1
|
Partridge JD, Harshey RM. Flagellar protein FliL: A many-splendored thing. Mol Microbiol 2024. [PMID: 39096095 DOI: 10.1111/mmi.15301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/09/2024] [Accepted: 07/16/2024] [Indexed: 08/04/2024]
Abstract
FliL is a bacterial flagellar protein demonstrated to associate with, and regulate ion flow through, the stator complex in a diverse array of bacterial species. FliL is also implicated in additional functions such as stabilizing the flagellar rod, modulating rotor bias, sensing the surface, and regulating gene expression. How can one protein do so many things? Its location is paramount to understanding its numerous functions. This review will look at the evidence, attempt to resolve some conflicting findings, and offer new thoughts on FliL.
Collapse
Affiliation(s)
- Jonathan D Partridge
- Department of Molecular Biosciences and the LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, Texas, USA
| | - Rasika M Harshey
- Department of Molecular Biosciences and the LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, Texas, USA
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Montgomery VA, Cain E, Styczynski MP, Prausnitz MR. Bacillus subtilis engineered for topical delivery of an antifungal agent. PLoS One 2023; 18:e0293664. [PMID: 38032939 PMCID: PMC10688720 DOI: 10.1371/journal.pone.0293664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/14/2023] [Indexed: 12/02/2023] Open
Abstract
Fungal skin infections are a common condition affecting 20-25 percent of the world population. While these conditions are treatable with regular application of an antifungal medication, we sought to develop a more convenient, longer-lasting topical antifungal platform that could increase patient adherence to treatment regimens by using Bacillus subtilis, a naturally antifungal bacteria found on the skin, for drug production and delivery. In this study, we engineered B. subtilis for increased production of the antifungal lipopeptide iturin A by overexpression of the pleiotropic regulator DegQ. The engineered strain had an over 200% increase in iturin A production as detected by HPLC, accompanied by slower growth but the same terminal cell density as determined by absorbance measurements of liquid culture. In an in vitro antifungal assay, we found that despite its higher iturin A production, the engineered strain was less effective at reducing the growth of a plug of the pathogenic fungus Trichophyton mentagrophytes on an agar plate compared to the parent strain. The reduced efficacy of the engineered strain may be explained by its reduced growth rate, which highlights the need to address trade-offs between titers (e.g. measured drug production) and other figures of merit (e.g. growth rate) during metabolic engineering.
Collapse
Affiliation(s)
- Veronica A. Montgomery
- Wallace H. Coulter Department of Biomedical Engineering at Emory University and Georgia Tech, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Ethan Cain
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Mark P. Styczynski
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Mark R. Prausnitz
- Wallace H. Coulter Department of Biomedical Engineering at Emory University and Georgia Tech, Georgia Institute of Technology, Atlanta, GA, United States of America
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United States of America
| |
Collapse
|
4
|
Shen Y, Shi Z, Zhao J, Li M, Tang J, Wang N, Mo Y, Yang T, Zhou X, Chen Q, Yang P. Whole genome sequencing provides evidence for Bacillus velezensis SH-1471 as a beneficial rhizosphere bacterium in plants. Sci Rep 2023; 13:20929. [PMID: 38017088 PMCID: PMC10684890 DOI: 10.1038/s41598-023-48171-9] [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: 07/10/2023] [Accepted: 11/23/2023] [Indexed: 11/30/2023] Open
Abstract
Bacillus is widely used in agriculture due to its diverse biological activities. We isolated a Bacillus velezensis SH-1471 from the rhizosphere soil of healthy tobacco, which has broad-spectrum antagonistic activity against a variety of plant pathogenic fungi such as Fusarium oxysporum, and can be colonized in the rhizosphere of a variety of plants. This study will further explore its mechanism by combining biological and molecular biology methods. SH-1471 contains a ring chromosome of 4,181,346 bp with a mean G + C content of 46.18%. We identified 14 homologous genes related to biosynthesis of resistant secondary metabolite, and three clusters encoded potential new antibacterial substances. It also contains a large number of genes from colonizing bacteria and genes related to plant bacterial interactions. It also contains genes related to environmental stress, as well as genes related to drug resistance. We also found that there are many metabolites in the strain that can inhibit the growth of pathogens. In addition, our indoor pot test found that SH-1471 has a good control effect on tomato wilt, and could significantly improve plant height, stem circumference, root length, root weight, and fresh weight and dry weight of the aboveground part of tomato seedlings. Therefore, SH-1471 is a potential biological control strain with important application value. The results of this study will help to further study the mechanism of SH-1471 in biological control of plant diseases and promote its application.
Collapse
Affiliation(s)
- Yunxin Shen
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming, 650204, China
- College of Plant Protection, Yunnan Agricultural University, Kunming, 655508, China
| | - Zhufeng Shi
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming, 650204, China
| | - Jiangyuan Zhao
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650106, China
| | - Minggang Li
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650106, China
| | - Jiacai Tang
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming, 650204, China
| | - Nan Wang
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming, 650204, China
- College of Plant Protection, Yunnan Agricultural University, Kunming, 655508, China
| | - Yanfang Mo
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming, 650204, China
- College of Plant Protection, Yunnan Agricultural University, Kunming, 655508, China
| | - Tongyu Yang
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming, 650204, China
- College of Plant Protection, Yunnan Agricultural University, Kunming, 655508, China
| | - Xudong Zhou
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming, 650204, China
| | - Qibin Chen
- College of Plant Protection, Yunnan Agricultural University, Kunming, 655508, China.
| | - Peiweng Yang
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming, 650204, China.
| |
Collapse
|
5
|
Partridge JD, Dufour Y, Hwang Y, Harshey RM. Flagellar motor remodeling during swarming requires FliL. Mol Microbiol 2023; 120:670-683. [PMID: 37675594 PMCID: PMC10942728 DOI: 10.1111/mmi.15148] [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: 07/14/2023] [Revised: 08/18/2023] [Accepted: 08/20/2023] [Indexed: 09/08/2023]
Abstract
FliL is an essential component of the flagellar machinery in some bacteria, but a conditional one in others. The conditional role is for optimal swarming in some bacteria. During swarming, physical forces associated with movement on a surface are expected to exert a higher load on the flagellum, requiring more motor torque to move. FliL was reported to enhance motor output in several bacteria and observed to assemble as a ring around ion-conducting stators that power the motor. In this study we identify a common new function for FliL in diverse bacteria-Escherichia coli, Bacillus subtilis, and Proteus mirabilis. During swarming, all these bacteria show increased cell speed and a skewed motor bias that suppresses cell tumbling. We demonstrate that these altered motor parameters, or "motor remodeling," require FliL. Both swarming and motor remodeling can be restored in an E. coli fliL mutant by complementation with fliL genes from P. mirabilis and B. subtilis, showing conservation of a swarming-associated FliL function across phyla. In addition, we demonstrate that the strong interaction we reported earlier between FliL and the flagellar MS-ring protein FliF is confined to the RBM-3 domain of FliF that links the periplasmic rod to the cytoplasmic C-ring. This interaction may explain several phenotypes associated with the absence of FliL.
Collapse
Affiliation(s)
- Jonathan D. Partridge
- Department of Molecular Biosciences and the LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, Texas, USA
| | - Yann Dufour
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - YuneSahng Hwang
- Department of Molecular Biosciences and the LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, Texas, USA
| | - Rasika M. Harshey
- Department of Molecular Biosciences and the LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, Texas, USA
| |
Collapse
|
6
|
Partridge JD, Dufour Y, Hwang Y, Harshey RM. Flagellar motor remodeling during swarming requires FliL. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.549092. [PMID: 37503052 PMCID: PMC10370021 DOI: 10.1101/2023.07.14.549092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
FliL is an essential component of the flagellar machinery in some bacteria, but a conditional one in others. The conditional role is for optimal swarming in some bacteria. During swarming, physical forces associated with movement on a surface are expected to exert a higher load on the flagellum, requiring more motor torque to move. Bacterial physiology and morphology are also altered during swarming to cope with the challenges of surface navigation. FliL was reported to enhance motor output in several bacteria and observed to assemble as a ring around ion-conducting stators that power the motor. In this study we identify a common new function for FliL in diverse bacteria - Escherichia coli, Bacillus subtilis and Proteus mirabilis . During swarming, all these bacteria show increased cell speed and a skewed motor bias that suppresses cell tumbling. We demonstrate that these altered motor parameters, or 'motor remodeling', require FliL. Both swarming and motor remodeling can be restored in an E. coli fliL mutant by complementation with fliL genes from P. mirabilis and B. subtilis , showing conservation of swarming-associated FliL function across phyla. In addition, we demonstrate that the strong interaction we reported earlier between FliL and the flagellar MS-ring protein FliF is confined to the RBM-3 domain of FliF that links the periplasmic rod to the cytoplasmic C-ring. This interaction may explain several phenotypes associated with the absence of FliL.
