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Abstract
The dispersal of bacterial cells from a matured biofilm can be mediated either by active or passive mechanisms. In this issue of the Journal of Bacteriology, Nishikawa and Kobayashi demonstrate that the presence of calcium influences the dispersal of spores from the pellicle biofilm of Bacillus subtilis (M. Nishikawa and K. Kobayashi, J Bacteriol 203:e00114-21, 2021, https://doi.org/10.1128/JB.00114-21). The authors propose that temporal heterogeneity in matrix production and chelation of calcium by dipicolinic acid in spores weakens the biofilm matrix and causes passive dispersal.
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52
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Abstract
Biofilm dispersion is the final stage of biofilm development, during which biofilm cells actively escape from biofilms in response to deteriorating conditions within the biofilm. Biofilm dispersion allows cells to spread to new locations and form new biofilms in better locations. However, dispersal mechanisms have been elucidated only in a limited number of bacteria. Here, we investigated biofilm dispersion in Bacillus subtilis. Biofilm dispersion was clearly observed when B. subtilis was grown under static conditions in modified LB medium containing glycerol and manganese. Biofilm dispersion was synergistically caused by two mechanisms: decreased expression of the epsA operon encoding exopolysaccharide synthetases and the induction of sporulation. Indeed, constitutive expression of the epsA operon in the sporulation-defective ΔsigK mutant prevented biofilm dispersion. The addition of calcium to the medium prevented biofilm dispersion without significantly affecting the expression of the epsA operon and sporulation genes. In synthetic medium, eliminating calcium did not prevent the expression of biofilm matrix genes and, thereby, biofilm formation, but it attenuated biofilm architecture. These results indicate that calcium structurally stabilizes biofilms and causes resistance to biofilm dispersion mechanisms. Sporulation-dependent biofilm dispersion required the spoVF operon, encoding dipicolinic acid (DPA) synthase. During sporulation, an enormous amount of DPA is synthesized and stored in spores as a chelate with calcium. We speculate that, during sporulation, calcium bound to biofilm matrix components may be transported to spores as a calcium-DPA complex, which weakens biofilm structure and leads to biofilm dispersion. IMPORTANCE Bacteria growing as biofilms are notoriously difficult to eradicate and sometimes pose serious threats to public health. Bacteria escape from biofilms by degrading them when biofilm conditions deteriorate. This process, called biofilm dispersion, has been studied as a promising strategy for safely controlling biofilms. However, the regulation and mechanism of biofilm dispersion has been elucidated only in a limited number of bacteria. Here, we identified two biofilm dispersion mechanisms in the Gram-positive, spore-forming bacterium Bacillus subtilis. The addition of calcium to the medium stabilized biofilms and caused resistance to dispersal mechanisms. Our findings provide new insights into biofilm dispersion and biofilm control.
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53
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Nordgaard M, Mortensen RMR, Kirk NK, Gallegos‐Monterrosa R, Kovács ÁT. Deletion of Rap-Phr systems in Bacillus subtilis influences in vitro biofilm formation and plant root colonization. Microbiologyopen 2021; 10:e1212. [PMID: 34180604 PMCID: PMC8236291 DOI: 10.1002/mbo3.1212] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 12/19/2022] Open
Abstract
Natural isolates of the soil-dwelling bacterium Bacillus subtilis form robust biofilms under laboratory conditions and colonize plant roots. B. subtilis biofilm gene expression displays phenotypic heterogeneity that is influenced by a family of Rap-Phr regulatory systems. Most Rap-Phr systems in B. subtilis have been studied independently, in different genetic backgrounds and under distinct conditions, hampering true comparison of the Rap-Phr systems' impact on bacterial cell differentiation. Here, we investigated each of the 12 Rap-Phr systems of B.subtilis NCIB 3610 for their effect on biofilm formation. By studying single ∆rap-phr mutants, we show that despite redundancy between the cell-cell communication systems, deletion of each of the 12 Rap-Phr systems influences matrix gene expression. These Rap-Phr systems therefore enable fine-tuning of the timing and level of matrix production in response to specific conditions. Furthermore, some of the ∆rap-phr mutants demonstrated altered biofilm formation in vitro and colonization of Arabidopsis thaliana roots, but not necessarily similarly in both processes, indicating that the pathways regulating matrix gene expression and other factors important for biofilm formation may be differently regulated under these distinct conditions.
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Affiliation(s)
- Mathilde Nordgaard
- Bacterial Interactions and Evolution GroupDTU BioengineeringTechnical University of DenmarkLyngbyDenmark
| | | | - Nikolaj Kaae Kirk
- Bacterial Interactions and Evolution GroupDTU BioengineeringTechnical University of DenmarkLyngbyDenmark
| | | | - Ákos T. Kovács
- Bacterial Interactions and Evolution GroupDTU BioengineeringTechnical University of DenmarkLyngbyDenmark
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54
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Khambhati K, Patel J, Saxena V, A P, Jain N. Gene Regulation of Biofilm-Associated Functional Amyloids. Pathogens 2021; 10:490. [PMID: 33921583 PMCID: PMC8072697 DOI: 10.3390/pathogens10040490] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/15/2021] [Accepted: 04/15/2021] [Indexed: 01/01/2023] Open
Abstract
Biofilms are bacterial communities encased in a rigid yet dynamic extracellular matrix. The sociobiology of bacterial communities within a biofilm is astonishing, with environmental factors playing a crucial role in determining the switch from planktonic to a sessile form of life. The mechanism of biofilm biogenesis is an intriguingly complex phenomenon governed by the tight regulation of expression of various biofilm-matrix components. One of the major constituents of the biofilm matrix is proteinaceous polymers called amyloids. Since the discovery, the significance of biofilm-associated amyloids in adhesion, aggregation, protection, and infection development has been much appreciated. The amyloid expression and assembly is regulated spatio-temporarily within the bacterial cells to perform a diverse function. This review provides a comprehensive account of the genetic regulation associated with the expression of amyloids in bacteria. The stringent control ensures optimal utilization of amyloid scaffold during biofilm biogenesis. We conclude the review by summarizing environmental factors influencing the expression and regulation of amyloids.
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Affiliation(s)
- Khushal Khambhati
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur NH 65, Nagaur Road, Karwar, Rajasthan 342037, India
| | - Jaykumar Patel
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur NH 65, Nagaur Road, Karwar, Rajasthan 342037, India
| | - Vijaylaxmi Saxena
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur NH 65, Nagaur Road, Karwar, Rajasthan 342037, India
| | - Parvathy A
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur NH 65, Nagaur Road, Karwar, Rajasthan 342037, India
| | - Neha Jain
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur NH 65, Nagaur Road, Karwar, Rajasthan 342037, India
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55
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Shi L, Derouiche A, Pandit S, Rahimi S, Kalantari A, Futo M, Ravikumar V, Jers C, Mokkapati VRSS, Vlahoviček K, Mijakovic I. Evolutionary Analysis of the Bacillus subtilis Genome Reveals New Genes Involved in Sporulation. Mol Biol Evol 2021; 37:1667-1678. [PMID: 32061128 PMCID: PMC7426031 DOI: 10.1093/molbev/msaa035] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Bacilli can form dormant, highly resistant, and metabolically inactive spores to cope with extreme environmental challenges. In this study, we examined the evolutionary age of Bacillus subtilis sporulation genes using the approach known as genomic phylostratigraphy. We found that B. subtilis sporulation genes cluster in several groups that emerged at distant evolutionary time-points, suggesting that the sporulation process underwent several stages of expansion. Next, we asked whether such evolutionary stratification of the genome could be used to predict involvement in sporulation of presently uncharacterized genes (y-genes). We individually inactivated a representative sample of uncharacterized genes that arose during the same evolutionary periods as the known sporulation genes and tested the resulting strains for sporulation phenotypes. Sporulation was significantly affected in 16 out of 37 (43%) tested strains. In addition to expanding the knowledge base on B. subtilis sporulation, our findings suggest that evolutionary age could be used to help with genome mining.
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Affiliation(s)
- Lei Shi
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Abderahmane Derouiche
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Santosh Pandit
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Shadi Rahimi
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Aida Kalantari
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Momir Futo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Vaishnavi Ravikumar
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Carsten Jers
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Venkata R S S Mokkapati
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Kristian Vlahoviček
- Bioinformatics group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Croatia.,School of Bioscience, University of Skövde, Skövde, Sweden
| | - Ivan Mijakovic
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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56
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Grobas I, Polin M, Asally M. Swarming bacteria undergo localized dynamic phase transition to form stress-induced biofilms. eLife 2021; 10:62632. [PMID: 33722344 PMCID: PMC7963483 DOI: 10.7554/elife.62632] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/26/2021] [Indexed: 12/23/2022] Open
Abstract
Self-organized multicellular behaviors enable cells to adapt and tolerate stressors to a greater degree than isolated cells. However, whether and how cellular communities alter their collective behaviors adaptively upon exposure to stress is largely unclear. Here, we investigate this question using Bacillus subtilis, a model system for bacterial multicellularity. We discover that, upon exposure to a spatial gradient of kanamycin, swarming bacteria activate matrix genes and transit to biofilms. The initial stage of this transition is underpinned by a stress-induced multilayer formation, emerging from a biophysical mechanism reminiscent of motility-induced phase separation (MIPS). The physical nature of the process suggests that stressors which suppress the expansion of swarms would induce biofilm formation. Indeed, a simple physical barrier also induces a swarm-to-biofilm transition. Based on the gained insight, we propose a strategy of antibiotic treatment to inhibit the transition from swarms to biofilms by targeting the localized phase transition.
