hilkmann M, Krull J, Stühle C, Brott S, Dürwald A, Reisky L, Hehemann JH, Becher D, Schweder T, Bornscheuer UT. Metabolic engineering enables Bacillus licheniformis to grow on the marine polysaccharide ulvan. Microb Cell Fact 2022; 21:207. [PMID: 36217189 PMCID: PMC9549685 DOI: 10.1186/s12934-022-01931-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/26/2022] [Indexed: 11/10/2022] Open
Abstract
Background Marine algae are responsible for half of the global primary production, converting carbon dioxide into organic compounds like carbohydrates. Particularly in eutrophic waters, they can grow into massive algal blooms. This polysaccharide rich biomass represents a cheap and abundant renewable carbon source. In nature, the diverse group of polysaccharides is decomposed by highly specialized microbial catabolic systems. We elucidated the complete degradation pathway of the green algae-specific polysaccharide ulvan in previous studies using a toolbox of enzymes discovered in the marine flavobacterium Formosa agariphila and recombinantly expressed in Escherichia coli. Results In this study we show that ulvan from algal biomass can be used as feedstock for a biotechnological production strain using recombinantly expressed carbohydrate-active enzymes. We demonstrate that Bacillus licheniformis is able to grow on ulvan-derived xylose-containing oligosaccharides. Comparative growth experiments with different ulvan hydrolysates and physiological proteogenomic analyses indicated that analogues of the F. agariphila ulvan lyase and an unsaturated β-glucuronylhydrolase are missing in B. licheniformis. We reveal that the heterologous expression of these two marine enzymes in B. licheniformis enables an efficient conversion of the algal polysaccharide ulvan as carbon and energy source. Conclusion Our data demonstrate the physiological capability of the industrially relevant bacterium B. licheniformis to grow on ulvan. We present a metabolic engineering strategy to enable ulvan-based biorefinery processes using this bacterial cell factory. With this study, we provide a stepping stone for the development of future bioprocesses with Bacillus using the abundant marine renewable carbon source ulvan. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01931-0.
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Affiliation(s)
- Theresa Dutschei
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Marie-Katherin Zühlke
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17487, Greifswald, Germany.,Institute of Marine Biotechnology e.V., 17489, Greifswald, Germany
| | - Norma Welsch
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17487, Greifswald, Germany.,Institute of Marine Biotechnology e.V., 17489, Greifswald, Germany
| | - Tom Eisenack
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17487, Greifswald, Germany
| | - Maximilian Hilkmann
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17487, Greifswald, Germany.,Institute of Marine Biotechnology e.V., 17489, Greifswald, Germany
| | - Joris Krull
- Institute of Marine Biotechnology e.V., 17489, Greifswald, Germany.,Max Planck-Institute for Marine Microbiology, 28359, Bremen, Germany.,Center for Marine Environmental Sciences (MARUM), University of Bremen, 28359, Bremen, Germany
| | - Carlo Stühle
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Stefan Brott
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Alexandra Dürwald
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17487, Greifswald, Germany
| | - Lukas Reisky
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Jan-Hendrik Hehemann
- Institute of Marine Biotechnology e.V., 17489, Greifswald, Germany.,Max Planck-Institute for Marine Microbiology, 28359, Bremen, Germany.,Center for Marine Environmental Sciences (MARUM), University of Bremen, 28359, Bremen, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, Institute for Microbiology, University of Greifswald, 17487, Greifswald, Germany
| | - Thomas Schweder
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17487, Greifswald, Germany. .,Institute of Marine Biotechnology e.V., 17489, Greifswald, Germany.
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany. .,Institute of Marine Biotechnology e.V., 17489, Greifswald, Germany.
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2
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The restriction modification system of Bacillus licheniformis MS1 and generation of a readily transformable deletion mutant. Appl Microbiol Biotechnol 2017; 101:7933-7944. [PMID: 28942561 DOI: 10.1007/s00253-017-8532-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 01/19/2023]
Abstract
Restriction modification systems (R-M systems), consisting of a restriction endonuclease and a cognate methyltransferase, constitute an effective means of a cell to protect itself from foreign DNA. Identification, characterization, and deletion of the restriction modification system BliMSI, a putative isoschizomer of ClaI from Caryophanon latum, were performed in the wild isolate Bacillus licheniformis MS1. BliMSI was produced as recombinant protein in Escherichia coli, purified, and in vitro analysis demonstrated identical restriction endonuclease activity as for ClaI. A recombinant E. coli strain, expressing the heterologous bliMSIM gene, was constructed and used as the host for in vivo methylation of plasmids prior to their introduction into B. licheniformis to improve transformation efficiencies. The establishment of suicide plasmids in the latter was rendered possible. The subsequent deletion of the restriction endonuclease encoding gene, bliMSIR, caused doubled transformation efficiencies in the respective mutant B. licheniformis MS2 (∆bliMSIR). Along with above in vivo methylation, the establishment of further gene deletions (∆upp, ∆yqfD) was performed. The constructed triple mutant (∆bliMSIR, ∆upp, ∆yqfD) enables rapid genome manipulation, a requirement for genetic engineering of industrially important strains.