Collapse
Affiliation(s)
- Jonathan D Partridge
- Department of Molecular Biosciences and the LaMontagne Center for Infectious Diseases The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Yann Dufour
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - YuneSahng Hwang
- Department of Molecular Biosciences and the LaMontagne Center for Infectious Diseases The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Rasika M Harshey
- Department of Molecular Biosciences and the LaMontagne Center for Infectious Diseases The University of Texas at Austin, Austin, Texas, 78712, USA
| |
Collapse
|
7
|
Cuellar-Gaviria TZ, García-Botero C, Ju KS, Villegas-Escobar V. The genome of Bacillus tequilensis EA-CB0015 sheds light into its epiphytic lifestyle and potential as a biocontrol agent. Front Microbiol 2023; 14:1135487. [PMID: 37051516 PMCID: PMC10083409 DOI: 10.3389/fmicb.2023.1135487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/06/2023] [Indexed: 03/29/2023] Open
Abstract
Different Bacillus species have successfully been used as biopesticides against a broad range of plant pathogens. Among these, Bacillus tequilensis EA-CB0015 has shown to efficiently control Black sigatoka disease in banana plants, presumably by mechanisms of adaptation that involve modifying the phyllosphere environment. Here, we report the complete genome of strain EA-CB0015, its precise taxonomic identity, and determined key genetic features that may contribute to its effective biocontrol of plant pathogens. We found that B. tequilensis EA-CB0015 harbors a singular 4 Mb circular chromosome, with 3,951 protein-coding sequences. Multi-locus sequence analysis (MLSA) and average nucleotide identity (ANI) analysis classified strain EA-CB0015 as B. tequilensis. Encoded within its genome are biosynthetic gene clusters (BGCs) for surfactin, iturin, plipastatin, bacillibactin, bacilysin, subtilosin A, sporulation killing factor, and other natural products that may facilitate inter-microbial warfare. Genes for indole-acetic acid (IAA) synthesis, the use of diverse carbon sources, and a multicellular lifestyle involving motility, biofilm formation, quorum sensing, competence, and sporulation suggest EA-CB0015 is adept at colonizing plant surfaces. Defensive mechanisms to survive invading viral infections and preserve genome integrity include putative type I and type II restriction modification (RM) and toxin/antitoxin (TA) systems. The presence of bacteriophage sequences, genomic islands, transposable elements, virulence factors, and antibiotic resistance genes indicate prior occurrences of genetic exchange. Altogether, the genome of EA-CB0015 supports its function as a biocontrol agent against phytopathogens and suggest it has adapted to thrive within phyllosphere environments.
Collapse
Affiliation(s)
- Tatiana Z. Cuellar-Gaviria
- CIBIOP Group, Department of Biological Sciences, Universidad EAFIT, Medellin, Colombia
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
- Banana Research Center, Augura, Conjunto Residencial Los Almendros, Carepa, Colombia
| | - Camilo García-Botero
- CIBIOP Group, Department of Biological Sciences, Universidad EAFIT, Medellin, Colombia
| | - Kou-San Ju
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, Columbus, OH, United States
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States
- *Correspondence: Kou-San Ju, ; Valeska Villegas-Escobar,
| | - Valeska Villegas-Escobar
- CIBIOP Group, Department of Biological Sciences, Universidad EAFIT, Medellin, Colombia
- *Correspondence: Kou-San Ju, ; Valeska Villegas-Escobar,
| |
Collapse
|
8
|
Songwattana P, Boonchuen P, Piromyou P, Wongdee J, Greetatorn T, Inthaisong S, Alisha Tantasawat P, Teamtisong K, Tittabutr P, Boonkerd N, Teaumroong N. Insights into Antifungal Mechanisms of Bacillus velezensis S141 against Cercospora Leaf Spot in Mungbean (V. radiata). Microbes Environ 2023; 38. [PMID: 36935122 PMCID: PMC10037098 DOI: 10.1264/jsme2.me22079] [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] [Indexed: 03/21/2023] Open
Abstract
Cercospora leaf spot (CLS) is caused by Cercospora canescens and is one of the most important diseases of mungbean (Vigna radiata). Cercospora leaf spot may result in economic loss in production areas. The present study investigated the potential of Bacillus velezensis S141 as a biocontrol agent for C. canescens PAK1 growth on culture plates. Cell-free secretions from a dual culture of S141+PAK1 inhibited fungal growth more than those from a single culture of S141. The biocontrol efficiency of S141 against Cercospora leaf spot on mungbean was then evaluated by spraying. The disease severity of Cercospora leaf spot was significantly reduced in plants treated with S141, with a control efficiency of 83% after 2 days of infection. Comparative transcriptomics and qRT-PCR ana-lyses of S141 during C. canescens inhibition were performed to elucidate the antifungal mechanisms underlying its antifungal activity against Cercospora leaf spot. According to the differentially expressed genes, most up-regulated genes involved in the biosynthetic genes encoding enzymatic hydrolases, including protease, β-glucanase, and N-acyl glucosaminase, were detected in strain S141 following its interaction. Moreover, genes related to secondary metabolites (surfactin, bacilysin, and bacillomycin D) were up-regulated. Collectively, these results suggest that S141 exhibited strong antifungal activity against C. canescens due to multiple enzymatic hydrolases and secondary metabolites. Therefore, the present study provides insights into the biological network responsible for the antifungal activity of B. velezensis S141 against C. canescens.
Collapse
Affiliation(s)
- Pongpan Songwattana
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Pakpoom Boonchuen
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Pongdet Piromyou
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Jenjira Wongdee
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Teerana Greetatorn
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Sukanya Inthaisong
- School of Crop Production Technology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Piyada Alisha Tantasawat
- School of Crop Production Technology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Kamonluck Teamtisong
- The Center for Scientific and Technological Equipment, Suranaree University of Technology
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| |
Collapse
|
9
|
Antifungal activity and genomic characterization of the biocontrol agent Bacillus velezensis CMRP 4489. Sci Rep 2022; 12:17401. [PMID: 36257999 PMCID: PMC9579199 DOI: 10.1038/s41598-022-22380-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 10/13/2022] [Indexed: 01/10/2023] Open
Abstract
The development of bio-based products has increased in recent years, and species of the Bacillus genus have been widely used for product development due to their elevated production of antimicrobial molecules and resistance to extreme environmental conditions through endospore formation. In this context, the antifungal potential of Bacillus velezensis CMRP 4489 was investigated using in silico predictions of secondary metabolites in its genome and in vitro tests against the following phytopathogenic fungi: Sclerotinia sclerotiorum, Macrophomina phaseolina, and Botrytis cinerea. The in-silico predictions indicated that CMRP 4489 possesses several Biosynthetic Gene Clusters (BGCs) capable of producing molecules with antifungal properties and other non-identified BGCs. The in vitro assay results evidenced strong antifungal activity, inhibiting more than 60% of the tested fungi, and the isolate's molecules were stable under diverse physicochemical conditions. The in vitro assay evidenced significant antifungal activity, deformation of the hyphal structure in SS, biofilm formation capacity, and swarming motility. In the colonization assay, we observed attachment, colonization, and net-shaped biofilm formation, with the strain transitioning from the seeds to nearby structures. Therefore, CMRP 4489 showed to be a potential biocontrol agent against various diseases with agronomic importance and can be used under adverse environmental conditions.
Collapse
|
10
|
Rahman MA, Heme UH, Parvez MAK. In silico functional annotation of hypothetical proteins from the Bacillus paralicheniformis strain Bac84 reveals proteins with biotechnological potentials and adaptational functions to extreme environments. PLoS One 2022; 17:e0276085. [PMID: 36228026 PMCID: PMC9560612 DOI: 10.1371/journal.pone.0276085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/28/2022] [Indexed: 11/26/2022] Open
Abstract
Members of the Bacillus genus are industrial cell factories due to their capacity to secrete significant quantities of biomolecules with industrial applications. The Bacillus paralicheniformis strain Bac84 was isolated from the Red Sea and it shares a close evolutionary relationship with Bacillus licheniformis. However, a significant number of proteins in its genome are annotated as functionally uncharacterized hypothetical proteins. Investigating these proteins' functions may help us better understand how bacteria survive extreme environmental conditions and to find novel targets for biotechnological applications. Therefore, the purpose of our research was to functionally annotate the hypothetical proteins from the genome of B. paralicheniformis strain Bac84. We employed a structured in-silico approach incorporating numerous bioinformatics tools and databases for functional annotation, physicochemical characterization, subcellular localization, protein-protein interactions, and three-dimensional structure determination. Sequences of 414 hypothetical proteins were evaluated and we were able to successfully attribute a function to 37 hypothetical proteins. Moreover, we performed receiver operating characteristic analysis to assess the performance of various tools used in this present study. We identified 12 proteins having significant adaptational roles to unfavorable environments such as sporulation, formation of biofilm, motility, regulation of transcription, etc. Additionally, 8 proteins were predicted with biotechnological potentials such as coenzyme A biosynthesis, phenylalanine biosynthesis, rare-sugars biosynthesis, antibiotic biosynthesis, bioremediation, and others. Evaluation of the performance of the tools showed an accuracy of 98% which represented the rationality of the tools used. This work shows that this annotation strategy will make the functional characterization of unknown proteins easier and can find the target for further investigation. The knowledge of these hypothetical proteins' potential functions aids B. paralicheniformis strain Bac84 in effectively creating a new biotechnological target. In addition, the results may also facilitate a better understanding of the survival mechanisms in harsh environmental conditions.
Collapse
Affiliation(s)
- Md. Atikur Rahman
- Institute of Microbiology, Friedrich Schiller University Jena, Thuringia, Germany
| | - Uzma Habiba Heme
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Thuringia, Germany
| | | |
Collapse
|
11
|
Engelhardt IC, Patko D, Liu Y, Mimault M, de Las Heras Martinez G, George TS, MacDonald M, Ptashnyk M, Sukhodub T, Stanley-Wall NR, Holden N, Daniell TJ, Dupuy LX. Novel form of collective movement by soil bacteria. THE ISME JOURNAL 2022; 16:2337-2347. [PMID: 35798939 PMCID: PMC9478162 DOI: 10.1038/s41396-022-01277-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 06/07/2022] [Accepted: 06/17/2022] [Indexed: 04/16/2023]
Abstract
Although migrations are essential for soil microorganisms to exploit scarce and heterogeneously distributed resources, bacterial mobility in soil remains poorly studied due to experimental limitations. In this study, time-lapse images collected using live microscopy techniques captured collective and coordinated groups of B. subtilis cells exhibiting "crowd movement". Groups of B. subtilis cells moved through transparent soil (nafion polymer with particle size resembling sand) toward plant roots and re-arranged dynamically around root tips in the form of elongating and retracting "flocks" resembling collective behaviour usually associated with higher organisms (e.g., bird flocks or fish schools). Genetic analysis reveals B. subtilis flocks are likely driven by the diffusion of extracellular signalling molecules (e.g., chemotaxis, quorum sensing) and may be impacted by the physical obstacles and hydrodynamics encountered in the soil like environment. Our findings advance understanding of bacterial migration through soil matrices and expand known behaviours for coordinated bacterial movement.
