1
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Messer LF, Wattiez R, Matallana-Surget S. A closer look at plastic colonisation: Prokaryotic dynamics in established versus newly synthesised marine plastispheres and their planktonic state. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 358:124479. [PMID: 38960113 DOI: 10.1016/j.envpol.2024.124479] [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: 03/21/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/05/2024]
Abstract
The taxonomy of marine plastisphere communities has been extensively studied, demonstrating the ubiquity of hydrocarbonoclastic bacteria of potential biotechnological significance. However, prokaryotic functioning on plastic surfaces has received limited attention, and the question of whether these microorganisms are active and expressing specific molecular mechanisms underpinning plastisphere colonisation remains to be addressed. The aim of this study was to investigate the plastic colonisation process, to identify the active taxa involved in biofilm formation and the mechanisms used to initiate colonisation. To achieve this, a marine plastisphere characterised by active hydrocarbonoclastic genera was used as the inoculum for a short-term microcosm experiment using virgin low-density polyethylene as the sole carbon source. Following incubation for 1 and 2 weeks (representing early and late colonisation, respectively), a taxonomic and comparative metaproteomic approach revealed a significant shift in plastisphere diversity and composition, yet highlighted stability in the predominance of active Proteobacteria spanning 16 genera, including Marinomonas, Pseudomonas, and Pseudoalteromonas. Relative quantification of 1762 proteins shared between the initial plastisphere inoculum, the microcosm plastisphere and the planktonic cells in the surrounding artificial seawater, provided insights into the differential regulation of proteins associated with plastisphere formation. This included the upregulation of proteins mediating cellular attachment in the plastisphere, for example flagellin expressed by Marinomonas, Cobetia, Pseudoalteromonas, and Pseudomonas, and curli expressed by Cobetia. In addition to the differential regulation of energy metabolism in Marinomonas, Psychrobacter, Pseudomonas and Cobetia within the plastisphere relative to the surrounding seawater. Further, we identified the upregulation of amino acid metabolism and transport, including glutamine hydrolysis to glutamate in Marinomonas and unclassified Halomonadaceae, potentially coupled to ammonia availability and oxidative stress experienced within the plastisphere. Our study provides novel insights into the dynamics of plastisphere formation and function, highlighting potential targets for regulating plastisphere growth to enhance plastic bioremediation processes.
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Affiliation(s)
- Lauren F Messer
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA, United Kingdom.
| | - Ruddy Wattiez
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Place du Parc 20, 7000, Mons, Belgium
| | - Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA, United Kingdom.
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2
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Zhang L, Li X, Gao H, Chang W, Li P. Gut microbiota-lncRNA/circRNA crosstalk: implications for different diseases. Crit Rev Microbiol 2024:1-15. [PMID: 38967384 DOI: 10.1080/1040841x.2024.2375516] [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: 07/04/2023] [Accepted: 06/26/2024] [Indexed: 07/06/2024]
Abstract
The gut microbiota features an abundance of diverse microorganisms and represents an important component of human physiology and metabolic homeostasis, indicating their roles in a wide array of physiological and pathological processes in the host. Maintaining balance in the gut microbiota is critical for normal functionality as microbial dysbiosis can lead to the occurrence and development of diseases through various mechanisms. Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are non-coding RNAs that perform important regulatory functions for many processes. Furthermore, the gut microbiota and lncRNAs/circRNAs are known to interact in a range of both physiological and pathological activities. In this article, we review existing research relevant to the interaction between the gut microbiota and lncRNAs/circRNAs and investigate the role of their crosstalk in the pathogenesis of different diseases. Studies have shown that, the gut microbiota can target lncRNAs ENO1-IT1, BFAL1, and LINC00152 to regulate colorectal cancer development via various signaling pathways. In addition, the gut microbiota can influence mental diseases and lung tumor metastasis by modulating circRNAs such as circNF1-419, circ_0001239, circHIPK2 and mmu_circ_0000730. These findings provide a theoretical basis for disease prevention and treatment and suggest that gut microbiota-lncRNA/circRNA crosstalk has high clinical value.
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Affiliation(s)
- Lei Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Xin Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Huijuan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Wenguang Chang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
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3
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Karim AS, Brown DM, Archuleta CM, Grannan S, Aristilde L, Goyal Y, Leonard JN, Mangan NM, Prindle A, Rocklin GJ, Tyo KJ, Zoloth L, Jewett MC, Calkins S, Kamat NP, Tullman-Ercek D, Lucks JB. Deconstructing synthetic biology across scales: a conceptual approach for training synthetic biologists. Nat Commun 2024; 15:5425. [PMID: 38926339 PMCID: PMC11208543 DOI: 10.1038/s41467-024-49626-x] [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: 12/01/2023] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Synthetic biology allows us to reuse, repurpose, and reconfigure biological systems to address society's most pressing challenges. Developing biotechnologies in this way requires integrating concepts across disciplines, posing challenges to educating students with diverse expertise. We created a framework for synthetic biology training that deconstructs biotechnologies across scales-molecular, circuit/network, cell/cell-free systems, biological communities, and societal-giving students a holistic toolkit to integrate cross-disciplinary concepts towards responsible innovation of successful biotechnologies. We present this framework, lessons learned, and inclusive teaching materials to allow its adaption to train the next generation of synthetic biologists.
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Affiliation(s)
- Ashty S Karim
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA.
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA.
| | - Dylan M Brown
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Chloé M Archuleta
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Sharisse Grannan
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Independent Evaluator, Lake Geneva, WI, 53147, USA
| | - Ludmilla Aristilde
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Yogesh Goyal
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Josh N Leonard
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Niall M Mangan
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, 60201, USA
| | - Arthur Prindle
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, 60611, USA
| | - Gabriel J Rocklin
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Pharmacology, Northwestern University, Chicago, IL, 60611, USA
| | - Keith J Tyo
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Laurie Zoloth
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- The Divinity School, University of Chicago, Chicago, IL, 60637, USA
| | - Michael C Jewett
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Susanna Calkins
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Searle Center for Advancing Learning and Teaching, Northwestern University, Evanston, IL, 60208, USA
- Nexus for Faculty Success, Rosalind Franklin University of Medicine and Science, Chicago, IL, USA
| | - Neha P Kamat
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Biomedical Engineering Northwestern University, Evanston, IL, 60208, USA
| | - Danielle Tullman-Ercek
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Julius B Lucks
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA.
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA.
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4
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Rai LS, Chauvel M, Sanchez H, van Wijlick L, Maufrais C, Cokelaer T, Sertour N, Legrand M, Sanyal K, Andes DR, Bachellier-Bassi S, d’Enfert C. Metabolic reprogramming during Candida albicans planktonic-biofilm transition is modulated by the transcription factors Zcf15 and Zcf26. PLoS Biol 2024; 22:e3002693. [PMID: 38905306 PMCID: PMC11221756 DOI: 10.1371/journal.pbio.3002693] [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: 08/04/2023] [Revised: 07/03/2024] [Accepted: 05/29/2024] [Indexed: 06/23/2024] Open
Abstract
Candida albicans is a commensal of the human microbiota that can form biofilms on implanted medical devices. These biofilms are tolerant to antifungals and to the host immune system. To identify novel genes modulating C. albicans biofilm formation, we performed a large-scale screen with 2,454 C. albicans doxycycline-dependent overexpression strains and identified 16 genes whose overexpression significantly hampered biofilm formation. Among those, overexpression of the ZCF15 and ZCF26 paralogs that encode transcription factors and have orthologs only in biofilm-forming species of the Candida clade, caused impaired biofilm formation both in vitro and in vivo. Interestingly, overexpression of ZCF15 impeded biofilm formation without any defect in hyphal growth. Transcript profiling, transcription factor binding, and phenotypic microarray analyses conducted upon overexpression of ZCF15 and ZCF26 demonstrated their role in reprogramming cellular metabolism by regulating central metabolism including glyoxylate and tricarboxylic acid cycle genes. Taken together, this study has identified a new set of biofilm regulators, including ZCF15 and ZCF26, that appear to control biofilm development through their specific role in metabolic remodeling.
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Affiliation(s)
- Laxmi Shanker Rai
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, Paris, France
- Department of Life Sciences, GITAM University, Bengaluru, Karnataka 561203, India
| | - Murielle Chauvel
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, Paris, France
| | - Hiram Sanchez
- Department of Medicine, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Lasse van Wijlick
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, Paris, France
| | - Corinne Maufrais
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, Paris, France
| | - Thomas Cokelaer
- Institut Pasteur, Université Paris Cité, Hub de Bioinformatique et Biostatistique, Paris, France
| | - Natacha Sertour
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, Paris, France
| | - Mélanie Legrand
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, Paris, France
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India
- Department of Biological Sciences, Bose Institute, Unified Academic Campus, EN-80, Sector-V, Salt Lake City, Kolkata, India
| | - David R. Andes
- Department of Medicine, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Sophie Bachellier-Bassi
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, Paris, France
| | - Christophe d’Enfert
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, Paris, France
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5
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Wan Q, Zhai S, Chen M, Xu M, Guo S. Comparative phenotype and transcriptome analysis revealed the role of ferric uptake regulator (Fur) in the virulence of Vibrio harveyi isolated from diseased American eel (Anguilla rostrata). JOURNAL OF FISH DISEASES 2024; 47:e13931. [PMID: 38373044 DOI: 10.1111/jfd.13931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/20/2024]
Abstract
Vibrio harveyi is commonly found in salt and brackish water and is recognized as a serious bacterial pathogen in aquaculture worldwide. In this study, we cloned the ferric uptake regulator (fur) gene from V. harveyi wild-type strain HA_1, which was isolated from diseased American eels (Anguilla rostrata) and has a length of 450 bp, encoding 149 amino acids. Then, a mutant strain, HA_1-Δfur, was constructed through homologous recombination of a suicide plasmid (pCVD442). The HA_1-Δfur mutant exhibited weaker biofilm formation and swarming motility, and 18-fold decrease (5.5%) in virulence to the American eels; compared to the wild-type strain, the mutant strain showed time and diameter differences in growth and haemolysis, respectively. Additionally, the adhesion ability of the mutant strain was significantly decreased. Moreover, there were 15 different biochemical indicators observed between the two strains. Transcriptome analysis revealed that 875 genes were differentially expressed in the Δfur mutant, with 385 up-regulated and 490 down-regulated DEGs. GO and KEGG enrichment analysis revealed that, compared to the wild-type strain, the type II and type VI secretion systems (T2SS and T6SS), amino acid synthesis and transport and energy metabolism pathways were significantly down-regulated, but the ABC transporters and biosynthesis of siderophore group non-ribosomal peptides pathways were up-regulated in the Δfur strain. The qRT-PCR results further confirmed that DEGs responsible for amino acid transport and energy metabolism were positively regulated, but DEGs involved in iron acquisition were negatively regulated in the Δfur strain. These findings suggest that the virulence of the Δfur strain was significantly decreased, which is closely related to phenotype changing and gene transcript regulation.
