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Mishra A, Hughes AC, Amon JD, Rudner DZ, Wang X, Kearns DB. SwrA-mediated Multimerization of DegU and an Upstream Activation Sequence Enhance Flagellar Gene Expression in Bacillus subtilis. J Mol Biol 2024; 436:168419. [PMID: 38141873 DOI: 10.1016/j.jmb.2023.168419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 12/25/2023]
Abstract
The earliest genes in bacterial flagellar assembly are activated by narrowly-conserved proteins called master regulators that often act as heteromeric complexes. A complex of SwrA and the response-regulator transcription factor DegU is thought to form the master flagellar regulator in Bacillus subtilis but how the two proteins co-operate to activate gene expression is poorly-understood. Here we find using ChIP-Seq that SwrA interacts with a subset of DegU binding sites in the chromosome and does so in a DegU-dependent manner. Using this information, we identify a DegU-specific inverted repeat DNA sequence in the Pflache promoter region and show that SwrA synergizes with DegU phosphorylation to increase binding affinity. We further demonstrate that the SwrA/DegU footprint extends from the DegU binding site towards the promoter, likely through SwrA-induced DegU multimerization. The location of the DegU inverted repeat was critical and moving the binding site closer to the promoter impaired transcription by disrupting a previously-unrecognized upstream activation sequence (UAS). Thus, the SwrA-DegU heteromeric complex likely enables both remote binding and interaction between the activator and RNA polymerase. Small co-activator proteins like SwrA may allow selective activation of subsets of genes where activator multimerization is needed. Why some promoters require activator multimerization and some require UAS sequences is unknown.
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Affiliation(s)
- Ayushi Mishra
- Department of Biology, Indiana University, Bloomington, IN 47408, USA
| | - Anna C Hughes
- Department of Biology, Indiana University, Bloomington, IN 47408, USA
| | - Jeremy D Amon
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - David Z Rudner
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, IN 47408, USA
| | - Daniel B Kearns
- Department of Biology, Indiana University, Bloomington, IN 47408, USA.
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Walgraeve J, Ferrero-Bordera B, Maaß S, Becher D, Schwerdtfeger R, van Dijl JM, Seefried M. Diamide-based screening method for the isolation of improved oxidative stress tolerance phenotypes in Bacillus mutant libraries. Microbiol Spectr 2023; 11:e0160823. [PMID: 37819171 PMCID: PMC10714788 DOI: 10.1128/spectrum.01608-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 08/30/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE During their life cycle, bacteria are exposed to a range of different stresses that need to be managed appropriately in order to ensure their growth and viability. This applies not only to bacteria in their natural habitats but also to bacteria employed in biotechnological production processes. Oxidative stress is one of these stresses that may originate either from bacterial metabolism or external factors. In biotechnological settings, it is of critical importance that production strains are resistant to oxidative stresses. Accordingly, this also applies to the major industrial cell factory Bacillus subtilis. In the present study, we, therefore, developed a screen for B. subtilis strains with enhanced oxidative stress tolerance. The results show that our approach is feasible and time-, space-, and resource-efficient. We, therefore, anticipate that it will enhance the development of more robust industrial production strains with improved robustness under conditions of oxidative stress.
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Affiliation(s)
| | | | - Sandra Maaß
- Department of Microbial Proteomics, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, University of Greifswald, Greifswald, Germany
| | | | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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Jeckel H, Nosho K, Neuhaus K, Hastewell AD, Skinner DJ, Saha D, Netter N, Paczia N, Dunkel J, Drescher K. Simultaneous spatiotemporal transcriptomics and microscopy of Bacillus subtilis swarm development reveal cooperation across generations. Nat Microbiol 2023; 8:2378-2391. [PMID: 37973866 PMCID: PMC10686836 DOI: 10.1038/s41564-023-01518-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023]
Abstract
Development of microbial communities is a complex multiscale phenomenon with wide-ranging biomedical and ecological implications. How biological and physical processes determine emergent spatial structures in microbial communities remains poorly understood due to a lack of simultaneous measurements of gene expression and cellular behaviour in space and time. Here we combined live-cell microscopy with a robotic arm for spatiotemporal sampling, which enabled us to simultaneously acquire phenotypic imaging data and spatiotemporal transcriptomes during Bacillus subtilis swarm development. Quantitative characterization of the spatiotemporal gene expression patterns revealed correlations with cellular and collective properties, and phenotypic subpopulations. By integrating these data with spatiotemporal metabolome measurements, we discovered a spatiotemporal cross-feeding mechanism fuelling swarm development: during their migration, earlier generations deposit metabolites which are consumed by later generations that swarm across the same location. These results highlight the importance of spatiotemporal effects during the emergence of phenotypic subpopulations and their interactions in bacterial communities.
