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Rosazza T, Earl C, Eigentler L, Davidson FA, Stanley-Wall NR. Reciprocal sharing of extracellular proteases and extracellular matrix molecules facilitates Bacillus subtilis biofilm formation. Mol Microbiol 2024. [PMID: 38922753 DOI: 10.1111/mmi.15288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
Extracellular proteases are a class of public good that support growth of Bacillus subtilis when nutrients are in a polymeric form. Bacillus subtilis biofilm matrix molecules are another class of public good that are needed for biofilm formation and are prone to exploitation. In this study, we investigated the role of extracellular proteases in B. subtilis biofilm formation and explored interactions between different public good producer strains across various conditions. We confirmed that extracellular proteases support biofilm formation even when glutamic acid provides a freely available nitrogen source. Removal of AprE from the NCIB 3610 secretome adversely affects colony biofilm architecture, while sole induction of WprA activity into an otherwise extracellular protease-free strain is sufficient to promote wrinkle development within the colony biofilm. We found that changing the nutrient source used to support growth affected B. subtilis biofilm structure, hydrophobicity and architecture. We propose that the different phenotypes observed may be due to increased protease dependency for growth when a polymorphic protein presents the sole nitrogen source. We however cannot exclude that the phenotypic changes are due to alternative matrix molecules being made. Co-culture of biofilm matrix and extracellular protease mutants can rescue biofilm structure, yet reliance on extracellular proteases for growth influences population coexistence dynamics. Our findings highlight the intricate interplay between these two classes of public goods, providing insights into microbial social dynamics during biofilm formation across different ecological niches.
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Affiliation(s)
- Thibault Rosazza
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Chris Earl
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Lukas Eigentler
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
- Mathematics, School of Science and Engineering, University of Dundee, Dundee, UK
| | - Fordyce A Davidson
- Mathematics, School of Science and Engineering, University of Dundee, Dundee, UK
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
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2
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Hou B, Li B, Deng W, Li B, Ren B, Hu C, Zhang G, Yang F, Xiao M, Xie S, Xie D. DHTPY-Cu@ZOL-Enhanced Photodynamic Therapy: A Strategic Platform for Advanced Treatment of Drug-Resistant Bacterial Wound Infections. Int J Nanomedicine 2024; 19:6319-6336. [PMID: 38919773 PMCID: PMC11198012 DOI: 10.2147/ijn.s458520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 06/16/2024] [Indexed: 06/27/2024] Open
Abstract
Purpose This research was to innovate a nanozyme-based therapeutic strategy that combines aggregation-induced emission (AIE) photosensitizers with copper nanozymes. This approach is designed to address the hypoxic conditions often found in bacterial infections and aims to boost the effectiveness of photodynamic therapy (PDT) by ensuring sufficient oxygen supply for reactive oxygen species (ROS) generation. Methods Our approach involved the synthesis of dihydroxyl triphenyl vinyl pyridine (DHTPY)-Cu@zoledronic acid (ZOL) nanozyme particles. We initially synthesized DHTPY and then combined it with copper nanozymes to form the DHTPY-Cu@ZOL composite. The nanozyme's size, morphology, and chemical properties were characterized using various techniques, including dynamic light scattering, transmission electron microscopy, and X-ray photoelectron spectroscopy. We conducted a series of in vitro and in vivo tests to evaluate the photodynamic, antibacterial, and wound-healing properties of the DHTPY-Cu@ZOL nanozymes, including their oxygen-generation capacity, ROS production, and antibacterial efficacy against methicillin-resistant Staphylococcus aureus (MRSA). Results The DHTPY-Cu@ZOL exhibited proficient H2O2 scavenging and oxygen generation, crucial for enhancing PDT in oxygen-deprived infection environments. Our in vitro analysis revealed a notable antibacterial effect against MRSA, suggesting the nanozymes' potential to disrupt bacterial cell membranes. Further, in vivo studies using a diabetic rat model with MRSA-infected wounds showed that DHTPY-Cu@ZOL markedly improved wound healing and reduced bacterial presence, underscoring its efficacy as a non-antibiotic approach for chronic infections. Conclusion Our study suggests that DHTPY-Cu@ZOL is a highly promising approach for combating antibiotic-resistant microbial pathogens and biofilms. The biocompatibility and stability of these nanozyme particles, coupled with their improved PDT efficacy position them as a promising candidate for clinical applications.
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Affiliation(s)
- Biao Hou
- Department of Joint Surgery and Sports Medicine, Center for Orthopedic Surgery, Orthopedic Hospital of Guangdong Province, The Third Affiliated Hospital of Southern Medical University, Guangzhou, People’s Republic of China
- Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, Academy of Orthopedics, Guangzhou, Guangdong Province, People’s Republic of China
- Department of Hand and Foot Microsurgery, The affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, People’s Republic of China
| | - Bo Li
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, People’s Republic of China
| | - Wanjun Deng
- Department of Hand and Foot Microsurgery, The affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, People’s Republic of China
| | - Bo Li
- Department of Joint Surgery and Sports Medicine, Center for Orthopedic Surgery, Orthopedic Hospital of Guangdong Province, The Third Affiliated Hospital of Southern Medical University, Guangzhou, People’s Republic of China
- Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, Academy of Orthopedics, Guangzhou, Guangdong Province, People’s Republic of China
| | - Bibo Ren
- College of Biomass Science and Engineering, Sichuan University, Chengdu, People’s Republic of China
| | - Chao Hu
- Department of Hand and Foot Microsurgery, The affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, People’s Republic of China
| | - Guowei Zhang
- Department of Joint Surgery and Sports Medicine, Center for Orthopedic Surgery, Orthopedic Hospital of Guangdong Province, The Third Affiliated Hospital of Southern Medical University, Guangzhou, People’s Republic of China
- Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, Academy of Orthopedics, Guangzhou, Guangdong Province, People’s Republic of China
| | - Fen Yang
- Department of Infectious Diseases, The Affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, Hunan, People’s Republic of China
| | - Meimei Xiao
- Department of Hand and Foot Microsurgery, The affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, People’s Republic of China
| | - Songlin Xie
- Department of Hand and Foot Microsurgery, The affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, People’s Republic of China
| | - Denghui Xie
- Department of Joint Surgery and Sports Medicine, Center for Orthopedic Surgery, Orthopedic Hospital of Guangdong Province, The Third Affiliated Hospital of Southern Medical University, Guangzhou, People’s Republic of China
- Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, Academy of Orthopedics, Guangzhou, Guangdong Province, People’s Republic of China
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3
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Fernandez NL, Simmons LA. Two distinct regulatory systems control pulcherrimin biosynthesis in Bacillus subtilis. PLoS Genet 2024; 20:e1011283. [PMID: 38753885 PMCID: PMC11135676 DOI: 10.1371/journal.pgen.1011283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/29/2024] [Accepted: 05/03/2024] [Indexed: 05/18/2024] Open
Abstract
Regulation of transcription is a fundamental process that allows bacteria to respond to external stimuli with appropriate timing and magnitude of response. In the soil bacterium Bacillus subtilis, transcriptional regulation is at the core of developmental processes needed for cell survival. Gene expression in cells transitioning from exponential phase to stationary phase is under the control of a group of transcription factors called transition state regulators (TSRs). TSRs influence numerous developmental processes including the decision between biofilm formation and motility, genetic competence, and sporulation, but the extent to which TSRs influence bacterial physiology remains to be fully elucidated. Here, we demonstrate two TSRs, ScoC and AbrB, along with the MarR-family transcription factor PchR negatively regulate production of the iron chelator pulcherrimin in B. subtilis. Genetic analysis of the relationship between the three transcription factors indicate that all are necessary to limit pulcherrimin production during exponential phase and influence the rate and total amount of pulcherrimin produced. Similarly, expression of the pulcherrimin biosynthesis gene yvmC was found to be under control of ScoC, AbrB, and PchR and correlated with the amount of pulcherrimin produced by each background. Lastly, our in vitro data indicate a weak direct role for ScoC in controlling pulcherrimin production along with AbrB and PchR. The layered regulation by two distinct regulatory systems underscores the important role for pulcherrimin in B. subtilis physiology.