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Affiliation(s)
- Qijuan Wan
- Fisheries College of Jimei University/Engineering Research Center of the Modern Industry Technology for Eel, Ministry of Education of PRC, Xiamen, China
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, China
| | - Shaowei Zhai
- Fisheries College of Jimei University/Engineering Research Center of the Modern Industry Technology for Eel, Ministry of Education of PRC, Xiamen, China
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, China
| | - Minxia Chen
- Fisheries College of Jimei University/Engineering Research Center of the Modern Industry Technology for Eel, Ministry of Education of PRC, Xiamen, China
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, China
| | - Ming Xu
- Fisheries College of Jimei University/Engineering Research Center of the Modern Industry Technology for Eel, Ministry of Education of PRC, Xiamen, China
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, China
| | - Songlin Guo
- Fisheries College of Jimei University/Engineering Research Center of the Modern Industry Technology for Eel, Ministry of Education of PRC, Xiamen, China
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, China
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6
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Shen B, Coruzzi GM, Shasha D. Bipartite networks represent causality better than simple networks: evidence, algorithms, and applications. Front Genet 2024; 15:1371607. [PMID: 38798697 PMCID: PMC11120958 DOI: 10.3389/fgene.2024.1371607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/17/2024] [Indexed: 05/29/2024] Open
Abstract
A network, whose nodes are genes and whose directed edges represent positive or negative influences of a regulatory gene and its targets, is often used as a representation of causality. To infer a network, researchers often develop a machine learning model and then evaluate the model based on its match with experimentally verified "gold standard" edges. The desired result of such a model is a network that may extend the gold standard edges. Since networks are a form of visual representation, one can compare their utility with architectural or machine blueprints. Blueprints are clearly useful because they provide precise guidance to builders in construction. If the primary role of gene regulatory networks is to characterize causality, then such networks should be good tools of prediction because prediction is the actionable benefit of knowing causality. But are they? In this paper, we compare prediction quality based on "gold standard" regulatory edges from previous experimental work with non-linear models inferred from time series data across four different species. We show that the same non-linear machine learning models have better predictive performance, with improvements from 5.3% to 25.3% in terms of the reduction in the root mean square error (RMSE) compared with the same models based on the gold standard edges. Having established that networks fail to characterize causality properly, we suggest that causality research should focus on four goals: (i) predictive accuracy; (ii) a parsimonious enumeration of predictive regulatory genes for each target gene g; (iii) the identification of disjoint sets of predictive regulatory genes for each target g of roughly equal accuracy; and (iv) the construction of a bipartite network (whose node types are genes and models) representation of causality. We provide algorithms for all goals.
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Affiliation(s)
- Bingran Shen
- Courant Institute of Mathematical Sciences, Department of Computer Science, New York University, New York, United States
| | - Gloria M. Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Dennis Shasha
- Courant Institute of Mathematical Sciences, Department of Computer Science, New York University, New York, United States
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7
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Xue Y, Yu C, Ouyang H, Huang J, Kang X. Uncovering the Molecular Composition and Architecture of the Bacillus subtilis Biofilm via Solid-State NMR Spectroscopy. J Am Chem Soc 2024; 146:11906-11923. [PMID: 38629727 DOI: 10.1021/jacs.4c00889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The complex and dynamic compositions of biofilms, along with their sophisticated structural assembly mechanisms, endow them with exceptional capabilities to thrive in diverse conditions that are typically unfavorable for individual cells. Characterizing biofilms in their native state is significantly challenging due to their intrinsic complexities and the limited availability of noninvasive techniques. Here, we utilized solid-state nuclear magnetic resonance (NMR) spectroscopy to analyze Bacillus subtilis biofilms in-depth. Our data uncover a dynamically distinct organization within the biofilm: a dominant, hydrophilic, and mobile framework interspersed with minor, rigid cores of limited water accessibility. In these heterogeneous rigid cores, the major components are largely self-assembled. TasA fibers, the most robust elements, further provide a degree of mechanical support for the cell aggregates and some lipid vesicles. Notably, rigid cell aggregates can persist even without the major extracellular polymeric substance (EPS) polymers, although this leads to slight variations in their rigidity and water accessibility. Exopolysaccharides are exclusively present in the mobile domain, playing a pivotal role in its water retention property. Specifically, all water molecules are tightly bound within the biofilm matrix. These findings reveal a dual-layered defensive strategy within the biofilm: a diffusion barrier through limited water mobility in the mobile phase and a physical barrier posed by limited water accessibility in the rigid phase. Complementing these discoveries, our comprehensive, in situ compositional analysis is not only essential for delineating the sophisticated biofilm architecture but also reveals the presence of alternative genetic mechanisms for synthesizing exopolysaccharides beyond the known pathway.
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Affiliation(s)
- Yi Xue
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Chenjie Yu
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Han Ouyang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Jiaofang Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xue Kang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
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8
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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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9
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Bassu G, Laurati M, Fratini E. Transition from active motion to anomalous diffusion for Bacillus subtilis confined in hydrogel matrices. Colloids Surf B Biointerfaces 2024; 236:113797. [PMID: 38431996 DOI: 10.1016/j.colsurfb.2024.113797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/06/2023] [Accepted: 02/11/2024] [Indexed: 03/05/2024]
Abstract
We investigate the motility of B. subtilis under different degrees of confinement induced by transparent porous hydrogels. The dynamical behavior of the bacteria at short times is linked to characteristic parameters describing the hydrogel porosity. Mean squared displacements (MSDs) reveal that the run-and-tumble dynamics of unconfined B. subtilis progressively turns into sub-diffusive motion with increasing confinement. Correspondingly, the median instantaneous velocity of bacteria decreases and becomes more narrowly distributed, while the reorientation rate increases and reaches a plateau value. Analyzing single-trajectories, we show that the average dynamical behavior is the result of complex displacements, in which active, diffusive and sub-diffusive segments coexist. For small and moderate confinements, the number of active segments reduces, while the diffusive and sub-diffusive segments increase. The alternation of sub-diffusion, diffusion and active motion along the same trajectory can be described as a hopping ad trapping motion, in which hopping events correspond to displacements with an instantaneous velocity exceeding the corresponding mean value along a trajectory. Different from previous observations, escape from local trapping occurs for B. subtilis through active runs but also diffusion. Interestingly, the contribution of diffusion is maximum at intermediate confinements. At sufficiently long times transport coefficients estimated from the experimental MSDs under different degrees of confinement can be reproduced using a recently proposed hopping and trapping model. Finally, we propose a quantitative relationship linking the median velocity of confined and unconfined bacteria through the characteristic confinement length of the hydrogel matrix. Our work provides new insights for the bacterial motility in complex media that mimic natural environments and are relevant to important problems like sterilization, water purification, biofilm formation, membrane permeation and bacteria separation.
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Affiliation(s)
- Gavino Bassu
- Department of Chemistry "Ugo Schiff", Via della Lastruccia 3, Sesto Fiorentino 50019, Italy; Consorzio per lo Sviluppo dei Sistemi a Grande Interfase (CSGI)), Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Marco Laurati
- Department of Chemistry "Ugo Schiff", Via della Lastruccia 3, Sesto Fiorentino 50019, Italy; Consorzio per lo Sviluppo dei Sistemi a Grande Interfase (CSGI)), Via della Lastruccia 3, Sesto Fiorentino 50019, Italy.
| | - Emiliano Fratini
- Department of Chemistry "Ugo Schiff", Via della Lastruccia 3, Sesto Fiorentino 50019, Italy; Consorzio per lo Sviluppo dei Sistemi a Grande Interfase (CSGI)), Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
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10
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Chen R, Liu N, Ren Y, Cui T. Transcriptomic and biochemical analysis of metabolic remodeling in Bacillus subtilis MSC4 under Benzo[a]pyrene stress. CHEMOSPHERE 2024; 353:141637. [PMID: 38462177 DOI: 10.1016/j.chemosphere.2024.141637] [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: 09/27/2023] [Revised: 01/25/2024] [Accepted: 03/01/2024] [Indexed: 03/12/2024]
Abstract
Polyaromatic benzo[a]pyrene (B[a]P) is a toxic carcinogenic environmental pollutant, and the use of microorganisms to remediate B[a]P contamination is considered to be one of the most effective strategies. However, there is still a gap in studying the metabolic remodeling of microorganisms under B[a]P stress. In this study, our systematically investigated the effects of B[a]P on the metabolism of Bacillus subtilis MSC4 based on transcriptomic, molecular and biochemical analyses. The results showed that in response to B[a]P stress, MSC4 formed more biofilm matrix and endospores, the structure of the endospores also was changed, which led to a reduction in their resistance and made them more difficult to germinate. In addition to an increase in glycolysis activity, the activities of tricarboxylic acid cycle, pentose phosphate pathway and the electron transport chain were decreased. B[a]P stress forced MSC4 to strengthen arginine synthesis, urea cycle, and urea decomposition, meanwhile, synthesize more ribonucleotides. The activity of DNA replication, transcription activities and the expression of multiple ribosomal protein genes were reduced. Moreover, all of the reported enzymes involved in B[a]P degradation showed decreased transcript abundance, and the degradation of B[a]P caused significant up-regulation of the gene expression of the acid inducible enzyme OxdC and the synthesis of acetoin. In addition, the cytotoxicity of B[a]P to bacteria was directly displayed in four aspects: increased intracellular level of reactive oxygen species (ROS), elevated cell membrane permeability, up-regulation of the cell envelope stress-sensing two-component system LiaRS, and downregulation of siderophores biosynthesis. Finally, B[a]P also caused morphological changes in the cells, with some cells exhibiting significant deformation and concavity. These findings provide effective research directions for targeted improvement the cellular activity of B[a]P-degrading strains, and is beneficial for further application of microorganisms to remediate B[a]P -contaminated soils.
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Affiliation(s)
- Rui Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, PR China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, PR China
| | - Na Liu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, PR China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, PR China
| | - Yuan Ren
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China
| | - Tangbing Cui
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, PR China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, PR China.