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Kim JH, Won YB, Ji CJ, Yang YM, Ryu SH, Ju SY, Kwon Y, Lee YE, Lee JW. The difference in in vivo sensitivity between Bacillus licheniformis PerR and Bacillus subtilis PerR is due to the different cellular environments. Biochem Biophys Res Commun 2017; 484:125-131. [PMID: 28104400 DOI: 10.1016/j.bbrc.2017.01.060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 01/13/2017] [Indexed: 11/16/2022]
Abstract
PerR, a member of Fur family of metal-dependent regulators, is a major peroxide sensor in many Gram positive bacteria, and controls the expression of genes involved in peroxide resistance. Bacillus licheniformis, a close relative to the well-studied model organism Bacillus subtilis, contains three PerR-like proteins (PerRBL, PerR2 and PerR3) in addition to Fur and Zur. In the present study, we characterized the role of PerRBL in B. licheniformis. In vitro and in vivo studies indicate that PerRBL, like PerRBS, uses either Fe2+ or Mn2+ as a corepressor and only the Fe2+-bound form of PerRBL senses low levels of H2O2 by iron-mediated histidine oxidation. Interestingly, regardless of the difference in H2O2 sensitivity, if any, between PerRBL and PerRBS, B. licheniformis expressing PerRBL or PerRBS could sense lower levels of H2O2 and was more sensitive to H2O2 than B. subtilis expressing PerRBL or PerRBS. This result suggests that the differences in cellular milieu between B. subtilis and B. licheniformis, rather than the intrinsic differences in PerRBS and PerRBLper se, affect the H2O2 sensing ability of PerR inside the cell and the H2O2 resistance of cell. In contrast, B. licheniformis and B. subtilis expressing Staphylococcus aureus PerR (PerRSA), which is more sensitive to H2O2 than PerRBL and PerRBS, were more resistant to H2O2 than those expressing either PerRBL or PerRBS. This result indicates that the sufficient difference in H2O2 susceptibility of PerR proteins can override the difference in cellular environment and affect the resistance of cell to H2O2.
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Affiliation(s)
- Jung-Hoon Kim
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Young-Bin Won
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Chang-Jun Ji
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Yoon-Mo Yang
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Su-Hyun Ryu
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Shin-Yeong Ju
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Yumi Kwon
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Yeh-Eun Lee
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Jin-Won Lee
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea.
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Helianti I, Ulfah M, Nurhayati N, Suhendar D, Finalissari AK, Wardani AK. Production of Xylanase by Recombinant Bacillus subtilis DB104 Cultivated in Agroindustrial Waste Medium. HAYATI JOURNAL OF BIOSCIENCES 2016. [DOI: 10.1016/j.hjb.2016.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Küppers T, Steffen V, Hellmuth H, O'Connell T, Bongaerts J, Maurer KH, Wiechert W. Developing a new production host from a blueprint: Bacillus pumilus as an industrial enzyme producer. Microb Cell Fact 2014; 13:46. [PMID: 24661794 PMCID: PMC3987833 DOI: 10.1186/1475-2859-13-46] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 03/18/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Since volatile and rising cost factors such as energy, raw materials and market competitiveness have a significant impact on the economic efficiency of biotechnological bulk productions, industrial processes need to be steadily improved and optimized. Thereby the current production hosts can undergo various limitations. To overcome those limitations and in addition increase the diversity of available production hosts for future applications, we suggest a Production Strain Blueprinting (PSB) strategy to develop new production systems in a reduced time lapse in contrast to a development from scratch.To demonstrate this approach, Bacillus pumilus has been developed as an alternative expression platform for the production of alkaline enzymes in reference to the established industrial production host Bacillus licheniformis. RESULTS To develop the selected B. pumilus as an alternative production host the suggested PSB strategy was applied proceeding in the following steps (dedicated product titers are scaled to the protease titer of Henkel's industrial production strain B. licheniformis at lab scale): Introduction of a protease production plasmid, adaptation of a protease production process (44%), process optimization (92%) and expression optimization (114%). To further evaluate the production capability of the developed B. pumilus platform, the target protease was substituted by an α-amylase. The expression performance was tested under the previously optimized protease process conditions and under subsequently adapted process conditions resulting in a maximum product titer of 65% in reference to B. licheniformis protease titer. CONCLUSIONS In this contribution the applied PSB strategy performed very well for the development of B. pumilus as an alternative production strain. Thereby the engineered B. pumilus expression platform even exceeded the protease titer of the industrial production host B. licheniformis by 14%. This result exhibits a remarkable potential of B. pumilus to be the basis for a next generation production host, since the strain has still a large potential for further genetic engineering. The final amylase titer of 65% in reference to B. licheniformis protease titer suggests that the developed B. pumilus expression platform is also suitable for an efficient production of non-proteolytic enzymes reaching a final titer of several grams per liter without complex process modifications.