Collapse
Affiliation(s)
- I C Engelhardt
- Ecological Sciences, The James Hutton Institute, Dundee, UK
- Department of Conservation of Natural Resources, Neiker, Bilbao, Spain
| | - D Patko
- Ecological Sciences, The James Hutton Institute, Dundee, UK
- Department of Conservation of Natural Resources, Neiker, Bilbao, Spain
| | - Y Liu
- Ecological Sciences, The James Hutton Institute, Dundee, UK
- ICS, The James Hutton Institute, Dundee, UK
| | - M Mimault
- ICS, The James Hutton Institute, Dundee, UK
| | | | - T S George
- Ecological Sciences, The James Hutton Institute, Dundee, UK
| | - M MacDonald
- School of Science and Engineering, University of Dundee, Dundee, UK
| | - M Ptashnyk
- School of Mathematical & Computer Sciences, Heriot-Watt University, Edinburgh, UK
| | - T Sukhodub
- School of Life Sciences, University of Dundee, Dundee, UK
| | | | - N Holden
- Ecological Sciences, The James Hutton Institute, Dundee, UK
- North Faculty, Scotland's Rural College, Aberdeen, UK
| | - T J Daniell
- Plants, Photosynthesis and Soil, School of Biosciences, The University of Sheffield, Sheffield, UK
| | - L X Dupuy
- Ecological Sciences, The James Hutton Institute, Dundee, UK.
- Department of Conservation of Natural Resources, Neiker, Bilbao, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
| |
Collapse
|
12
|
Bacillus velezensis: A Treasure House of Bioactive Compounds of Medicinal, Biocontrol and Environmental Importance. FORESTS 2021. [DOI: 10.3390/f12121714] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Bacillus velezensis gram-positive bacterium, is frequently isolated from diverse niches mainly soil, water, plant roots, and fermented foods. B. velezensis is ubiquitous, non-pathogenic and endospore forming. Being frequently isolated from diverse plant holobionts it is considered host adapted microorganism and recognized of high economic importance given its ability to promote plant growth under diverse biotic and abiotic stress conditions. Additionally, the species suppress many plant diseases, including bacterial, oomycete, and fungal diseases. It is also able after plant host root colonization to induce unique physiological situation of host plant called primed state. Primed host plants are able to respond more rapidly and/or effectively to biotic or abiotic stress. Moreover, B. velezenis have the ability to resist diverse environmental stresses and help host plants to cope with, including metal and xenobiotic stresses. Within species B. velezensis strains have unique abilities allowing them to adopt different life styles. Strain level abilities knowledge is warranted and could be inferred using the ever-expanding new genomes list available in genomes databases. Pangenome analysis and subsequent identification of core, accessory and unique genomes is actually of paramount importance to decipher species full metabolic capacities and fitness across diverse environmental conditions shaping its life style. Despite the crucial importance of the pan genome, its assessment among large number of strains remains sparse and systematic studies still needed. Extensive knowledge of the pan genome is needed to translate genome sequencing efforts into developing more efficient biocontrol agents and bio-fertilizers. In this study, a genome survey of B. velezensis allowed us to (a) highlight B. velezensis species boundaries and show that Bacillus suffers taxonomic imprecision that blurs the debate over species pangenome; (b) identify drivers of their successful acquisition of specific life styles and colonization of new niches; (c) describe strategies they use to promote plant growth and development; (d) reveal the unlocked strain specific orphan secondary metabolite gene clusters (biosynthetic clusters with corresponding metabolites unknown) that product identification is still awaiting to amend our knowledge of their putative role in suppression of pathogens and plant growth promotion, and (e) to describe a dynamic pangenome with a secondary metabolite rich accessory genome.
Collapse
|
13
|
Chen M, Zheng M, Chen Y, Xiao R, Zheng X, Liu B, Wang J, Zhu Y. Effect of metal ions on lipopeptide secretion from Bacillus subtilis strain FJAT-4: Negative regulation by Ca 2. J Appl Microbiol 2021; 132:2167-2176. [PMID: 34716970 DOI: 10.1111/jam.15347] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 10/24/2021] [Indexed: 11/27/2022]
Abstract
AIMS This study aimed to investigate the effect of metal ions on lipopeptide production by Bacillus subtilis strain FJAT-4 and the mechanism of negative regulation by Ca2+ . METHODS AND RESULTS The quantitative measurement of lipopeptides in response to K+ , Na+ , Mg2+ and Ca2+ addition was carried out by LC-MS. The contents of fengycin and surfactin varied within the range of 116.24-129.80 mg/L and 34.03-63.11 mg/L in the culture media containing K+ , Na+ and Mg2+ , while the levels were 0.86 and 0.63 mg/L in the media containing Ca2+ . Ca2+ at a high concentration (45 mM) did not adversely affect the growth of strain FJAT-4, but caused significant downregulation of lipopeptide synthesis-related gene expression, corresponding to a decrease in lipopeptide production. This inhibition by Ca2+ was further investigated by proteomic analysis. In total, 112 proteins were upregulated and 524 proteins were downregulated in the presence of additional Ca2+ (45 mM). Among these differentially expressed proteins (DEPs), 28 were related to phosphotransferase activity, and 42 were related to kinase activity. The proteomics results suggested that altered levels of three two-component signal-transduction systems (ResD/ResE, PhoP/PhoR and DegU/DegS) might be involved in the control of expression of the fen and srfA operons of FJAT-4 under high calcium stress. CONCLUSIONS The Ca2+ at the high concentration (45 mM) triggers a decrease in lipopeptide production, which might be attributed to the regulation of three two-component signal-transduction systems ResD/ResE, PhoP/PhoR and DegU/DegS. SIGNIFICANCE AND IMPACT OF THE STUDY The regulatory effect of calcium on the expression of genes encoding lipopeptide synthetases can be applied to optimize the production of lipopeptides.
Collapse
Affiliation(s)
- Meichun Chen
- Agricultural Bioresources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Meixia Zheng
- Agricultural Bioresources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yanping Chen
- Agricultural Bioresources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Rongfeng Xiao
- Agricultural Bioresources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Xuefang Zheng
- Agricultural Bioresources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Bo Liu
- Agricultural Bioresources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jieping Wang
- Agricultural Bioresources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yujing Zhu
- Agricultural Bioresources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| |
Collapse
|
14
|
The Role of Surfactin Production by Bacillus velezensis on Colonization, Biofilm Formation on Tomato Root and Leaf Surfaces and Subsequent Protection (ISR) against Botrytis cinerea. Microorganisms 2021; 9:microorganisms9112251. [PMID: 34835375 PMCID: PMC8626045 DOI: 10.3390/microorganisms9112251] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/14/2021] [Accepted: 10/14/2021] [Indexed: 11/17/2022] Open
Abstract
Many aspects regarding the role of lipopeptides (LPs) in bacterial interaction with plants are not clear yet. Of particular interest is the LP family of surfactin, immunogenic molecules involved in induced systemic resistance (ISR) and the bacterial colonization of plant surfaces. We hypothesize that the concentration of surfactin produced by a strain correlates directly with its ability to colonize and persist on different plant surfaces, which conditions its capacity to trigger ISR. We used two Bacillus velezensis strains (BBC023 and BBC047), whose antagonistic potential in vitro is practically identical, but not on plant surfaces. The surfactin production of BBC047 is 1/3 higher than that of BBC023. Population density and SEM images revealed stable biofilms of BBC047 on leaves and roots, activating ISR on both plant surfaces. Despite its lower surfactin production, strain BBC023 assembled stable biofilms on roots and activated ISR. However, on leaves only isolated, unstructured populations were observed, which could not activate ISR. Thus, the ability of a strain to effectively colonize a plant surface is not only determined through its production of surfactin. Multiple aspects, such as environmental stressors or compensation mechanisms may influence the process. Finally, the importance of surfactin lies in its impacts on biofilm formation and stable colonization, which finally enables its activity as an elicitor of ISR.
Collapse
|
15
|
Ferreira WT, Hong HA, Hess M, Adams JRG, Wood H, Bakun K, Tan S, Baccigalupi L, Ferrari E, Brisson A, Ricca E, Teresa Rejas M, Meijer WJJ, Soloviev M, Cutting SM. Micellar Antibiotics of Bacillus. Pharmaceutics 2021; 13:pharmaceutics13081296. [PMID: 34452257 PMCID: PMC8399155 DOI: 10.3390/pharmaceutics13081296] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/24/2022] Open
Abstract
Members of the Bacillus genus, particularly the “Bacillus subtilis group”, are known to produce amphipathic lipopeptides with biosurfactant activity. This includes the surfactins, fengycins and iturins that have been associated with antibacterial, antifungal, and anti-viral properties. We have screened a large collection of Bacillus, isolated from human, animal, estuarine water and soil samples and found that the most potent lipopeptide producers are members of the species Bacillus velezensis. B. velezensis lipopeptides exhibited anti-bacterial activity which was localised on the surface of both vegetative cells and spores. Interestingly, lipopeptide micelles (6–10 nm diameter) were detectable in strains exhibiting the highest levels of activity. Micelles were stable (heat and gastric stable) and shown to entrap other antimicrobials produced by the host bacterium (exampled here was the dipeptide antibiotic chlorotetaine). Commercially acquired lipopeptides did not exhibit similar levels of inhibitory activity and we suspect that micelle formation may relate to the particular isomeric forms produced by individual bacteria. Using naturally produced micelle formulations we demonstrated that they could entrap antimicrobial compounds (e.g., clindamycin, vancomycin and resveratrol). Micellar incorporation of antibiotics increased activity. Bacillus is a prolific producer of antimicrobials, and this phenomenon could be exploited naturally to augment antimicrobial activity. From an applied perspective, the ability to readily produce Bacillus micelles and formulate with drugs enables a possible strategy for enhanced drug delivery.