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11
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Bisht K, Elmassry MM, Al Mahmud H, Bhattacharjee S, Deonarine A, Black C, San Francisco MJ, Hamood AN, Wakeman CA. Global stress response in Pseudomonas aeruginosa upon malonate utilization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586813. [PMID: 38585990 PMCID: PMC10996706 DOI: 10.1101/2024.03.26.586813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Versatility in carbon source utilization assists Pseudomonas aeruginosa in its adaptation to various niches. Recently, we characterized the role of malonate, an understudied carbon source, in quorum sensing regulation, antibiotic resistance, and virulence factor production in P. aeruginosa . These results indicate that global responses to malonate metabolism remain to be uncovered. We leveraged a publicly available metabolomic dataset on human airway and found malonate to be as abundant as glycerol, a common airway metabolite and carbon source for P. aeruginosa . Here, we explored and compared adaptations of P. aeruginosa UCBPP-PA14 (PA14) in response to malonate or glycerol as a sole carbon source using transcriptomics and phenotypic assays. Malonate utilization activated glyoxylate and methylcitrate cycles and induced several stress responses, including oxidative, anaerobic, and metal stress responses associated with increases in intracellular aluminum and strontium. Some induced genes were required for optimal growth of P. aeruginosa in malonate. To assess the conservation of malonate-associated responses among P. aeruginosa strains, we compared our findings in strain PA14 with other lab strains and cystic fibrosis isolates of P. aeruginosa . Most strains grew on malonate as a sole carbon source as efficiently as or better than glycerol. While not all responses to malonate were conserved among strains, formation of biomineralized biofilm-like aggregates, increased tolerance to kanamycin, and increased susceptibility to norfloxacin were the most frequently observed phenotypes. Our findings reveal global remodeling of P. aeruginosa gene expression during its growth on malonate as a sole carbon source that is accompanied by several important phenotypic changes. These findings add to accumulating literature highlighting the role of different carbon sources in the physiology of P. aeruginosa and its niche adaptation. Importance Pseudomonas aeruginosa is a notorious pathogen that causes local and systemic infections in immunocompromised individuals. Different carbon sources can uniquely modulate metabolic and virulence pathways in P. aeruginosa , highlighting the importance of the environment that the pathogen occupies. In this work, we used a combination of transcriptomic analysis and phenotypic assays to determine how malonate utilization impacts P. aeruginosa, as recent evidence indicates this carbon source may be relevant to certain niches associated within the human host. We found that malonate utilization can induce global stress responses, alter metabolic circuits, and influence various phenotypes of P. aeruginosa that could influence host colonization. Investigating the metabolism of malonate provides insight into P. aeruginosa adaptations to specific niches where this substrate is abundant, and how it can be leveraged in the development of much-needed antimicrobial agents or identification of new therapeutic targets of this difficult-to-eradicate pathogen.
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12
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Liu Y, LaBonte S, Brake C, LaFayette C, Rosebrock AP, Caudy AA, Straight PD. MOB rules: Antibiotic Exposure Reprograms Metabolism to Mobilize Bacillus subtilis in Competitive Interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585991. [PMID: 38562742 PMCID: PMC10983992 DOI: 10.1101/2024.03.20.585991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Antibiotics have dose-dependent effects on exposed bacteria. The medicinal use of antibiotics relies on their growth-inhibitory activities at sufficient concentrations. At subinhibitory concentrations, exposure effects vary widely among different antibiotics and bacteria. Bacillus subtilis responds to bacteriostatic translation inhibitors by mobilizing a population of cells (MOB-Mobilized Bacillus) to spread across a surface. How B. subtilis regulates the antibiotic-induced mobilization is not known. In this study, we used chloramphenicol to identify regulatory functions that B. subtilis requires to coordinate cell mobilization following subinhibitory exposure. We measured changes in gene expression and metabolism and mapped the results to a network of regulatory proteins that direct the mobile response. Our data reveal that several transcriptional regulators coordinately control the reprogramming of metabolism to support mobilization. The network regulates changes in glycolysis, nucleotide metabolism, and amino acid metabolism that are signature features of the mobilized population. Among the hundreds of genes with changing expression, we identified two, pdhA and pucA, where the magnitudes of their changes in expression, and in the abundance of associated metabolites, reveal hallmark metabolic features of the mobilized population. Using reporters of pdhA and pucA expression, we visualized the separation of major branches of metabolism in different regions of the mobilized population. Our results reveal a regulated response to chloramphenicol exposure that enables a population of bacteria in different metabolic states to mount a coordinated mobile response.
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Affiliation(s)
- Yongjin Liu
- Biochemistry and Biophysics Department, Texas A&M University, AgriLife Research, College Station, Texas, USA
| | - Sandra LaBonte
- Biochemistry and Biophysics Department, Texas A&M University, AgriLife Research, College Station, Texas, USA
- Interdisciplinary Program in Genetics and Genomics,Texas A&M University, College Station, Texas, USA
| | - Courtney Brake
- Department of Visualization, Institute for Applied Creativity, Texas A&M University, College Station, Texas, USA
| | - Carol LaFayette
- Department of Visualization, Institute for Applied Creativity, Texas A&M University, College Station, Texas, USA
| | | | - Amy A. Caudy
- Maple Flavored Solutions, LLC, Indianapolis, Indiana, USA
| | - Paul D. Straight
- Biochemistry and Biophysics Department, Texas A&M University, AgriLife Research, College Station, Texas, USA
- Interdisciplinary Program in Genetics and Genomics,Texas A&M University, College Station, Texas, USA
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13
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Tran P, Lander SM, Prindle A. Active pH regulation facilitates Bacillus subtilis biofilm development in a minimally buffered environment. mBio 2024; 15:e0338723. [PMID: 38349175 PMCID: PMC10936434 DOI: 10.1128/mbio.03387-23] [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: 12/18/2023] [Accepted: 01/12/2024] [Indexed: 03/14/2024] Open
Abstract
Biofilms provide individual bacteria with many advantages, yet dense cellular proliferation can also create intrinsic metabolic challenges including excessive acidification. Because such pH stress can be masked in buffered laboratory media-such as MSgg commonly used to study Bacillus subtilis biofilms-it is not always clear how such biofilms cope with minimally buffered natural environments. Here, we report how B. subtilis biofilms overcome this intrinsic metabolic challenge through an active pH regulation mechanism. Specifically, we find that these biofilms can modulate their extracellular pH to the preferred neutrophile range, even when starting from acidic and alkaline initial conditions, while planktonic cells cannot. We associate this behavior with dynamic interplay between acetate and acetoin biosynthesis and show that this mechanism is required to buffer against biofilm acidification. Furthermore, we find that buffering-deficient biofilms exhibit dysregulated biofilm development when grown in minimally buffered conditions. Our findings reveal an active pH regulation mechanism in B. subtilis biofilms that could lead to new targets to control unwanted biofilm growth.IMPORTANCEpH is known to influence microbial growth and community dynamics in multiple bacterial species and environmental contexts. Furthermore, in many bacterial species, rapid cellular proliferation demands the use of overflow metabolism, which can often result in excessive acidification. However, in the case of bacterial communities known as biofilms, these acidification challenges can be masked when buffered laboratory media are employed to stabilize the pH environment for optimal growth. Our study reveals that B. subtilis biofilms use an active pH regulation mechanism to mitigate both growth-associated acidification and external pH challenges. This discovery provides new opportunities for understanding microbial communities and could lead to new methods for controlling biofilm growth outside of buffered laboratory conditions.
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Affiliation(s)
- Peter Tran
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois, USA
| | - Stephen M Lander
- Medical Scientist Training Program, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Arthur Prindle
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Chicago, Illinois, USA
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Li Y, Narayanan M, Shi X, Chen X, Li Z, Ma Y. Biofilms formation in plant growth-promoting bacteria for alleviating agro-environmental stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167774. [PMID: 37848152 DOI: 10.1016/j.scitotenv.2023.167774] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/02/2023] [Accepted: 10/10/2023] [Indexed: 10/19/2023]
Abstract
Biofilm formation represents a pivotal and adaptable trait among microorganisms within natural environments. This attribute plays a multifaceted role across diverse contexts, including environmental, aquatic, industrial, and medical systems. While previous research has primarily focused on the adverse impacts of biofilms, harnessing their potential effectively could confer substantial advantages to humanity. In the face of escalating environmental pressures (e.g., drought, salinity, extreme temperatures, and heavy metal pollution), which jeopardize global crop yields, enhancing crop stress tolerance becomes a paramount endeavor for restoring sufficient food production. Recently, biofilm-forming plant growth-promoting bacteria (PGPB) have emerged as promising candidates for agricultural application. These biofilms are evidence of microorganism colonization on plant roots. Their remarkable stress resilience empowers crops to thrive and yield even in harsh conditions. This is accomplished through increased root colonization, improved soil properties, and the synthesis of valuable secondary metabolites (e.g., ACC deaminase, acetin, 2,3-butanediol, proline, etc.). This article elucidates the mechanisms underpinning the role of biofilm-forming PGPB in bolstering plant growth amidst environmental challenges. Furthermore, it explores the tangible applications of these biofilms in agriculture and delves into strategies for manipulating biofilm formation to extract maximal benefits in practical crop production scenarios.
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Affiliation(s)
- Yujia Li
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Mathiyazhagan Narayanan
- Division of Research and Innovation, Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Science, Chennai 602105, Tamil Nadu, India
| | - Xiaojun Shi
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Xinping Chen
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Zhenlun Li
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Ying Ma
- College of Resources and Environment, Southwest University, Chongqing 400716, China.