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6
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Wiegand S, Voigt B, Albrecht D, Bongaerts J, Evers S, Hecker M, Daniel R, Liesegang H. Fermentation stage-dependent adaptations of Bacillus licheniformis during enzyme production. Microb Cell Fact 2013; 12:120. [PMID: 24313996 PMCID: PMC3878961 DOI: 10.1186/1475-2859-12-120] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 12/01/2013] [Indexed: 11/10/2022] Open
Abstract
Background Industrial fermentations can generally be described as dynamic biotransformation processes in which microorganisms convert energy rich substrates into a desired product. The knowledge of active physiological pathways, reflected by corresponding gene activities, allows the identification of beneficial or disadvantageous performances of the microbial host. Whole transcriptome RNA-Seq is a powerful tool to accomplish in-depth quantification of these gene activities, since the low background noise and the absence of an upper limit of quantification allow the detection of transcripts with high dynamic ranges. Such data enable the identification of potential bottlenecks and futile energetic cycles, which in turn can lead to targets for rational approaches to productivity improvement. Here we present an overview of the dynamics of gene activity during an industrial-oriented fermentation process with Bacillus licheniformis, an important industrial enzyme producer. Thereby, valuable insights which help to understand the complex interactions during such processes are provided. Results Whole transcriptome RNA-Seq has been performed to study the gene expression at five selected growth stages of an industrial-oriented protease production process employing a germination deficient derivative of B. licheniformis DSM13. Since a significant amount of genes in Bacillus strains are regulated posttranscriptionally, the generated data have been confirmed by 2D gel-based proteomics. Regulatory events affecting the coordinated activity of hundreds of genes have been analyzed. The data enabled the identification of genes involved in the adaptations to changing environmental conditions during the fermentation process. A special focus of the analyses was on genes contributing to central carbon metabolism, amino acid transport and metabolism, starvation and stress responses and protein secretion. Genes contributing to lantibiotics production and Tat-dependent protein secretion have been pointed out as potential optimization targets. Conclusions The presented data give unprecedented insights into the complex adaptations of bacterial production strains to the changing physiological demands during an industrial-oriented fermentation. These are, to our knowledge, the first publicly available data that document quantifiable transcriptional responses of the commonly employed production strain B. licheniformis to changing conditions over the course of a typical fermentation process in such extensive depth.
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Affiliation(s)
| | | | | | | | | | | | | | - Heiko Liesegang
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Norddeutsches Zentrum für Mikrobielle Genomforschung, Georg-August-Universität Göttingen, Grisebachstr, 8, D-37077 Göttingen, Germany.
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7
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Wiegand S, Dietrich S, Hertel R, Bongaerts J, Evers S, Volland S, Daniel R, Liesegang H. RNA-Seq of Bacillus licheniformis: active regulatory RNA features expressed within a productive fermentation. BMC Genomics 2013; 14:667. [PMID: 24079885 PMCID: PMC3871023 DOI: 10.1186/1471-2164-14-667] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 09/25/2013] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The production of enzymes by an industrial strain requires a complex adaption of the bacterial metabolism to the conditions within the fermenter. Regulatory events within the process result in a dynamic change of the transcriptional activity of the genome. This complex network of genes is orchestrated by proteins as well as regulatory RNA elements. Here we present an RNA-Seq based study considering selected phases of an industry-oriented fermentation of Bacillus licheniformis. RESULTS A detailed analysis of 20 strand-specific RNA-Seq datasets revealed a multitude of transcriptionally active genomic regions. 3314 RNA features encoded by such active loci have been identified and sorted into ten functional classes. The identified sequences include the expected RNA features like housekeeping sRNAs, metabolic riboswitches and RNA switches well known from studies on Bacillus subtilis as well as a multitude of completely new candidates for regulatory RNAs. An unexpectedly high number of 855 RNA features are encoded antisense to annotated protein and RNA genes, in addition to 461 independently transcribed small RNAs. These antisense transcripts contain molecules with a remarkable size range variation from 38 to 6348 base pairs in length. The genome of the type strain B. licheniformis DSM13 was completely reannotated using data obtained from RNA-Seq analyses and from public databases. CONCLUSION The hereby generated data-sets represent a solid amount of knowledge on the dynamic transcriptional activities during the investigated fermentation stages. The identified regulatory elements enable research on the understanding and the optimization of crucial metabolic activities during a productive fermentation of Bacillus licheniformis strains.