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Affiliation(s)
- Iago Grobas
- Warwick Medical School, Universityof Warwick, Coventry, United Kingdom
| | - Marco Polin
- Warwick Medical School, Universityof Warwick, Coventry, United Kingdom.,Centre for Mechanochemical Cell Biology, University of Warwick, Coventry, United Kingdom.,Physics Department, University of Warwick, Coventry, United Kingdom.,Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), C/ Miquel Marqués, Balearic Islands, Spain
| | - Munehiro Asally
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry, United Kingdom.,Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, United Kingdom.,School of Life Sciences, University of Warwick, Coventry, United Kingdom
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57
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Sharipova MR, Mardanova AM, Rudakova NL, Pudova DS. Bistability and Formation of the Biofilm Matrix as Adaptive Mechanisms during the Stationary Phase of Bacillus subtilis. Microbiology (Reading) 2021. [DOI: 10.1134/s002626172006017x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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58
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Arjes HA, Willis L, Gui H, Xiao Y, Peters J, Gross C, Huang KC. Three-dimensional biofilm colony growth supports a mutualism involving matrix and nutrient sharing. eLife 2021; 10:e64145. [PMID: 33594973 PMCID: PMC7925131 DOI: 10.7554/elife.64145] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/15/2021] [Indexed: 12/16/2022] Open
Abstract
Life in a three-dimensional biofilm is typical for many bacteria, yet little is known about how strains interact in this context. Here, we created essential gene CRISPR interference knockdown libraries in biofilm-forming Bacillus subtilis and measured competitive fitness during colony co-culture with wild type. Partial knockdown of some translation-related genes reduced growth rates and led to out-competition. Media composition led some knockdowns to compete differentially as biofilm versus non-biofilm colonies. Cells depleted for the alanine racemase AlrA died in monoculture but survived in a biofilm colony co-culture via nutrient sharing. Rescue was enhanced in biofilm colony co-culture with a matrix-deficient parent due to a mutualism involving nutrient and matrix sharing. We identified several examples of mutualism involving matrix sharing that occurred in three-dimensional biofilm colonies but not when cultured in two dimensions. Thus, growth in a three-dimensional colony can promote genetic diversity through sharing of secreted factors and may drive evolution of mutualistic behavior.
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Affiliation(s)
- Heidi A Arjes
- Department of Bioengineering, Stanford University School of MedicineStanfordUnited States
| | - Lisa Willis
- Department of Bioengineering, Stanford University School of MedicineStanfordUnited States
| | - Haiwen Gui
- Department of Bioengineering, Stanford University School of MedicineStanfordUnited States
| | - Yangbo Xiao
- Department of Bioengineering, Stanford University School of MedicineStanfordUnited States
| | - Jason Peters
- Department of Cell and Tissue Biology, University of California San FranciscoSan FranciscoUnited States
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-MadisonMadisonUnited States
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-MadisonMadisonUnited States
- Department of Bacteriology, University of Wisconsin-MadisonMadisonUnited States
- Department of Medical Microbiology and Immunology, University of Wisconsin-MadisonMadisonUnited States
| | - Carol Gross
- Department of Cell and Tissue Biology, University of California San FranciscoSan FranciscoUnited States
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University School of MedicineStanfordUnited States
- Department of Microbiology & Immunology, Stanford University School of MedicineStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
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59
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Newton R, Amstutz J, Patrick JE. Biofilm formation by Bacillus subtilis is altered in the presence of pesticides. Access Microbiol 2021; 2:acmi000175. [PMID: 33490870 PMCID: PMC7818241 DOI: 10.1099/acmi.0.000175] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 10/21/2020] [Indexed: 11/18/2022] Open
Abstract
Bacillus subtilis uses swarming motility and biofilm formation to colonize plant roots and form a symbiotic relationship with the plant. Swarming motility and biofilm formation are group behaviours made possible through the use of chemical messengers. We investigated whether chemicals applied to plants would interfere with the swarming motility and biofilm-forming capabilities of B. subtilis in vitro. We hypothesized that pesticides could act as chemical signals that influence bacterial behaviour; this research investigates whether swarming motility and biofilm formation of B. subtilis is affected by the application of the commercial pesticides with the active ingredients of neem oil, pyrethrin, or malathion. The results indicate that all three pesticides inhibit biofilm formation. Swarming motility is not affected by the application of pyrethrin or malathion, but swarm expansion and pattern is altered in the presence of neem oil. Future studies to investigate the mechanism by which pesticides alter biofilm formation are warranted.
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Affiliation(s)
- Rachael Newton
- Truman State University, 100 E Normal Kirksville, MO 63501, USA
| | | | - Joyce E Patrick
- Truman State University, 100 E Normal Kirksville, MO 63501, USA
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60
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Zhang C, Wang C, Zhao S, Xiu Z. Role of c-di-GMP in improving stress resistance of alginate-chitosan microencapsulated Bacillus subtilis cells in simulated digestive fluids. Biotechnol Lett 2021; 43:677-690. [PMID: 33385252 DOI: 10.1007/s10529-020-03055-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/10/2020] [Indexed: 11/27/2022]
Abstract
OBJECTIVES Probiotics (Bacillus subtilis 04178) were entrapped in alginate-chitosan microcapsules by high-voltage electrostatic process. The encapsulation pattern was established as entrapped low density cells with culture (ELDCwc). The performance of ELDCwc cells was investigated against stress environments of simulated digestive fluids. RESULTS After incubation in simulated gastric (pH 2.5) and intestinal fluids (4% bile salt) for 2 h, the survival rate of ELDCwc cells (18.19% and 27.54%) was significantly higher than that of the free cells (0.0000009% and 0.0005%). The reason why B. subtilis embedded in microcapsules can resist the stress environments was that the mass production of extracellular proteins and polysaccharides prompted B. subtilis to form cell aggregates. The production of extracellular proteins and polysaccharides were regulated by the concentration of c-di-GMP and the expression of ydaJKLMN operon, abbA, sinI, slrA, slrB, abrR and sinR. CONCLUSIONS c-di-GMP is important for the production of extracellular polymer substance to enhance probiotic viability in stress environments.
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Affiliation(s)
- Chaolei Zhang
- School of Life Science and Biotechnology, Dalian University of Technology, Linggong Road 2, Dalian, 116024, China
| | - Chao Wang
- Laboratory of Environmental Technology, INET, Tsinghua University, Beijing, 100084, China
| | - Shan Zhao
- Dalian Institute of Chemical Physics, Chinese Academy of Science, 116023, Dalian, China
| | - Zhilong Xiu
- School of Life Science and Biotechnology, Dalian University of Technology, Linggong Road 2, Dalian, 116024, China.
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61
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Ren P, Chen T, Liu N, Sun W, Hu G, Yu Y, Yu B, Ouyang P, Liu D, Chen Y. Efficient Biofilm-Based Fermentation Strategies by eDNA Formation for l-Proline Production with Corynebacterium glutamicum. ACS OMEGA 2020; 5:33314-33322. [PMID: 33403293 PMCID: PMC7774248 DOI: 10.1021/acsomega.0c05095] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
Biofilms could provide favorable conditions for the growth of cells during industrial fermentation. However, biofilm-immobilized fermentation has not yet been reported in Corynebacterium glutamicum (C. glutamicum), one of the main strains for amino acid production. This is mainly because C. glutamicum has a poor capability of adsorption onto materials or forming an extracellular polymeric substance (EPS). Here, an engineered strain, C. glutamicum Pro-ΔexeM, was created by removing the extracellular nuclease gene exeM, which effectively increased extracellular DNA (eDNA) in the EPS and cell adhesiveness onto carrier materials. In repeated-batch fermentation using the biofilm, l-proline production increased from 10.2 to 17.1 g/L. In summary, this research demonstrated that a synthetic C. glutamicum biofilm could be favorable for l-proline production, which could be extended to other industrial applications of C. glutamicum, and the strategy may also be applicable to the engineering of other strains.
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Affiliation(s)
- Peifang Ren
- State
Key Laboratory of Materials-Oriented Chemical Engineering, College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Tianpeng Chen
- State
Key Laboratory of Materials-Oriented Chemical Engineering, College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Na Liu
- State
Key Laboratory of Materials-Oriented Chemical Engineering, College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Wenjun Sun
- State
Key Laboratory of Materials-Oriented Chemical Engineering, College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Guang Hu
- Nanjing
Iaso Biotherapeutics Co., Ltd., Nanjing 210000, P.R. China
| | - Ying Yu
- State
Key Laboratory of Materials-Oriented Chemical Engineering, College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Bin Yu
- State
Key Laboratory of Materials-Oriented Chemical Engineering, College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Pingkai Ouyang
- State
Key Laboratory of Materials-Oriented Chemical Engineering, College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
- National
Engineering Research Center for Biotechnology, College of Biotechnology
and Pharmaceutical Engineering, Nanjing
Tech University, Nanjing 211816, P.R. China
| | - Dong Liu
- State
Key Laboratory of Materials-Oriented Chemical Engineering, College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
- National
Engineering Research Center for Biotechnology, College of Biotechnology
and Pharmaceutical Engineering, Nanjing
Tech University, Nanjing 211816, P.R. China
| | - Yong Chen
- State
Key Laboratory of Materials-Oriented Chemical Engineering, College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
- National
Engineering Research Center for Biotechnology, College of Biotechnology
and Pharmaceutical Engineering, Nanjing
Tech University, Nanjing 211816, P.R. China
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62
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Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome. Nat Commun 2020; 11:6338. [PMID: 33311500 PMCID: PMC7732839 DOI: 10.1038/s41467-020-20153-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 10/29/2020] [Indexed: 12/24/2022] Open
Abstract
The transcriptional regulatory network (TRN) of Bacillus subtilis coordinates cellular functions of fundamental interest, including metabolism, biofilm formation, and sporulation. Here, we use unsupervised machine learning to modularize the transcriptome and quantitatively describe regulatory activity under diverse conditions, creating an unbiased summary of gene expression. We obtain 83 independently modulated gene sets that explain most of the variance in expression and demonstrate that 76% of them represent the effects of known regulators. The TRN structure and its condition-dependent activity uncover putative or recently discovered roles for at least five regulons, such as a relationship between histidine utilization and quorum sensing. The TRN also facilitates quantification of population-level sporulation states. As this TRN covers the majority of the transcriptome and concisely characterizes the global expression state, it could inform research on nearly every aspect of transcriptional regulation in B. subtilis. The systems-level regulatory structure underlying gene expression in bacteria can be inferred using machine learning algorithms. Here we show this structure for Bacillus subtilis, present five hypotheses gleaned from it, and analyse the process of sporulation from its perspective.