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15
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Verstraeten S, Layec S, Auger S, Juste C, Henry C, Charif S, Jaszczyszyn Y, Sokol H, Beney L, Langella P, Thomas M, Huillet E. Faecalibacterium duncaniae A2-165 regulates the expression of butyrate synthesis, ferrous iron uptake, and stress-response genes based on acetate consumption. Sci Rep 2024; 14:987. [PMID: 38200051 PMCID: PMC10781979 DOI: 10.1038/s41598-023-51059-3] [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: 06/23/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
The promising next-generation probiotic Faecalibacterium prausnitzii is one of the most abundant acetate-consuming, butyrate-producing bacteria in the healthy human gut. Yet, little is known about how acetate availability affects this bacterium's gene expression strategies. Here, we investigated the effect of acetate on temporal changes in the transcriptome of F. duncaniae A2-165 cultures using RNA sequencing. We compared gene expression patterns between two growth phases (early stationary vs. late exponential) and two acetate levels (low: 3 mM vs. high: 23 mM). Only in low-acetate conditions, a general stress response was activated. In high-acetate conditions, there was greater expression of genes related to butyrate synthesis and to the importation of B vitamins and iron. Specifically, expression was strongly activated in the case of the feoAABC operon, which encodes a FeoB ferrous iron transporter, but not in the case of the feoAB gene, which encodes a second putative FeoAB transporter. Moreover, excess ferrous iron repressed feoB expression but not feoAB. Lastly, FeoB but not FeoAB peptides from strain A2-165 were found in abundance in a healthy human fecal metaproteome. In conclusion, we characterized two early-stationary transcriptomes based on acetate consumption and this work highlights the regulation of feoB expression in F. duncaniae A2-165.
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Affiliation(s)
- Sophie Verstraeten
- Micalis Institute, INRAe, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Séverine Layec
- Micalis Institute, INRAe, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Sandrine Auger
- Micalis Institute, INRAe, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- Paris Center for Microbiome Medecine (PaCeMM) FHU, AP-HP, Paris, France
| | - Catherine Juste
- Micalis Institute, INRAe, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Céline Henry
- Micalis Institute, INRAe, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Sawiya Charif
- Micalis Institute, INRAe, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Yan Jaszczyszyn
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-Sur-Yvette, France
| | - Harry Sokol
- Micalis Institute, INRAe, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- Paris Center for Microbiome Medecine (PaCeMM) FHU, AP-HP, Paris, France
| | - Laurent Beney
- UMR PAM, INRAe, Université Bourgogne Franche-Conté, AgroSup Dijon, Dijon, France
| | - Philippe Langella
- Micalis Institute, INRAe, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- Paris Center for Microbiome Medecine (PaCeMM) FHU, AP-HP, Paris, France
| | - Muriel Thomas
- Micalis Institute, INRAe, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- Paris Center for Microbiome Medecine (PaCeMM) FHU, AP-HP, Paris, France
| | - Eugénie Huillet
- Micalis Institute, INRAe, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
- Paris Center for Microbiome Medecine (PaCeMM) FHU, AP-HP, Paris, France.
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16
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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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17
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Li JG, Chen XF, Lu TY, Zhang J, Dai SH, Sun J, Liu YH, Liao XP, Zhou YF. Increased Activity of β-Lactam Antibiotics in Combination with Carvacrol against MRSA Bacteremia and Catheter-Associated Biofilm Infections. ACS Infect Dis 2023; 9:2482-2493. [PMID: 38019707 DOI: 10.1021/acsinfecdis.3c00338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
β-Lactam antibiotics are the mainstay for the treatment of staphylococcal infections, but their utility is greatly limited by the emergence and rapid dissemination of methicillin-resistant Staphylococcus aureus (MRSA). Herein, we evaluated the ability of the plant-derived monoterpene carvacrol to act as an antibiotic adjuvant, revitalizing the anti-MRSA activity of β-lactam antibiotics. Increased susceptibility of MRSA to β-lactam antibiotics and significant synergistic activities were observed with carvacrol-based combinations. Carvacrol significantly inhibited MRSA biofilms and reduced the production of exopolysaccharide, polysaccharide intercellular adhesin, and extracellular DNA and showed synergistic biofilm inhibition in combination with β-lactams. Transcriptome analysis revealed profound downregulation in the expression of genes involved in two-component systems and S. aureus infection. Mechanistic studies indicate that carvacrol inhibits the expression of staphylococcal accessory regulator sarA and interferes with SarA-mecA promoter binding that decreases mecA-mediated β-lactam resistance. Consistently, the in vivo experiment also supported that carvacrol restored MRSA sensitivity to β-lactam antibiotic treatments in both murine models of bacteremia and biofilm-associated infection. Our results indicated that carvacrol has a potential role as a combinatorial partner with β-lactam antibiotics to address MRSA infections.
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Affiliation(s)
- Jian-Guo Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Xiao-Feng Chen
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Ting-Yin Lu
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Jing Zhang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Yantai Fushan Center for Animal Disease Control and Prevention, Fushan, Yantai, Shandong 265500, China
| | - Shu-He Dai
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Jian Sun
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Ya-Hong Liu
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Xiao-Ping Liao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Yu-Feng Zhou
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
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18
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Dergham Y, Le Coq D, Nicolas P, Bidnenko E, Dérozier S, Deforet M, Huillet E, Sanchez-Vizuete P, Deschamps J, Hamze K, Briandet R. Direct comparison of spatial transcriptional heterogeneity across diverse Bacillus subtilis biofilm communities. Nat Commun 2023; 14:7546. [PMID: 37985771 PMCID: PMC10661151 DOI: 10.1038/s41467-023-43386-w] [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: 01/09/2023] [Accepted: 11/08/2023] [Indexed: 11/22/2023] Open
Abstract
Bacillus subtilis can form various types of spatially organised communities on surfaces, such as colonies, pellicles and submerged biofilms. These communities share similarities and differences, and phenotypic heterogeneity has been reported for each type of community. Here, we studied spatial transcriptional heterogeneity across the three types of surface-associated communities. Using RNA-seq analysis of different regions or populations for each community type, we identified genes that are specifically expressed within each selected population. We constructed fluorescent transcriptional fusions for 17 of these genes, and observed their expression in submerged biofilms using time-lapse confocal laser scanning microscopy (CLSM). We found mosaic expression patterns for some genes; in particular, we observed spatially segregated cells displaying opposite regulation of carbon metabolism genes (gapA and gapB), indicative of distinct glycolytic or gluconeogenic regimes coexisting in the same biofilm region. Overall, our study provides a direct comparison of spatial transcriptional heterogeneity, at different scales, for the three main models of B. subtilis surface-associated communities.
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Affiliation(s)
- Yasmine Dergham
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Lebanese University, Faculty of Science, Beirut, Lebanon
| | - Dominique Le Coq
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS), INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pierre Nicolas
- Université Paris-Saclay, INRAE, MAIAGE, Jouy-en-Josas, France
| | - Elena Bidnenko
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Sandra Dérozier
- Université Paris-Saclay, INRAE, MAIAGE, Jouy-en-Josas, France
| | - Maxime Deforet
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean Perrin, Paris, France
| | - Eugénie Huillet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pilar Sanchez-Vizuete
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Julien Deschamps
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Kassem Hamze
- Lebanese University, Faculty of Science, Beirut, Lebanon.
| | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.
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19
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Zanditenas E, Trebicz-Geffen M, Kolli D, Domínguez-García L, Farhi E, Linde L, Romero D, Chapman M, Kolodkin-Gal I, Ankri S. Digestive exophagy of biofilms by intestinal amoeba and its impact on stress tolerance and cytotoxicity. NPJ Biofilms Microbiomes 2023; 9:77. [PMID: 37813896 PMCID: PMC10562373 DOI: 10.1038/s41522-023-00444-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023] Open
Abstract
The human protozoan parasite Entamoeba histolytica is responsible for amebiasis, a disease endemic to developing countries. E. histolytica trophozoites colonize the large intestine, primarily feeding on bacteria. However, in the gastrointestinal tract, bacterial cells form aggregates or structured communities called biofilms too large for phagocytosis. Remarkably, trophozoites are still able to invade and degrade established biofilms, utilizing a mechanism that mimics digestive exophagy. Digestive exophagy refers to the secretion of digestive enzymes that promote the digestion of objects too large for direct phagocytosis by phagocytes. E. histolytica cysteine proteinases (CPs) play a crucial role in the degradation process of Bacillus subtilis biofilm. These proteinases target TasA, a major component of the B. subtilis biofilm matrix, also contributing to the adhesion of the parasite to the biofilm. In addition, they are also involved in the degradation of biofilms formed by Gram-negative and Gram-positive enteric pathogens. Furthermore, biofilms also play an important role in protecting trophozoites against oxidative stress. This specific mechanism suggests that the amoeba has adapted to prey on biofilms, potentially serving as an untapped reservoir for novel therapeutic approaches to treat biofilms. Consistently, products derived from the amoeba have been shown to restore antibiotic sensitivity to biofilm cells. In addition, our findings reveal that probiotic biofilms can act as a protective shield for mammalian cells, hindering the progression of the parasite towards them.
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Affiliation(s)
- Eva Zanditenas
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Meirav Trebicz-Geffen
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Divya Kolli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, USA
| | - Laura Domínguez-García
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga, Spain
| | - Einan Farhi
- Technion Genomics Center, Technion - Israel Institute of Technology, Haifa, Israel
| | - Liat Linde
- Technion Genomics Center, Technion - Israel Institute of Technology, Haifa, Israel
| | - Diego Romero
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga, Spain
| | - Matthew Chapman
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, USA
| | - Ilana Kolodkin-Gal
- Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
- Scojen Institute for Synthetic Biology, Reichman University, Herzliya, Israel.
| | - Serge Ankri
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel.
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20
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Belcher LJ, Dewar AE, Hao C, Ghoul M, West SA. Signatures of kin selection in a natural population of the bacteria Bacillus subtilis. Evol Lett 2023; 7:315-330. [PMID: 37829498 PMCID: PMC10565896 DOI: 10.1093/evlett/qrad029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/14/2023] [Accepted: 07/07/2023] [Indexed: 10/14/2023] Open
Abstract
Laboratory experiments have suggested that bacteria perform a range of cooperative behaviors, which are favored because they are directed toward relatives (kin selection). However, there is a lack of evidence for cooperation and kin selection in natural bacterial populations. Molecular population genetics offers a promising method to study natural populations because the theory predicts that kin selection will lead to relaxed selection, which will result in increased polymorphism and divergence at cooperative genes. Examining a natural population of Bacillus subtilis, we found consistent evidence that putatively cooperative traits have higher polymorphism and greater divergence than putatively private traits expressed at the same rate. In addition, we were able to eliminate alternative explanations for these patterns and found more deleterious mutations in genes controlling putatively cooperative traits. Overall, our results suggest that cooperation is favored by kin selection, with an average relatedness of r = .79 between interacting individuals.