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Affiliation(s)
- Sandra Wiegand
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Norddeutsches Zentrum für Mikrobielle Genomforschung, Georg-August-Universität Göttingen, Grisebachstr, 8, D-37077 Göttingen, Germany.
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Rachinger M, Bauch M, Strittmatter A, Bongaerts J, Evers S, Maurer KH, Daniel R, Liebl W, Liesegang H, Ehrenreich A. Size unlimited markerless deletions by a transconjugative plasmid-system in Bacillus licheniformis. J Biotechnol 2013; 167:365-9. [PMID: 23916947 DOI: 10.1016/j.jbiotec.2013.07.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 07/22/2013] [Accepted: 07/23/2013] [Indexed: 11/26/2022]
Abstract
Conjugative shuttle vectors of the pKVM series, based on an IncP transfer origin and the pMAD vector with a temperature sensitive replication were constructed to establish a markerless gene deletion protocol for Bacilli without natural competence such as the exoenzyme producer Bacillus licheniformis. The pKVM plasmids can be conjugated to strains of B. licheniformis and B. subtilis. For chromosomal gene deletion, regions flanking the target gene are fused and cloned in a pKVM vector prior to conjugative transfer from Escherichia coli to B. licheniformis. Appropriate markers on the vector backbone allow for the identification of the integration at the target locus and thereafter the vector excision, both events taking place via homologous recombination. The functionality of the deletion system was demonstrated with B. licheniformis by a markerless 939 bp in-frame deletion of the yqfD gene and the deletion of a 31 kbp genomic segment carrying a PBSX-like prophage.
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9
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Buchholz M, Nahrstedt H, Pillukat MH, Deppe V, Meinhardt F. yneA mRNA instability is involved in temporary inhibition of cell division during the SOS response of Bacillus megaterium. MICROBIOLOGY-SGM 2013; 159:1564-1574. [PMID: 23728628 DOI: 10.1099/mic.0.064766-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The SOS response, a mechanism enabling bacteria to cope with DNA damage, is strictly regulated by the two major players, RecA and LexA (Bacillus homologue DinR). Genetic stress provokes formation of ssDNA-RecA nucleoprotein filaments, the coprotease activity of which mediates the autocatalytic cleavage of the transcriptional repressor DinR and ensures the expression of a set of din (damage-inducible) genes, which encode proteins that enhance repair capacity, accelerate mutagenesis rate and cause inhibition of cell division (ICD). In Bacillus subtilis, the transcriptional activation of the yneAB-ynzC operon is part of the SOS response, with YneA being responsible for the ICD. Pointing to its cellular function in Bacillus megaterium, overexpression of homologous YneA led to filamentous growth, while ICD was temporary during the SOS response. Genetic knockouts of the individual open reading frames of the yneAB-ynzC operon increased the mutagenic sensitivity, proving - for the first time in a Bacillus species - that each of the three genes is in fact instrumental in coping with genetic stress. Northern- and quantitative real-time PCR analyses revealed - in contrast to other din genes (exemplified for dinR, uvrBA) - transient mRNA-presence of the yneAB-ynzC operon irrespective of persisting SOS-inducing conditions. Promoter test assays and Northern analyses suggest that the decline of the ICD is at least partly due to yneAB-ynzC mRNA instability.