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Affiliation(s)
- Nicolas L. Fernandez
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lyle A. Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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4
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He P, Hu S, Zhang Y, Xiang Z, Zhang Z, Wang D, Chen S. A new ROS response factor YvmB protects Bacillus licheniformis against oxidative stress under adverse environment. Appl Environ Microbiol 2024; 90:e0146823. [PMID: 38193675 PMCID: PMC10880666 DOI: 10.1128/aem.01468-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/30/2023] [Indexed: 01/10/2024] Open
Abstract
Bacillus spp., a class of aerobic bacteria, is widely used as a biocontrol microbe in the world. However, the reactive oxygen species (ROS) will accumulate once the aerobic bacteria are exposed to environmental stresses, which can decrease cell activity or lead to cell death. Hydroxyl radical (·OH), the strongest oxide in the ROS, can damage DNA directly, which is generated through Fenton Reaction by H2O2 and free iron. Here, we proved that the synthesis of pulcherriminic acid (PA), an iron chelator produced by Bacillus spp., could reduce DNA damage to protect cells from oxidative stress by sequestrating excess free iron, which enhanced the cell survival rates in stressful conditions (salt, antibiotic, and high temperature). It was worth noting that the synthesis of PA was found to be increased under oxidative stress. Thus, we demonstrated that the YvmB, a direct negative regulator of PA synthesis cluster yvmC-cypX, could be oxidized at cysteine residue (C57) to form a dimer losing the DNA-binding activity, which led to an improvement in PA production. Collectively, our findings highlight that YvmB senses ROS to regulate PA synthesis is one of the evolved proactive defense systems in bacteria against adverse environments.IMPORTANCEUnder environment stress, the electron transfer chain will be perturbed resulting in the accumulation of H2O2 and rapidly transform to ·OH through Fenton Reaction. How do bacteria deal with oxidative stress? At present, several iron chelators have been reported to decrease the ·OH generation by sequestrating iron, while how bacteria control the synthesis of iron chelators to resist oxidative stress is still unclear. Our study found that the synthesis of iron chelator PA is induced by reactive oxygen species (ROS), which means that the synthesis of iron chelator is a proactive defense mechanism against environment stress. Importantly, YvmB is the first response factor found to protect cells by reducing the ROS generation, which present a new perspective in antioxidation studies.
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Affiliation(s)
- Penghui He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, China
| | - Shiying Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, China
| | - Yongjia Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, China
| | - Zhengwei Xiang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, China
| | - Zheng Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, China
| | - Dong Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, China
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, China
- Key Laboratory of Green Chemical Technology of Fujian Province University, College of Ecological and Resource Engineering, Wuyi University, Wuyishan, China
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5
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Freimoser FM, Mahler M, McCullough M, Brachmann AO, Nägeli L, Hilber-Bodmer M, Piel J, Hoffmann SA, Cai Y. Heterologous pulcherrimin production in Saccharomyces cerevisiae confers inhibitory activity on Botrytis conidiation. FEMS Yeast Res 2024; 24:foad053. [PMID: 38140959 PMCID: PMC10786192 DOI: 10.1093/femsyr/foad053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 12/01/2023] [Accepted: 12/21/2023] [Indexed: 12/24/2023] Open
Abstract
Pulcherrimin is an iron (III) chelate of pulcherriminic acid that plays a role in antagonistic microbial interactions, iron metabolism, and stress responses. Some bacteria and yeasts produce pulcherriminic acid, but so far, pulcherrimin could not be produced in Saccharomyces cerevisiae. Here, multiple integrations of the Metschnikowia pulcherrima PUL1 and PUL2 genes in the S. cerevisiae genome resulted in red colonies, which indicated pulcherrimin formation. The coloration correlated positively and significantly with the number of PUL1 and PUL2 genes. The presence of pulcherriminic acid was confirmed by mass spectrometry. In vitro competition assays with the plant pathogenic fungus Botrytis caroliana revealed inhibitory activity on conidiation by an engineered, strong pulcherrimin-producing S. cerevisiae strain. We demonstrate that the PUL1 and PUL2 genes from M. pulcherrima, in multiple copies, are sufficient to transfer pulcherrimin production to S. cerevisiae and represent the starting point for engineering and optimizing this biosynthetic pathway in the future.
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Affiliation(s)
- Florian M Freimoser
- Agroscope, Research Division Plant Protection, Route de Duillier 60, 1260 Nyon 1, Switzerland
| | - Marina Mahler
- Agroscope, Research Division Plant Protection, Route de Duillier 60, 1260 Nyon 1, Switzerland
| | - Mark McCullough
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street Manchester M1 7DN, UK
| | - Alexander O Brachmann
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Lukas Nägeli
- Agroscope, Research Division Plant Protection, Route de Duillier 60, 1260 Nyon 1, Switzerland
| | - Maja Hilber-Bodmer
- Agroscope, Research Division Plant Protection, Route de Duillier 60, 1260 Nyon 1, Switzerland
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Stefan A Hoffmann
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street Manchester M1 7DN, UK
| | - Yizhi Cai
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street Manchester M1 7DN, UK
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6
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Fernandez NL, Simmons LA. Two Distinct Regulatory Systems Control Pulcherrimin Biosynthesis in Bacillus subtilis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.574033. [PMID: 38260623 PMCID: PMC10802322 DOI: 10.1101/2024.01.03.574033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Regulation of transcription is a fundamental process that allows bacteria to respond to external stimuli with appropriate timing and magnitude of response. In the soil bacterium Bacillus subtilis, transcriptional regulation is at the core of developmental processes needed for cell survival. Gene expression in cells transitioning from exponential phase to stationary phase is under the control of a group of transcription factors called transition state regulators (TSRs). TSRs influence numerous developmental processes including the decision between biofilm formation and motility, genetic competence, and sporulation, but the extent to which TSRs influence bacterial physiology remains to be fully elucidated. Here, we demonstrate two TSRs, ScoC and AbrB, along with the MerR-family transcription factor PchR negatively regulate production of the iron chelator pulcherrimin in B. subtilis. Genetic analysis of the relationship between the three transcription factors indicate that all are necessary to limit pulcherrimin production during exponential phase and influence the rate and total amount of pulcherrimin produced. Similarly, expression of the pulcherrimin biosynthesis gene yvmC was found to be under control of ScoC, AbrB, and PchR and correlated with the amount of pulcherrimin produced by each background. Lastly, our in vitro data indicate a weak direct role for ScoC in controlling pulcherrimin production along with AbrB and PchR. The layered regulation by two distinct regulatory systems underscores the important, and somewhat enigmatic, role for pulcherrimin in B. subtilis physiology.
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Affiliation(s)
- Nicolas L. Fernandez
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Lyle A. Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
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7
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Kang X, Yang X, He Y, Guo C, Li Y, Ji H, Qin Y, Wu L. Strategies and materials for the prevention and treatment of biofilms. Mater Today Bio 2023; 23:100827. [PMID: 37859998 PMCID: PMC10582481 DOI: 10.1016/j.mtbio.2023.100827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023] Open
Abstract
Biofilms are aggregates of organized microbial growth that function as barriers and create a stable internal environment for cell survival. The bacteria in the biofilms exhibit characteristics that are quite different from the planktonic bacteria, such as strong resistance to antibiotics and other bactericides, getting out of host immunity, and developing in harsh environments, which all contribute to the persistent and intractable treatment. Hence, there is an urgent need to develop novel materials and strategies to combat biofilms. However, most of the reviews on anti-biofilms published in recent years are based on specific fields or materials. Microorganisms are ubiquitous, except in the context of medical and health issues; however, biofilms exert detrimental effects on the advancement and progress of various fields. Therefore, this review aims to provide a comprehensive summary of effective strategies and methodologies applicable across all industries. Firstly, the process of biofilms formation was introduced to enhance our comprehension of the "enemy". Secondly, strategies to intervene in the important links of biofilms formation were discussed, taking timely action during the early weak stages of the "enemy". Thirdly, treatment strategies for mature biofilms were summarized to deal with biofilms that break through the defense line. Finally, several substances with antibacterial properties were presented. The review concludes with the standpoint of the author about potential developments of anti-biofilms strategies. This review may help researchers quickly understand the research progress and challenges in the field of anti-biofilms to design more efficient methods and strategies to combat biofilms.