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63
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Emerging Roles of Functional Bacterial Amyloids in Gene Regulation, Toxicity, and Immunomodulation. Microbiol Mol Biol Rev 2020; 85:85/1/e00062-20. [PMID: 33239434 DOI: 10.1128/mmbr.00062-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bacteria often reside in multicellular communities, called biofilms, held together by an extracellular matrix. In many bacteria, the major proteinaceous component of the biofilm are amyloid fibers. Amyloids are highly stable and structured protein aggregates which were known mostly to be associated with neurodegenerative diseases, such as Alzheimer's, Parkinson's, and Huntington's diseases. In recent years, microbial amyloids were identified also in other species and shown to play major roles in microbial physiology and virulence. For example, amyloid fibers assemble on the bacterial cell surface as a part of the extracellular matrix and are extremely important to the scaffolding and structural integrity of biofilms, which contribute to microbial resilience and resistance. Furthermore, microbial amyloids play fundamental nonscaffold roles that contribute to the development of biofilms underlying numerous persistent infections. Here, we review several nonscaffold roles of bacterial amyloid proteins, including bridging cells during collective migration, acting as regulators of cell fate, as toxins against other bacteria or against host immune cells, and as modulators of the hosts' immune system. These overall points on the complexity of the amyloid fold in encoding numerous activities, which offer approaches for the development of a novel repertoire of antivirulence therapeutics.
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64
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Abe K, Nomura N, Suzuki S. Biofilms: hot spots of horizontal gene transfer (HGT) in aquatic environments, with a focus on a new HGT mechanism. FEMS Microbiol Ecol 2020; 96:5766226. [PMID: 32109282 PMCID: PMC7189800 DOI: 10.1093/femsec/fiaa031] [Citation(s) in RCA: 159] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/27/2020] [Indexed: 12/21/2022] Open
Abstract
Biofilms in water environments are thought to be hot spots for horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). ARGs can be spread via HGT, though mechanisms are known and have been shown to depend on the environment, bacterial communities and mobile genetic elements. Classically, HGT mechanisms include conjugation, transformation and transduction; more recently, membrane vesicles (MVs) have been reported as DNA reservoirs implicated in interspecies HGT. Here, we review the current knowledge on the HGT mechanisms with a focus on the role of MVs and the methodological innovations in the HGT research.
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Affiliation(s)
- Kimihiro Abe
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8577 Japan
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8577 Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, 305-8577 Japan
| | - Satoru Suzuki
- Center for Marine Environmental Studies, Ehime University, Matsuyama, 790-8577 Japan
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65
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Sharma M, Saleh D, Charron JB, Jabaji S. A Crosstalk Between Brachypodium Root Exudates, Organic Acids, and Bacillus velezensis B26, a Growth Promoting Bacterium. Front Microbiol 2020; 11:575578. [PMID: 33123106 PMCID: PMC7573104 DOI: 10.3389/fmicb.2020.575578] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/10/2020] [Indexed: 12/23/2022] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) are associated with plant roots and use organic compounds that are secreted from root exudates as food and energy source. Root exudates can chemoattract and help bacteria to colonize the surface of plant roots by inducing chemotactic responses of rhizospheric bacteria. In this study, we show that root colonization of Brachypodium distachyon by Bacillus velezensis strain B26 depends on several factors. These include root exudates, organic acids, and their biosynthetic genes, chemotaxis, biofilm formation and the induction of biofilm encoding genes. Analysis of root exudates by GC-MS identified five intermediates of the TCA cycle; malic, fumaric, citric, succinic, oxaloacetic acids, and were subsequently evaluated. The strongest chemotactic responses were induced by malic, succinic, citric, and fumaric acids. In comparison, the biofilm formation was induced by all organic acids with maximal induction by citric acid. Relative to the control, the individual organic acids, succinic and citric acids activated the epsD gene related to EPS biofilm, and also the genes encoding membrane protein (yqXM) and hydrophobin component (bslA) of the biofilm of strain B26. Whereas epsA and epsB genes were highly induced genes by succinic acid. Similarly, concentrated exudates released from inoculated roots after 48 h post-inoculation also induced all biofilm-associated genes. The addition of strain B26 to wild type and to icdh mutant line led to a slight induction but not biologically significant relative to their respective controls. Thus, B26 has no effect on the expression of the ICDH gene, both in the wild type and the mutant backgrounds. Our results indicate that root exudates and individual organic acids play an important role in selective recruitment and colonization of PGPR and inducing biofilm. The current study increases the understanding of molecular mechanisms behind biofilm induction by organic acids.
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Affiliation(s)
- Meha Sharma
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
| | - Dina Saleh
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
| | - Jean-Benoit Charron
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
| | - Suha Jabaji
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
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66
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Negative Interplay between Biofilm Formation and Competence in the Environmental Strains of Bacillus subtilis. mSystems 2020; 5:5/5/e00539-20. [PMID: 32873610 PMCID: PMC7470987 DOI: 10.1128/msystems.00539-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The soil bacterium Bacillus subtilis can form robust biofilms, which are important for its survival in the environment. B. subtilis also exhibits natural competence. By investigating competence development in B. subtilisin situ during biofilm formation, we reveal that robust biofilm formation often greatly reduces the frequency of competent cells within the biofilm. We then characterize a cross-pathway regulation that allows cells in these two developmental events to undergo mutually exclusive cell differentiation during biofilm formation. Finally, we discuss potential biological implications of limiting competence in a bacterial biofilm. Environmental strains of the soil bacterium Bacillus subtilis have valuable applications in agriculture, industry, and biotechnology; however, environmental strains are genetically less accessible. This reduced accessibility is in sharp contrast to laboratory strains, which are well known for their natural competence, and a limitation in their applications. In this study, we observed that robust biofilm formation by environmental strains of B. subtilis greatly reduced the frequency of competent cells in the biofilm. By using model strain 3610, we revealed a cross-pathway regulation that allows biofilm matrix producers and competence-developing cells to undergo mutually exclusive cell differentiation. We further demonstrated that the competence activator ComK represses the key biofilm regulatory gene sinI by directly binding to the sinI promoter, thus blocking competent cells from simultaneously becoming matrix producers. In parallel, the biofilm activator SlrR represses competence through three distinct mechanisms involving both genetic regulation and cell morphological changes. Finally, we discuss the potential implications of limiting competence in a bacterial biofilm. IMPORTANCE The soil bacterium Bacillus subtilis can form robust biofilms, which are important for its survival in the environment. B. subtilis also exhibits natural competence. By investigating competence development in B. subtilisin situ during biofilm formation, we reveal that robust biofilm formation often greatly reduces the frequency of competent cells within the biofilm. We then characterize a cross-pathway regulation that allows cells in these two developmental events to undergo mutually exclusive cell differentiation during biofilm formation. Finally, we discuss potential biological implications of limiting competence in a bacterial biofilm.
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Špacapan M, Danevčič T, Štefanic P, Porter M, Stanley-Wall NR, Mandic-Mulec I. The ComX Quorum Sensing Peptide of Bacillus subtilis Affects Biofilm Formation Negatively and Sporulation Positively. Microorganisms 2020; 8:E1131. [PMID: 32727033 PMCID: PMC7463575 DOI: 10.3390/microorganisms8081131] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/08/2020] [Accepted: 07/22/2020] [Indexed: 01/01/2023] Open
Abstract
Quorum sensing (QS) is often required for the formation of bacterial biofilms and is a popular target of biofilm control strategies. Previous studies implicate the ComQXPA quorum sensing system of Bacillus subtilis as a promoter of biofilm formation. Here, we report that ComX signaling peptide deficient mutants form thicker and more robust pellicle biofilms that contain chains of cells. We confirm that ComX positively affects the transcriptional activity of the PepsA promoter, which controls the synthesis of the major matrix polysaccharide. In contrast, ComX negatively controls the PtapA promoter, which drives the production of TasA, a fibrous matrix protein. Overall, the biomass of the mutant biofilm lacking ComX accumulates more monosaccharide and protein content than the wild type. We conclude that this QS phenotype might be due to extended investment into growth rather than spore development. Consistent with this, the ComX deficient mutant shows a delayed activation of the pre-spore specific promoter, PspoIIQ, and a delayed, more synchronous commitment to sporulation. We conclude that ComX mediated early commitment to sporulation of the wild type slows down biofilm formation and modulates the coexistence of multiple biological states during the early stages of biofilm development.
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Affiliation(s)
- Mihael Špacapan
- Chair of Microbiology, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Vecna pot 111, 1000 Ljubljana, Slovenia; (M.Š.); (T.D.); (P.Š.)
| | - Tjaša Danevčič
- Chair of Microbiology, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Vecna pot 111, 1000 Ljubljana, Slovenia; (M.Š.); (T.D.); (P.Š.)
| | - Polonca Štefanic
- Chair of Microbiology, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Vecna pot 111, 1000 Ljubljana, Slovenia; (M.Š.); (T.D.); (P.Š.)
| | - Michael Porter
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; (M.P.); (N.R.S.-W.)
| | - Nicola R. Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; (M.P.); (N.R.S.-W.)
| | - Ines Mandic-Mulec
- Chair of Microbiology, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Vecna pot 111, 1000 Ljubljana, Slovenia; (M.Š.); (T.D.); (P.Š.)
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68
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Pavlova M, Asaturova A, Allakhverdian V, Sidorova T. Physiological and biochemical aspects of the fungicidal action of promising biocontrol Bacillus subtilis strains against phytopathogenic fungi pp. Fusarium and Pyrenophora. BIO WEB OF CONFERENCES 2020. [DOI: 10.1051/bioconf/20202100016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The article presents some aspects of the interaction between biocontrol Bacillus subtilis strains and phytopathogenic fungi Fusarium and Pyrenophora. The presence of antifungal metabolites complexes in the culture fluid of the strains, including surfactin and iturin A has been found. The nature of the changes in the mycelium of phytopathogenic fungi is examined when co-cultivated with B.subtilis strains.
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69
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Earl C, Arnaouteli S, Bamford NC, Porter M, Sukhodub T, MacPhee CE, Stanley-Wall NR. The majority of the matrix protein TapA is dispensable for Bacillus subtilis colony biofilm architecture. Mol Microbiol 2020; 114:920-933. [PMID: 32491277 DOI: 10.1111/mmi.14559] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/26/2020] [Accepted: 05/26/2020] [Indexed: 01/08/2023]
Abstract
Biofilm formation is a co-operative behaviour, where microbial cells become embedded in an extracellular matrix. This biomolecular matrix helps manifest the beneficial or detrimental outcome mediated by the collective of cells. Bacillus subtilis is an important bacterium for understanding the principles of biofilm formation. The protein components of the B. subtilis matrix include the secreted proteins BslA, which forms a hydrophobic coat over the biofilm, and TasA, which forms protease-resistant fibres needed for structuring. TapA is a secreted protein also needed for biofilm formation and helps in vivo TasA-fibre formation but is dispensable for in vitro TasA-fibre assembly. We show that TapA is subjected to proteolytic cleavage in the colony biofilm and that only the first 57 amino acids of the 253-amino acid protein are required for colony biofilm architecture. Through the construction of a strain which lacks all eight extracellular proteases, we show that proteolytic cleavage by these enzymes is not a prerequisite for TapA function. It remains unknown why TapA is synthesised at 253 amino acids when the first 57 are sufficient for colony biofilm structuring; the findings do not exclude the core conserved region of TapA having a second role beyond structuring the B. subtilis colony biofilm.