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Affiliation(s)
- Hannah Jeckel
- Biozentrum, University of Basel, Basel, Switzerland
- Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Kazuki Nosho
- Biozentrum, University of Basel, Basel, Switzerland
| | - Konstantin Neuhaus
- Biozentrum, University of Basel, Basel, Switzerland
- Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Alasdair D Hastewell
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dominic J Skinner
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, USA
| | - Dibya Saha
- Biozentrum, University of Basel, Basel, Switzerland
| | | | - Nicole Paczia
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Knut Drescher
- Biozentrum, University of Basel, Basel, Switzerland.
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Xie CY, Li WJ, Feng H. Tuning transcription factor DegU for developing extracellular protease overproducer in Bacillus pumilus. Microb Cell Fact 2023; 22:163. [PMID: 37635205 PMCID: PMC10464342 DOI: 10.1186/s12934-023-02177-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/11/2023] [Indexed: 08/29/2023] Open
Abstract
BACKGROUND Global transcription machinery engineering (gTME) is an effective approach employed in strain engineering to rewire gene expression and reshape cellular metabolic fluxes at the transcriptional level. RESULTS In this study, we utilized gTME to engineer the positive transcription factor, DegU, in the regulation network of major alkaline protease, AprE, in Bacillus pumilus. To validate its functionality when incorporated into the chromosome, we performed several experiments. First, three negative transcription factors, SinR, Hpr, and AbrB, were deleted to promote AprE synthesis. Second, several hyper-active DegU mutants, designated as DegU(hy), were selected using the fluorescence colorimetric method with the host of the Bacillus subtilis ΔdegSU mutant. Third, we integrated a screened degU(L113F) sequence into the chromosome of the Δhpr mutant of B. pumilus SCU11 to replace the original degU gene using a CRISPR/Cas9 system. Finally, based on transcriptomic and molecular dynamic analysis, we interpreted the possible mechanism of high-yielding and found that the strain produced alkaline proteases 2.7 times higher than that of the control strain (B. pumilus SCU11) in LB medium. CONCLUSION Our findings serve as a proof-of-concept that tuning the global regulator is feasible and crucial for improving the production performance of B. pumilus. Additionally, our study established a paradigm for gene function research in strains that are difficult to handle.
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Affiliation(s)
- Chao-Ying Xie
- Key Laboratory for Bio-resources and Eco-Environment of the Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Wen-Jin Li
- Key Laboratory for Bio-resources and Eco-Environment of the Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Hong Feng
- Key Laboratory for Bio-resources and Eco-Environment of the Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China.
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Bremer E, Calteau A, Danchin A, Harwood C, Helmann JD, Médigue C, Palsson BO, Sekowska A, Vallenet D, Zuniga A, Zuniga C. A model industrial workhorse:
Bacillus subtilis
strain 168 and its genome after a quarter of a century. Microb Biotechnol 2023; 16:1203-1231. [PMID: 37002859 DOI: 10.1111/1751-7915.14257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/20/2023] [Indexed: 04/04/2023] Open
Abstract
The vast majority of genomic sequences are automatically annotated using various software programs. The accuracy of these annotations depends heavily on the very few manual annotation efforts that combine verified experimental data with genomic sequences from model organisms. Here, we summarize the updated functional annotation of Bacillus subtilis strain 168, a quarter century after its genome sequence was first made public. Since the last such effort 5 years ago, 1168 genetic functions have been updated, allowing the construction of a new metabolic model of this organism of environmental and industrial interest. The emphasis in this review is on new metabolic insights, the role of metals in metabolism and macromolecule biosynthesis, functions involved in biofilm formation, features controlling cell growth, and finally, protein agents that allow class discrimination, thus allowing maintenance management, and accuracy of all cell processes. New 'genomic objects' and an extensive updated literature review have been included for the sequence, now available at the International Nucleotide Sequence Database Collaboration (INSDC: AccNum AL009126.4).
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Affiliation(s)
- Erhard Bremer
- Department of Biology, Laboratory for Microbiology and Center for Synthetic Microbiology (SYNMIKRO) Philipps‐University Marburg Marburg Germany
| | - Alexandra Calteau
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Antoine Danchin
- School of Biomedical Sciences, Li KaShing Faculty of Medicine Hong Kong University Pokfulam SAR Hong Kong China
| | - Colin Harwood
- Centre for Bacterial Cell Biology, Biosciences Institute Newcastle University Baddiley Clark Building Newcastle upon Tyne UK
| | - John D. Helmann
- Department of Microbiology Cornell University Ithaca New York USA
| | - Claudine Médigue
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Bernhard O. Palsson
- Department of Bioengineering University of California San Diego La Jolla USA
| | | | - David Vallenet
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Abril Zuniga
- Department of Biology San Diego State University San Diego California USA
| | - Cristal Zuniga
- Bioinformatics and Medical Informatics Graduate Program San Diego State University San Diego California USA
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