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Affiliation(s)
- Meike Buchholz
- Institut für Molekulare Mikrobiologie und Biotechnologie Westfälische Wilhelms-Universität Münster Corrensstraße 3, 48149 Münster, Germany
| | - Hannes Nahrstedt
- Institut für Molekulare Mikrobiologie und Biotechnologie Westfälische Wilhelms-Universität Münster Corrensstraße 3, 48149 Münster, Germany
| | - Mike H Pillukat
- Institut für Molekulare Mikrobiologie und Biotechnologie Westfälische Wilhelms-Universität Münster Corrensstraße 3, 48149 Münster, Germany
| | - Veronika Deppe
- Institut für Molekulare Mikrobiologie und Biotechnologie Westfälische Wilhelms-Universität Münster Corrensstraße 3, 48149 Münster, Germany
| | - Friedhelm Meinhardt
- Institut für Molekulare Mikrobiologie und Biotechnologie Westfälische Wilhelms-Universität Münster Corrensstraße 3, 48149 Münster, Germany
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Wemhoff S, Meinhardt F. Generation of biologically contained, readily transformable, and genetically manageable mutants of the biotechnologically important Bacillus pumilus. Appl Microbiol Biotechnol 2013; 97:7805-19. [PMID: 23644770 DOI: 10.1007/s00253-013-4935-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 04/12/2013] [Accepted: 04/15/2013] [Indexed: 11/25/2022]
Abstract
Bacillus pumilus mutants were generated by targeted deletion of a set of genes eventually facilitating genetic handling and assuring biological containment. The well-defined and stable mutants do not form functional endospores due to the deletion of yqfD, an essential sporulation gene; they are affected in DNA repair, as ΔuvrBA rendered them UV hypersensitive and, thus, biologically contained; they are deficient for the uracil phosphoribosyl-transferase (Δupp), allowing for 5-fluorouracil-based counterselection facilitating rapid allelic exchanges; and they are readily transformable due to the deletion of the restrictase encoding locus (ΔhsdR) of a type I restriction modification system. Vegetative growth as well as extracellular enzyme production and secretion are in no case affected. The combination of such gene deletions allows for development of B. pumilus strains suited for industrial use and further improvements.
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Affiliation(s)
- Stephanie Wemhoff
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, 48149, Münster, Germany
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Korneli C, David F, Biedendieck R, Jahn D, Wittmann C. Getting the big beast to work--systems biotechnology of Bacillus megaterium for novel high-value proteins. J Biotechnol 2012; 163:87-96. [PMID: 22750448 DOI: 10.1016/j.jbiotec.2012.06.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 06/18/2012] [Accepted: 06/20/2012] [Indexed: 12/31/2022]
Abstract
The high industrial relevance of the soil bacterium Bacillus megaterium as host for recombinant proteins is driving systems-wide analyses of its metabolic and regulatory networks. The present review highlights novel systems biology tools available to unravel the various cellular components on the level of metabolic and regulatory networks. These provide a rational platform for systems metabolic engineering of B. megaterium. In line, a number of interesting studies have particularly focused on studying recombinant B. megaterium in its industrial bioprocess environment thus integrating systems metabolic engineering with systems biotechnology and providing the full picture toward optimal processes.
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Affiliation(s)
- Claudia Korneli
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
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Genetic analysis of the Bacillus licheniformis degSU operon and the impact of regulatory mutations on protease production. J Biotechnol 2012; 159:12-20. [DOI: 10.1016/j.jbiotec.2012.02.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 01/16/2012] [Accepted: 02/16/2012] [Indexed: 11/20/2022]
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Borgmeier C, Biedendieck R, Hoffmann K, Jahn D, Meinhardt F. Transcriptome profiling of degU expression reveals unexpected regulatory patterns in Bacillus megaterium and discloses new targets for optimizing expression. Appl Microbiol Biotechnol 2011; 92:583-96. [PMID: 21935588 DOI: 10.1007/s00253-011-3575-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 08/17/2011] [Accepted: 09/08/2011] [Indexed: 11/24/2022]
Abstract
The first whole transcriptome assessment of a Bacillus megaterium strain provides unanticipated insights into the degSU regulon considered to be of central importance for exo-enzyme production. Regulatory patterns as well as the transcription of degSU itself deviate from the model organism Bacillus subtilis; the number of DegU-regulated secretory enzymes is rather small. Targets for productivity optimization, besides degSU itself, arise from the unexpected DegU-dependent induction of the transition-state regulator AbrB during exponential growth. Induction of secretion-assisting factors, such as the translocase subunit SecY or the signal peptidase SipM, promote hypersecretion. B. megaterium DegSU transcriptional control is advantageous for production purposes, since the degU32 constitutively active mutant conferred hypersecretion of a heterologous Bacillus amyloliquefaciens amylase without the detrimental rise, as for B. subtilis and Bacillus licheniformis, in extracellular proteolytic activities.