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Affiliation(s)
- Chris Earl
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Sofia Arnaouteli
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Natalie C Bamford
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Michael Porter
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Tetyana Sukhodub
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Cait E MacPhee
- James Clerk Maxwell Building, School of Physics, University of Edinburgh, Edinburgh, UK
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
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70
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Rath H, Sappa PK, Hoffmann T, Gesell Salazar M, Reder A, Steil L, Hecker M, Bremer E, Mäder U, Völker U. Impact of high salinity and the compatible solute glycine betaine on gene expression of Bacillus subtilis. Environ Microbiol 2020; 22:3266-3286. [PMID: 32419322 DOI: 10.1111/1462-2920.15087] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/30/2020] [Accepted: 05/13/2020] [Indexed: 12/15/2022]
Abstract
The Gram-positive bacterium Bacillus subtilis is frequently exposed to hyperosmotic conditions. In addition to the induction of genes involved in the accumulation of compatible solutes, high salinity exerts widespread effects on B. subtilis physiology, including changes in cell wall metabolism, induction of an iron limitation response, reduced motility and suppression of sporulation. We performed a combined whole-transcriptome and proteome analysis of B. subtilis 168 cells continuously cultivated at low or high (1.2 M NaCl) salinity. Our study revealed significant changes in the expression of more than one-fourth of the protein-coding genes and of numerous non-coding RNAs. New aspects in understanding the impact of high salinity on B. subtilis include a sustained low-level induction of the SigB-dependent general stress response and strong repression of biofilm formation under high-salinity conditions. The accumulation of compatible solutes such as glycine betaine aids the cells to cope with water stress by maintaining physiologically adequate levels of turgor and also affects multiple cellular processes through interactions with cellular components. Therefore, we additionally analysed the global effects of glycine betaine on the transcriptome and proteome of B. subtilis and revealed that it influences gene expression not only under high-salinity, but also under standard growth conditions.
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Affiliation(s)
- Hermann Rath
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Praveen K Sappa
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Tamara Hoffmann
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Manuela Gesell Salazar
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Alexander Reder
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Leif Steil
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Michael Hecker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology e.V. (IMaB), Greifswald, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Ulrike Mäder
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology e.V. (IMaB), Greifswald, Germany
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71
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Effects of Spo0A on Clostridium acetobutylicum with an emphasis on biofilm formation. World J Microbiol Biotechnol 2020; 36:80. [PMID: 32444896 DOI: 10.1007/s11274-020-02859-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 05/18/2020] [Indexed: 02/08/2023]
Abstract
Clostridium acetobutylicum is a well-known strain for biofuel production. In previous work, it was found that this strain formed biofilm readily during fermentation processes. Biofilm formation could protect cells and enhance productivities under environmental stresses in our previous work. To explore the molecular mechanism of biofilm formation, Spo0A of C. acetobutylicum was selected to investigate its influences on biofilm formation and other physiological performances. When spo0A gene was disrupted, the spo0A mutant could hardly form biofilm. The aggregation and adhesion abilities of the spo0A mutant as well as its swarming motility were dramatically reduced compared to those of wild type strain. Sporulation was also negatively influenced by spo0A disruption, and solvent production was almost undetectable in the spo0A mutant fermentation. Furthermore, proteomic differences between wild type strain and the spo0A mutant were consistent with physiological performances. This is the first study confirming a genetic clue to C. acetobutylicum biofilm and will be valuable for biofilm optimization through genetic engineering in the future.
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72
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Kyriakopoulos AM, Nagl M, Orth-Höller D, Marcinkiewicz J, Baliou S, Zoumbourlis V. Successful treatment of a unique chronic multi-bacterial scalp infection with N-chlorotaurine, N-bromotaurine and bromamine T. Access Microbiol 2020; 2:acmi000126. [PMID: 32974590 PMCID: PMC7497830 DOI: 10.1099/acmi.0.000126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/11/2020] [Indexed: 12/19/2022] Open
Abstract
Microbial species can act in synergy to circumvent environmental stress conditions and survive. In addition, biofilms are a serious public-health issue globally and constitute a clinical emergency. Infection persistence, increased morbidity and mortality, and antibiotic resistance are consequences of poly-microbial synergy. Due to inherited complexity and synergy between numerous species, newer antimicrobial agents of increased efficacy and tolerability are needed. In this unique medical case, a chronic (9 year) multi-bacterial scalp infection was differentially diagnosed from other inflammatory skin disorders by prolonged microbiological culture. The bacterial species found seem to have caused lesions of visible biofilm not documented previously in the medical literature. This complicated infection was treated successfully and rapidly with the combined topical application of the active halogen compounds N-chlorotaurine, N-bromotaurine and bromamine T, which is in contrast to the previous failed systemic and topical therapeutic approaches. This study strengthens the case for the use of active halogen compounds against multi-bacterial infections of the skin in the future, without the occurrence of resistance.
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Affiliation(s)
| | - Markus Nagl
- Department of Hygiene, Microbiology and Social Medicine, Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Dorothea Orth-Höller
- Department of Hygiene, Microbiology and Social Medicine, Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Janusz Marcinkiewicz
- Department of Immunology, Jagiellonian University Medical College, Krakow, Poland
| | - Stella Baliou
- National Hellenic Research Foundation, 48 Vasileos Konstantinou Str., Athens, Greece
| | - Vassilis Zoumbourlis
- National Hellenic Research Foundation, 48 Vasileos Konstantinou Str., Athens, Greece
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73
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Kretschmer M, Lieleg O. Chelate chemistry governs ion-specific stiffening of Bacillus subtilis B-1 and Azotobacter vinelandii biofilms. Biomater Sci 2020; 8:1923-1933. [PMID: 32031543 DOI: 10.1039/c9bm01763a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Unwanted formation of bacterial biofilms can cause problems in both the medical sector and industrial settings. However, removing them from surfaces remains an ongoing challenge since biofilm bacteria efficiently protect themselves from external influences such as mechanical shear forces by embedding themselves into a matrix of extracellular polymeric substances. Here, we discuss microscopic principles, which are responsible for alterations in the viscoelastic properties of biofilms upon contact with metal ions. We suggest that it is a combination of mainly two parameters, that decides if biofilm stiffening occurs or not: the ion size and the detailed configuration of polyanionic macromolecules from the biofilm matrix. Our results provide new insights in the molecular mechanisms that govern the mechanical properties of biofilms. Also, they indicate that hydrogels comprising purified biopolymers can serve as suitable model systems to reproduce certain aspects of biofilm mechanics - provided that the correct biopolymer is chosen.
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Affiliation(s)
- Martin Kretschmer
- Munich School of Bioengineering and Department of Mechanical Engineering, Technical University of Munich, 85748 Garching, Germany.
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74
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Whitfield GB, Marmont LS, Bundalovic-Torma C, Razvi E, Roach EJ, Khursigara CM, Parkinson J, Howell PL. Discovery and characterization of a Gram-positive Pel polysaccharide biosynthetic gene cluster. PLoS Pathog 2020; 16:e1008281. [PMID: 32236137 PMCID: PMC7112168 DOI: 10.1371/journal.ppat.1008281] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/11/2019] [Indexed: 12/14/2022] Open
Abstract
Our understanding of the biofilm matrix components utilized by Gram-positive bacteria, and the signalling pathways that regulate their production are largely unknown. In a companion study, we developed a computational pipeline for the unbiased identification of homologous bacterial operons and applied this algorithm to the analysis of synthase-dependent exopolysaccharide biosynthetic systems. Here, we explore the finding that many species of Gram-positive bacteria have operons with similarity to the Pseudomonas aeruginosa pel locus. Our characterization of the pelDEADAFG operon from Bacillus cereus ATCC 10987, presented herein, demonstrates that this locus is required for biofilm formation and produces a polysaccharide structurally similar to Pel. We show that the degenerate GGDEF domain of the B. cereus PelD ortholog binds cyclic-3',5'-dimeric guanosine monophosphate (c-di-GMP), and that this binding is required for biofilm formation. Finally, we identify a diguanylate cyclase, CdgF, and a c-di-GMP phosphodiesterase, CdgE, that reciprocally regulate the production of Pel. The discovery of this novel c-di-GMP regulatory circuit significantly contributes to our limited understanding of c-di-GMP signalling in Gram-positive organisms. Furthermore, conservation of the core pelDEADAFG locus amongst many species of bacilli, clostridia, streptococci, and actinobacteria suggests that Pel may be a common biofilm matrix component in many Gram-positive bacteria.
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Affiliation(s)
- Gregory B Whitfield
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Lindsey S Marmont
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Cedoljub Bundalovic-Torma
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Erum Razvi
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Elyse J Roach
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Cezar M Khursigara
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - John Parkinson
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - P Lynne Howell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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75
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Matoz-Fernandez D, Arnaouteli S, Porter M, MacPhee CE, Stanley-Wall NR, Davidson FA. Comment on "Rivalry in Bacillus subtilis colonies: enemy or family?". SOFT MATTER 2020; 16:3344-3346. [PMID: 32207471 PMCID: PMC8522905 DOI: 10.1039/c9sm02141h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/24/2020] [Indexed: 06/10/2023]
Abstract
It is well known that biofilms are one of the most widespread forms of life on Earth, capable of colonising almost any environment from humans to metals.
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Affiliation(s)
- Daniel Matoz-Fernandez
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK. and Division of Mathematics, School of Science and Engineering, University of Dundee, Dundee DD1 4HN, UK.
| | - Sofia Arnaouteli
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
| | - Michael Porter
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
| | | | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
| | - Fordyce A Davidson
- Division of Mathematics, School of Science and Engineering, University of Dundee, Dundee DD1 4HN, UK.