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Affiliation(s)
- Xiaoxia Kang
- School of Public Health, Nantong Key Laboratory of Public Health and Medical Analysis, Nantong University, Nantong, 226019, China
| | - Xiaoxiao Yang
- School of Public Health, Nantong Key Laboratory of Public Health and Medical Analysis, Nantong University, Nantong, 226019, China
| | - Yue He
- School of Public Health, Nantong Key Laboratory of Public Health and Medical Analysis, Nantong University, Nantong, 226019, China
| | - Conglin Guo
- School of Public Health, Nantong Key Laboratory of Public Health and Medical Analysis, Nantong University, Nantong, 226019, China
| | - Yuechen Li
- School of Public Health, Nantong Key Laboratory of Public Health and Medical Analysis, Nantong University, Nantong, 226019, China
| | - Haiwei Ji
- School of Public Health, Nantong Key Laboratory of Public Health and Medical Analysis, Nantong University, Nantong, 226019, China
| | - Yuling Qin
- School of Public Health, Nantong Key Laboratory of Public Health and Medical Analysis, Nantong University, Nantong, 226019, China
| | - Li Wu
- School of Public Health, Nantong Key Laboratory of Public Health and Medical Analysis, Nantong University, Nantong, 226019, China
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8
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Zhu XC, Xu SG, Wang YR, Zou MT, Mridha MAU, Javed K, Wang Y. Unveiling the Potential of Bacillus safensis Y246 for Enhanced Suppression of Rhizoctonia solani. J Fungi (Basel) 2023; 9:1085. [PMID: 37998890 PMCID: PMC10672523 DOI: 10.3390/jof9111085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023] Open
Abstract
Rhizoctonia solani is a significant pathogen affecting various crops, including tobacco. In this study, a bacterial strain, namely Y246, was isolated from the soil of healthy plants and exhibited high antifungal activity. Based on morphological identification and DNA sequencing, this bacterial strain was identified as Bacillus safensis. The aim of this investigation was to explore the antifungal potential of strain Y246, to test the antifungal stability of Y246 by adjusting different cultivation conditions, and to utilize gas chromatography-mass spectrometry (GC-MS) to predict the volatile compounds related to antifungal activity in Y246. In vitro assays demonstrated that strain Y246 exhibited a high fungal inhibition rate of 76.3%. The fermentation broth and suspension of strain Y246 inhibited the mycelial growth of R. solani by 66.59% and 63.75%, respectively. Interestingly, treatment with volatile compounds derived from the fermentation broth of strain Y246 resulted in abnormal mycelial growth of R. solani. Scanning electron microscopy analysis revealed bent and deformed mycelium structures with a rough surface. Furthermore, the stability of antifungal activity of the fermentation broth of strain Y246 was assessed. Changes in temperature, pH value, and UV irradiation time had minimal impact on the antifungal activity, indicating the stability of the antifungal activity of strain Y246. A GC-MS analysis of the volatile organic compounds (VOCs) produced by strain Y246 identified a total of 34 compounds with inhibitory effects against different fungi. Notably, the strain demonstrated broad-spectrum activity, exhibiting varying degrees of inhibition against seven pathogens (Alternaria alternata, Phomopsis. sp., Gloeosporium musarum, Dwiroopa punicae, Colletotrichum karstii, Botryosphaeria auasmontanum, and Botrytis cinerea). In our extensive experiments, strain Y246 not only exhibited strong inhibition against R. solani but also demonstrated remarkable inhibitory effects on A. alternata-induced tobacco brown spot and kiwifruit black spot, with impressive inhibition rates of 62.96% and 46.23%, respectively. Overall, these findings highlight the significant antifungal activity of B. safensis Y246 against R. solani. In addition, Y246 has an excellent antifungal stability, with an inhibition rate > 30% under different treatments (temperature, pH, UV). The results showed that the VOCs of strain Y246 had a strong inhibitory effect on the colony growth of R. solani, and the volatile substances produced by strain Y246 had an inhibitory effect on R. solani at rate of 70.19%. Based on these results, we can conclude that Y246 inhibits the normal growth of R. solani. These findings can provide valuable insights for developing sustainable agricultural strategies.
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Affiliation(s)
- Xing-Cheng Zhu
- Department of Plant Pathology, Agriculture College, Guizhou University, Guiyang 550025, China; (X.-C.Z.); (S.-G.X.); (Y.-R.W.); (M.-T.Z.)
| | - Shu-Gang Xu
- Department of Plant Pathology, Agriculture College, Guizhou University, Guiyang 550025, China; (X.-C.Z.); (S.-G.X.); (Y.-R.W.); (M.-T.Z.)
| | - Yu-Ru Wang
- Department of Plant Pathology, Agriculture College, Guizhou University, Guiyang 550025, China; (X.-C.Z.); (S.-G.X.); (Y.-R.W.); (M.-T.Z.)
| | - Meng-Ting Zou
- Department of Plant Pathology, Agriculture College, Guizhou University, Guiyang 550025, China; (X.-C.Z.); (S.-G.X.); (Y.-R.W.); (M.-T.Z.)
| | | | - Khadija Javed
- Department of Plant Pathology, Agriculture College, Guizhou University, Guiyang 550025, China; (X.-C.Z.); (S.-G.X.); (Y.-R.W.); (M.-T.Z.)
- Julius Kühn-Institut (JKI) for Biological Control, 64287 Darmstadt, Germany
| | - Yong Wang
- Department of Plant Pathology, Agriculture College, Guizhou University, Guiyang 550025, China; (X.-C.Z.); (S.-G.X.); (Y.-R.W.); (M.-T.Z.)
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9
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Angelini LL, Dos Santos RAC, Fox G, Paruthiyil S, Gozzi K, Shemesh M, Chai Y. Pulcherrimin protects Bacillus subtilis against oxidative stress during biofilm development. NPJ Biofilms Microbiomes 2023; 9:50. [PMID: 37468524 PMCID: PMC10356805 DOI: 10.1038/s41522-023-00418-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 07/04/2023] [Indexed: 07/21/2023] Open
Abstract
Pulcherrimin is an iron-binding reddish pigment produced by various bacterial and yeast species. In the soil bacterium Bacillus subtilis, this pigment is synthesized intracellularly as the colorless pulcherriminic acid by using two molecules of tRNA-charged leucine as the substrate; pulcherriminic acid molecules are then secreted and bind to ferric iron extracellularly to form the red-colored pigment pulcherrimin. The biological importance of pulcherrimin is not well understood. A previous study showed that secretion of pulcherrimin caused iron depletion in the surroundings and growth arrest on cells located at the edge of a B. subtilis colony biofilm. In this study, we identified that pulcherrimin is primarily produced under biofilm conditions and provides protection to cells in the biofilm against oxidative stress. We presented molecular evidence on how pulcherrimin lowers the level of reactive oxygen species (ROS) and alleviates oxidative stress and DNA damage caused by ROS accumulation in a mature biofilm. We also performed global transcriptome profiling to identify differentially expressed genes in the pulcherrimin-deficient mutant compared with the wild type, and further characterized the regulation of genes by pulcherrimin that are related to iron homeostasis, DNA damage response (DDR), and oxidative stress response. Based on our findings, we propose pulcherrimin as an important antioxidant that modulates B. subtilis biofilm development.
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Affiliation(s)
| | | | - Gabriel Fox
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Srinand Paruthiyil
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
- Medical Scientist Training Program (MSTP), Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO, 63110, USA
| | - Kevin Gozzi
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
- The Rowland Institute at Harvard, 100 Edwin H. Land Blvd., Cambridge, MA, 02142, USA
| | - Moshe Shemesh
- Department of Food Science, Agricultural Research Organization The Volcani Institute, Derech Hamacabim, POB 15159, Rishon LeZion, 7528809, Israel
| | - Yunrong Chai
- Department of Biology, Northeastern University, Boston, MA, 02115, USA.
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10
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Kregiel D, Czarnecka-Chrebelska KH, Schusterová H, Vadkertiová R, Nowak A. The Metschnikowia pulcherrima Clade as a Model for Assessing Inhibition of Candida spp. and the Toxicity of Its Metabolite, Pulcherrimin. Molecules 2023; 28:5064. [PMID: 37446724 DOI: 10.3390/molecules28135064] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Candidiasis is one of the most frequent infections worldwide. In this study, the antimicrobial properties of six strains belonging to the Metschnikowia pulcherrima clade were evaluated against twenty Candida and Candida-related Filobasidiella neoformans var. bacillispora (syn. Cryptococcus neoformans) of different origins, employing the agar cross method. The toxic effect of pulcherrimin, a red metabolite that is responsible for the antimicrobial activities of Metschnikowia spp., was evaluated in various experimental models. The results of agar tests showed that the selected M. pulcherrima strains inhibited the growth of the Candida and non-Candida strains. However, inhibition was dependent on the strain and the environment. The presence of peptone, sodium silicate, and a higher incubation temperature decreased the antifungal action of the M. pulcherrima strains. Pulcherrimin showed cytotoxic and antiproliferative activity, with oxidative stress in cells leading to apoptosis. More research is needed on the mechanism of action of pulcherrimin on somatic cells.
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Affiliation(s)
- Dorota Kregiel
- Department of Environmental Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
- Culture Collection of Yeasts, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 38 Bratislava, Slovakia
| | | | - Hana Schusterová
- Culture Collection of Yeasts, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 38 Bratislava, Slovakia
| | - Renáta Vadkertiová
- Culture Collection of Yeasts, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 38 Bratislava, Slovakia
| | - Adriana Nowak
- Department of Environmental Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
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11
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Charron-Lamoureux V, Haroune L, Pomerleau M, Hall L, Orban F, Leroux J, Rizzi A, Bourassa JS, Fontaine N, d'Astous ÉV, Dauphin-Ducharme P, Legault CY, Bellenger JP, Beauregard PB. Pulcherriminic acid modulates iron availability and protects against oxidative stress during microbial interactions. Nat Commun 2023; 14:2536. [PMID: 37137890 PMCID: PMC10156857 DOI: 10.1038/s41467-023-38222-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 04/20/2023] [Indexed: 05/05/2023] Open
Abstract
Siderophores are soluble or membrane-embedded molecules that bind the oxidized form of iron, Fe(III), and play roles in iron acquisition by microorganisms. Fe(III)-bound siderophores bind to specific receptors that allow microbes to acquire iron. However, certain soil microbes release a compound (pulcherriminic acid, PA) that, upon binding to Fe(III), forms a precipitate (pulcherrimin) that apparently functions by reducing iron availability rather than contributing to iron acquisition. Here, we use Bacillus subtilis (PA producer) and Pseudomonas protegens as a competition model to show that PA is involved in a peculiar iron-managing system. The presence of the competitor induces PA production, leading to precipitation of Fe(III) as pulcherrimin, which prevents oxidative stress in B. subtilis by restricting the Fenton reaction and deleterious ROS formation. In addition, B. subtilis uses its known siderophore bacillibactin to retrieve Fe(III) from pulcherrimin. Our findings indicate that PA plays multiple roles by modulating iron availability and conferring protection against oxidative stress during inter-species competition.