Collapse
Affiliation(s)
- William T. Ferreira
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (M.H.); (J.R.G.A.); (M.S.)
| | - Huynh A. Hong
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (M.H.); (J.R.G.A.); (M.S.)
| | - Mateusz Hess
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (M.H.); (J.R.G.A.); (M.S.)
| | - James R. G. Adams
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (M.H.); (J.R.G.A.); (M.S.)
| | - Hannah Wood
- SporeGen Ltd., London Bioscience Innovation Centre, 2 Royal College Street, London NW1 0NH, UK; (H.W.); (K.B.)
| | - Karolina Bakun
- SporeGen Ltd., London Bioscience Innovation Centre, 2 Royal College Street, London NW1 0NH, UK; (H.W.); (K.B.)
| | - Sisareuth Tan
- Laboratoire d’Imagerie Moléculaire et Nano-Bio-Technologie, UMR-CBMN CNRS-Université de Bordeaux-IPB, 33607 Pessac, France; (S.T.); (A.B.)
| | - Loredana Baccigalupi
- Department of Molecular Medicine and Medical Biotechnology, Federico II University of Naples, 80126 Napoli, Italy;
| | - Enrico Ferrari
- School of Life Sciences, University of Lincoln, Lincoln LN6 7TS, UK;
| | - Alain Brisson
- Laboratoire d’Imagerie Moléculaire et Nano-Bio-Technologie, UMR-CBMN CNRS-Université de Bordeaux-IPB, 33607 Pessac, France; (S.T.); (A.B.)
| | - Ezio Ricca
- Department of Biology, Federico II University of Naples, 80126 Napoli, Italy;
| | - María Teresa Rejas
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain; (M.T.R.); (W.J.J.M.)
| | - Wilfried J. J. Meijer
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain; (M.T.R.); (W.J.J.M.)
| | - Mikhail Soloviev
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (M.H.); (J.R.G.A.); (M.S.)
| | - Simon M. Cutting
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (M.H.); (J.R.G.A.); (M.S.)
- SporeGen Ltd., London Bioscience Innovation Centre, 2 Royal College Street, London NW1 0NH, UK; (H.W.); (K.B.)
- Correspondence:
| |
Collapse
|
16
|
Sucrose triggers a novel signaling cascade promoting Bacillus subtilis rhizosphere colonization. ISME JOURNAL 2021; 15:2723-2737. [PMID: 33772107 PMCID: PMC8397739 DOI: 10.1038/s41396-021-00966-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/02/2021] [Accepted: 03/15/2021] [Indexed: 11/26/2022]
Abstract
Beneficial rhizobacteria promote plant growth and protect plants against phytopathogens. Effective colonization on plant roots is critical for the rhizobacteria to exert beneficial activities. How bacteria migrate swiftly in the soil of semisolid or solid nature remains unclear. Here we report that sucrose, a disaccharide ubiquitously deployed by photosynthetic plants for fixed carbon transport and storage, and abundantly secreted from plant roots, promotes solid surface motility (SSM) and root colonization by Bacillus subtilis through a previously uncharacterized mechanism. Sucrose induces robust SSM by triggering a signaling cascade, first through extracellular synthesis of polymeric levan, which in turn stimulates strong production of surfactin and hyper-flagellation of the cells. B. subtilis poorly colonizes the roots of Arabidopsis thaliana mutants deficient in root-exudation of sucrose, while exogenously added sucrose selectively shapes the rhizomicrobiome associated with the tomato plant roots, promoting specifically bacilli and pseudomonad. We propose that sucrose activates a signaling cascade to trigger SSM and promote rhizosphere colonization by B. subtilis. Our findings also suggest a practicable approach to boost prevalence of beneficial Bacillus species in plant protection.
Collapse
|
17
|
Gutiérrez-Chávez C, Benaud N, Ferrari BC. The ecological roles of microbial lipopeptides: Where are we going? Comput Struct Biotechnol J 2021; 19:1400-1413. [PMID: 33777336 PMCID: PMC7960500 DOI: 10.1016/j.csbj.2021.02.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 02/18/2021] [Accepted: 02/20/2021] [Indexed: 12/30/2022] Open
Abstract
Lipopeptides (LPs) are secondary metabolites produced by a diversity of bacteria and fungi. Their unique chemical structure comprises both a peptide and a lipid moiety. LPs are of major biotechnological interest owing to their emulsification, antitumor, immunomodulatory, and antimicrobial activities. To date, these versatile compounds have been applied across multiple industries, from pharmaceuticals through to food processing, cosmetics, agriculture, heavy metal, and hydrocarbon bioremediation. The variety of LP structures and the diversity of the environments from which LP-producing microorganisms have been isolated suggest important functions in their natural environment. However, our understanding of the ecological role of LPs is limited. In this review, the mode of action and the role of LPs in motility, antimicrobial activity, heavy metals removal and biofilm formation are addressed. We include discussion on the need to characterise LPs from a diversity of microorganisms, with a focus on taxa inhabiting 'extreme' environments. We introduce the use of computational target fishing and molecular dynamics simulations as powerful tools to investigate the process of interaction between LPs and cell membranes. Together, these advances will provide new understanding of the mechanism of action of novel LPs, providing greater insights into the roles of LPs in the natural environment.
Collapse
Affiliation(s)
| | - Nicole Benaud
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney 2052, Australia
| | - Belinda C Ferrari
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney 2052, Australia
| |
Collapse
|
18
|
Théatre A, Hoste ACR, Rigolet A, Benneceur I, Bechet M, Ongena M, Deleu M, Jacques P. Bacillus sp.: A Remarkable Source of Bioactive Lipopeptides. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 181:123-179. [DOI: 10.1007/10_2021_182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
19
|
Xu S, Xie X, Zhao Y, Shi Y, Chai A, Li L, Li B. Whole-genome analysis of bacillus velezensis ZF2, a biocontrol agent that protects cucumis sativus against corynespora leaf spot diseases. 3 Biotech 2020; 10:186. [PMID: 32257742 DOI: 10.1007/s13205-020-2165-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/11/2020] [Indexed: 12/17/2022] Open
Abstract
Bacillus spp. have been widely described for their potentials to protect plants against pathogens. Here, we reported the whole genome sequence of Bacillus velezensis ZF2, which was isolated from the stem of a healthy cucumber plant. Strain ZF2 showed a broad spectrum of antagonistic activities against many plant bacterial and fungal pathogens, including the cucumber leaf spot fungus Corynespora cassiicola. The complete genome of B. velezensis ZF2 contained a 3,931,418-bp circular chromosome, with an average G + C content of 46.50%. Genome comparison revealed closest similarity between ZF2 and other B. velezensis strains. Genes homologous to 14 gene clusters for biosynthesis of secondary metabolites were identified in the ZF2 genome. Also identified were a number of genes involved in bacterial colonization, including the genes for motility, biofilm formation, flagella biosynthesis, and capsular biosynthesis. Numerous genes associated with plant-bacteria interactions, including cellulase or protease biosynthesis, and plant growth promotion were also identified in the ZF2 genome. Overall, our data will aid future studies of the biocontrol mechanisms of B. velezensis ZF2 and promote its application in vegetable disease control.
Collapse
Affiliation(s)
- Shuai Xu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xuewen Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yurong Zhao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yanxia Shi
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Ali Chai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Lei Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Baoju Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| |
Collapse
|
20
|
Thérien M, Kiesewalter HT, Auria E, Charron-Lamoureux V, Wibowo M, Maróti G, Kovács ÁT, Beauregard PB. Surfactin production is not essential for pellicle and root-associated biofilm development of Bacillus subtilis. Biofilm 2020; 2:100021. [PMID: 33447807 PMCID: PMC7798449 DOI: 10.1016/j.bioflm.2020.100021] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/11/2020] [Accepted: 02/17/2020] [Indexed: 02/06/2023] Open
Abstract
Secondary metabolites have an important impact on the biocontrol potential of soil-derived microbes. In addition, various microbe-produced chemicals have been suggested to impact the development and phenotypic differentiation of bacteria, including biofilms. The non-ribosomal synthesized lipopeptide of Bacillus subtilis, surfactin, has been described to impact the plant promoting capacity of the bacterium. Here, we investigated the impact of surfactin production on biofilm formation of B. subtilis using the laboratory model systems; pellicle formation at the air-medium interface and architecturally complex colony development, in addition to plant root-associated biofilms. We found that the production of surfactin by B. subtilis is not essential for pellicle biofilm formation neither in the well-studied strain, NCIB 3610, nor in the newly isolated environmental strains, but lack of surfactin reduces colony expansion. Further, plant root colonization was comparable both in the presence or absence of surfactin synthesis. Our results suggest that surfactin-related biocontrol and plant promotion in B. subtilis strains are independent of biofilm formation.