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Affiliation(s)
| | - Anna E Dewar
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Chunhui Hao
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Melanie Ghoul
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Stuart A West
- Department of Biology, University of Oxford, Oxford, United Kingdom
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21
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Gadar K, McCarthy RR. Using next generation antimicrobials to target the mechanisms of infection. NPJ ANTIMICROBIALS AND RESISTANCE 2023; 1:11. [PMID: 38686217 PMCID: PMC11057201 DOI: 10.1038/s44259-023-00011-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 07/28/2023] [Indexed: 05/02/2024]
Abstract
The remarkable impact of antibiotics on human health is being eroded at an alarming rate by the emergence of multidrug resistant pathogens. There is a recognised consensus that new strategies to tackle infection are urgently needed to limit the devasting impact of antibiotic resistance on our global healthcare infrastructure. Next generation antimicrobials (NGAs) are compounds that target bacterial virulence factors to disrupt pathogenic potential without impacting bacterial viability. By disabling the key virulence factors required to establish and maintain infection, NGAs make pathogens more vulnerable to clearance by the immune system and can potentially render them more susceptible to traditional antibiotics. In this review, we discuss the developing field of NGAs and how advancements in this area could offer a viable standalone alternative to traditional antibiotics or an effective means to prolong antibiotic efficacy when used in combination.
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Affiliation(s)
- Kavita Gadar
- Division of Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UB8 3PH United Kingdom
| | - Ronan R. McCarthy
- Division of Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UB8 3PH United Kingdom
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22
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Sun H, Si F, Zhao X, Li F, Qi G. The cellular redox state in Bacillus amyloliquefaciens WH1 affects biofilm formation indirectly in a surfactant direct manner. J Basic Microbiol 2023. [PMID: 37189223 DOI: 10.1002/jobm.202300064] [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: 02/10/2023] [Revised: 03/30/2023] [Accepted: 04/27/2023] [Indexed: 05/17/2023]
Abstract
Surfactin is a signal to trigger biofilm formation against harsh environments. Generally, harsh environments can result in change of the cellular redox state to induce biofilm formation, but we know little about whether the cellular redox state influences biofilm formation via surfactin. Here, the reductant glucose could reduce surfactin and enhance biofilm formation by a surfactin-indirect way. The oxidant H2 O2 led to a decrease of surfactin accompanying with weakened biofilm formation. Spx and PerR were both necessary for surfactin production and biofilm formation. H2 O2 improved surfactin production but inhibited biofilm formation by a surfactin-indirect manner in Δspx, while it reduced surfactin production without obvious influence on biofilm formation in ΔperR. The ability against H2 O2 stress was enhanced in Δspx, but weakened in ΔperR. Thereby, PerR was favorable for resisting oxidative stress, while Spx played a negative role in this action. Knockout and compensation of rex also supported that the cells could form biofilm by a surfactin-indirect way. Collectively, surfactin is not a unique signal to trigger biofilm formation, and the cellular redox state can influence biofilm formation by a surfactin-direct or -indirect way in Bacillus amyloliquefaciens WH1.
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Affiliation(s)
- Huiwan Sun
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fengmei Si
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiuyun Zhao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Feng Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Gaofu Qi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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23
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Yang P, Geng C, Zhu S, Zhou Z, Bilal M, Gu C, Xu H, Ji L, Xiao B, Wang J, Qian Z, Zhao L, Zhao Y, Lu H. Identification and functional analysis of non-coding regulatory small RNA FenSr3 in Bacillus amyloliquefaciens LPB-18. PeerJ 2023; 11:e15236. [PMID: 37214100 PMCID: PMC10194069 DOI: 10.7717/peerj.15236] [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: 11/28/2022] [Accepted: 03/28/2023] [Indexed: 05/24/2023] Open
Abstract
Bacillus amyloliquefaciens is an interesting microbe in the food processing and manufacturing industries. Non-coding small RNAs (sRNAs) have been shown to play a crucial role in the physiology and metabolism of bacteria by post-transcriptionally regulating gene expression. This study investigated the function of novel sRNA FenSr3 by constructing fenSr3 deficient strain and complementary strains in B. amyloliquefaciens LPB-18 , which were named LPN-18N and LPB-18P, respectively. The result showed significant differences in fengycin yield between strain LPB -18N and LPB-18P. The production of fengycin was significantly enhanced in B. amyloliquefaciens LPB-18N, compared with that of the strain LPB-18 from 190.908 mg/L to 327.598 mg/L. Moreover, the production of fengycin decreased from 190.464 mg/L to 38.6 mg/L in B . amyloliquefaciens LPB-18P. A comparative transcriptome sequencing was carried out to better understand the complex regulatory mechanism. Transcription analysis revealed that 1037 genes were differentially expressed between B. amyloliquefaciens LPB-18 and B. amyloliquefaciens LPB-18N, including the key regulatory genes in fatty acid, amino acid biosynthesis, and central carbon metabolism, which could provide sufficient quantities of building precursors for fengycin biosynthesis. The biofilm formation and sporulation was also enhanced in the strain LPB-18N, which indicates that FenSr3 could play a vital role in stress resistance and promotes survival in B. amyloliquefaciens. Some sRNAs involved in stress response have been identified in the literature, but their regulatory roles in fengycin production remain unclear. The study will contribute a novel perspective to the regulation mechanism of biosynthesis and the optimization of key metabolites of B. amyloliquefaciens.
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Affiliation(s)
- Panping Yang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaiyin Institute of Technology, Huaian, Jiangsu, China
| | - Chengxin Geng
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaiyin Institute of Technology, Huaian, Jiangsu, China
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Weigang, China
| | - Shaohui Zhu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaiyin Institute of Technology, Huaian, Jiangsu, China
| | - Zhen Zhou
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaiyin Institute of Technology, Huaian, Jiangsu, China
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaiyin Institute of Technology, Huaian, Jiangsu, China
| | - Chengyuan Gu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaiyin Institute of Technology, Huaian, Jiangsu, China
| | - Hai Xu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaiyin Institute of Technology, Huaian, Jiangsu, China
| | - Linchun Ji
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaiyin Institute of Technology, Huaian, Jiangsu, China
| | - Benchang Xiao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaiyin Institute of Technology, Huaian, Jiangsu, China
| | - Jingye Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaiyin Institute of Technology, Huaian, Jiangsu, China
| | - Zhoujie Qian
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaiyin Institute of Technology, Huaian, Jiangsu, China
| | - Li Zhao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaiyin Institute of Technology, Huaian, Jiangsu, China
| | - Yuping Zhao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaiyin Institute of Technology, Huaian, Jiangsu, China
| | - Hedong Lu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaiyin Institute of Technology, Huaian, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan College, Wuxi, Jiangsu, China
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24
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Su Z, Liu G, Liu X, Li S, Lu X, Wang P, Zhao W, Zhang X, Dong L, Qu Y, Zhang J, Mo S, Guo Q, Ma P. Functional Analyses of the Bacillus velezensis HMB26553 Genome Provide Evidence That Its Genes Are Potentially Related to the Promotion of Plant Growth and Prevention of Cotton Rhizoctonia Damping-Off. Cells 2023; 12:cells12091301. [PMID: 37174701 PMCID: PMC10177454 DOI: 10.3390/cells12091301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/18/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Bacillus spp. is one kind of the important representative biocontrol agents against plant diseases and promoting plant growth. In this study, the whole genomic sequence of bacterial strain HMB26553 was obtained. A phylogenetic tree based on the genome and ANI (average nucleotide identity), as well as dDDH (digital DNA-DNA hybridization), was constructed, and strain HMB26553 was identified as Bacillus velezensis. Fourteen biosynthetic gene clusters responsible for secondary metabolite were predicted via anti-SMASH, and six secondary metabolites were identified by UHPLC-QTOF-MS/MS (ultra-high-performance liquid chromatography coupled to quadrupole-time-of-flight tandem mass spectrometry). When the phytopathogen Rhizoctonia solani was treated with B. velezensis HMB26553, the mycelial structure changed, ROS (reactive oxygen species) accumulated, and the mitochondrial membrane potential decreased. Characteristics of strain HMB26553 were predicted and confirmed by genomic information and experiments, such as producing IAA, siderophore, extracellular enzymes and biofilm, as well as moving and promoting cotton growth. All these results suggested the mechanisms by which B. velezensis HMB26553 inhibits pathogen growth and promotes cotton growth, which likely provided the potential biocontrol agent to control cotton Rhizoctonia damping-off.
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Affiliation(s)
- Zhenhe Su
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding 071000, China
| | - Gaoge Liu
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding 071000, China
| | - Xiaomeng Liu
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding 071000, China
| | - Shezeng Li
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding 071000, China
| | - Xiuyun Lu
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding 071000, China
| | - Peipei Wang
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding 071000, China
| | - Weisong Zhao
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding 071000, China
| | - Xiaoyun Zhang
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding 071000, China
| | - Lihong Dong
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding 071000, China
| | - Yuanhang Qu
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding 071000, China
| | - Jiaqi Zhang
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding 071000, China
| | - Shaojing Mo
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding 071000, China
| | - Qinggang Guo
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding 071000, China
| | - Ping Ma
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Integrated Pest Management Innovation Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs of China, Baoding 071000, China
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25
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Transcript profiling reveals the role of PDB1, a subunit of the pyruvate dehydrogenase complex, in Candida albicans biofilm formation. Res Microbiol 2023; 174:104014. [PMID: 36535619 DOI: 10.1016/j.resmic.2022.104014] [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: 10/24/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Candida albicans, the most prevalent fungal pathogen in the human microbiota can form biofilms on implanted medical devices. These biofilms are tolerant to conventional antifungal drugs and the host immune system as compared to the free-floating planktonic cells. Several in vitro models of biofilm formation have been used to determine the C. albicans biofilm-forming process, regulatory networks, and their properties. Here, we performed a genome-wide transcript profiling with C. albicans cells grown in YPD medium both in planktonic and biofilm condition. Transcript profiling of YPD-grown biofilms was further compared with published Spider medium-grown biofilm transcriptome data. This comparative analysis highlighted the differentially expressed genes and the pathways altered during biofilm formation. In addition, we demonstrated that overexpression of the PDB1 gene encoding a subunit of the pyruvate dehydrogenase resulted in defective biofilm formation. Altogether, this comparative analysis of transcript profiles from two different studies provides a robust reading on biofilm-altered genes and pathways during C. albicans biofilm development.