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Affiliation(s)
- Claudia Borgmeier
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms Universität, Corrensstrasse 3, 48149, Münster, Germany
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Functional analysis of the response regulator DegU in Bacillus megaterium DSM319 and comparative secretome analysis of degSU mutants. Appl Microbiol Biotechnol 2011; 91:699-711. [DOI: 10.1007/s00253-011-3302-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 04/01/2011] [Accepted: 04/01/2011] [Indexed: 10/18/2022]
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Hoffmann K, Daum G, Köster M, Kulicke WM, Meyer-Rammes H, Bisping B, Meinhardt F. Genetic improvement of Bacillus licheniformis strains for efficient deproteinization of shrimp shells and production of high-molecular-mass chitin and chitosan. Appl Environ Microbiol 2010; 76:8211-21. [PMID: 20971870 PMCID: PMC3008253 DOI: 10.1128/aem.01404-10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 10/14/2010] [Indexed: 11/20/2022] Open
Abstract
By targeted deletion of the polyglutamate operon (pga) in Bacillus licheniformis F11, a derivative form, F11.1 (Δpga), was obtained that, along with lacking polyglutamate (PGA) formation, displayed enhanced proteolytic activities. The phenotypic properties were maintained in a strain in which the chiBA operon was additionally deleted: F11.4 (ΔchiBA Δpga). These genetically modified strains, carrying the Δpga deletion either alone (F11.1) or together with the ΔchiBA (F11.4) deletion, were used in fermentations (20-liter scale) aiming at the deproteinization of shrimp shells in order to obtain long-chain chitin. After chemical deacetylation, the resulting chitosan samples were analyzed by nuclear magnetic resonance spectroscopy, size exclusion chromatography, and viscometry and compared to a chitosan preparation that was produced in parallel by chemical methods by a commercial chitosan supplier (GSRmbH). Though faint lipid impurities were present in the fermented polysaccharides, the viscosity of the material produced with the double-deletion mutant F11.4 (Δpga ΔchiBA) was higher than that of the chemically produced and commercially available samples (Cognis GmbH). Thus, enhanced proteolytic activities and a lack of chitinase activity render the double mutant F11.4 a powerful tool for the production of long-chain chitosan.
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Affiliation(s)
- Kerstin Hoffmann
- Westfälische Wilhelms-Universität Münster, Institut für Molekulare Mikrobiologie und Biotechnologie, D-48149 Münster, Germany, Universität Hamburg, Biozentrum Klein Flottbek, Institut für Lebensmittelchemie, Abteilung Lebensmittelmikrobiologie und Biotechnologie, Ohnhorststr. 18, 22609 Hamburg, Germany, Universität Hamburg, Institut für Technische und Makromolekulare Chemie, Bundesstr. 45, 20146 Hamburg, Germany
| | - Gabriele Daum
- Westfälische Wilhelms-Universität Münster, Institut für Molekulare Mikrobiologie und Biotechnologie, D-48149 Münster, Germany, Universität Hamburg, Biozentrum Klein Flottbek, Institut für Lebensmittelchemie, Abteilung Lebensmittelmikrobiologie und Biotechnologie, Ohnhorststr. 18, 22609 Hamburg, Germany, Universität Hamburg, Institut für Technische und Makromolekulare Chemie, Bundesstr. 45, 20146 Hamburg, Germany
| | - Marina Köster
- Westfälische Wilhelms-Universität Münster, Institut für Molekulare Mikrobiologie und Biotechnologie, D-48149 Münster, Germany, Universität Hamburg, Biozentrum Klein Flottbek, Institut für Lebensmittelchemie, Abteilung Lebensmittelmikrobiologie und Biotechnologie, Ohnhorststr. 18, 22609 Hamburg, Germany, Universität Hamburg, Institut für Technische und Makromolekulare Chemie, Bundesstr. 45, 20146 Hamburg, Germany
| | - Werner-Michael Kulicke
- Westfälische Wilhelms-Universität Münster, Institut für Molekulare Mikrobiologie und Biotechnologie, D-48149 Münster, Germany, Universität Hamburg, Biozentrum Klein Flottbek, Institut für Lebensmittelchemie, Abteilung Lebensmittelmikrobiologie und Biotechnologie, Ohnhorststr. 18, 22609 Hamburg, Germany, Universität Hamburg, Institut für Technische und Makromolekulare Chemie, Bundesstr. 45, 20146 Hamburg, Germany
| | - Heike Meyer-Rammes
- Westfälische Wilhelms-Universität Münster, Institut für Molekulare Mikrobiologie und Biotechnologie, D-48149 Münster, Germany, Universität Hamburg, Biozentrum Klein Flottbek, Institut für Lebensmittelchemie, Abteilung Lebensmittelmikrobiologie und Biotechnologie, Ohnhorststr. 18, 22609 Hamburg, Germany, Universität Hamburg, Institut für Technische und Makromolekulare Chemie, Bundesstr. 45, 20146 Hamburg, Germany