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76
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Vyas R, Pandya M, Pohnerkar J, Kumar GN. Vitreoscilla hemoglobin promotes biofilm expansion and mitigates sporulation in Bacillus subtilis DK1042. 3 Biotech 2020; 10:118. [PMID: 32117679 DOI: 10.1007/s13205-020-2115-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/02/2020] [Indexed: 11/29/2022] Open
Abstract
Biofilm formation is considered as a stress combating strategy adopted by bacteria in response to variety of cellular and environmental signals. Impaired respiration due to low oxygen concentrations is one such signal that triggers wrinkling and robust biofilm formation in Bacillus subtilis. Vitreoscilla hemoglobin (VHb) improves microaerobic growth and bioproduct synthesis in a variety of bacteria by supplying oxygen to the respiratory chain. Present study was carried out to determine the effect of VHb on multicellularity of B. subtilis. Thus, B. subtilis DK1042 (WT) was genetically modified to express vgb and gfp genes under the control of P43 promoter at amyE locus by double cross over events. Biofilm formation by the integrant NRM1113 and WT was monitored on Lysogeny broth (LB) and LB containing glycerol and manganese (LBGM) medium. The WT produced more wrinkled colonies than NRM1113 on LB and LBGM medium. Concomitantly, biofilm-associated sporulation and production of pulcherriminic acid was decreased in NRM1113 as compared to WT on LB as well as LBGM. Expression studies of genes encoding structural components of biofilms revealed ~ 70% down-regulation of bslA gene in NRM1113 on both LB and LBGM which is correlated with reduced wrinkling in NRM1113. Moreover, NRM1113 showed increased colony expansion compared to WT in LB, LBGM and high osmolarity conditions. VHb expression alters various processes in different host cells, our study represents that VHb modulates biofilm formation, sporulation and pulcherriminic acid formation in B. subtilis DK1042.
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Affiliation(s)
- Riddhi Vyas
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat 390002 India
| | - Maharshi Pandya
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat 390002 India
| | - Jayashree Pohnerkar
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat 390002 India
| | - G Naresh Kumar
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat 390002 India
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77
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Majumdar M, Khan SA, Biswas SC, Roy DN, Panja AS, Misra TK. In vitro and in silico investigation of anti-biofilm activity of Citrus macroptera fruit extract mediated silver nanoparticles. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112586] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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78
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Cell Membrane and Electron Transfer Engineering for Improved Synthesis of Menaquinone-7 in Bacillus subtilis. iScience 2020; 23:100918. [PMID: 32109677 PMCID: PMC7044751 DOI: 10.1016/j.isci.2020.100918] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/09/2020] [Accepted: 02/11/2020] [Indexed: 11/23/2022] Open
Abstract
The formation of biofilm facilitates the synthesis of valuable natural product menaquinone-7 (MK-7) in static culture of Bacillus subtilis, whereas the essential role and mechanism of biofilm in MK-7 synthesis have not been revealed. Herein, comparative transcriptomics show that the formation of biofilm affected MK-7 synthesis by changing the transcription levels of signal receptor (BSU02010), transmembrane transporter (BSU29340, BSU03070), and signal transduction (BSU02630). Moreover, we also found that oxalate decarboxylase OxdC has an important effect on electron generation and MK-7 synthesis, when the transcriptional level of NADH dehydrogenase decreases in static culture. Our results revealed that cell membrane and electron transfer are important factors in promoting MK-7 synthesis. Transcriptome analysis shows the relationship between biofilm and MK-7 synthesis Electron transfer significantly affects the synthesis of MK-7 Oxalate decarboxylase OxdC plays a role in electron generation and MK-7 synthesis
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79
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Fancello F, Multineddu C, Santona M, Deiana P, Zara G, Mannazzu I, Budroni M, Dettori S, Zara S. Bacterial Biodiversity of Extra Virgin Olive Oils and Their Potential Biotechnological Exploitation. Microorganisms 2020; 8:E97. [PMID: 31936728 PMCID: PMC7022595 DOI: 10.3390/microorganisms8010097] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/22/2019] [Accepted: 01/07/2020] [Indexed: 12/16/2022] Open
Abstract
Bacterial diversity of 15 extra virgin olive oils, obtained from different Italian varieties, including Frantoio, Coratina, Bosana, and Semidana, was analyzed in this study. All bacterial isolates were genotyped using RAPD and REP-PCR method and grouped by means of cluster analyses. Sequencing of 16S rDNA of 51 isolates, representative of 36 clusters, led to the identification of Bacillus spp., Brevibacillus spp., Micrococcus spp., Staphylococcus spp., Pantoea spp., Kocuria spp., Lysinbacillus spp., and Lactobacillus spp., most of which reported for first time in olive oils. Phenotypic characterization of the 51 isolates, some of which ascribed to potentially probiotic species, indicate that two of them have beta-glucosidase activity while 37% present lipolytic activity. Preliminary evaluation of probiotic potential indicates that 31% of the isolates show biofilm formation ability, 29% acidic pH resistance, and 25% bile salt resistance. Finally, 29% of the isolates were sensitive to antibiotics while the remaining 71%, that include bacterial species well-recognized for their ability to disseminate resistance genes in the environment, showed a variable pattern of antibiotic resistance. The results obtained underline that microbial diversity of extra virgin olive oils represents an unexpected sink of microbial diversity and poses safety issues on the possible biotechnological exploitation of this microbial biodiversity.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Severino Zara
- Dipartimento di Agraria, Viale Italia 39, University of Sassari, 07100 Sassari, Italy; (F.F.); (C.M.); (M.S.); (P.D.); (G.Z.); (I.M.); (M.B.); (S.D.)
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Bich L, Pradeu T, Moreau JF. Understanding Multicellularity: The Functional Organization of the Intercellular Space. Front Physiol 2019; 10:1170. [PMID: 31620013 PMCID: PMC6759637 DOI: 10.3389/fphys.2019.01170] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/29/2019] [Indexed: 01/08/2023] Open
Abstract
The aim of this paper is to provide a theoretical framework to understand how multicellular systems realize functionally integrated physiological entities by organizing their intercellular space. From a perspective centered on physiology and integration, biological systems are often characterized as organized in such a way that they realize metabolic self-production and self-maintenance. The existence and activity of their components rely on the network they realize and on the continuous management of the exchange of matter and energy with their environment. One of the virtues of the organismic approach focused on organization is that it can provide an understanding of how biological systems are functionally integrated into coherent wholes. Organismic frameworks have been primarily developed by focusing on unicellular life. Multicellularity, however, presents additional challenges to our understanding of biological systems, related to how cells are capable to live together in higher-order entities, in such a way that some of their features and behaviors are constrained and controlled by the system they realize. Whereas most accounts of multicellularity focus on cell differentiation and increase in size as the main elements to understand biological systems at this level of organization, we argue that these factors are insufficient to provide an understanding of how cells are physically and functionally integrated in a coherent system. In this paper, we provide a new theoretical framework to understand multicellularity, capable to overcome these issues. Our thesis is that one of the fundamental theoretical principles to understand multicellularity, which is missing or underdeveloped in current accounts, is the functional organization of the intercellular space. In our view, the capability to be organized in space plays a central role in this context, as it enables (and allows to exploit all the implications of) cell differentiation and increase in size, and even specialized functions such as immunity. We argue that the extracellular matrix plays a crucial active role in this respect, as an evolutionary ancient and specific (non-cellular) control subsystem that contributes as a key actor to the functional specification of the multicellular space and to modulate cell fate and behavior. We also analyze how multicellular systems exert control upon internal movement and communication. Finally, we show how the organization of space is involved in some of the failures of multicellular organization, such as aging and cancer.
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Affiliation(s)
- Leonardo Bich
- Department of Logic and Philosophy of Science, IAS-Research Centre for Life, Mind and Society, University of the Basque Country (UPV/EHU), Donostia-San Sebastian, Spain
| | - Thomas Pradeu
- ImmunoConcept, CNRS UMR 5164, Bordeaux University, Bordeaux, France.,CNRS UMR8590, Institut d'Histoire et de Philosophie des Sciences et des Techniques, Pantheon-Sorbonne University, Paris, France
| | - Jean-François Moreau
- ImmunoConcept, CNRS UMR 5164, Bordeaux University, Bordeaux, France.,CHU Bordeaux, Bordeaux, France
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81
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Milton ME, Draughn GL, Bobay BG, Stowe SD, Olson AL, Feldmann EA, Thompson RJ, Myers KH, Santoro MT, Kearns DB, Cavanagh J. The Solution Structures and Interaction of SinR and SinI: Elucidating the Mechanism of Action of the Master Regulator Switch for Biofilm Formation in Bacillus subtilis. J Mol Biol 2019; 432:343-357. [PMID: 31493408 DOI: 10.1016/j.jmb.2019.08.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/09/2019] [Accepted: 08/29/2019] [Indexed: 02/04/2023]
Abstract
Bacteria have developed numerous protection strategies to ensure survival in harsh environments, with perhaps the most robust method being the formation of a protective biofilm. In biofilms, bacterial cells are embedded within a matrix that is composed of a complex mixture of polysaccharides, proteins, and DNA. The gram-positive bacterium Bacillus subtilis has become a model organism for studying regulatory networks directing biofilm formation. The phenotypic transition from a planktonic to biofilm state is regulated by the activity of the transcriptional repressor, SinR, and its inactivation by its primary antagonist, SinI. In this work, we present the first full-length structural model of tetrameric SinR using a hybrid approach combining high-resolution solution nuclear magnetic resonance (NMR), chemical cross-linking, mass spectrometry, and molecular docking. We also present the solution NMR structure of the antagonist SinI dimer and probe the mechanism behind the SinR-SinI interaction using a combination of biochemical and biophysical techniques. As a result of these findings, we propose that SinI utilizes a residue replacement mechanism to block SinR multimerization, resulting in diminished DNA binding and concomitant decreased repressor activity. Finally, we provide an evidence-based mechanism that confirms how disruption of the SinR tetramer by SinI regulates gene expression.
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Affiliation(s)
- Morgan E Milton
- Department of Biochemistry and Molecular Biology, The Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
| | - G Logan Draughn
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Benjamin G Bobay
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA; Duke University NMR Center, Duke University, Durham, NC 27710, USA
| | - Sean D Stowe
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Andrew L Olson
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Erik A Feldmann
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Richele J Thompson
- Department of Biochemistry and Molecular Biology, The Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
| | - Katherine H Myers
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Michael T Santoro
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Daniel B Kearns
- Department of Biology, Indiana University Bloomington, Bloomington, IN 47405, USA
| | - John Cavanagh
- Department of Biochemistry and Molecular Biology, The Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA.