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26
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Shibamura-Fujiogi M, Wang X, Maisat W, Koutsogiannaki S, Li Y, Chen Y, Lee JC, Yuki K. GltS regulates biofilm formation in methicillin-resistant Staphylococcus aureus. Commun Biol 2022; 5:1284. [PMID: 36418899 PMCID: PMC9684512 DOI: 10.1038/s42003-022-04239-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 11/08/2022] [Indexed: 11/25/2022] Open
Abstract
Biofilm-based infection is a major healthcare burden. Methicillin-resistant Staphylococcus aureus (MRSA) is one of major organisms responsible for biofilm infection. Although biofilm is induced by a number of environmental signals, the molecule responsible for environmental sensing is not well delineated. Here we examined the role of ion transporters in biofilm formation and found that the sodium-glutamate transporter gltS played an important role in biofilm formation in MRSA. This was shown by gltS transposon mutant as well as its complementation. The lack of exogenous glutamate also enhanced biofilm formation in JE2 strain. The deficiency of exogenous glutamate intake accelerated endogenous glutamate/glutamine production, which led to the activation of the urea cycle. We also showed that urea cycle activation was critical for biofilm formation. In conclusion, we showed that gltS was a critical regulator of biofilm formation by controlling the intake of exogenous glutamate. An intervention to target glutamate intake may be a potential useful approach against biofilm.
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Affiliation(s)
- Miho Shibamura-Fujiogi
- Department of Anesthesiology, Critical Care and Pain Medicine, Cardiac Anesthesia Division, Boston Children's Hospital, Boston, MA, USA
- Department of Anaesthesia and Immunology, Harvard Medical School, Boston, MA, USA
| | - Xiaogang Wang
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Wiriya Maisat
- Department of Anesthesiology, Critical Care and Pain Medicine, Cardiac Anesthesia Division, Boston Children's Hospital, Boston, MA, USA
- Department of Anaesthesia and Immunology, Harvard Medical School, Boston, MA, USA
| | - Sophia Koutsogiannaki
- Department of Anesthesiology, Critical Care and Pain Medicine, Cardiac Anesthesia Division, Boston Children's Hospital, Boston, MA, USA
- Department of Anaesthesia and Immunology, Harvard Medical School, Boston, MA, USA
| | - Yunan Li
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Yue Chen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Jean C Lee
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Koichi Yuki
- Department of Anesthesiology, Critical Care and Pain Medicine, Cardiac Anesthesia Division, Boston Children's Hospital, Boston, MA, USA.
- Department of Anaesthesia and Immunology, Harvard Medical School, Boston, MA, USA.
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27
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Su Y, Yrastorza JT, Matis M, Cusick J, Zhao S, Wang G, Xie J. Biofilms: Formation, Research Models, Potential Targets, and Methods for Prevention and Treatment. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203291. [PMID: 36031384 PMCID: PMC9561771 DOI: 10.1002/advs.202203291] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/31/2022] [Indexed: 05/28/2023]
Abstract
Due to the continuous rise in biofilm-related infections, biofilms seriously threaten human health. The formation of biofilms makes conventional antibiotics ineffective and dampens immune clearance. Therefore, it is important to understand the mechanisms of biofilm formation and develop novel strategies to treat biofilms more effectively. This review article begins with an introduction to biofilm formation in various clinical scenarios and their corresponding therapy. Established biofilm models used in research are then summarized. The potential targets which may assist in the development of new strategies for combating biofilms are further discussed. The novel technologies developed recently for the prevention and treatment of biofilms including antimicrobial surface coatings, physical removal of biofilms, development of new antimicrobial molecules, and delivery of antimicrobial agents are subsequently presented. Finally, directions for future studies are pointed out.
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Affiliation(s)
- Yajuan Su
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | - Jaime T. Yrastorza
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | - Mitchell Matis
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | - Jenna Cusick
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | - Siwei Zhao
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | - Guangshun Wang
- Department of Pathology and MicrobiologyCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | - Jingwei Xie
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
- Department of Mechanical and Materials EngineeringCollege of EngineeringUniversity of Nebraska‐LincolnLincolnNE68588USA
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28
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Wang N, Gao J, Xiao S, Zhuang G. Overexpression of pdeR promotes biofilm formation of Paracoccus denitrificans by promoting ATP production and iron acquisition. Front Microbiol 2022; 13:966976. [PMID: 36033861 PMCID: PMC9399729 DOI: 10.3389/fmicb.2022.966976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 07/21/2022] [Indexed: 12/02/2022] Open
Abstract
Bacterial biofilms are ubiquitous in natural environments and play an essential role in bacteria’s environmental adaptability. Quorum sensing (QS), as the main signaling mechanism bacteria used for cell-to-cell communication, plays a key role in bacterial biofilm formation. However, little is known about the role of QS circuit in the N-transformation type strain, Paracoccus denitrificans, especially for the regulatory protein PdeR. In this study, we found the overexpression of pdeR promoted bacterial aggregation and biofilm formation. Through RNA-seq analysis, we demonstrated that PdeR is a global regulator which could regulate 656 genes expression, involved in multiple metabolic pathways. Combined with transcriptome as well as biochemical experiments, we found the overexpressed pdeR mainly promoted the intracellular degradation of amino acids and fatty acids, as well as siderophore biosynthesis and transportation, thus providing cells enough energy and iron for biofilm development. These results revealed the underlying mechanism for PdeR in biofilm formation of P. denitrificans, adding to our understanding of QS regulation in biofilm development.
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Affiliation(s)
- Na Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Jie Gao
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Jie Gao,
| | - Shujie Xiao
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Guoqiang Zhuang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Guoqiang Zhuang,
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29
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Wu P, Rane NR, Xing C, Patil SM, Roh HS, Jeon BH, Li X. Integrative chemical and omics analyses reveal copper biosorption and tolerance mechanisms of Bacillus cereus strain T6. JOURNAL OF HAZARDOUS MATERIALS 2022; 435:129002. [PMID: 35490635 DOI: 10.1016/j.jhazmat.2022.129002] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 06/14/2023]
Abstract
A comprehensive understanding of the cellular response of microbes to metal stress is necessary for the rational development of microbe-based biosorbents for metal removal. The present study investigated the copper (Cu) sorption and resistance mechanism of Bacillus cereus strain T6, a newly isolated Cu-resistant bacterium, by integrative analyses of physiochemistry, genomics, transcriptomics, and metabolomics. The growth inhibition assay and biosorption determination showed that this bacterium exhibited high tolerance to Cu, with a minimum inhibitory concentration of 4.0 mM, and accumulated Cu by both extracellular adsorption and intracellular binding. SEM microscopic images and FTIR spectra showed significant cellular surface changes at the high Cu level but not at low, and the involvement of surface functional groups in the biosorption of Cu, respectively. Transcriptomic and untargeted metabolomic analyses detected 362 differentially expressed genes and 60 significantly altered metabolites, respectively. Integrative omics analyses revealed that Cu exposure dramatically induced a broad spectrum of genes involved in Cu transport and iron homeostasis, and suppressed the denitrification pathway, leading to significant accumulation of metabolites for metal transporter synthesis, membrane remolding, and antioxidant activities. The results presented here provide a new perspective on the intricate regulatory network of Cu homeostasis in bacteria.
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Affiliation(s)
- Ping Wu
- Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Niraj R Rane
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Chao Xing
- Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Swapnil M Patil
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Hyun-Seog Roh
- Department of Environmental Engineering, Yonsei University, 1 Yonseidae-gil, Wonju, Gangwon 26493, Republic of Korea
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea.
| | - Xiaofang Li
- Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China.
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30
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Kutnu M, İşlerel ET, Tunçbağ N, Özcengiz G. Comparative biological network analysis for differentially expressed proteins as a function of bacilysin biosynthesis in Bacillus subtilis. Integr Biol (Camb) 2022; 14:99-110. [PMID: 35901454 DOI: 10.1093/intbio/zyac010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 12/07/2021] [Accepted: 01/05/2022] [Indexed: 06/15/2023]
Abstract
The Gram-positive bacterium Bacillus subtilis produces a diverse range of secondary metabolites with different structures and activities. Among them, bacilysin is an enzymatically synthesized dipeptide that consists of L-alanine and L-anticapsin. Previous research by our group has suggested bacilysin's role as a pleiotropic molecule in its producer, B. subtilis PY79. However, the nature of protein interactions in the absence of bacilysin has not been defined. In the present work, we constructed a protein-protein interaction subnetwork by using Omics Integrator based on our recent comparative proteomics data obtained from a bacilysin-silenced strain, OGU1. Functional enrichment analyses on the resulting networks pointed to certain putatively perturbed pathways such as citrate cycle, quorum sensing and secondary metabolite biosynthesis. Various molecules, which were absent from the experimental data, were included in the final network. We believe that this study can guide further experiments in the identification and confirmation of protein-protein interactions in B. subtilis.
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Affiliation(s)
- Meltem Kutnu
- Department of Biological Sciences/Molecular Biology and Genetics, Middle East Technical University, Ankara 06800, Turkey
| | - Elif Tekin İşlerel
- Department of Biological Sciences/Molecular Biology and Genetics, Middle East Technical University, Ankara 06800, Turkey
- Department of Medical Microbiology, Faculty of Medicine, Maltepe University, Istanbul 34857, Turkey
| | - Nurcan Tunçbağ
- Department of Chemical and Biological Engineering, Koc University, Istanbul 34450, Turkey
| | - Gülay Özcengiz
- Department of Biological Sciences/Molecular Biology and Genetics, Middle East Technical University, Ankara 06800, Turkey
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31
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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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32
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Lamba S, Mundanda Muthappa D, Fanning S, Scannell AGM. Sporulation and Biofilms as Survival Mechanisms of Bacillus Species in Low-Moisture Food Production Environments. Foodborne Pathog Dis 2022; 19:448-462. [PMID: 35819266 DOI: 10.1089/fpd.2022.0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Low-moisture foods (LMF) have clear advantages with respect to limiting the growth of foodborne pathogens. However, the incidences of Bacillus species in LMF reported in recent years raise concerns about food quality and safety, particularly when these foods are used as ingredients in more complex higher moisture products. This literature review describes the interlinked pathways of sporulation and biofilm formation by Bacillus species and their underlying molecular mechanisms that contribute to the bacteriums' persistence in LMF production environments. The long-standing challenges of food safety and quality in the LMF industry are also discussed with a focus on the bakery industry.