| | - Bernward Bisping
- Westfälische Wilhelms-Universität Münster, Institut für Molekulare Mikrobiologie und Biotechnologie, D-48149 Münster, Germany, Universität Hamburg, Biozentrum Klein Flottbek, Institut für Lebensmittelchemie, Abteilung Lebensmittelmikrobiologie und Biotechnologie, Ohnhorststr. 18, 22609 Hamburg, Germany, Universität Hamburg, Institut für Technische und Makromolekulare Chemie, Bundesstr. 45, 20146 Hamburg, Germany
| | - Friedhelm Meinhardt
- Westfälische Wilhelms-Universität Münster, Institut für Molekulare Mikrobiologie und Biotechnologie, D-48149 Münster, Germany, Universität Hamburg, Biozentrum Klein Flottbek, Institut für Lebensmittelchemie, Abteilung Lebensmittelmikrobiologie und Biotechnologie, Ohnhorststr. 18, 22609 Hamburg, Germany, Universität Hamburg, Institut für Technische und Makromolekulare Chemie, Bundesstr. 45, 20146 Hamburg, Germany
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Facilitation of direct conditional knockout of essential genes in Bacillus licheniformis DSM13 by comparative genetic analysis and manipulation of genetic competence. Appl Environ Microbiol 2010; 76:5046-57. [PMID: 20543043 DOI: 10.1128/aem.00660-10] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The genetic manageability of the biotechnologically important Bacillus licheniformis is hampered due to its poor transformability, whereas Bacillus subtilis efficiently takes up DNA during genetic competence, a quorum-sensing-dependent process. Since the sensor histidine kinase ComP, encoded by a gene of the quorum-sensing module comQXPA of B. licheniformis DSM13, was found to be inactive due to an insertion element within comP, the coding region was exchanged with a functional copy. Quorum sensing was restored, but the already-poor genetic competence dropped further. The inducible expression of the key regulator for the transcription of competence genes, ComK, in trans resulted in highly competent strains and facilitated the direct disruption of genes, as well as the conditional knockout of an essential operon. As ComK is inhibited at low cell densities by a proteolytic complex in which MecA binds ComK and such inhibition is antagonized by the interaction of MecA with ComS (the expression of the latter is controlled by cell density in B. subtilis), we performed an in silico analysis of MecA and the hitherto unidentified ComS, which revealed differences for competent and noncompetent strains, indicating that the reduced competence possibly is due to a nonfunctional coupling of the comQXPA-encoded quorum module and ComK. The obtained increased genetic tractability of this industrial workhorse should improve a wide array of scientific investigations.
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Evidence-based biosafety: a review of the principles and effectiveness of microbiological containment measures. Clin Microbiol Rev 2008; 21:403-25. [PMID: 18625678 DOI: 10.1128/cmr.00014-08] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We examined the available evidence on the effectiveness of measures aimed at protecting humans and the environment against the risks of working with genetically modified microorganisms (GMOs) and with non-GMO pathogenic microorganisms. A few principles and methods underlie the current biosafety practice: risk assessment, biological containment, concentration and enclosure, exposure minimization, physical containment, and hazard minimization. Many of the current practices are based on experience and expert judgment. The effectiveness of biosafety measures may be evaluated at the level of single containment equipment items and procedures, at the level of the laboratory as a whole, or at the clinical-epidemiological level. Data on the containment effectiveness of equipment and laboratories are scarce and fragmented. Laboratory-acquired infections (LAIs) are therefore important for evaluating the effectiveness of biosafety. For the majority of LAIs there appears to be no direct cause, suggesting that failures of biosafety were not noticed or that containment may have been insufficient. The number of reported laboratory accidents associated with GMOs is substantially lower than that of those associated with non-GMOs. It is unknown to what extent specific measures contribute to the overall level of biosafety. We therefore recommend that the evidence base of biosafety practice be strengthened.