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Affiliation(s)
| | - Lounès Haroune
- Département de chimie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
- Institut de pharmacologie de Sherbrooke, Faculté de médecine, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Maude Pomerleau
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Léo Hall
- Département de chimie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Frédéric Orban
- Département de chimie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Julie Leroux
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Adrien Rizzi
- Département de chimie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Jean-Sébastien Bourassa
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Nicolas Fontaine
- Département de chimie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Élodie V d'Astous
- Département de chimie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | | | - Claude Y Legault
- Département de chimie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Jean-Philippe Bellenger
- Département de chimie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Pascale B Beauregard
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada.
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12
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Zhang Z, He P, Hu S, Yu Y, Wang X, Ishaq AR, Chen S. Promoting cell growth for bio-chemicals production via boosting the synthesis of L/D-alanine and D-alanyl-D-alanine in Bacillus licheniformis. World J Microbiol Biotechnol 2023; 39:115. [PMID: 36918439 DOI: 10.1007/s11274-023-03560-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 02/28/2023] [Indexed: 03/16/2023]
Abstract
Metabolic engineering is a substantial approach for escalating the production of biochemical products. Cell biomass is lowered by system constraints and toxication carried on by the aggregation of metabolites that serve as inhibitors of product synthesis. In order to increase the production of biochemical products, it is important to trace the relationship between alanine metabolism and biomass. According to our investigation, the appropriate concentration of additional L/D-alanine (0.1 g/L) raised the cell biomass (OD600) in Bacillus licheniformis in contrast to the control strain. Remarkably, it was also determined that high levels of intracellular L/D-alanine and D-alanyl-D-alanine were induced by the overexpression of the ald, dal, and ddl genes to accelerate cell proliferation. Our findings clearly revealed that 0.2 g/L of L-alanine and D-alanine substantially elevated the titer of poly-γ-glutamic acid (γ-PGA) by 14.89% and 6.19%, correspondingly. And the levels of γ-PGA titer were hastened by the overexpression of the ald, dal, and ddl genes by 19.72%, 15.91%, and 16.64%, respectively. Furthermore, overexpression of ald, dal, and ddl genes decreased the by-products (acetoin, 2,3-butanediol, acetic acid and lactic acid) formation by about 14.10%, 8.77%, and 8.84% for augmenting the γ-PGA production. Our results also demonstrated that overexpression of ald gene amplified the production of lichenysin, pulcherrimin and nattokinase by about 18.71%, 19.82% and 21.49%, respectively. This work delineated the importance of the L/D-alanine and D-alanyl-D-alanine synthesis to the cell growth and the high production of bio-products, and provided an effective strategy for producing bio-products.
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Affiliation(s)
- Zheng Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 430062, Wuhan, China
| | - Penghui He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 430062, Wuhan, China
| | - Shiying Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 430062, Wuhan, China
| | - Yanqing Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 430062, Wuhan, China
| | - Xiaoting Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 430062, Wuhan, China
| | - Ali Raza Ishaq
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 430062, Wuhan, China
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 430062, Wuhan, China. .,, 368 Youyi Avenue, Wuchang District, 430062, Wuhan, Hubei, PR China.
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13
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New perspectives for mechanisms, ingredients, and their preparation for promoting the formation of beneficial bacterial biofilm. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2023. [DOI: 10.1007/s11694-022-01777-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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14
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Eigentler L, Davidson FA, Stanley-Wall NR. Mechanisms driving spatial distribution of residents in colony biofilms: an interdisciplinary perspective. Open Biol 2022; 12:220194. [PMID: 36514980 PMCID: PMC9748781 DOI: 10.1098/rsob.220194] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Biofilms are consortia of microorganisms that form collectives through the excretion of extracellular matrix compounds. The importance of biofilms in biological, industrial and medical settings has long been recognized due to their emergent properties and impact on surrounding environments. In laboratory situations, one commonly used approach to study biofilm formation mechanisms is the colony biofilm assay, in which cell communities grow on solid-gas interfaces on agar plates after the deposition of a population of founder cells. The residents of a colony biofilm can self-organize to form intricate spatial distributions. The assay is ideally suited to coupling with mathematical modelling due to the ability to extract a wide range of metrics. In this review, we highlight how interdisciplinary approaches have provided deep insights into mechanisms causing the emergence of these spatial distributions from well-mixed inocula.
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Affiliation(s)
- Lukas Eigentler
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK,Mathematics, School of Science and Engineering, University of Dundee, Dundee DD1 4HN, UK
| | - Fordyce A. Davidson
- Mathematics, School of Science and Engineering, University of Dundee, Dundee DD1 4HN, UK
| | - Nicola R. Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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15
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Chen T, Zhang Z, Li W, Chen J, Chen X, Wang B, Ma J, Dai Y, Ding H, Wang W, Long Y. Biocontrol potential of Bacillus subtilis CTXW 7-6-2 against kiwifruit soft rot pathogens revealed by whole-genome sequencing and biochemical characterisation. Front Microbiol 2022; 13:1069109. [PMID: 36532498 PMCID: PMC9751376 DOI: 10.3389/fmicb.2022.1069109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/14/2022] [Indexed: 09/05/2023] Open
Abstract
Soft rot causes significant economic losses in the kiwifruit industry. This study isolated strain CTXW 7-6-2 from healthy kiwifruit tissue; this was a gram-positive bacterium that produced the red pigment pulcherrimin. The phylogenetic tree based on 16S ribosomal RNA, gyrA, rpoB, and purH gene sequences identified CTXW 7-6-2 as a strain of Bacillus subtilis. CTXW 7-6-2 inhibited hyphal growth of pathogenic fungi that cause kiwifruit soft rot, namely, Botryosphaeria dothidea, Phomopsis sp., and Alternaria alternata, by 81.76, 69.80, and 32.03%, respectively. CTXW 7-6-2 caused the hyphal surface to become swollen and deformed. Volatile compounds (VOC) produced by the strain inhibited the growth of A. alternata and Phomopsis sp. by 65.74 and 54.78%, respectively. Whole-genome sequencing revealed that CTXW 7-6-2 possessed a single circular chromosome of 4,221,676 bp that contained 4,428 protein-coding genes, with a guanine and cytosine (GC) content of 43.41%. Gene functions were annotated using the National Center for Biotechnology Information (NCBI) non-redundant protein, Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes, Clusters of Orthologous Groups of proteins, Gene Ontology, Pathogen-Host Interactions, Carbohydrate-Active enZYmes, and Rapid Annotations using Subsystem Technology databases, revealing non-ribosomal pathways associated with antifungal mechanisms, biofilm formation, chemotactic motility, VOC 3-hydroxy-2-butanone, cell wall-associated enzymes, and synthesis of various secondary metabolites. antiSMASH analysis predicted that CTXW 7-6-2 can produce the active substances bacillaene, bacillibactin, subtilosin A, bacilysin, and luminmide and has four gene clusters of unknown function. Quantitative real-time PCR (qRT-PCR) analysis verified that yvmC and cypX, key genes involved in the production of pulcherrimin, were highly expressed in CTXW 7-6-2. This study elucidates the mechanism by which B. subtilis strain CTXW 7-6-2 inhibits pathogenic fungi that cause kiwifruit soft rot, suggesting the benefit of further studying its antifungal active substances.