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82
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van Gestel J, Ackermann M, Wagner A. Microbial life cycles link global modularity in regulation to mosaic evolution. Nat Ecol Evol 2019; 3:1184-1196. [PMID: 31332330 DOI: 10.1038/s41559-019-0939-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 06/03/2019] [Indexed: 11/09/2022]
Abstract
Microbes are exposed to changing environments, to which they can respond by adopting various lifestyles such as swimming, colony formation or dormancy. These lifestyles are often studied in isolation, thereby giving a fragmented view of the life cycle as a whole. Here, we study lifestyles in the context of this whole. We first use machine learning to reconstruct the expression changes underlying life cycle progression in the bacterium Bacillus subtilis, based on hundreds of previously acquired expression profiles. This yields a timeline that reveals the modular organization of the life cycle. By analysing over 380 Bacillales genomes, we then show that life cycle modularity gives rise to mosaic evolution in which life stages such as motility and sporulation are conserved and lost as discrete units. We postulate that this mosaic conservation pattern results from habitat changes that make these life stages obsolete or detrimental. Indeed, when evolving eight distinct Bacillales strains and species under laboratory conditions that favour colony growth, we observe rapid and parallel losses of the sporulation life stage across species, induced by mutations that affect the same global regulator. We conclude that a life cycle perspective is pivotal to understanding the causes and consequences of modularity in both regulation and evolution.
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Affiliation(s)
- Jordi van Gestel
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland. .,Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland.
| | - Martin Ackermann
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.,Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,The Santa Fe Institute, Santa Fe, NM, USA.
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83
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Ma Y, McClure DD, Somerville MV, Proschogo NW, Dehghani F, Kavanagh JM, Coleman NV. Metabolic Engineering of the MEP Pathway in Bacillus subtilis for Increased Biosynthesis of Menaquinone-7. ACS Synth Biol 2019; 8:1620-1630. [PMID: 31250633 DOI: 10.1021/acssynbio.9b00077] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Vitamin K is essential for blood coagulation and plays important roles in bone and cardiovascular health. Menaquinone-7 (MK-7) is one form of vitamin K that is especially useful due to its long half-life in the circulation. MK-7 is difficult to make via organic synthesis, and is thus commonly produced by fermentation. This study aimed to genetically modify Bacillus subtilis cultures to increase their MK-7 yield and reduce production costs. We constructed 12 different strains of B. subtilis 168 by overexpressing different combinations of the rate-limiting enzymes Dxs, Dxr, Idi, and MenA. We observed an 11-fold enhancement of production in the best-performing strain, resulting in 50 mg/L MK-7. Metabolite analysis revealed new bottlenecks in the pathway at IspG and IspH, which suggest avenues for further optimization. This work highlights the usefulness of Bacillus subtilis for industrial production of high value compounds.
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Affiliation(s)
- Yanwei Ma
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - Dale D. McClure
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - Mark V. Somerville
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Fariba Dehghani
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - John M. Kavanagh
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - Nicholas V. Coleman
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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84
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Gómez-Godínez LJ, Fernandez-Valverde SL, Martinez Romero JC, Martínez-Romero E. Metatranscriptomics and nitrogen fixation from the rhizoplane of maize plantlets inoculated with a group of PGPRs. Syst Appl Microbiol 2019; 42:517-525. [DOI: 10.1016/j.syapm.2019.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 10/26/2022]
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85
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Abstract
The cytoplasm of bacterial cells is a highly crowded cellular compartment that possesses considerable osmotic potential. As a result, and owing to the semipermeable nature of the cytoplasmic membrane and the semielastic properties of the cell wall, osmotically driven water influx will generate turgor, a hydrostatic pressure considered critical for growth and viability. Both increases and decreases in the external osmolarity inevitably trigger water fluxes across the cytoplasmic membrane, thus impinging on the degree of cellular hydration, molecular crowding, magnitude of turgor, and cellular integrity. Here, we assess mechanisms that permit the perception of osmotic stress by bacterial cells and provide an overview of the systems that allow them to genetically and physiologically cope with this ubiquitous environmental cue. We highlight recent developments implicating the secondary messenger c-di-AMP in cellular adjustment to osmotic stress and the role of osmotic forces in the life of bacteria-assembled in biofilms.
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Affiliation(s)
- Erhard Bremer
- Laboratory for Microbiology, Department of Biology; and Center for Synthetic Microbiology, Philipps-Universität Marburg, 35043 Marburg, Germany;
| | - Reinhard Krämer
- Institute of Biochemistry, University of Cologne, 50674 Cologne, Germany;
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86
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Abstract
Bacterial biofilms are ubiquitous in natural environments and play an important role in many clinical, industrial, and ecological settings. Although much is known about the transcriptional regulatory networks that control biofilm formation in model bacteria such as Bacillus subtilis, very little is known about the role of metabolism in this complex developmental process. To address this important knowledge gap, we performed a time-resolved analysis of the metabolic changes associated with bacterial biofilm development in B. subtilis by combining metabolomic, transcriptomic, and proteomic analyses. Here, we report a widespread and dynamic remodeling of metabolism affecting central carbon metabolism, primary biosynthetic pathways, fermentation pathways, and secondary metabolism. This report serves as a unique hypothesis-generating resource for future studies on bacterial biofilm physiology. Outside the biofilm research area, this work should also prove relevant to any investigators interested in microbial physiology and metabolism. Biofilms are structured communities of tightly associated cells that constitute the predominant state of bacterial growth in natural and human-made environments. Although the core genetic circuitry that controls biofilm formation in model bacteria such as Bacillus subtilis has been well characterized, little is known about the role that metabolism plays in this complex developmental process. Here, we performed a time-resolved analysis of the metabolic changes associated with pellicle biofilm formation and development in B. subtilis by combining metabolomic, transcriptomic, and proteomic analyses. We report surprisingly widespread and dynamic remodeling of metabolism affecting central carbon metabolism, primary biosynthetic pathways, fermentation pathways, and secondary metabolism. Most of these metabolic alterations were hitherto unrecognized as biofilm associated. For example, we observed increased activity of the tricarboxylic acid (TCA) cycle during early biofilm growth, a shift from fatty acid biosynthesis to fatty acid degradation, reorganization of iron metabolism and transport, and a switch from acetate to acetoin fermentation. Close agreement between metabolomic, transcriptomic, and proteomic measurements indicated that remodeling of metabolism during biofilm development was largely controlled at the transcriptional level. Our results also provide insights into the transcription factors and regulatory networks involved in this complex metabolic remodeling. Following upon these results, we demonstrated that acetoin production via acetolactate synthase is essential for robust biofilm growth and has the dual role of conserving redox balance and maintaining extracellular pH. This report represents a comprehensive systems-level investigation of the metabolic remodeling occurring during B. subtilis biofilm development that will serve as a useful road map for future studies on biofilm physiology.
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87
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Stress-Responsive Alternative Sigma Factor SigB Plays a Positive Role in the Antifungal Proficiency of Bacillus subtilis. Appl Environ Microbiol 2019; 85:AEM.00178-19. [PMID: 30824454 DOI: 10.1128/aem.00178-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 02/16/2019] [Indexed: 01/05/2023] Open
Abstract
Different Bacillus species with PGPR (plant growth-promoting rhizobacterium) activity produce potent biofungicides and stimulate plant defense responses against phytopathogenic fungi. However, very little is known about how these PGPRs recognize phytopathogens and exhibit the antifungal response. Here, we report the antagonistic interaction between Bacillus subtilis and the phytopathogenic fungus Fusarium verticillioides We demonstrate that this bacterial-fungal interaction triggers the induction of the SigB transcription factor, the master regulator of B. subtilis stress adaptation. Dual-growth experiments performed with live or dead mycelia or culture supernatants of F. verticillioides showed that SigB was activated and required for the biocontrol of fungal growth. Mutations in the different regulatory pathways of SigB activation in the isogenic background revealed that only the energy-related RsbP-dependent arm of SigB activation was responsible for specific fungal detection and triggering the antagonistic response. The activation of SigB increased the expression of the operon responsible for the production of the antimicrobial cyclic lipopeptide surfactin (the srfA operon). SigB-deficient B. subtilis cultures produced decreased amounts of surfactin, and B. subtilis cultures defective in surfactin production (ΔsrfA) were unable to control the growth of F. verticillioides In vivo experiments of seed germination efficiency and early plant growth inhibition in the presence of F. verticillioides confirmed the physiological importance of SigB activity for plant bioprotection.IMPORTANCE Biological control using beneficial bacteria (PGPRs) represents an attractive and environment-friendly alternative to pesticides for controlling plant diseases. Different PGPR Bacillus species produce potent biofungicides and stimulate plant defense responses against phytopathogenic fungi. However, very little is known about how PGPRs recognize phytopathogens and process the antifungal response. Here, we report how B. subtilis triggers the induction of the stress-responsive sigma B transcription factor and the synthesis of the lipopeptide surfactin to fight the phytopathogen. Our findings show the participation of the stress-responsive regulon of PGPR Bacillus in the detection and biocontrol of a phytopathogenic fungus of agronomic impact.
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88
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Dinh ТL, Akhmetova GR, Martykanova DS, Rudakova NL, Sharipova МR. Influence of Divalent Metal Ions on Biofilm Formation by Bacillus subtilis. BIONANOSCIENCE 2019. [DOI: 10.1007/s12668-019-00621-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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89
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Bucher T, Keren-Paz A, Hausser J, Olender T, Cytryn E, Kolodkin-Gal I. An active β-lactamase is a part of an orchestrated cell wall stress resistance network of Bacillus subtilis and related rhizosphere species. Environ Microbiol 2019; 21:1068-1085. [PMID: 30637927 DOI: 10.1111/1462-2920.14526] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/12/2018] [Indexed: 11/29/2022]
Abstract
A hallmark of the Gram-positive bacteria, such as the soil-dwelling bacterium Bacillus subtilis, is their cell wall. Here, we report that d-leucine and flavomycin, biofilm inhibitors targeting the cell wall, activate the β-lactamase PenP. This β-lactamase contributes to ampicillin resistance in B. subtilis under all conditions tested. In contrast, both Spo0A, a master regulator of nutritional stress, and the general cell wall stress response, differentially contribute to β-lactam resistance under different conditions. To test whether β-lactam resistance and β-lactamase genes are widespread in other Bacilli, we isolated Bacillus species from undisturbed soils, and found that their genomes can encode up to five β-lactamases with differentiated activity spectra. Surprisingly, the activity of environmental β-lactamases and PenP, as well as the general stress response, resulted in a similarly reduced lag phase of the culture in the presence of β-lactam antibiotics, with little or no impact on the logarithmic growth rate. The length of the lag phase may determine the outcome of the competition between β-lactams and β-lactamases producers. Overall, our work suggests that antibiotic resistance genes in B. subtilis and related species are ancient and widespread, and could be selected by interspecies competition in undisturbed soils.