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Affiliation(s)
- Sakshi Lamba
- UCD Institute of Food and Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD Centre for Food Safety, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD School of Agriculture and Food Science, and Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Dechamma Mundanda Muthappa
- UCD Centre for Food Safety, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD School of Agriculture and Food Science, and Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Séamus Fanning
- UCD Institute of Food and Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD Centre for Food Safety, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Amalia G M Scannell
- UCD Institute of Food and Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD Centre for Food Safety, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD School of Agriculture and Food Science, and Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
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33
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Guo M, Tan S, Zhu J, Sun A, Du P, Liu X. Genes Involved in Biofilm Matrix Formation of the Food Spoiler Pseudomonas fluorescens PF07. Front Microbiol 2022; 13:881043. [PMID: 35733961 PMCID: PMC9207406 DOI: 10.3389/fmicb.2022.881043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
The extracellular matrix is essential for the biofilm formation of food spoilers. Pseudomonas fluorescens PF07 is a previous isolate from spoiled marine fish; however, the genes involved in the extracellular matrix formation of PF07 biofilms remain poorly defined. In this study, PF07 formed a wrinkled macrocolony biofilm through the high production of extracellular matrix. The genes involved in biofilm matrix formation and regulation were screened and identified by RNA-seq-dependent transcriptomic analysis and gene knock-out analysis. The macrocolony biofilms of PF07 grown for 5 days (PF07_5d) were compared with those grown for 1 day (PF07_1d). A total of 1,403 genes were significantly differentially expressed during biofilm formation. These mainly include the genes related to biofilm matrix proteins, polysaccharides, rhamnolipids, secretion system, biofilm regulation, and metabolism. Among them, functional amyloid genes fapABCDE were highly upregulated in the mature biofilm, and the operon fapA-E had a –24/–12 promoter dependent on the sigma factor RpoN. Moreover, the RNA-seq analyses of the rpoN mutant, compared with PF07, revealed 159 genes were differentially expressed in the macrocolony biofilms, and fapA-E genes were positively regulated by RpoN. In addition, the deletion mutants of fapC, rpoN, and brfA (a novel gene coding for an RpoN-dependent transcriptional regulator) were defective in forming mature macrocolony biofilms, solid surface-associated (SSA) biofilms, and pellicles, and they showed significantly reduced biofilm matrices. The fap genes were significantly downregulated in ΔbrfA, as in ΔrpoN. These findings suggest that the functional amyloid Fap is the main component of PF07 biofilm matrices, and RpoN may directly regulate the transcription of fap genes, in conjunction with BrfA. These genes may serve as potential molecular targets for screening new anti-biofilm agents or for biofilm detection in food environments.
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Affiliation(s)
- Miao Guo
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
- School of Public Health, Hangzhou Medical College, Hangzhou, China
| | - Siqi Tan
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
- School of Public Health, Hangzhou Medical College, Hangzhou, China
| | - Junli Zhu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Aihua Sun
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Peng Du
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Xiaoxiang Liu
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
- *Correspondence: Xiaoxiang Liu,
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Wang N, Gao J, Wang Q, Xiao S, Zhuang G. Antimicrobial peptide antibiotics inhibit aerobic denitrification via affecting electron transportation and remolding carbon metabolism. JOURNAL OF HAZARDOUS MATERIALS 2022; 431:128616. [PMID: 35359112 DOI: 10.1016/j.jhazmat.2022.128616] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/17/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
The harmful effects of antibiotics on biological denitrification have attracted widespread attention due to their excessive usage. Polymyxin B (PMB) as the typical antimicrobial peptides having been regarded as the "last hope" for treatment of multidrug-resistance bacteria, has also been detected in wastewater. However, little is known about the influence of PMB on aerobic denitrification. In this study, the impact of PMB on aerobic denitrification performance was investigated. Results showed 0.50 mg/L PMB decreased nitrate removal efficiency from 97.4% to 85.3%, and drove denitrifiers to transform more nitrate to biomass instead of producing gas-N. The live/dead staining method showed PMB damaged bacterial membrane. Transcriptome analysis further indicated the key enzymes participating in denitrification and aerobic respiratory chains were suppressed by PMB. To resist the PMB stress, denitrifiers formed thicker biofilm to protect cells from PMB damaging and thus remodeling the central carbon metabolism. Further investigation revealed denitrifiers have different preference on various carbon sources when PMB is present. Subsequently, the underlying mechanism of the distinctive carbon sources preference was explored by the combination of transcriptome and metabolism analysis. Overall, our data suggested denitrifiers have distinctive carbon sources preference under PMB treatment conditions, reminding us that carbon source selection should be cautious in practical applications.
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Affiliation(s)
- Na Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Gao
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Qiuying Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shujie Xiao
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoqiang Zhuang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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35
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Identification of metabolite extraction method for targeted exploration of antimicrobial resistance associated metabolites of Klebsiella pneumoniae. Sci Rep 2022; 12:8939. [PMID: 35624184 PMCID: PMC9142494 DOI: 10.1038/s41598-022-12153-0] [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: 01/06/2022] [Accepted: 04/22/2022] [Indexed: 11/08/2022] Open
Abstract
Antimicrobial resistant Klebsiella pneumoniae (K. pneumoniae), as being a pathogen of critical clinical concern, urgently demands effective therapeutic options. However, the discovery of novel antibiotics over the last three decades has declined drastically and necessitates exploring novel strategies. Metabolomic modulation has been the promising approach for the development of effective therapeutics to deal with AMR; however, only limited efforts have been made to-date, possibly due to the unavailability of suitable metabolites extraction protocols. Therefore, in order to establish a detailed metabolome of K. pneumoniae and identify a method for targeted exploration of metabolites that are involved in the regulation of AMR associated processes, metabolites were extracted using multiple methods of metabolites extraction (freeze-thaw cycle (FTC) and sonication cycle (SC) method alone or in combination (FTC followed by SC; FTC + SC)) from K. pneumoniae cells and then identified using an orbitrap mass analyzer (ESI-LC-MS/MS). A total of 151 metabolites were identified by using FTC, 132 metabolites by using FTC+SC, 103 metabolites by using SC and 69 metabolites common among all the methods used which altogether enabled the identification of 199 unique metabolites. Of these 199, 70 metabolites were known to have an association with AMR phenotype and among these, the FTC + SC method yielded better (identified 55 metabolites), quantitatively and qualitatively compared to FTC and SC alone (identified 51 and 41 metabolites respectively). Each method of metabolite extraction showed a definite degree of biasness and specificity towards chemical classes of metabolites and jointly contributed to the development of a detailed metabolome of the pathogen. FTC method was observed to give higher metabolomic coverage as compared to SC alone and FTC + SC. However, FTC + SC resulted in the identification of a higher number of AMR associated metabolites of K. pneumoniae compared to FTC and SC alone.
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36
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Characterization of Staphylococcus aureus biofilms via crystal violet binding and biochemical composition assays of isolates from hospitals, raw meat, and biofilm-associated gene mutants. Microb Pathog 2022; 167:105554. [DOI: 10.1016/j.micpath.2022.105554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 11/18/2022]
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37
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Systems view of Bacillus subtilis pellicle development. NPJ Biofilms Microbiomes 2022; 8:25. [PMID: 35414070 PMCID: PMC9005697 DOI: 10.1038/s41522-022-00293-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/19/2022] [Indexed: 11/08/2022] Open
Abstract
In this study, we link pellicle development at the water-air interface with the vertical distribution and viability of the individual B. subtilis PS-216 cells throughout the water column. Real-time interfacial rheology and time-lapse confocal laser scanning microscopy were combined to correlate mechanical properties with morphological changes (aggregation status, filament formation, pellicle thickness, spore formation) of the growing pellicle. Six key events were identified in B. subtilis pellicle formation that are accompanied by a major change in viscoelastic and morphology behaviour of the pellicle. The results imply that pellicle development is a multifaceted response to a changing environment induced by bacterial growth that causes population redistribution within the model system, reduction of the viable habitat to the water-air interface, cell development, and morphogenesis. The outcome is a build-up of mechanical stress supporting structure that eventually, due to nutrient deprivation, reaches the finite thickness. After prolonged incubation, the formed pellicle collapses, which correlates with the spore releasing process. The pellicle loses the ability to support mechanical stress, which marks the end of the pellicle life cycle and entry of the system into the dormant state.
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38
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Recent Strategies to Combat Biofilms Using Antimicrobial Agents and Therapeutic Approaches. Pathogens 2022; 11:pathogens11030292. [PMID: 35335616 PMCID: PMC8955104 DOI: 10.3390/pathogens11030292] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 02/01/2023] Open
Abstract
Biofilms are intricate bacterial assemblages that attach to diverse surfaces using an extracellular polymeric substance that protects them from the host immune system and conventional antibiotics. Biofilms cause chronic infections that result in millions of deaths around the world every year. Since the antibiotic tolerance mechanism in biofilm is different than that of the planktonic cells due to its multicellular structure, the currently available antibiotics are inadequate to treat biofilm-associated infections which have led to an immense need to find newer treatment options. Over the years, various novel antibiofilm compounds able to fight biofilms have been discovered. In this review, we have focused on the recent and intensively researched therapeutic techniques and antibiofilm agents used for biofilm treatment and grouped them according to their type and mode of action. We also discuss some therapeutic approaches that have the potential for future advancement.
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Ramírez-Larrota JS, Eckhard U. An Introduction to Bacterial Biofilms and Their Proteases, and Their Roles in Host Infection and Immune Evasion. Biomolecules 2022; 12:306. [PMID: 35204806 PMCID: PMC8869686 DOI: 10.3390/biom12020306] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/03/2022] [Accepted: 02/10/2022] [Indexed: 12/15/2022] Open
Abstract
Bacterial biofilms represent multicellular communities embedded in a matrix of extracellular polymeric substances, conveying increased resistance against environmental stress factors but also antibiotics. They are shaped by secreted enzymes such as proteases, which can aid pathogenicity by degrading host proteins of the connective tissue or the immune system. Importantly, both secreted proteases and the capability of biofilm formation are considered key virulence factors. In this review, we focus on the basic aspects of proteolysis and protein secretion, and highlight various secreted bacterial proteases involved in biofilm establishment and dispersal, and how they aid bacteria in immune evasion by degrading immunoglobulins and components of the complement system. Thus, secreted proteases represent not only prominent antimicrobial targets but also enzymes that can be used for dedicated applications in biotechnology and biomedicine, including their use as laundry detergents, in mass spectrometry for the glycoprofiling of antibodies, and the desensitization of donor organs intended for positive crossmatch patients.