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Affiliation(s)
- Tingting Chen
- Research Center for Engineering Technology of Kiwifruit, College of Agriculture, Institute of Crop Protection, Guizhou University, Guiyang, China
| | - Zhuzhu Zhang
- Research Center for Engineering Technology of Kiwifruit, College of Agriculture, Institute of Crop Protection, Guizhou University, Guiyang, China
| | - Wenzhi Li
- Research Center for Engineering Technology of Kiwifruit, College of Agriculture, Institute of Crop Protection, Guizhou University, Guiyang, China
| | - Jia Chen
- Research Center for Engineering Technology of Kiwifruit, College of Agriculture, Institute of Crop Protection, Guizhou University, Guiyang, China
| | - Xuetang Chen
- Research Center for Engineering Technology of Kiwifruit, College of Agriculture, Institute of Crop Protection, Guizhou University, Guiyang, China
| | - Bince Wang
- Research Center for Engineering Technology of Kiwifruit, College of Agriculture, Institute of Crop Protection, Guizhou University, Guiyang, China
| | - Jiling Ma
- Research Center for Engineering Technology of Kiwifruit, College of Agriculture, Institute of Crop Protection, Guizhou University, Guiyang, China
| | - Yunyun Dai
- Research Center for Engineering Technology of Kiwifruit, College of Agriculture, Institute of Crop Protection, Guizhou University, Guiyang, China
| | - Haixia Ding
- Research Center for Engineering Technology of Kiwifruit, College of Agriculture, Institute of Crop Protection, Guizhou University, Guiyang, China
- Department of Plant Pathology, Guizhou University, Guiyang, China
| | - Weizhen Wang
- Research Center for Engineering Technology of Kiwifruit, College of Agriculture, Institute of Crop Protection, Guizhou University, Guiyang, China
| | - Youhua Long
- Research Center for Engineering Technology of Kiwifruit, College of Agriculture, Institute of Crop Protection, Guizhou University, Guiyang, China
- Teaching Experimental Factory, Guizhou University, Guiyang, China
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16
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Villa F, Wu YL, Zerboni A, Cappitelli F. In Living Color: Pigment-Based Microbial Ecology At the Mineral-Air Interface. Bioscience 2022; 72:1156-1175. [PMID: 36451971 PMCID: PMC9699719 DOI: 10.1093/biosci/biac091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Pigment-based color is one of the most important phenotypic traits of biofilms at the mineral-air interface (subaerial biofilms, SABs), because it reflects the physiology of the microbial community. Because color is the hallmark of all SABs, we argue that pigment-based color could convey the mechanisms that drive microbial adaptation and coexistence across different terrestrial environments and link phenotypic traits to community fitness and ecological dynamics. Within this framework, we present the most relevant microbial pigments at the mineral-air interface and discuss some of the evolutionary landscapes that necessitate pigments as adaptive strategies for resource allocation and survivability. We report several pigment features that reflect SAB communities' structure and function, as well as pigment ecology in the context of microbial life-history strategies and coexistence theory. Finally, we conclude the study of pigment-based ecology by presenting its potential application and some of the key challenges in the research.
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17
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Cryptic specialized metabolites drive Streptomyces exploration and provide a competitive advantage during growth with other microbes. Proc Natl Acad Sci U S A 2022; 119:e2211052119. [PMID: 36161918 DOI: 10.1073/pnas.2211052119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Streptomyces bacteria have a complex life cycle that is intricately linked with their remarkable metabolic capabilities. Exploration is a recently discovered developmental innovation of these bacteria, that involves the rapid expansion of a structured colony on solid surfaces. Nutrient availability impacts exploration dynamics, and we have found that glycerol can dramatically increase exploration rates and alter the metabolic output of exploring colonies. We show here that glycerol-mediated growth acceleration is accompanied by distinct transcriptional signatures and by the activation of otherwise cryptic metabolites including the orange-pigmented coproporphyrin, the antibiotic chloramphenicol, and the uncommon, alternative siderophore foroxymithine. Exploring cultures are also known to produce the well-characterized desferrioxamine siderophore. Mutational studies of single and double siderophore mutants revealed functional redundancy when strains were cultured on their own; however, loss of the alternative foroxymithine siderophore imposed a more profound fitness penalty than loss of desferrioxamine during coculture with the yeast Saccharomyces cerevisiae. Notably, the two siderophores displayed distinct localization patterns, with desferrioxamine being confined within the colony area, and foroxymithine diffusing well beyond the colony boundary. The relative fitness advantage conferred by the alternative foroxymithine siderophore was abolished when the siderophore piracy capabilities of S. cerevisiae were eliminated (S. cerevisiae encodes a ferrioxamine-specific transporter). Our work suggests that exploring Streptomyces colonies can engage in nutrient-targeted metabolic arms races, deploying alternative siderophores that allow them to successfully outcompete other microbes for the limited bioavailable iron during coculture.
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18
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Porter M, Davidson FA, MacPhee CE, Stanley-Wall NR. Systematic microscopical analysis reveals obligate synergy between extracellular matrix components during Bacillus subtilis colony biofilm development. Biofilm 2022; 4:100082. [PMID: 36148433 PMCID: PMC9486643 DOI: 10.1016/j.bioflm.2022.100082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/11/2022] [Accepted: 08/11/2022] [Indexed: 12/03/2022] Open
Abstract
Single-species bacterial colony biofilms often present recurring morphologies that are thought to be of benefit to the population of cells within and are known to be dependent on the self-produced extracellular matrix. However, much remains unknown in terms of the developmental process at the single cell level. Here, we design and implement systematic time-lapse imaging and quantitative analyses of the growth of Bacillus subtilis colony biofilms. We follow the development from the initial deposition of founding cells through to the formation of large-scale complex structures. Using the model biofilm strain NCIB 3610, we examine the movement dynamics of the growing biomass and compare them with those displayed by a suite of otherwise isogenic matrix-mutant strains. Correspondingly, we assess the impact of an incomplete matrix on biofilm morphologies and sessile growth rate. Our results indicate that radial expansion of colony biofilms results from the division of bacteria at the biofilm periphery rather than being driven by swelling due to fluid intake. Moreover, we show that lack of exopolysaccharide production has a negative impact on cell division rate, and the extracellular matrix components act synergistically to give the biomass the structural strength to produce aerial protrusions and agar substrate-deforming ability.
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19
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Young E, Allen RJ. Lineage dynamics in growing biofilms: Spatial patterns of standing vs. de novo diversity. Front Microbiol 2022; 13:915095. [PMID: 35966660 PMCID: PMC9363821 DOI: 10.3389/fmicb.2022.915095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
Microbial biofilms show high phenotypic and genetic diversity, yet the mechanisms underlying diversity generation and maintenance remain unclear. Here, we investigate how spatial patterns of growth activity within a biofilm lead to spatial patterns of genetic diversity. Using individual-based computer simulations, we show that the active layer of growing cells at the biofilm interface controls the distribution of lineages within the biofilm, and therefore the patterns of standing and de novo diversity. Comparing biofilms of equal size, those with a thick active layer retain more standing diversity, while de novo diversity is more evenly distributed within the biofilm. In contrast, equal-sized biofilms with a thin active layer retain less standing diversity, and their de novo diversity is concentrated at the top of the biofilm, and in fewer lineages. In the context of antimicrobial resistance, biofilms with a thin active layer may be more prone to generate lineages with multiple resistance mutations, and to seed new resistant biofilms via sloughing of resistant cells from the upper layers. Our study reveals fundamental "baseline" mechanisms underlying the patterning of diversity within biofilms.
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Affiliation(s)
- Ellen Young
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Rosalind J. Allen
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
- Theoretical Microbial Ecology, Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
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20
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Xu S, Cao Q, Liu Z, Chen J, Yan P, Li B, Xu Y. Transcriptomic Analysis Reveals the Role of tmRNA on Biofilm Formation in Bacillus subtilis. Microorganisms 2022; 10:microorganisms10071338. [PMID: 35889057 PMCID: PMC9319509 DOI: 10.3390/microorganisms10071338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
Bacillus strains are widely distributed in terrestrial and marine environments, and some of them are used as biocontrol organisms for their biofilm-formation ability. In Bacillus subtilis, biofilm formation is fine-tuned by a complex network, a clear understanding of which still requires study. In bacteria, tmRNA, encoded by the ssrA gene, catalyzes trans-translation that can rescue ribosomes stalled on mRNA transcripts lacking a functional stop codon. tmRNA also affects physiological bioprocesses in some bacteria. In this study, we constructed a ssrA mutant in B. subtilis and found that the biofilm formation in the ssrA mutant was largely impaired. Moreover, we isolated a biofilm-formation suppressor of ssrA, in which the biofilm formation was restored to a level even stronger than that in the wild type. We further performed RNAseq assays with the wild type, ssrA mutant, and suppressor of ssrA for comparisons of their transcriptomes. By analyzing the transcriptomic data, we predicted the possible functions of some differentially expressed genes (DEGs) in the tmRNA regulation of biofilm formation in B. subtilis. Finally, we found that the overexpression of two DEGs, acoA and yhjR, could restore the biofilm formation in the ssrA mutant, indicating that AcoA and YhjR were immediate regulators involved in the tmRNA regulatory web controlling biofilm formation in B. subtilis. Our data can improve the knowledge about the molecular network involved in Bacillus biofilm formation and provide new targets for manipulation of Bacillus biofilms for future investigation.
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Affiliation(s)
- Shanshan Xu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (S.X.); (Q.C.); (Z.L.); (J.C.)
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China;
| | - Qianqian Cao
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (S.X.); (Q.C.); (Z.L.); (J.C.)
| | - Zengzhi Liu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (S.X.); (Q.C.); (Z.L.); (J.C.)