Collapse
Affiliation(s)
- Maude Thérien
- Centre SÈVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Heiko T Kiesewalter
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Emile Auria
- Centre SÈVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada.,Biology Department, Ecole Normale Supérieure Paris-Saclay, Paris-Saclay University, Cachan, France
| | - Vincent Charron-Lamoureux
- Centre SÈVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Mario Wibowo
- Natural Product Discovery Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Pascale B Beauregard
- Centre SÈVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada
| |
Collapse
|
21
|
Caro-Astorga J, Álvarez-Mena A, Hierrezuelo J, Guadix JA, Heredia-Ponce Z, Arboleda-Estudillo Y, González-Munoz E, de Vicente A, Romero D. Two genomic regions encoding exopolysaccharide production systems have complementary functions in B. cereus multicellularity and host interaction. Sci Rep 2020; 10:1000. [PMID: 31969664 PMCID: PMC6976573 DOI: 10.1038/s41598-020-57970-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/09/2020] [Indexed: 01/10/2023] Open
Abstract
Bacterial physiology and adaptation are influenced by the exopolysaccharides (EPS) they produce. These polymers are indispensable for the assembly of the biofilm extracellular matrix in multiple bacterial species. In a previous study, we described the profound gene expression changes leading to biofilm assembly in B. cereus ATCC14579 (CECT148). We found that a genomic region putatively dedicated to the synthesis of a capsular polysaccharide (eps2) was overexpressed in a biofilm cell population compared to in a planktonic population, while we detected no change in the transcript abundance from another genomic region (eps1) also likely to be involved in polysaccharide production. Preliminary biofilm assays suggested a mild role for the products of the eps2 region in biofilm formation and no function for the products of the eps1 region. The aim of this work was to better define the roles of these two regions in B. cereus multicellularity. We demonstrate that the eps2 region is indeed involved in bacterial adhesion to surfaces, cell-to-cell interaction, cellular aggregation and biofilm formation, while the eps1 region appears to be involved in a kind of social bacterial motility. Consistent with these results, we further demonstrate using bacterial-host cell interaction experiments that the eps2 region is more relevant to the adhesion to human epithelial cells and the zebrafish intestine, suggesting that this region encodes a bacterial factor that may potentiate gut colonization and enhance pathogenicity against humans.
Collapse
Affiliation(s)
- Joaquin Caro-Astorga
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" -Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071, Málaga, Spain
| | - Ana Álvarez-Mena
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" -Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071, Málaga, Spain
| | - Jesús Hierrezuelo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" -Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071, Málaga, Spain
| | - Juan Antonio Guadix
- Departamento de Biología Animal, Facultad de Ciencias, Universidad de Málaga - IBIMA, Campus de Teatinos s/n, 29071, Málaga, Spain
- Centro Andaluz de Nanomedicina y Biotecnología (BIONAND), Junta de Andalucía, Universidad de Málaga, C/ Severo Ochoa 35, 29590, Campanillas (Málaga), Spain
| | - Zahira Heredia-Ponce
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" -Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071, Málaga, Spain
| | - Yohanna Arboleda-Estudillo
- LARCEL, Andalusian Laboratory of Cell Reprogramming, Andalusian Center for Nanomedicine and Biotechnology-BIONAND, 29590, Málaga, Spain
| | - Elena González-Munoz
- LARCEL, Andalusian Laboratory of Cell Reprogramming, Andalusian Center for Nanomedicine and Biotechnology-BIONAND, 29590, Málaga, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" -Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071, Málaga, Spain
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" -Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071, Málaga, Spain.
| |
Collapse
|
22
|
Biofilm Formation and Synthesis of Antimicrobial Compounds by the Biocontrol Agent Bacillus velezensis QST713 in an Agaricus bisporus Compost Micromodel. Appl Environ Microbiol 2019; 85:AEM.00327-19. [PMID: 30979839 DOI: 10.1128/aem.00327-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/07/2019] [Indexed: 12/22/2022] Open
Abstract
Bacillus velezensis QST713 is widely used as a biological control agent for crop protection and disease suppression. This strain is used industrially in France for the protection of Agaricus bisporus against Trichoderma aggressivum f. europaeum, which causes green mold disease. The efficacy of this biocontrol process was evaluated in a previous study, yet the mode of its action has not been explored under production conditions. In order to decipher the underlying biocontrol mechanisms for effective biofilm formation by strain QST713 in the compost and for the involvement of antimicrobial compounds, we developed a simplified micromodel for the culture of A. bisporus during its early culture cycle. By using this micromodel system, we studied the transcriptional response of strain QST713 in the presence or absence of A. bisporus and/or T. aggressivum in axenic industrial compost. We report the overexpression of several genes of the biocontrol agent involved in biofilm formation in the compost compared to their expression during growth in broth compost extract either in the exponential growth phase (the epsC, blsA, and tapA genes) or in the stationary growth phase (the tapA gene), while a gene encoding a flagellar protein (hag) was underexpressed. We also report the overexpression of Bacillus velezensis QST713 genes related to surfactin (srfAA) and fengycin (fenA) production in the presence of the fungal pathogen in the compost.IMPORTANCE Biocontrol agents are increasingly used to replace chemical pesticides to prevent crop diseases. In the button mushroom field in France, the use of Bacillus velezensis QST713 as a biocontrol agent against the green mold Trichoderma aggressivum has been shown to be efficient. However, the biocontrol mechanisms effective in the Agaricus bisporus/Trichoderma aggressivum/Bacillus velezensis QST713 pathosystem are still unknown. Our paper focuses on the exploration of the bioprotection mechanisms of the biocontrol agent Bacillus velezensis QST713 during culture of the button mushroom (Agaricus bisporus) in a micromodel culture system to study the specific response of strain QST713 in the presence of T. aggressivum and/or A. bisporus.
Collapse
|
23
|
Feng X, Guo W, Zheng H, Du J, Luo H, Wu Q, Ren N. Inhibition of biofilm formation by chemical uncoupler, 3, 3′, 4′, 5-tetrachlorosalicylanilide (TCS): From the perspective of quorum sensing and biofilm related genes. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.05.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
|
24
|
Osman KM, Kappell AD, Orabi A, Al-Maary KS, Mubarak AS, Dawoud TM, Hemeg HA, Moussa IMI, Hessain AM, Yousef HMY, Hristova KR. Poultry and beef meat as potential seedbeds for antimicrobial resistant enterotoxigenic Bacillus species: a materializing epidemiological and potential severe health hazard. Sci Rep 2018; 8:11600. [PMID: 30072706 PMCID: PMC6072766 DOI: 10.1038/s41598-018-29932-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 07/18/2018] [Indexed: 12/17/2022] Open
Abstract
Although Bacillus cereus is of particular concern in food safety and public health, the role of other Bacillus species was overlooked. Therefore, we investigated the presence of eight enterotoxigenic genes, a hemolytic gene and phenotypic antibiotic resistance profiles of Bacillus species in retail meat samples. From 255 samples, 124 Bacillus isolates were recovered, 27 belonged to B. cereus and 97 were non-B. cereus species. Interestingly, the non-B. cereus isolates carried the virulence genes and exhibited phenotypic virulence characteristics as the B. cereus. However, correlation matrix analysis revealed the B. cereus group positively correlates with the presence of the genes hblA, hblC, and plc, and the detection of hemolysis (p < 0.05), while the other Bacillus sp. groups are negatively correlated. Tests for antimicrobial resistance against ten antibiotics revealed extensive drug and multi-drug resistant isolates. Statistical analyses didn't support a correlation of antibiotic resistance to tested virulence factors suggesting independence of these phenotypic markers and virulence genes. Of special interest was the isolation of Paenibacillus alvei and Geobacillus stearothermophilus from the imported meat samples being the first recorded. The isolation of non-B. cereus species carrying enterotoxigenic genes in meat within Egypt, suggests their impact on food safety and public health and should therefore not be minimised, posing an area that requires further research.
Collapse
Affiliation(s)
- Kamelia M Osman
- Department of Microbiology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Anthony D Kappell
- Department of Civil, Construction, and Environmental Engineering, Marquette University, Milwaukee, WI, USA
| | - Ahmed Orabi
- Department of Microbiology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Khalid S Al-Maary
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ayman S Mubarak
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Turki M Dawoud
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Hassan A Hemeg
- Department of Clinical Laboratory sciences, college of Applied Medical sciences, Taibah University, Taibah, Saudi Arabia
| | - Ihab M I Moussa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ashgan M Hessain
- Department of Health Science, College of Applied Studies and Community Service, King Saud University, Riyadh, Saudi Arabia
| | - Hend M Y Yousef
- Central Administration of Preventive Medicine, General Organization for Veterinary Service, Giza, Egypt.
| | | |
Collapse
|
25
|
Complete genome sequence of Bacillus velezensis QST713: A biocontrol agent that protects Agaricus bisporus crops against the green mould disease. J Biotechnol 2018; 278:10-19. [DOI: 10.1016/j.jbiotec.2018.04.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 04/19/2018] [Accepted: 04/22/2018] [Indexed: 12/14/2022]
|
26
|
Mattingly AE, Weaver AA, Dimkovikj A, Shrout JD. Assessing Travel Conditions: Environmental and Host Influences On Bacterial Surface Motility. J Bacteriol 2018; 200:e00014-18. [PMID: 29555698 PMCID: PMC5952383 DOI: 10.1128/jb.00014-18] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The degree to which surface motile bacteria explore their surroundings is influenced by aspects of their local environment. Accordingly, regulation of surface motility is controlled by numerous chemical, physical, and biological stimuli. Discernment of such regulation due to these multiple cues is a formidable challenge. Additionally inherent ambiguity and variability from the assays used to assess surface motility can be an obstacle to clear delineation of regulated surface motility behavior. Numerous studies have reported single environmental determinants of microbial motility and lifestyle behavior but the translation of these data to understand surface motility and bacterial colonization of human host or environmental surfaces is unclear. Here, we describe the current state of the field and our understanding of exogenous factors that influence bacterial surface motility.