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Waschkau B, Waldeck J, Wieland S, Eichstädt R, Meinhardt F. Generation of readily transformable Bacillus licheniformis mutants. Appl Microbiol Biotechnol 2008; 78:181-8. [DOI: 10.1007/s00253-007-1278-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Revised: 11/06/2007] [Accepted: 11/06/2007] [Indexed: 11/29/2022]
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Waldeck J, Meyer-Rammes H, Wieland S, Feesche J, Maurer KH, Meinhardt F. Targeted deletion of genes encoding extracellular enzymes in Bacillus licheniformis and the impact on the secretion capability. J Biotechnol 2007; 130:124-32. [PMID: 17481763 DOI: 10.1016/j.jbiotec.2007.03.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Revised: 02/13/2007] [Accepted: 03/09/2007] [Indexed: 10/23/2022]
Abstract
The general secretory pathway is routinely concerned with a multitude of extracellular enzymes. By eliminating obstructive competitors the export machinery may transport larger quantities of remaining proteins under circumstances in which the secretion machinery is fully loaded. Hence, in this study, genes encoding efficiently expressed but dispensable exoenzymes were knocked out in Bacillus licheniformis MD1. Single, double, and triple mutants with deletions of celA, chiA, and amyB, respectively, were generated via in vivo recombination by making use of a vector with a temperature sensitive origin of replication. Overexpression of a heterologous amylase gene on a multi-copy plasmid, a common scenario in biotechnological processes, resulted in an articulate reduction of chromosomally encoded extracellular enzyme activities indicating that the secretion machinery works to capacity in such transformants. Deletion mutants with the expression plasmid displayed enhanced amylase activities compared to the strain with the wild type genetic background. In addition, the chromosomally encoded protease activity was clearly higher in transformants with deletions.
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Affiliation(s)
- Jens Waldeck
- Westfälische Wilhelms-Universität Münster, Institut für Molekulare Mikrobiologie und Biotechnologie, Corrensstrasse 3, 48149 Münster, Germany
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Waldeck J, Daum G, Bisping B, Meinhardt F. Isolation and molecular characterization of chitinase-deficient Bacillus licheniformis strains capable of deproteinization of shrimp shell waste to obtain highly viscous chitin. Appl Environ Microbiol 2006; 72:7879-85. [PMID: 17028230 PMCID: PMC1694268 DOI: 10.1128/aem.00938-06] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2006] [Accepted: 09/26/2006] [Indexed: 11/20/2022] Open
Abstract
Proteolytic but chitinase-deficient microbial cultures were isolated from shrimp shell waste and characterized. The most efficient isolate was found to be a mixed culture consisting of two Bacillus licheniformis strains, which were first determined microscopically and physiologically. Molecular characterization was carried out by sequencing the 16S rRNA gene of both strains. According to the residual protein and ash content, the chitin obtained by fermentation of such a mixed culture was found to be comparable to a commercially available, chemically processed product. However, the strikingly high viscosity (80 versus 10 mPa of the commercially available sample) indicates its superior quality. The two strains differed in colony morphology and in their secretion capabilities for degradative extracellular enzymes. Sequencing of the loci encoding amylase, cellulase, chitinases, and proteases, as well as the degS/degU operon, which is instrumental in the regulation of degradative enzymes, and the pga operon, which is responsible for polyglutamic acid production, revealed no differences. However, a frameshift mutation in chiA, encoding a chitinase, was validated for both strains, providing an explanation for the ascertained absence of chitinolytic activities and the concomitant possibility of producing highly viscous chitin in a fermentational deproteinization process.
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Affiliation(s)
- Jens Waldeck
- Westfälische Wilhelms-Universität Münster, Institut für Molekulare Mikrobiologie und Biotechnologie, Corrensstrasse 3, D-48149 Münster, Germany
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Waldeck J, Meyer-Rammes H, Nahrstedt H, Eichstädt R, Wieland S, Meinhardt F. Targeted deletion of the uvrBA operon and biological containment in the industrially important Bacillus licheniformis. Appl Microbiol Biotechnol 2006; 73:1340-7. [PMID: 17004053 DOI: 10.1007/s00253-006-0602-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Revised: 07/20/2006] [Accepted: 08/07/2006] [Indexed: 10/24/2022]
Abstract
From a Bacillus licheniformis wild type as well as a defined asporogenous derivative, stable UV hypersensitive mutants were generated by targeted deletion of the uvrBA operon, encoding highly conserved key components of the nucleotide excision repair. Comparative studies, which included the respective parental strains, revealed no negative side effects of the deletion, neither on enzyme secretion nor on vegetative propagation. Thus, the uvrBA locus proved to be a useful deletion target for achieving biological containment in this industrially exploited bacterium. In contrast to recA mutants, which also display UV hypersensitivity, further strain development via homologous recombination techniques will be still possible in such uvr mutants.
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Affiliation(s)
- Jens Waldeck
- Westfälische Wilhelms-Universität Münster, Institut für Molekulare Mikrobiologie und Biotechnologie, Corrensstrasse 3, 48149, Münster, Germany
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