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China;
| | - Junpeng Chen
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (S.X.); (Q.C.); (Z.L.); (J.C.)
| | - Peiguang Yan
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China;
| | - Bingyu Li
- Guangdong Key Laboratory for Genome Stability and Disease Prevention, Health Science Center, Shenzhen University, Shenzhen 518055, China
- Correspondence: (B.L.); (Y.X.)
| | - Ying Xu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (S.X.); (Q.C.); (Z.L.); (J.C.)
- Correspondence: (B.L.); (Y.X.)
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21
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Kregiel D, Nowacka M, Rygala A, Vadkertiová R. Biological Activity of Pulcherrimin from the Meschnikowia pulcherrima Clade. Molecules 2022; 27:molecules27061855. [PMID: 35335219 PMCID: PMC8949601 DOI: 10.3390/molecules27061855] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/27/2022] [Accepted: 03/09/2022] [Indexed: 12/21/2022] Open
Abstract
Pulcherrimin is a secondary metabolite of yeasts belonging to the Metschnikowia pulcherrima clade, and pulcherrimin formation is responsible for the antimicrobial action of its producers. Understanding the environmental function of this metabolite can provide insight into various microbial interactions and enables the efficient development of new effective bioproducts and methods. In this study, we evaluated the antimicrobial and antiadhesive action of yeast pulcherrimin, as well as its protective properties under selected stressful conditions. Classical microbiological plate methods, microscopy, and physico-chemical testing were used. The results show that pure pulcherrimin does not have antimicrobial properties, but its unique hydrophilic nature may hinder the adhesion of hydrophilic bacterial cells to abiotic surfaces. Pulcherrimin also proved to be a good cell protectant against UV–C radiation at both high and low temperatures.
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Affiliation(s)
- Dorota Kregiel
- Department of Environmental Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland;
- Culture Collection of Yeasts, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 38 Bratislava, Slovakia;
- Correspondence: ; Tel.: +48-426-313-247
| | - Maria Nowacka
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland;
| | - Anna Rygala
- Department of Environmental Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland;
| | - Renáta Vadkertiová
- Culture Collection of Yeasts, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 38 Bratislava, Slovakia;
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22
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Amoah YS, Rajasekharan SK, Reifen R, Shemesh M. Chickpea-Derived Prebiotic Substances Trigger Biofilm Formation by Bacillus subtilis. Nutrients 2021; 13:nu13124228. [PMID: 34959781 PMCID: PMC8704855 DOI: 10.3390/nu13124228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/19/2021] [Accepted: 11/21/2021] [Indexed: 11/16/2022] Open
Abstract
Chickpea-based foods are known for their low allergenicity and rich nutritional package. As an essential dietary legume, chickpea is often processed into milk or hummus or as an industrial source of protein and starch. The current study explores the feasibility of using the chickpea-derived prebiotic substances as a scaffold for growing Bacillus subtilis (a prospective probiotic bacterium) to develop synbiotic chickpea-based functional food. We report that the chickpea-derived fibers enhance the formation of the B. subtilis biofilms and the production of the antimicrobial pigment pulcherrimin. Furthermore, electron micrograph imaging confirms the bacterial embedding onto the chickpea fibers, which may provide a survival tactic to shield and protect the bacterial population from environmental insults. Overall, it is believed that chickpea-derived prebiotic substances provide a staple basis for developing functional probiotics and synbiotic food.
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Affiliation(s)
- Yaa Serwaah Amoah
- Department of Food Sciences, Institute for Postharvest Technology and Food Sciences, Agricultural Research Organization (ARO), Volcani Institute, Rishon LeZion 7528809, Israel; (Y.S.A.); (S.K.R.)
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel;
| | - Satish Kumar Rajasekharan
- Department of Food Sciences, Institute for Postharvest Technology and Food Sciences, Agricultural Research Organization (ARO), Volcani Institute, Rishon LeZion 7528809, Israel; (Y.S.A.); (S.K.R.)
| | - Ram Reifen
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel;
| | - Moshe Shemesh
- Department of Food Sciences, Institute for Postharvest Technology and Food Sciences, Agricultural Research Organization (ARO), Volcani Institute, Rishon LeZion 7528809, Israel; (Y.S.A.); (S.K.R.)
- Correspondence:
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23
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The Intertwined Roles of Specialized Metabolites within the Bacillus subtilis Biofilm. J Bacteriol 2021; 203:e0043121. [PMID: 34460313 DOI: 10.1128/jb.00431-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Bacteria produce specialized metabolites with a range of functions. In this issue of the Journal of Bacteriology, Schoenborn et al. study the production and role of secondary metabolites during biofilm development and sporulation in Bacillus subtilis (A. A. Schoenborn, S. M. Yannarell, E. D. Wallace, H. Clapper, et al., J Bacteriol 203:e00337-21, 2021, https://doi.org/https://doi.org/10.1128/JB.00337-21). Most metabolites studied are produced during differentiation, and six are required for the development of biofilms and/or spores. The authors propose a model for the timing of production and role in differentiation exerted by each secondary metabolite.
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Luo C, Liu J, Bilal M, Liu X, Wang X, Dong F, Liu Y, Zang S, Yin X, Yang X, Zhu T, Zhang S, Zhang W, Li B. Extracellular lipopeptide bacillomycin L regulates serial expression of genes for modulating multicellular behavior in Bacillus velezensis Bs916. Appl Microbiol Biotechnol 2021; 105:6853-6870. [PMID: 34477941 DOI: 10.1007/s00253-021-11524-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/30/2021] [Accepted: 08/05/2021] [Indexed: 11/29/2022]
Abstract
In wild strains of Bacillus, a handful of extracellular natural products act as signals that can regulate multicellular behavior, but relatively little is known about molecular mechanisms' detail. We proposed a previously unreported molecular mechanism for triggering multicellularity in B. velezensis Bs916 by an endogenous cyclic lipopeptide, bacillomycin L. The genome-wide effect on gene expression was caused by the disruption of bacillomycin L gene cluster, and 100 µg/mL bacillomycin L was revealed by quantitative transcriptomics. A total of 878 differentially expressed genes among Bs916, Δbl, and Δbl + 100BL were identified and grouped into 9 functional categories. The transcription levels of 40 candidate genes were further evaluated by RT-qPCR analysis. The expression of eight candidate genes regulated by bacillomycin L in a dose-dependent manner was revealed by LacZ fusion experiment. Although the addition of bacillomycin L could not completely restore the expression levels of the differentially regulated genes in △bl, our results strongly suggest that bacillomycin L acts as a tuning signal of swarming motility and complex biofilm formation by indirectly regulating the expression levels of some two-component systems (TCSs) connector genes, particularly including several Raps that potentially regulate the phosphorylation levels of three major regulators ComA, DegU, and Spo0A.Key points• Proposed model for bacillomycin L regulation in B. velezensis Bs916.• Bacillomycin L can act as an extracellular signal to regulate the phosphorylation levels of three major regulators, ComA, DegU, and Spo0A and control the multicellular processes of vegetative growth, competent, motility, matrix production, sporulation, and autolysis.
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Affiliation(s)
- Chuping Luo
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China. .,Institute of Veterinary Medicine, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Jiachen Liu
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Muhammad Bilal
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Xuehui Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaohua Wang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Fei Dong
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Yuan Liu
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China.,Institute of Veterinary Medicine, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Shanshan Zang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiulian Yin
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Xueting Yang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Tao Zhu
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Shuangyu Zhang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Weifeng Zhang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Bin Li
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China. .,Institute of Veterinary Medicine, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
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25
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Arnaouteli S, Bamford NC, Stanley-Wall NR, Kovács ÁT. Bacillus subtilis biofilm formation and social interactions. Nat Rev Microbiol 2021; 19:600-614. [PMID: 33824496 DOI: 10.1038/s41579-021-00540-9] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2021] [Indexed: 02/03/2023]
Abstract
Biofilm formation is a process in which microbial cells aggregate to form collectives that are embedded in a self-produced extracellular matrix. Bacillus subtilis is a Gram-positive bacterium that is used to dissect the mechanisms controlling matrix production and the subsequent transition from a motile planktonic cell state to a sessile biofilm state. The collective nature of life in a biofilm allows emergent properties to manifest, and B. subtilis biofilms are linked with novel industrial uses as well as probiotic and biocontrol processes. In this Review, we outline the molecular details of the biofilm matrix and the regulatory pathways and external factors that control its production. We explore the beneficial outcomes associated with biofilms. Finally, we highlight major advances in our understanding of concepts of microbial evolution and community behaviour that have resulted from studies of the innate heterogeneity of biofilms.
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Affiliation(s)
- 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
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK.
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark.