Collapse
Affiliation(s)
- Anne E. Mattingly
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Abigail A. Weaver
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Aleksandar Dimkovikj
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Joshua D. Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana, USA
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| |
Collapse
|
27
|
Fan H, Zhang Z, Li Y, Zhang X, Duan Y, Wang Q. Biocontrol of Bacterial Fruit Blotch by Bacillus subtilis 9407 via Surfactin-Mediated Antibacterial Activity and Colonization. Front Microbiol 2017; 8:1973. [PMID: 29075242 PMCID: PMC5641556 DOI: 10.3389/fmicb.2017.01973] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/25/2017] [Indexed: 01/08/2023] Open
Abstract
In this study, Bacillus subtilis 9407 showed a strong antibacterial activity against Acidovorax citrulli in vitro and 61.7% biocontrol efficacy on melon seedlings 4 days post inoculation under greenhouse conditions. To understand the biocontrol mechanism of B. subtilis 9407, identify the primary antibacterial compound and determine its role in controlling bacterial fruit blotch (BFB), a srfAB deletion mutant (ΔsrfAB) was constructed. The ΔsrfAB which was deficient in production of surfactin, not only showed almost no ability to inhibit growth of A. citrulli but also decreased biofilm formation and reduced swarming motility. Colonization assay demonstrated that B. subtilis 9407 could conlonize on melon roots and leaves in a large population, while ΔsrfAB showed a four- to ten-fold reduction in colonization of melon roots and leaves. Furthermore, a biocontrol assay showed that ΔsrfAB lost the biocontrol efficacy. In summary, our results indicated that surfactin, which consists of C13- to C16-surfactin A was the primary antibacterial compound of B. subtilis 9407, and it played a major role in biofilm formation, swarming motility, colonization and suppressing BFB. We propose that the biocontrol activity of B. subtilis 9407 is the results of the coordinated action of surfactin-mediated antibacterial activity and colonization. This study reveals for the first time that the use of a B. subtilis strain as a potential biological control agent could efficiently control BFB by producing surfactin.
Collapse
Affiliation(s)
| | | | | | | | | | - Qi Wang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| |
Collapse
|
28
|
Belbahri L, Chenari Bouket A, Rekik I, Alenezi FN, Vallat A, Luptakova L, Petrovova E, Oszako T, Cherrad S, Vacher S, Rateb ME. Comparative Genomics of Bacillus amyloliquefaciens Strains Reveals a Core Genome with Traits for Habitat Adaptation and a Secondary Metabolites Rich Accessory Genome. Front Microbiol 2017; 8:1438. [PMID: 28824571 PMCID: PMC5541019 DOI: 10.3389/fmicb.2017.01438] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 07/17/2017] [Indexed: 12/04/2022] Open
Abstract
The Gram positive, non-pathogenic endospore-forming soil inhabiting prokaryote Bacillus amyloliquefaciens is a plant growth-promoting rhizobacterium. Bacillus amyloliquefaciens processes wide biocontrol abilities and numerous strains have been reported to suppress diverse bacterial, fungal and fungal-like pathogens. Knowledge about strain level biocontrol abilities is warranted to translate this knowledge into developing more efficient biocontrol agents and bio-fertilizers. Ever-expanding genome studies of B. amyloliquefaciens are showing tremendous increase in strain-specific new secondary metabolite clusters which play key roles in the suppression of pathogens and plant growth promotion. In this report, we have used genome mining of all sequenced B. amyloliquefaciens genomes to highlight species boundaries, the diverse strategies used by different strains to promote plant growth and the diversity of their secondary metabolites. Genome composition of the targeted strains suggest regions of genomic plasticity that shape the structure and function of these genomes and govern strain adaptation to different niches. Our results indicated that B. amyloliquefaciens: (i) suffer taxonomic imprecision that blurs the debate over inter-strain genome diversity and dynamics, (ii) have diverse strategies to promote plant growth and development, (iii) have an unlocked, yet to be delimited impressive arsenal of secondary metabolites and products, (iv) have large number of so-called orphan gene clusters, i.e., biosynthetic clusters for which the corresponding metabolites are yet unknown, and (v) have a dynamic pan genome with a secondary metabolite rich accessory genome.
Collapse
Affiliation(s)
- Lassaad Belbahri
- Laboratory of Soil Biology, University of NeuchatelNeuchatel, Switzerland.,NextBiotechAgareb, Tunisia
| | - Ali Chenari Bouket
- NextBiotechAgareb, Tunisia.,Graduate School of Life and Environmental Sciences, Osaka Prefecture UniversitySakai, Japan.,Young Researchers and Elite Club, Tabriz Branch, Islamic Azad UniversityTabriz, Iran
| | | | | | - Armelle Vallat
- Neuchâtel Platform of Analytical Chemistry, Institute of Chemistry, University of NeuchâtelNeuchâtel, Switzerland
| | - Lenka Luptakova
- NextBiotechAgareb, Tunisia.,Department of Biology and Genetics, Institute of Biology, Zoology and Radiobiology, University of Veterinary Medicine and PharmacyKosice, Slovakia
| | - Eva Petrovova
- Institute of Anatomy, University of Veterinary Medicine and PharmacyKosice, Slovakia
| | | | | | | | - Mostafa E Rateb
- School of Science and Sport, University of the West of ScotlandPaisley, United Kingdom
| |
Collapse
|
29
|
Isolated Bacillus subtilis strain 330-2 and its antagonistic genes identified by the removing PCR. Sci Rep 2017; 7:1777. [PMID: 28496135 PMCID: PMC5431837 DOI: 10.1038/s41598-017-01940-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/04/2017] [Indexed: 11/25/2022] Open
Abstract
Plant growth-promoting bacteria (PGPB) may trigger tolerance against biotic/abiotic stresses and growth enhancement in plants. In this study, an endophytic bacterial strain from rapeseed was isolated to assess its role in enhancing plant growth and tolerance to abiotic stresses, as well as banded leaf and sheath blight disease in maize. Based on 16S rDNA and BIOLOG test analysis, the 330-2 strain was identified as Bacillus subtilis. The strain produced indole-3-acetic acid, siderophores, lytic enzymes and solubilized different sources of organic/inorganic phosphates and zinc. Furthermore, the strain strongly suppressed the in vitro growth of Rhizoctonia solani AG1-IA, Botrytis cinerea, Fusarium oxysporum, Alternaria alternata, Cochliobolus heterostrophus, and Nigrospora oryzae. The strain also significantly increased the seedling growth (ranging 14–37%) of rice and maize. Removing PCR analysis indicated that 114 genes were differentially expressed, among which 10%, 32% and 10% were involved in antibiotic production (e.g., srfAA, bae, fen, mln, and dfnI), metabolism (e.g., gltA, pabA, and ggt) and transportation of nutrients (e.g., fhu, glpT, and gltT), respectively. In summary, these results clearly indicate the effectiveness and mechanisms of B. subtilis strain 330-2 in enhancing plant growth, as well as tolerance to biotic/abiotic stresses, which suggests that the strain has great potential for commercialization as a vital biological control agent.
Collapse
|
30
|
Pan HQ, Li QL, Hu JC. The complete genome sequence of Bacillus velezensis 9912D reveals its biocontrol mechanism as a novel commercial biological fungicide agent. J Biotechnol 2017; 247:25-28. [DOI: 10.1016/j.jbiotec.2017.02.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 02/16/2017] [Accepted: 02/19/2017] [Indexed: 11/26/2022]
|
31
|
Ma W, Peng D, Walker SL, Cao B, Gao CH, Huang Q, Cai P. Bacillus subtilis biofilm development in the presence of soil clay minerals and iron oxides. NPJ Biofilms Microbiomes 2017. [PMID: 28649405 PMCID: PMC5445608 DOI: 10.1038/s41522-017-0013-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Clay minerals and metal oxides, as important parts of the soil matrix, play crucial roles in the development of microbial communities. However, the mechanism underlying such a process, particularly on the formation of soil biofilm, remains poorly understood. Here, we investigated the effects of montmorillonite, kaolinite, and goethite on the biofilm formation of the representative soil bacteria Bacillus subtilis. The bacterial biofilm formation in goethite was found to be impaired in the initial 24 h but burst at 48 h in the liquid-air interface. Confocal laser scanning microscopy showed that the biofilm biomass in goethite was 3-16 times that of the control, montmorillonite, and kaolinite at 48 h. Live/Dead staining showed that cells had the highest death rate of 60% after 4 h of contact with goethite, followed by kaolinite and montmorillonite. Atomic force microscopy showed that the interaction between goethite and bacteria may injure bacterial cells by puncturing cell wall, leading to the swarming of bacteria toward the liquid-air interface. Additionally, the expressions of abrB and sinR, key players in regulating the biofilm formation, were upregulated at 24 h and downregulated at 48 h in goethite, indicating the initial adaptation of the cells to minerals. A model was proposed to describe the effects of goethite on the biofilm formation. Our findings may facilitate a better understanding of the roles of soil clays in biofilm development and the manipulation of bacterial compositions through controlling the biofilm in soils.