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Affiliation(s)
- Tabitha Bucher
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl Street, Rehovot, 76100, Israel
| | - Alona Keren-Paz
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl Street, Rehovot, 76100, Israel
| | - Jean Hausser
- Department of Molecular Cell Biology, Weizmann Institute of Science, 234 Herzl Street, Rehovot, 76100, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl Street, Rehovot, 76100, Israel
| | - Eddie Cytryn
- Institute of Soil and Water and Environmental Sciences, Volcani Research Center, 68 HaMakabim Road, 7505101, Rishon Lezion, Israel
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl Street, Rehovot, 76100, Israel
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90
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Kaundinya CR, Savithri HS, Rao KK, Balaji PV. EpsN from Bacillus subtilis 168 has UDP-2,6-dideoxy 2-acetamido 4-keto glucose aminotransferase activity in vitro. Glycobiology 2019; 28:802-812. [PMID: 29982582 DOI: 10.1093/glycob/cwy063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/04/2018] [Indexed: 01/08/2023] Open
Abstract
The gene epsN of Bacillus subtilis 168 was cloned and overexpressed in Escherichia coli. Purified recombinant EpsN is shown to be a pyridoxal 5'-phosphate (PLP)-dependent aminotransferase by absorption spectroscopy, l-cycloserine inhibition and reverse phase HPLC studies. EpsN catalyzes the conversion of UDP-2,6-dideoxy 2-acetamido 4-keto glucose to UDP-2,6-dideoxy 2-acetamido 4-amino glucose. Lys190 was found by sequence comparison and site-directed mutagenesis to form Schiff base with PLP. Mutagenesis studies showed that, in addition to Lys190, Ser185, Glu164, Gly58 and Thr59 are essential for aminotransferase activity.
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Affiliation(s)
- Chinmayi R Kaundinya
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Handanahal S Savithri
- Department of Biochemistry, Indian Institute of Science, CV Raman Road, Bengaluru, India
| | - K Krishnamurthy Rao
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Petety V Balaji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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91
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Gilbert C, Ellis T. Biological Engineered Living Materials: Growing Functional Materials with Genetically Programmable Properties. ACS Synth Biol 2019; 8:1-15. [PMID: 30576101 DOI: 10.1021/acssynbio.8b00423] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Natural biological materials exhibit remarkable properties: self-assembly from simple raw materials, precise control of morphology, diverse physical and chemical properties, self-repair, and the ability to sense-and-respond to environmental stimuli. Despite having found numerous uses in human industry and society, the utility of natural biological materials is limited. But, could it be possible to genetically program microbes to create entirely new and useful biological materials? At the intersection between microbiology, material science, and synthetic biology, the emerging field of biological engineered living materials (ELMs) aims to answer this question. Here we review recent efforts to program cells to produce living materials with novel functional properties, focusing on microbial systems that can be engineered to grow materials and on new genetic circuits for pattern formation that could be used to produce the more complex systems of the future.
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Affiliation(s)
- Charlie Gilbert
- Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Tom Ellis
- Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
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92
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Klotz M, Kretschmer M, Goetz A, Ezendam S, Lieleg O, Opitz M. Importance of the biofilm matrix for the erosion stability of Bacillus subtilis NCIB 3610 biofilms. RSC Adv 2019; 9:11521-11529. [PMID: 35520264 PMCID: PMC9063333 DOI: 10.1039/c9ra01955c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 04/02/2019] [Indexed: 12/12/2022] Open
Abstract
Erosion of bacterial biofilms is dependent on the composition of the biofilm matrix and the surrounding chemical environment.
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Affiliation(s)
- M. Klotz
- Center for NanoScience
- Faculty of Physics
- Ludwig-Maximilians-Universität München
- Munich
- Germany
| | - M. Kretschmer
- Munich School of BioEngineering and Department of Mechanical Engineering
- Technische Universität München
- Garching
- Germany
| | - A. Goetz
- Center for NanoScience
- Faculty of Physics
- Ludwig-Maximilians-Universität München
- Munich
- Germany
| | - S. Ezendam
- Center for NanoScience
- Faculty of Physics
- Ludwig-Maximilians-Universität München
- Munich
- Germany
| | - O. Lieleg
- Munich School of BioEngineering and Department of Mechanical Engineering
- Technische Universität München
- Garching
- Germany
| | - M. Opitz
- Center for NanoScience
- Faculty of Physics
- Ludwig-Maximilians-Universität München
- Munich
- Germany
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93
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Regulation of Biofilm Aging and Dispersal in Bacillus subtilis by the Alternative Sigma Factor SigB. J Bacteriol 2018; 201:JB.00473-18. [PMID: 30396900 DOI: 10.1128/jb.00473-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/25/2018] [Indexed: 11/20/2022] Open
Abstract
Bacterial biofilms are important in natural settings, biotechnology, and medicine. However, regulation of biofilm development and its persistence in different niches is complex and only partially understood. One key step during the biofilm life cycle is dispersal, when motile cells abandon the mature biofilm to spread out and colonize new niches. Here, we show that in the model bacterium Bacillus subtilis the general stress transcription factor SigB is essential for halting detrimental overgrowth of mature biofilm and for triggering dispersal when nutrients become limited. Specifically, SigB-deficient biofilms were larger than wild-type biofilms but exhibited accelerated cell death, significantly greater sensitivity to different stresses, and reduced dispersal. Interestingly, the signal detected by SigB to limit biofilm growth was transduced through the RsbP-dependent metabolic arm of the SigB regulatory cascade, which in turn positively controlled expression of SinR, the master regulator of biofilm formation and cell motility. This novel SigB-SinR regulatory circuit might be important in controlling the fitness of biofilms (either beneficial or harmful) in diverse environments.IMPORTANCE Biofilms are crucial for bacterial survival, adaptation, and dissemination in natural, industrial, and medical systems. Sessile cells embedded in the self-produced extracellular matrix of the biofilm benefit from a division of labor and are protected from environmental insults. However, as the biofilm ages, cells become stressed because of overcrowding, starvation, and accumulation of waste products. How does the sessile biofilm community sense and respond to stressful conditions? Here, we show that in Bacillus subtilis, the transcription factors SigB and SinR control whether cells remain in or leave a biofilm when metabolic conditions become unfavorable. This novel SigB-SinR regulatory circuit might be important for controlling the fitness of biofilms (either beneficial or harmful) in diverse environments.
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94
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Programmable and printable Bacillus subtilis biofilms as engineered living materials. Nat Chem Biol 2018; 15:34-41. [PMID: 30510190 DOI: 10.1038/s41589-018-0169-2] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 10/09/2018] [Indexed: 11/09/2022]
Abstract
Bacterial biofilms can be programmed to produce living materials with self-healing and evolvable functionalities. However, the wider use of artificial biofilms has been hindered by limitations on processability and functional protein secretion capacity. We describe a highly flexible and tunable living functional materials platform based on the TasA amyloid machinery of the bacterium Bacillus subtilis. We demonstrate that genetically programmable TasA fusion proteins harboring diverse functional proteins or domains can be secreted and can assemble into diverse extracellular nano-architectures with tunable physicochemical properties. Our engineered biofilms have the viscoelastic behaviors of hydrogels and can be precisely fabricated into microstructures having a diversity of three-dimensional (3D) shapes using 3D printing and microencapsulation techniques. Notably, these long-lasting and environmentally responsive fabricated living materials remain alive, self-regenerative, and functional. This new tunable platform offers previously unattainable properties for a variety of living functional materials having potential applications in biomaterials, biotechnology, and biomedicine.
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95
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Erskine E, Morris RJ, Schor M, Earl C, Gillespie RMC, Bromley KM, Sukhodub T, Clark L, Fyfe PK, Serpell LC, Stanley‐Wall NR, MacPhee CE. Formation of functional, non-amyloidogenic fibres by recombinant Bacillus subtilis TasA. Mol Microbiol 2018; 110:897-913. [PMID: 29802781 PMCID: PMC6334530 DOI: 10.1111/mmi.13985] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2018] [Indexed: 01/06/2023]
Abstract
Bacterial biofilms are communities of microbial cells encased within a self-produced polymeric matrix. In the Bacillus subtilis biofilm matrix, the extracellular fibres of TasA are essential. Here, a recombinant expression system allows interrogation of TasA, revealing that monomeric and fibre forms of TasA have identical secondary structure, suggesting that fibrous TasA is a linear assembly of globular units. Recombinant TasA fibres form spontaneously, and share the biological activity of TasA fibres extracted from B. subtilis, whereas a TasA variant restricted to a monomeric form is inactive and subjected to extracellular proteolysis. The biophysical properties of both native and recombinant TasA fibres indicate that they are not functional amyloid-like fibres. A gel formed by TasA fibres can recover after physical shear force, suggesting that the biofilm matrix is not static and that these properties may enable B. subtilis to remodel its local environment in response to external cues. Using recombinant fibres formed by TasA orthologues we uncover species variability in the ability of heterologous fibres to cross-complement the B. subtilis tasA deletion. These findings are indicative of specificity in the biophysical requirements of the TasA fibres across different species and/or reflect the precise molecular interactions needed for biofilm matrix assembly.