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26
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Elemosho R, Suwanto A, Thenawidjaja M. Extracellular expression in Bacillus subtilis of a thermostable Geobacillus stearothermophilus lipase. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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27
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Rajasekharan SK, Paz‐Aviram T, Galili S, Berkovich Z, Reifen R, Shemesh M. Biofilm formation onto starch fibres by Bacillus subtilis governs its successful adaptation to chickpea milk. Microb Biotechnol 2021; 14:1839-1846. [PMID: 33080087 PMCID: PMC8313274 DOI: 10.1111/1751-7915.13665] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/04/2020] [Accepted: 08/23/2020] [Indexed: 11/28/2022] Open
Abstract
Beneficial biofilms may confer effective adaptation to food matrices that assist bacteria in enduring hostile environmental conditions. The matrices, for instance, dietary fibres of various food products, might serve as a natural scaffold for bacterial cells to adhere and grow as biofilms. Here, we report on a unique interaction of Bacillus subtilis cells with the resistant starch fibresof chickpea milk (CPM), herein CPM fibres, along with the production of a reddish-pink pigment. Genetic analysis identified the pigment as pulcherrimin, and also revealed the involvement of Spo0A/SinI pathway in modulating the observed phenotypes. Besides, through successful colonization of the CPM fibres, the wild-type cells of B. subtilis displayed enhanced survivability and resilience to environmental stress, such as heat and in vitro gastrointestinal treatments. In total, we infer that the biofilm formation on CPM fibres is an adaptation response of B. subtilis for strategic survival.
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Affiliation(s)
- Satish Kumar Rajasekharan
- Departmet of Food ScienceInstitute of Postharvvest Technology and Food SciencesAgricultural Research Organization (ARO)The Volcani CenterRishon LeZion7528809Israel
| | - Tali Paz‐Aviram
- Departmet of Food ScienceInstitute of Postharvvest Technology and Food SciencesAgricultural Research Organization (ARO)The Volcani CenterRishon LeZion7528809Israel
| | - Shmuel Galili
- Department of Vegetable and Field CropsInstitute of Plant SciencesAgricultural Research Organization (ARO)The Volcani CenterRishon LeZion7528809Israel
| | - Zipi Berkovich
- Institute of Biochemistry, Food Science and NutritionThe Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovotIsrael
| | - Ram Reifen
- Institute of Biochemistry, Food Science and NutritionThe Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovotIsrael
| | - Moshe Shemesh
- Departmet of Food ScienceInstitute of Postharvvest Technology and Food SciencesAgricultural Research Organization (ARO)The Volcani CenterRishon LeZion7528809Israel
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28
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Harding CJ, Sutherland E, Hanna JG, Houston DR, Czekster CM. Bypassing the requirement for aminoacyl-tRNA by a cyclodipeptide synthase enzyme. RSC Chem Biol 2021; 2:230-240. [PMID: 33937777 PMCID: PMC8084100 DOI: 10.1039/d0cb00142b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Cyclodipeptide synthases (CDPSs) produce a variety of cyclic dipeptide products by utilising two aminoacylated tRNA substrates. We sought to investigate the minimal requirements for substrate usage in this class of enzymes as the relationship between CDPSs and their substrates remains elusive. Here, we investigated the Bacillus thermoamylovorans enzyme, BtCDPS, which synthesises cyclo(l-Leu–l-Leu). We systematically tested where specificity arises and, in the process, uncovered small molecules (activated amino esters) that will suffice as substrates, although catalytically poor. We solved the structure of BtCDPS to 1.7 Å and combining crystallography, enzymatic assays and substrate docking experiments propose a model for how the minimal substrates interact with the enzyme. This work is the first report of a CDPS enzyme utilizing a molecule other than aa-tRNA as a substrate; providing insights into substrate requirements and setting the stage for the design of improved simpler substrates. Cyclodipeptide synthases recognize a minimalistic substrate to produce cyclic dipeptides in a tRNA-independent manner.![]()
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Affiliation(s)
- Christopher J Harding
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews Fife KY16 9ST UK
| | - Emmajay Sutherland
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews Fife KY16 9ST UK
| | - Jane G Hanna
- Arab Academy for Science, Technology, and Maritime Transport (AASTMT) Cairo Campus Egypt
| | - Douglas R Houston
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh Waddington 1 Building, King's Buildings Edinburgh EH9 3BF UK
| | - Clarissa M Czekster
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews Fife KY16 9ST UK
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29
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Rychel K, Decker K, Sastry AV, Phaneuf PV, Poudel S, Palsson BO. iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning. Nucleic Acids Res 2021; 49:D112-D120. [PMID: 33045728 PMCID: PMC7778901 DOI: 10.1093/nar/gkaa810] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/10/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022] Open
Abstract
Independent component analysis (ICA) of bacterial transcriptomes has emerged as a powerful tool for obtaining co-regulated, independently-modulated gene sets (iModulons), inferring their activities across a range of conditions, and enabling their association to known genetic regulators. By grouping and analyzing genes based on observations from big data alone, iModulons can provide a novel perspective into how the composition of the transcriptome adapts to environmental conditions. Here, we present iModulonDB (imodulondb.org), a knowledgebase of prokaryotic transcriptional regulation computed from high-quality transcriptomic datasets using ICA. Users select an organism from the home page and then search or browse the curated iModulons that make up its transcriptome. Each iModulon and gene has its own interactive dashboard, featuring plots and tables with clickable, hoverable, and downloadable features. This site enhances research by presenting scientists of all backgrounds with co-expressed gene sets and their activity levels, which lead to improved understanding of regulator-gene relationships, discovery of transcription factors, and the elucidation of unexpected relationships between conditions and genetic regulatory activity. The current release of iModulonDB covers three organisms (Escherichia coli, Staphylococcus aureus and Bacillus subtilis) with 204 iModulons, and can be expanded to cover many additional organisms.
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Affiliation(s)
- Kevin Rychel
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Katherine Decker
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anand V Sastry
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Patrick V Phaneuf
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Saugat Poudel
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
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30
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Jacobs L, Meesters J, Parijs I, Hooyberghs G, Van der Eycken EV, Lories B, Steenackers HP. 2-Aminoimidazoles as potent inhibitors of contaminating brewery biofilms. BIOFOULING 2021; 37:61-77. [PMID: 33573402 DOI: 10.1080/08927014.2021.1874366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 12/23/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Cleaning and disinfection protocols are not always able to remove biofilm microbes present in breweries, indicating that novel anti-biofilm strategies are needed. The preventive activities of three in-house synthesized members of the 2-aminoimidazole class of anti-biofilm molecules were studied against 17 natural brewery biofilms and benchmarked against 18 known inhibitors. Two 2-aminoimidazoles belonged to the top six inhibitors, which were retested against 12 defined brewery biofilm models. For the three best inhibitors, tannic acid (n° 1), 2-aminoimidazole imi-AAC-5 (n° 2), and baicalein (n° 3), the effect on the microbial metabolic activity was evaluated. Here, the top three inhibitors showed similar effectiveness, with baicalein possessing a slightly higher efficacy. Even though the 2-aminoimidazole was the second-best inhibitor, it showed a lower biocidal activity than tannic acid, making it less prone to resistance evolution. Overall, this study supports the potential of 2-aminoimidazoles as a preventive anti-biofilm strategy.
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Affiliation(s)
- Lene Jacobs
- Centrum of Microbial and Plant Genetics, KU Leuven, Belgium
| | | | - Ilse Parijs
- Centrum of Microbial and Plant Genetics, KU Leuven, Belgium
| | - Geert Hooyberghs
- Laboratory for Organic and Microwave-Assisted Chemistry - LOMAC, KU Leuven, Belgium
| | - Erik V Van der Eycken
- Laboratory for Organic and Microwave-Assisted Chemistry - LOMAC, KU Leuven, Belgium
- Peoples' Friendship University of Russia (RUDN University), Moscow, Russia
| | - Bram Lories
- Centrum of Microbial and Plant Genetics, KU Leuven, Belgium
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31
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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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32
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Yuan S, Yong X, Zhao T, Li Y, Liu J. Research Progress of the Biosynthesis of Natural Bio-Antibacterial Agent Pulcherriminic Acid in Bacillus. Molecules 2020; 25:E5611. [PMID: 33260656 PMCID: PMC7731078 DOI: 10.3390/molecules25235611] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/13/2020] [Accepted: 11/15/2020] [Indexed: 11/16/2022] Open
Abstract
Pulcherriminic acid is a cyclic dipeptide found mainly in Bacillus and yeast. Due to the ability of pulcherriminic acid to chelate Fe3+ to produce reddish brown pulcherrimin, microorganisms capable of synthesizing pulcherriminic acid compete with other microorganisms for environmental iron ions to achieve bacteriostatic effects. Therefore, studying the biosynthetic pathway and their enzymatic catalysis, gene regulation in the process of synthesis of pulcherriminic acid in Bacillus can facilitate the industrial production, and promote the wide application in food, agriculture and medicine industries. After initially discussing, this review summarizes current research on the synthesis of pulcherriminic acid by Bacillus, which includes the crystallization of key enzymes, molecular catalytic mechanisms, regulation of synthetic pathways, and methods to improve efficiency in synthesizing pulcherriminic acid and its precursors. Finally, possible applications of pulcherriminic acid in the fermented food, such as Chinese Baijiu, applying combinatorial biosynthesis will be summarized.