Collapse
Affiliation(s)
- Wenting Ma
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070 China
| | - Donghai Peng
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070 China
| | - Sharon L Walker
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521 USA
| | - Bin Cao
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798 Singapore
| | - Chun-Hui Gao
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070 China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070 China
| | - Peng Cai
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070 China
| |
Collapse
|
32
|
Abstract
Protein degradation is essential for all living things. Bacteria use energy-dependent proteases to control protein destruction in a highly specific manner. Recognition of substrates is determined by the inherent specificity of the proteases and through adaptor proteins that alter the spectrum of substrates. In the α-proteobacterium Caulobacter crescentus, regulated protein degradation is required for stress responses, developmental transitions, and cell cycle progression. In this review, we describe recent progress in our understanding of the regulated and stress-responsive protein degradation pathways in Caulobacter. We discuss how organization of highly specific adaptors into functional hierarchies drives destruction of proteins during the bacterial cell cycle. Because all cells must balance the need for degradation of many true substrates with the toxic consequences of nonspecific protein destruction, principles found in one system likely generalize to others.
Collapse
Affiliation(s)
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003;
| |
Collapse
|
33
|
Gao W, Liu F, Zhang W, Quan Y, Dang Y, Feng J, Gu Y, Wang S, Song C, Yang C. Mutations in genes encoding antibiotic substances increase the synthesis of poly-γ-glutamic acid in Bacillus amyloliquefaciens LL3. Microbiologyopen 2016; 6. [PMID: 27539744 PMCID: PMC5300885 DOI: 10.1002/mbo3.398] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 07/11/2016] [Accepted: 07/22/2016] [Indexed: 11/09/2022] Open
Abstract
Poly‐γ‐glutamic acid (γ‐PGA) is an important natural biopolymer that is used widely in fields of foods, medicine, cosmetics, and agriculture. Several B. amyloliquefaciens LL3 mutants were constructed to improve γ‐PGA synthesis via single or multiple marker‐less in‐frame deletions of four gene clusters (itu, bae, srf, and fen) encoding antibiotic substances. γ‐PGA synthesis by the Δsrf mutant showed a slight increase (4.1 g/L) compared with that of the wild‐type strain (3.3 g/L). The ΔituΔsrf mutant showed increased γ‐PGA yield from 3.3 to 4.5 g/L, with an increase of 36.4%. The γ‐PGA yield of the ΔituΔsrfΔfen and ΔituΔsrfΔfenΔbae mutants did not show a further increase. The four gene clusters’ roles in swarming motility and biofilm formation were also studied. The Δsrf and Δbae mutant strains were both significantly defective in swarming, indicating that bacillaene and surfactin are involved in swarming motility of B. amyloliquefaciens LL3. Furthermore, Δsrf and Δitu mutant strains were obviously defective in biofilm formation; therefore, iturin and surfactin must play important roles in biofilm formation in B. amyloliquefaciens LL3.
Collapse
Affiliation(s)
- Weixia Gao
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin, China
| | - Fenghong Liu
- Key Laboratory of Bioactive Materials for Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Wei Zhang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin, China
| | - Yufen Quan
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin, China
| | - Yulei Dang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin, China
| | - Jun Feng
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin, China
| | - Yanyan Gu
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin, China
| | - Shufang Wang
- Key Laboratory of Bioactive Materials for Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Cunjiang Song
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin, China
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| |
Collapse
|
34
|
Mu D, Yu X, Xu Z, Du Z, Chen G. Physiological and transcriptomic analyses reveal mechanistic insight into the adaption of marine Bacillus subtilis C01 to alumina nanoparticles. Sci Rep 2016; 6:29953. [PMID: 27440502 PMCID: PMC4954987 DOI: 10.1038/srep29953] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 06/24/2016] [Indexed: 12/05/2022] Open
Abstract
An increasing number of studies have investigated the effects of nanoparticles (NPs) on microbial systems; however, few existing reports have focused on the defense mechanisms of bacteria against NPs. Whether secondary metabolism biosynthesis is a response to NP stress and contributes to the adaption of bacteria to NPs is unclear. Here, a significant induction in the surfactin production and biofilm formation were detected by adding Al2O3 NPs to the B. subtilis fermentation broth. Physiological analysis showed that Al2O3 NP stress could also affect the cell and colony morphogenesis and inhibit the motility and sporulation. Exogenously adding commercial surfactin restored the swarming motility. Additionally, a suite of toxicity assays analyzing membrane damage, cellular ROS generation, electron transport activity and membrane potential was used to determine the molecular mechanisms of toxicity of Al2O3 NPs. Furthermore, whole transcriptomic analysis was used to elucidate the mechanisms of B. subtilis adaption to Al2O3 NPs. These results revealed several mechanisms by which marine B. subtilis C01 adapt to Al2O3 NPs. Additionally, this study broadens the applications of nanomaterials and describes the important effects on secondary metabolism and multicellularity regulation by using Al2O3 NPs or other nano-products.
Collapse
Affiliation(s)
- Dashuai Mu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- College of Marine Science, Shandong University (Weihai), Weihai 264209, PR China
| | - Xiuxia Yu
- College of Marine Science, Shandong University (Weihai), Weihai 264209, PR China
| | - Zhenxing Xu
- College of Marine Science, Shandong University (Weihai), Weihai 264209, PR China
| | - Zongjun Du
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- College of Marine Science, Shandong University (Weihai), Weihai 264209, PR China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- College of Marine Science, Shandong University (Weihai), Weihai 264209, PR China
| |
Collapse
|
35
|
Aleti G, Lehner S, Bacher M, Compant S, Nikolic B, Plesko M, Schuhmacher R, Sessitsch A, Brader G. Surfactin variants mediate species-specific biofilm formation and root colonization in Bacillus. Environ Microbiol 2016; 18:2634-45. [PMID: 27306252 DOI: 10.1111/1462-2920.13405] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cyclic lipopeptides (cLP) and especially surfactins produced by Bacillus spp. trigger biofilm formation and root colonization and are crucial for biocontrol activity and systemic resistance in plants. Bacillus atrophaeus 176s isolated from the moss Tortella tortuosa produces the cLP fengycins, iturins and surfactins, possesses antifungal activities and can protect tomato, lettuce and sugar beet against Rhizoctonia solani infection. In B. atrophaeus we identified for the first time the variant surfactin C, which differs from surfactin A produced by B. subtilis and B. amyloliquefaciens by an isoleucine instead of a leucine at position 7 of the lipopeptide backbone. The analysis of the complete surfactin gene clusters revealed that the dissimilarity is encoded in the adenylation domain of srfC and show that surfactin variations are distributed in a species-specific manner in bacilli. We demonstrate that the surfactin A and C with subtle structural differences have varying signal strengths on biofilm formation and root colonization and act specifically on the respective producing strain. This became evident as biofilm formation and root colonization but not swarming motility in surfactin biosynthesis mutants was restored differentially in the presence of exogenously supplemented cognate and non-cognate surfactin variants.
Collapse
Affiliation(s)
- Gajender Aleti
- Health & Environment Department, Bioresources Unit, AIT Austrian Institute of Technology GmbH, AIT, Konrad Lorenz Strasse 24, Tulln, A-3430, Austria
| | - Sylvia Lehner
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences (BOKU), Konrad-Lorenz-Str. 20, 3430 Tulln, Austria
| | - Markus Bacher
- Department of Chemistry, University of Natural Resources and Life Sciences (BOKU), UFT Research Center Tulln, Konrad-Lorenz-Str. 24, Tulln, A-3430, Austria
| | - Stéphane Compant
- Health & Environment Department, Bioresources Unit, AIT Austrian Institute of Technology GmbH, AIT, Konrad Lorenz Strasse 24, Tulln, A-3430, Austria
| | - Branislav Nikolic
- Health & Environment Department, Bioresources Unit, AIT Austrian Institute of Technology GmbH, AIT, Konrad Lorenz Strasse 24, Tulln, A-3430, Austria
| | - Maja Plesko
- Health & Environment Department, Bioresources Unit, AIT Austrian Institute of Technology GmbH, AIT, Konrad Lorenz Strasse 24, Tulln, A-3430, Austria
| | - Rainer Schuhmacher
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences (BOKU), Konrad-Lorenz-Str. 20, 3430 Tulln, Austria
| | - Angela Sessitsch
- Health & Environment Department, Bioresources Unit, AIT Austrian Institute of Technology GmbH, AIT, Konrad Lorenz Strasse 24, Tulln, A-3430, Austria
| | - Günter Brader
- Health & Environment Department, Bioresources Unit, AIT Austrian Institute of Technology GmbH, AIT, Konrad Lorenz Strasse 24, Tulln, A-3430, Austria
| |
Collapse
|
36
|
Identification and Pathogenic Potential of Clinical Bacillus and Paenibacillus Isolates. PLoS One 2016; 11:e0152831. [PMID: 27031639 PMCID: PMC4816569 DOI: 10.1371/journal.pone.0152831] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/02/2016] [Indexed: 11/21/2022] Open
Abstract
The soil-related Bacillus and Paenibacillus species have increasingly been implicated in various human diseases. Nevertheless, their identification still poses problems in the clinical microbiology laboratory and, with the exception of Bacillus anthracis and Bacillus cereus, little is known on their pathogenicity for humans. In this study, we evaluated the use of matrix-assisted laser desorption—ionization time of flight mass spectrometry (MALDI-TOF MS) in the identification of clinical isolates of these genera and conducted genotypic and phenotypic analyses to highlight specific virulence properties. Seventy-five clinical isolates were subjected to biochemical and MALDI-TOF MS identification. 16S rDNA sequencing and supplemental tests were used to solve any discrepancies or failures in the identification results. MALDI-TOF MS significantly outperformed classical biochemical testing for correct species identification and no misidentification was obtained. One third of the collected strains belonged to the B. cereus species, but also Bacillus pumilus and Bacillus subtilis were isolated at high rate. Antimicrobial susceptibility testing showed that all the B. cereus, B. licheniformis, B. simplex, B. mycoides, Paenibacillus glucanolyticus and Paenibacillus lautus isolates are resistant to penicillin. The evaluation of toxin/enzyme secretion, toxin-encoding genes, motility, and biofilm formation revealed that B. cereus displays the highest virulence potential. However, although generally considered nonpathogenic, most of the other species were shown to swim, swarm, produce biofilms, and secrete proteases that can have a role in bacterial virulence. In conclusion, MALDI-TOF MS appears useful for fast and accurate identification of Bacillus and Paenibacillus strains whose virulence properties make them of increasing clinical relevance.