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Affiliation(s)
- Elliot Erskine
- Division of Molecular Microbiology, School of Life SciencesUniversity of DundeeDundeeDD1 4HNUK
| | - Ryan J. Morris
- James Clerk Maxwell Building, School of Physics, and AstronomyUniversity of Edinburgh, The Kings Buildings, Peter Guthrie Tait RoadEdinburghEH9 3FDUK
| | - Marieke Schor
- James Clerk Maxwell Building, School of Physics, and AstronomyUniversity of Edinburgh, The Kings Buildings, Peter Guthrie Tait RoadEdinburghEH9 3FDUK
| | - Chris Earl
- Division of Molecular Microbiology, School of Life SciencesUniversity of DundeeDundeeDD1 4HNUK
| | - Rachel M. C. Gillespie
- Division of Molecular Microbiology, School of Life SciencesUniversity of DundeeDundeeDD1 4HNUK
| | - Keith M. Bromley
- James Clerk Maxwell Building, School of Physics, and AstronomyUniversity of Edinburgh, The Kings Buildings, Peter Guthrie Tait RoadEdinburghEH9 3FDUK
| | - Tetyana Sukhodub
- Division of Molecular Microbiology, School of Life SciencesUniversity of DundeeDundeeDD1 4HNUK
| | - Lauren Clark
- James Clerk Maxwell Building, School of Physics, and AstronomyUniversity of Edinburgh, The Kings Buildings, Peter Guthrie Tait RoadEdinburghEH9 3FDUK
| | - Paul K. Fyfe
- Division of Molecular Microbiology, School of Life SciencesUniversity of DundeeDundeeDD1 4HNUK
| | | | - Nicola R. Stanley‐Wall
- Division of Molecular Microbiology, School of Life SciencesUniversity of DundeeDundeeDD1 4HNUK
| | - Cait E. MacPhee
- James Clerk Maxwell Building, School of Physics, and AstronomyUniversity of Edinburgh, The Kings Buildings, Peter Guthrie Tait RoadEdinburghEH9 3FDUK
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96
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Abstract
Bacillus subtilis has the capacity to choose between two mutually exclusive lifestyles: biofilm formation and flagellum-mediated swimming motility. Interestingly, this choice is made at the individual cell level, with bacterial cells in a population expressing genes required for biofilm formation or genes required for swimming motility but not both. A bistable switch controls the biofilm-versus-swimming decision, resulting in an evolutionarily favorable strategy known as "bet hedging" that ensures that subpopulations of bacteria continue to grow as conditions change and/or become unfavorable. In a recent issue of mBio, J. Kampf and colleagues (mBio 9:e01464-18, 2018, https://doi.org/10.1128/mBio.01464-18) reported the use of a combination of genetics and microfluidics to reveal that the interplay that occurs between the SinR and YmdB proteins underlies the B. subtilis choice between biofilm formation and swimming motility. Their report suggests that B. subtilis experiences selective pressure to form biofilms while maintaining reserve cell subpopulations with the capacity to swim away.
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97
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Kaundinya CR, Savithri HS, Rao KK, Balaji PV. EpsM from Bacillus subtilis 168 has UDP-2,4,6-trideoxy-2-acetamido-4-amino glucose acetyltransferase activity in vitro. Biochem Biophys Res Commun 2018; 505:1057-1062. [PMID: 30314705 DOI: 10.1016/j.bbrc.2018.09.185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 09/29/2018] [Indexed: 01/14/2023]
Abstract
Bacillus subtilis 168 EpsM (UniProt id P71063) has been electronically annotated as putative acetyltransferase in the UniProt database. The gene epsM was cloned and overexpressed in E. coli with an N-terminal GST tag. The purified fusion protein was shown by absorption spectroscopy, autoradiography and reverse phase HPLC to catalyse the conversion of UDP-2,4,6-trideoxy-2-acetamido-4-amino glucose to UDP-2,4,6-trideoxy-2,4-diacetamido glucose, commonly known as N,N'-diacetylbacillosamine, using acetyl coenzyme A as the donor substrate. His146 was shown by site-directed mutagenesis to be essential for acetyltransferase activity. It is hypothesized that EpsC (NAD+ dependent UDP GlcNAc 4,6-dehydratase), EpsN (PLP dependent aminotransferase) and EpsM, all of which are part of the eps operon, are involved in the biosynthesis of N,N'-diacetylbacillosamine.
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Affiliation(s)
- Chinmayi R Kaundinya
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Handanahal S Savithri
- Department of Biochemistry, Indian Institute of Science, CV Raman Road, Bengaluru 560012, India
| | - K Krishnamurthy Rao
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Petety V Balaji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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98
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Poquet I, Saujet L, Canette A, Monot M, Mihajlovic J, Ghigo JM, Soutourina O, Briandet R, Martin-Verstraete I, Dupuy B. Clostridium difficile Biofilm: Remodeling Metabolism and Cell Surface to Build a Sparse and Heterogeneously Aggregated Architecture. Front Microbiol 2018; 9:2084. [PMID: 30258415 PMCID: PMC6143707 DOI: 10.3389/fmicb.2018.02084] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 08/14/2018] [Indexed: 12/11/2022] Open
Abstract
Clostridium difficile is an opportunistic entero-pathogen causing post-antibiotic and nosocomial diarrhea upon microbiota dysbiosis. Although biofilms could contribute to colonization, little is known about their development and physiology. Strain 630Δerm is able to form, in continuous-flow micro-fermentors, macro-colonies and submersed biofilms loosely adhesive to glass. According to gene expression data, in biofilm/planktonic cells, central metabolism is active and fuels fatty acid biosynthesis rather than fermentations. Consistently, succinate is consumed and butyrate production is reduced. Toxin A expression, which is coordinated to metabolism, is down-regulated, while surface proteins, like adhesins and the primary Type IV pili subunits, are over-expressed. C-di-GMP level is probably tightly controlled through the expression of both diguanylate cyclase-encoding genes, like dccA, and phosphodiesterase-encoding genes. The coordinated expression of genes controlled by c-di-GMP and encoding the putative surface adhesin CD2831 and the major Type IV pilin PilA1, suggests that c-di-GMP could be high in biofilm cells. A Bacillus subtilis SinR-like regulator, CD2214, and/or CD2215, another regulator co-encoded in the same operon as CD2214, control many genes differentially expressed in biofilm, and in particular dccA, CD2831 and pilA1 in a positive way. After growth in micro-titer plates and disruption, the biofilm is composed of robust aggregated structures where cells are embedded into a polymorphic material. The intact biofilm observed in situ displays a sparse, heterogeneous and high 3D architecture made of rods and micro-aggregates. The biofilm is denser in a mutant of both CD2214 and CD2215 genes, but it is not affected by the inactivation of neither CD2831 nor pilA1. dccA, when over-expressed, not only increases the biofilm but also triggers its architecture to become homogeneous and highly aggregated, in a way independent of CD2831 and barely dependent of pilA1. Cell micro-aggregation is shown to play a major role in biofilm formation and architecture. This thorough analysis of gene expression reprogramming and architecture remodeling in biofilm lays the foundation for a deeper understanding of this lifestyle and could lead to novel strategies to limit C. difficile spread.
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Affiliation(s)
- Isabelle Poquet
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France
| | - Laure Saujet
- Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France.,Sorbonne Paris Cité, Université Paris Diderot, Paris, France
| | - Alexis Canette
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Marc Monot
- Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France.,Sorbonne Paris Cité, Université Paris Diderot, Paris, France
| | | | - Jean-Marc Ghigo
- Unité de Génétique des Biofilms, Institut Pasteur, Paris, France
| | - Olga Soutourina
- Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France.,Sorbonne Paris Cité, Université Paris Diderot, Paris, France
| | - Romain Briandet
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Isabelle Martin-Verstraete
- Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France.,Sorbonne Paris Cité, Université Paris Diderot, Paris, France
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France.,Sorbonne Paris Cité, Université Paris Diderot, Paris, France
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99
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Selective Pressure for Biofilm Formation in Bacillus subtilis: Differential Effect of Mutations in the Master Regulator SinR on Bistability. mBio 2018; 9:mBio.01464-18. [PMID: 30181249 PMCID: PMC6123443 DOI: 10.1128/mbio.01464-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Many bacteria are able to choose between two mutually exclusive lifestyles: biofilm formation and motility. In the model bacterium Bacillus subtilis, this choice is made by each individual cell rather than at the population level. The transcriptional repressor SinR is the master regulator in this decision-making process. The regulation of SinR activity involves complex control of its own expression and of its interaction with antagonist proteins. We show that the YmdB phosphodiesterase is required to allow the expression of SinR-repressed genes in a subpopulation of cells and that such subpopulations can switch between different SinR activity states. Suppressor analyses revealed that ymdB mutants readily acquire mutations affecting SinR, thus restoring biofilm formation. These findings suggest that B. subtilis cells experience selective pressure to form the extracellular matrix that is characteristic of biofilms and that YmdB is required for the homeostasis of SinR and/or its antagonists. Biofilm formation by Bacillus subtilis requires the expression of genes encoding enzymes for extracellular polysaccharide synthesis and for an amyloid-like protein. The master regulator SinR represses all the corresponding genes, and repression of these key biofilm genes is lifted when SinR interacts with its cognate antagonist proteins. The YmdB phosphodiesterase is a recently discovered factor that is involved in the control of SinR activity: cells lacking YmdB exhibit hyperactive SinR and are unable to relieve the repression of the biofilm genes. In this study, we have examined the dynamics of gene expression patterns in wild-type and ymdB mutant cells by microfluidic analysis coupled to time-lapse microscopy. Our results confirm the bistable expression pattern for motility and biofilm genes in the wild-type strain and the loss of biofilm gene expression in the mutant. Moreover, we demonstrated dynamic behavior in subpopulations of the wild-type strain that is characterized by switches in sets of the expressed genes. In order to gain further insights into the role of YmdB, we isolated a set of spontaneous suppressor mutants derived from ymdB mutants that had regained the ability to form complex colonies and biofilms. Interestingly, all of the mutations affected SinR. In some mutants, large genomic regions encompassing sinR were deleted, whereas others had alleles encoding SinR variants. Functional and biochemical studies with these SinR variants revealed how these proteins allowed biofilm gene expression in the ymdB mutant strains.
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100
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Basarab VY, Voronkova OS, Voronkova YS, Severynovska OV. The Characteristics of Growth of Bacilli Formed Fouling on Wooden Constructions. INTERNATIONAL LETTERS OF NATURAL SCIENCES 2018. [DOI: 10.56431/p-h657vz] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Problem of biofilm formation have a great significance for environmental microbiological research. Biospheric microorganisms can form biofilm, that provide bacteria resistance to influence of different environmental factors. Some of the most common bacteria in biosphere are bacilli, among them there are film-forming strains. Bacillus spp. ia a well-known film forming microorganisms that colonize environmental objects. The biofilm fouling of underwater elements of small wooden constructions located on the Dnieper River near the city of the Dnipro (Ukraine) was studied. It was found that biofilms from surfaces of water constructions include bacilli. It is established that the mean values of CFU in samples from running and still water were (1.81±0.52)×108 and (1.83±0.53)×108 CFU / ml respectively per area of wooden sample approximately 1 cm2, while during the laboratory cultivation of the film, formed by these cultures on the plate, the number of cells was (4.90±0.93)×107 and (4.60±1.07)×107 CFU / ml per 1 cm2 of the well’s bottom, which was an approximate limit of the content of cells of the Bacillus spp. film per unit of area.
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