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Affiliation(s)
- Siqi Yuan
- Sichuan University of Science & Engineering, Xueyuan Street 180#, Huixing Rd., Zigong 643000, China; (S.Y.); (X.Y.); (T.Z.)
- Luzhou Laojiao Group Co. Ltd., Airentang Square, Jiangyang District, Luzhou 646000, China
| | - Xihao Yong
- Sichuan University of Science & Engineering, Xueyuan Street 180#, Huixing Rd., Zigong 643000, China; (S.Y.); (X.Y.); (T.Z.)
| | - Ting Zhao
- Sichuan University of Science & Engineering, Xueyuan Street 180#, Huixing Rd., Zigong 643000, China; (S.Y.); (X.Y.); (T.Z.)
| | - Yuan Li
- Sichuan University of Science & Engineering, Xueyuan Street 180#, Huixing Rd., Zigong 643000, China; (S.Y.); (X.Y.); (T.Z.)
| | - Jun Liu
- Sichuan University of Science & Engineering, Xueyuan Street 180#, Huixing Rd., Zigong 643000, China; (S.Y.); (X.Y.); (T.Z.)
- Wuliangye Group Co. Ltd., No. 150 Minjiang West Road, Yibin 644000, China
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33
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Abstract
Pulcherrimin, a red iron chelate, is produced by some yeasts and bacteria. It plays important ecological roles in many ecosystems, including growth control, biofilm inhibition and photoprotection. In this study, fifteen yeast strains of the genus Metschnikowia were characterized based on their production of pulcherrimin. Yeast pulcherrimin was isolated and its purity assessed using 1H nuclear magnetic resonance spectroscopy. Under experimental conditions, pulcherrimin formation varied depending on both the tested strains and culture media. The best producers formed up to 240 mg/L of pulcherrimin in minimal medium with glucose as the carbon source, supplemented with 0.05% FeCl3 and 0.1% Tween 80. This study presents a new approach to producing high yields of pulcherrimin from yeasts.
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34
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Ferral-Pérez H, Galicia-García M, Alvarado-Tenorio B, Izaguirre-Pompa A, Aguirre-Ramírez M. Novel method to achieve crystallinity of calcite by Bacillus subtilis in coupled and non-coupled calcium-carbon sources. AMB Express 2020; 10:174. [PMID: 32990816 PMCID: PMC7524977 DOI: 10.1186/s13568-020-01111-6] [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: 09/05/2020] [Accepted: 09/15/2020] [Indexed: 12/19/2022] Open
Abstract
Bacteria mineralization is a promising biotechnological approach to apply in biomaterials development. In this investigation, we demonstrate that Bacillus subtilis 168 induces and influences CaCO3 composites precipitation. Crystals were formed in calcium-carbon non-coupled (glycerol + CaCl2, GLY; or glucose + CaCl2, GLC) and coupled (calcium lactate, LAC; or calcium acetate, ACE) agar-sources, only maintaining the same Ca2+ concentration. The mineralized colonies showed variations in morphology, size, and crystallinity form properties. The crystals presented spherulitic growth in all conditions, and botryoidal shapes in GLC one. Birefringence and diffraction patterns confirmed that all biogenic carbonate crystals (BCC) were organized as calcite. The CaCO3 in BCC was organized as calcite, amorphous calcium carbon (ACC) and organic matter (OM) of biofilm; all of them with relative abundance related to bacteria growth condition. BCC-GLY presented greatest OM composition, while BCC-ACE highest CaCO3 content. Nucleation mechanism and OM content impacted in BCC crystallinity.
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35
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Li Y, Yuan S, Yong X, zhao T, Liu J. Research progress on small peptides in Chinese Baijiu. J Funct Foods 2020. [DOI: 10.1016/j.jff.2020.104081] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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36
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Bergkessel M. Regulation of protein biosynthetic activity during growth arrest. Curr Opin Microbiol 2020; 57:62-69. [PMID: 32858411 DOI: 10.1016/j.mib.2020.07.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 07/18/2020] [Accepted: 07/20/2020] [Indexed: 01/10/2023]
Abstract
Heterotrophic bacteria grow and divide rapidly when resources are abundant. Yet resources are finite, and environments fluctuate, so bacteria need strategies to survive when nutrients become scarce. In fact, many bacteria spend most of their time in such conditions of nutrient limitation, and hence they need to optimise gene regulation and protein biosynthesis during growth arrest. An optimal strategy in these conditions must mitigate the challenges and risks of making new proteins, while the cell is severely limited for energy and substrates. Recently, ribosome abundance and activity were measured in these conditions, revealing very low amounts of new protein synthesis, which is nevertheless vital for survival. The underlying mechanisms are only now starting to be explored. Improving our understanding of the regulation of protein production during bacterial growth arrest could have important implications for a wide range of challenges, including the identification of new targets for antibiotic development.
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Affiliation(s)
- Megan Bergkessel
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK.
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37
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Role of Glutamate Synthase in Biofilm Formation by Bacillus subtilis. J Bacteriol 2020; 202:JB.00120-20. [PMID: 32393519 DOI: 10.1128/jb.00120-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/04/2020] [Indexed: 11/20/2022] Open
Abstract
Bacillus subtilis forms robust biofilms in the presence of large amounts of carbon sources, such as glycerol. However, little is known about the importance of the metabolic systems, or the relationship between metabolic systems and regulatory systems, involved in biofilm formation. Glutamate synthase, encoded by gltAB, is an enzyme that converts 2-ketoglutarate (a tricarboxylic acid [TCA] cycle intermediate) and glutamine into glutamate, which is a general amino group donor in metabolism. Here, we show that a ΔgltA mutant exhibited early arrest of biofilm formation in complex medium containing glycerol. This phenotype was not due to glutamate auxotrophy. Consistent with its biofilm formation phenotype, the ΔgltA mutant exhibited an early decrease in expression of the epsA and tapA operons, which are responsible for production of biofilm matrix polymers. This resulted from decreased activity of their regulator, Spo0A, as evidenced by reduced expression of other Spo0A-regulated genes in the ΔgltA mutant. The ΔgltA mutation prevented biofilm formation only in the presence of large amounts of glycerol. Moreover, limited expression of citrate synthase (but not other TCA enzymes) restored biofilm-forming ability to the ΔgltA mutant. These results indicate that the ΔgltA mutant accumulates an inhibitory intermediate (citrate) in the TCA cycle in the presence of large amounts of glycerol. The ΔgltA mutant formed biofilms when excess iron was added to the medium. Taken together, the data suggest that accumulation of citrate ions by the ΔgltA mutant causes iron shortage due to chelation, which prevents activation of Spo0A and causes defective biofilm formation.IMPORTANCE Bacillus subtilis, a model organism for bacterial biofilm formation, forms robust biofilms in a medium-dependent manner. Although the regulatory network that controls biofilm formation has been well studied, the importance of the underlying metabolic systems remains to be elucidated. The present study demonstrates that a metabolic disorder in a well-conserved metabolic system causes accumulation of an inhibitory metabolic intermediate that prevents activation of the system that regulates biofilm formation. These findings increase our understanding of the coordination between cellular metabolic status and the regulatory networks governing biofilm formation.
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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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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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Abstract
Understanding the processes that underpin the mechanism of biofilm formation, dispersal, and inhibition is critical to allow exploitation and to understand how microbes thrive in the environment. Here, we reveal that the formation of an extracellular iron chelate restricts the expansion of a biofilm. The countering benefit to self-restriction of growth is protection of an environmental niche. These findings highlight the complex options and outcomes that bacteria need to balance to modulate their local environment to maximize colonization, and therefore survival. Biofilm formation by Bacillus subtilis is a communal process that culminates in the formation of architecturally complex multicellular communities. Here we reveal that the transition of the biofilm into a nonexpanding phase constitutes a distinct step in the process of biofilm development. Using genetic analysis we show that B. subtilis strains lacking the ability to synthesize pulcherriminic acid form biofilms that sustain the expansion phase, thereby linking pulcherriminic acid to growth arrest. However, production of pulcherriminic acid is not sufficient to block expansion of the biofilm. It needs to be secreted into the extracellular environment where it chelates Fe3+ from the growth medium in a nonenzymatic reaction. Utilizing mathematical modeling and a series of experimental methodologies we show that when the level of freely available iron in the environment drops below a critical threshold, expansion of the biofilm stops. Bioinformatics analysis allows us to identify the genes required for pulcherriminic acid synthesis in other Firmicutes but the patchwork presence both within and across closely related species suggests loss of these genes through multiple independent recombination events. The seemingly counterintuitive self-restriction of growth led us to explore if there were any benefits associated with pulcherriminic acid production. We identified that pulcherriminic acid producers can prevent invasion by neighboring communities through the generation of an “iron-free” zone, thereby addressing the paradox of pulcherriminic acid production by B. subtilis.
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