Collapse
|
37
|
Traxler MF, Kolter R. Natural products in soil microbe interactions and evolution. Nat Prod Rep 2015; 32:956-70. [DOI: 10.1039/c5np00013k] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Gram positive bacteria from the soil have historically been a deep source of useful natural products. This article considers how natural products may mediate microbial interactions in the soil environment.
Collapse
Affiliation(s)
- Matthew F. Traxler
- Dept. of Plant and Microbial Biology
- University of California at Berkeley
- Berkeley
- USA
| | - Roberto Kolter
- Dept. of Microbiology and Immunobiology
- Harvard Medical School
- Boston
- USA
| |
Collapse
|
38
|
Niazi A, Manzoor S, Asari S, Bejai S, Meijer J, Bongcam-Rudloff E. Genome analysis of Bacillus amyloliquefaciens Subsp. plantarum UCMB5113: a rhizobacterium that improves plant growth and stress management. PLoS One 2014; 9:e104651. [PMID: 25119988 PMCID: PMC4138018 DOI: 10.1371/journal.pone.0104651] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 07/10/2014] [Indexed: 11/18/2022] Open
Abstract
The Bacillus amyloliquefaciens subsp. plantarum strain UCMB5113 is a Gram-positive rhizobacterium that can colonize plant roots and stimulate plant growth and defense based on unknown mechanisms. This reinforcement of plants may provide protection to various forms of biotic and abiotic stress. To determine the genetic traits involved in the mechanism of plant-bacteria association, the genome sequence of UCMB5113 was obtained by assembling paired-end Illumina reads. The assembled chromosome of 3,889,532 bp was predicted to encode 3,656 proteins. Genes that potentially contribute to plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, acetoin synthesis and siderophore production were identified. Moreover, annotation identified putative genes responsible for non-ribosomal synthesis of secondary metabolites and genes supporting environment fitness of UCMB5113 including drug and metal resistance. A large number of genes encoding a diverse set of secretory proteins, enzymes of primary and secondary metabolism and carbohydrate active enzymes were found which reflect a high capacity to degrade various rhizosphere macromolecules. Additionally, many predicted membrane transporters provides the bacterium with efficient uptake capabilities of several nutrients. Although, UCMB5113 has the possibility to produce antibiotics and biosurfactants, the protective effect of plants to pathogens seems to be indirect and due to priming of plant induced systemic resistance. The availability of the genome enables identification of genes and their function underpinning beneficial interactions of UCMB5113 with plants.
Collapse
Affiliation(s)
- Adnan Niazi
- Department of Animal Breeding and Genetics, SLU Global Bioinformatics Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
| | - Shahid Manzoor
- Department of Animal Breeding and Genetics, SLU Global Bioinformatics Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden
- University of the Punjab, Lahore, Pakistan
| | - Shashidar Asari
- Department of Plant Biology, Linnéan Center for Plant Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sarosh Bejai
- Department of Plant Biology, Linnéan Center for Plant Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Johan Meijer
- Department of Plant Biology, Linnéan Center for Plant Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics, SLU Global Bioinformatics Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden
| |
Collapse
|
39
|
Asadishad B, Olsson ALJ, Dusane DH, Ghoshal S, Tufenkji N. Transport, motility, biofilm forming potential and survival of Bacillus subtilis exposed to cold temperature and freeze-thaw. WATER RESEARCH 2014; 58:239-247. [PMID: 24768703 DOI: 10.1016/j.watres.2014.03.048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 02/27/2014] [Accepted: 03/18/2014] [Indexed: 06/03/2023]
Abstract
In cold climate regions, microorganisms in upper layers of soil are subject to low temperatures and repeated freeze-thaw (FT) conditions during the winter. We studied the effects of cold temperature and FT cycles on the viability and survival strategies (namely motility and biofilm formation) of the common soil bacterium and model pathogen Bacillus subtilis. We also examined the effect of FT on the transport behavior of B. subtilis at two solution ionic strengths (IS: 10 and 100 mM) in quartz sand packed columns. Finally, to study the mechanical properties of the bacteria-surface bond, a quartz crystal microbalance with dissipation monitoring (QCM-D) was used to monitor changes in bond stiffness when B. subtilis attached to a quartz substrate (model sand surface) under different environmental conditions. We observed that increasing the number of FT cycles decreased bacterial viability and that B. subtilis survived for longer time periods in higher IS solution. FT treatment decreased bacterial swimming motility and the transcription of flagellin encoding genes. Although FT exposure had no significant effect on the bacterial growth rate, it substantially decreased B. subtilis biofilm formation and correspondingly decreased the transcription of matrix production genes in higher IS solution. As demonstrated with QCM-D, the bond stiffness between B. subtilis and the quartz surface decreased after FT. Moreover, column transport studies showed higher bacterial retention onto sand grains after exposure to FT. This investigation demonstrates how temperature variations around the freezing point in upper layers of soil can influence key bacterial properties and behavior, including survival and subsequent transport.
Collapse
Affiliation(s)
- Bahareh Asadishad
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 2B2, Canada
| | - Adam L J Olsson
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 2B2, Canada
| | - Devendra H Dusane
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 2B2, Canada
| | - Subhasis Ghoshal
- Department of Civil Engineering, McGill University, Montreal, Quebec H3A 2K6, Canada
| | - Nathalie Tufenkji
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 2B2, Canada.
| |
Collapse
|
40
|
Steuten B, Hoch PG, Damm K, Schneider S, Köhler K, Wagner R, Hartmann RK. Regulation of transcription by 6S RNAs: insights from the Escherichia coli and Bacillus subtilis model systems. RNA Biol 2014; 11:508-21. [PMID: 24786589 DOI: 10.4161/rna.28827] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Whereas, the majority of bacterial non-coding RNAs and functional RNA elements regulate post-transcriptional processes, either by interacting with other RNAs via base-pairing or through binding of small ligands (riboswitches), 6S RNAs affect transcription itself by binding to the housekeeping holoenzyme of RNA polymerase (RNAP). Remarkably, 6S RNAs serve as RNA templates for bacterial RNAP, giving rise to the de novo synthesis of short transcripts, termed pRNAs (product RNAs). Hence, 6S RNAs prompt the enzyme to act as an RNA-dependent RNA polymerase (RdRP). Synthesis of pRNAs exceeding a certain length limit (~13 nt) persistently rearrange the 6S RNA structure, which in turn, disrupts the 6S RNA:RNAP complex. This pRNA synthesis-mediated "reanimation" of sequestered RNAP molecules represents the conceivably fastest mechanism for resuming transcription in cells that enter a new exponential growth phase. The many different 6S RNAs found in a wide variety of bacteria do not share strong sequence homology but have in common a conserved rod-shaped structure with a large internal loop, termed the central bulge; this architecture mediates specific binding to the active site of RNAP. In this article, we summarize the overall state of knowledge as well as very recent findings on the structure, function, and physiological effects of 6S RNA examples from the two model organisms, Escherichia coli and Bacillus subtilis. Comparison of the presently known properties of 6S RNAs in the two organisms highlights common principles as well as diverse features.
Collapse
Affiliation(s)
- Benedikt Steuten
- Heinrich-Heine-Universität Düsseldorf; Institut für Physikalische Biologie Universitätsstr; Düsseldorf, Germany
| | | | - Katrin Damm
- Philipps-Universität Marburg; Marburg, Germany
| | - Sabine Schneider
- Heinrich-Heine-Universität Düsseldorf; Institut für Physikalische Biologie Universitätsstr; Düsseldorf, Germany
| | | | - Rolf Wagner
- Heinrich-Heine-Universität Düsseldorf; Institut für Physikalische Biologie Universitätsstr; Düsseldorf, Germany
| | | |
Collapse
|
41
|
Abstract
Movement over an agar surface via swarming motility is subject to formidable challenges not encountered during swimming. Bacteria display a great deal of flexibility in coping with these challenges, which include attracting water to the surface, overcoming frictional forces, and reducing surface tension. Bacteria that swarm on "hard" agar surfaces (robust swarmers) display a hyperflagellated and hyperelongated morphology. Bacteria requiring a "softer" agar surface (temperate swarmers) do not exhibit such a dramatic morphology. For polarly flagellated robust swarmers, there is good evidence that restriction of flagellar rotation somehow signals the induction of a large number of lateral flagella, but this scenario is apparently not relevant to temperate swarmers. Swarming bacteria can be further subdivided by their requirement for multiple stators (Mot proteins) or a stator-associated protein (FliL), secretion of essential polysaccharides, cell density-dependent gene regulation including surfactant synthesis, a functional chemotaxis signaling pathway, appropriate cyclic (c)-di-GMP levels, induction of virulence determinants, and various nutritional requirements such as iron limitation or nitrate availability. Swarming strategies are as diverse as the bacteria that utilize them. The strength of these numerous designs stems from the vantage point they offer for understanding mechanisms for effective colonization of surface niches, acquisition of pathogenic potential, and identification of environmental signals that regulate swarming. The signature swirling and streaming motion within a swarm is an interesting phenomenon in and of itself, an emergent behavior with properties similar to flocking behavior in diverse systems, including birds and fish, providing a convenient new avenue for modeling such behavior.
Collapse
|