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Affiliation(s)
| | - Ulrich Eckhard
- Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Baldiri Reixac, 15-21, 08028 Barcelona, Spain;
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40
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Mahapatra S, Yadav R, Ramakrishna W. Bacillus subtilis Impact on Plant Growth, Soil Health and Environment: Dr. Jekyll and Mr. Hyde. J Appl Microbiol 2022; 132:3543-3562. [PMID: 35137494 DOI: 10.1111/jam.15480] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/04/2022] [Indexed: 11/29/2022]
Abstract
The increased dependence of farmers on chemical fertilizers poses a risk to soil fertility and ecosystem stability. Plant growth-promoting rhizobacteria (PGPR) are at the forefront of sustainable agriculture, providing multiple benefits for the enhancement of crop production and soil health. Bacillus subtilis is a common PGPR in soil that plays a key role in conferring biotic and abiotic stress tolerance to plants by induced systemic resistance (ISR), biofilm formation, and lipopeptide production. As a part of bioremediating technologies, Bacillus spp. can purify metal contaminated soil. It acts as a potent denitrifying agent in agroecosystems while improving the carbon sequestration process when applied in a regulated concentration. Although it harbors several antibiotic resistance genes (ARGs), it can reduce the horizontal transfer of ARGs during manure composting by modifying the genetic makeup of existing microbiota. In some instances, it affects the beneficial microbes of the rhizosphere. External inoculation of B. subtilis has both positive and negative impacts on the endophytic and semi-synthetic microbial community. Soil texture, type, pH, and bacterial concentration play a crucial role in the regulation of all these processes. Soil amendments and microbial consortia of Bacillus produced by microbial engineering could be used to lessen the negative effect on soil microbial diversity. The complex plant-microbe interactions could be decoded using transcriptomics, proteomics, metabolomics, and epigenomics strategies which would be beneficial for both crop productivity and the well-being of soil microbiota. Bacillus subtilis has more positive attributes similar to the character of Dr. Jekyll and some negative attributes on plant growth, soil health, and the environment akin to the character of Mr. Hyde.
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A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis. Nat Chem Biol 2022; 18:161-170. [PMID: 34931064 PMCID: PMC8810680 DOI: 10.1038/s41589-021-00919-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/12/2021] [Indexed: 12/18/2022]
Abstract
Multi-enzyme assemblies composed of metabolic enzymes catalyzing sequential reactions are being increasingly studied. Here, we report the discovery of a 1.6 megadalton multi-enzyme complex from Bacillus subtilis composed of two enzymes catalyzing opposite ('counter-enzymes') rather than sequential reactions: glutamate synthase (GltAB) and glutamate dehydrogenase (GudB), which make and break glutamate, respectively. In vivo and in vitro studies show that the primary role of complex formation is to inhibit the activity of GudB. Using cryo-electron microscopy, we elucidated the structure of the complex and the molecular basis of inhibition of GudB by GltAB. The complex exhibits unusual oscillatory progress curves and is necessary for both planktonic growth, in glutamate-limiting conditions, and for biofilm growth, in glutamate-rich media. The regulation of a key metabolic enzyme by complexing with its counter enzyme may thus enable cell growth under fluctuating glutamate concentrations.
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42
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The de novo Purine Biosynthesis Pathway Is the Only Commonly Regulated Cellular Pathway during Biofilm Formation in TSB-Based Medium in Staphylococcus aureus and Enterococcus faecalis. Microbiol Spectr 2021; 9:e0080421. [PMID: 34935415 PMCID: PMC8693917 DOI: 10.1128/spectrum.00804-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial biofilms are involved in chronic infections and confer 10 to 1,000 times more resistance to antibiotics compared with planktonic growth, leading to complications and treatment failure. When transitioning from a planktonic lifestyle to biofilms, some Gram-positive bacteria are likely to modulate several cellular pathways, including central carbon metabolism, biosynthesis pathways, and production of secondary metabolites. These metabolic adaptations might play a crucial role in biofilm formation by Gram-positive pathogens such as Staphylococcus aureus and Enterococcus faecalis. Here, we performed a transcriptomic approach to identify cellular pathways that might be similarly regulated during biofilm formation in these bacteria. Different strains and biofilm-inducing media were used to identify a set of regulated genes that are common and independent of the environment or accessory genomes analyzed. Our approach highlighted that the de novo purine biosynthesis pathway was upregulated in biofilms of both species when using a tryptone soy broth-based medium but not so when a brain heart infusion-based medium was used. We did not identify other pathways commonly regulated between both pathogens. Gene deletions and usage of a drug targeting a key enzyme showed the importance of this pathway in biofilm formation of S. aureus. The importance of the de novo purine biosynthesis pathway might reflect an important need for purine during biofilm establishment, and thus could constitute a promising drug target. IMPORTANCE Biofilms are often involved in nosocomial infections and can cause serious chronic infections if not treated properly. Current anti-biofilm strategies rely on antibiotic usage, but they have a limited impact because of the biofilm intrinsic tolerance to drugs. Metabolism remodeling likely plays a central role during biofilm formation. Using comparative transcriptomics of different strains of Staphylococcus aureus and Enterococcus faecalis, we determined that almost all cellular adaptations are not shared between strains and species. Interestingly, we observed that the de novo purine biosynthesis pathway was upregulated during biofilm formation by both species in a specific medium. The requirement for purine could constitute an interesting new anti-biofilm target with a wide spectrum that could also prevent resistance evolution. These results are also relevant to a better understanding of the physiology of biofilm formation.
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Martien JI, Trujillo EA, Jacobson TB, Tatli M, Hebert AS, Stevenson DM, Coon JJ, Amador-Noguez D. Metabolic Remodeling during Nitrogen Fixation in Zymomonas mobilis. mSystems 2021; 6:e0098721. [PMID: 34783580 PMCID: PMC8594446 DOI: 10.1128/msystems.00987-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/06/2021] [Indexed: 11/20/2022] Open
Abstract
Zymomonas mobilis is an ethanologenic bacterium currently being developed for production of advanced biofuels. Recent studies have shown that Z. mobilis can fix dinitrogen gas (N2) as a sole nitrogen source. During N2 fixation, Z. mobilis exhibits increased biomass-specific rates of ethanol production. In order to better understand the physiology of Z. mobilis during N2 fixation and during changes in ammonium (NH4+) availability, we performed liquid chromatography-mass spectrometry (LC-MS)-based targeted metabolomics and shotgun proteomics under three regimes of nitrogen availability: continuous N2 fixation, gradual NH4+ depletion, and acute NH4+ addition to N2-fixing cells. We report dynamic changes in abundance of proteins and metabolites related to nitrogen fixation, motility, ammonium assimilation, amino acid biosynthesis, nucleotide biosynthesis, isoprenoid biosynthesis, and Entner-Doudoroff (ED) glycolysis, providing insight into the regulatory mechanisms that control these processes in Z. mobilis. Our analysis identified potential physiological mechanisms that may contribute to increased specific ethanol production during N2 fixation, including decreased activity of biosynthetic pathways, increased protein abundance of alcohol dehydrogenase (ADHI), and increased thermodynamic favorability of the ED pathway. Of particular relevance to advanced biofuel production, we found that intermediates in the methylerythritol phosphate (MEP) pathway for isoprenoid biosynthesis were depleted during N2 fixation, coinciding with decreased protein abundance of deoxyxylulose 5-phosphate synthase (DXS), the first enzyme in the pathway. This implies that DXS protein abundance serves as a native control point in regulating MEP pathway activity in Z. mobilis. The results of this study will inform metabolic engineering to further develop Z. mobilis as a platform organism for biofuel production. IMPORTANCE Biofuels and bioproducts have the potential to serve as environmentally sustainable replacements for petroleum-derived fuels and commodity molecules. Advanced fuels such as higher alcohols and isoprenoids are more suitable gasoline replacements than bioethanol. Developing microbial systems to generate advanced biofuels requires metabolic engineering to reroute carbon away from ethanol and other native products and toward desired pathways, such as the MEP pathway for isoprenoid biosynthesis. However, rational engineering of microbial metabolism relies on understanding metabolic control points, in terms of both enzyme activity and thermodynamic favorability. In Z. mobilis, the factors that control glycolytic rates, ethanol production, and isoprenoid production are still not fully understood. In this study, we performed metabolomic, proteomic, and thermodynamic analysis of Z. mobilis during N2 fixation. This analysis identified key changes in metabolite levels, enzyme abundance, and glycolytic thermodynamic favorability that occurred during changes in NH4+ availability, helping to inform future efforts in metabolic engineering.
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Affiliation(s)
- Julia I. Martien
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Edna A. Trujillo
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Tyler B. Jacobson
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Mehmet Tatli
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Alexander S. Hebert
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - David M. Stevenson
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Joshua J. Coon
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Daniel Amador-Noguez
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
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Abstract
Bacillus subtilis is a soil bacterium that can form biofilms, which are communities of cells encased by an extracellular matrix. In these complex communities, cells perform numerous metabolic processes and undergo differentiation into functionally distinct phenotypes as a survival strategy. Because biofilms are often studied in bulk, it remains unclear how metabolite production spatially correlates with B. subtilis phenotypes within biofilm structures. In many cases, we still do not know where these biological processes are occurring in the biofilm. Here, we developed a method to analyze the localization of molecules within sagittal thin sections of B. subtilis biofilms using high-resolution mass spectrometry imaging. We correlated the organization of specific molecules to the localization of well-studied B. subtilis phenotypic reporters determined by confocal laser scanning fluorescence microscopy within analogous biofilm thin sections. The correlations between these two data sets suggest the role of surfactin as a signal for extracellular matrix gene expression in the biofilm periphery and the role of bacillibactin as an iron-scavenging molecule. Taken together, this method will help us generate hypotheses to discover relationships between metabolites and phenotypic cell states in B. subtilis and other biofilm-forming bacteria. IMPORTANCE Bacterial biofilms are complex and heterogeneous structures. Cells within biofilms carry out numerous metabolic processes in a nuanced and organized manner, details of which are still being discovered. Here, we used multimodal imaging to analyze B. subtilis biofilm processes at the metabolic and gene expression levels in biofilm sagittal thin sections. Often, imaging techniques analyze only the top of the surface of the biofilm and miss the multifaceted interactions that occur deep within the biofilm. Our analysis of the sagittal planes of B. subtilis biofilms revealed the distributions of metabolic processes throughout the depths of these structures and allowed us to draw correlations between metabolites and phenotypically important subpopulations of B. subtilis cells. This technique provides a platform to generate hypotheses about the role of specific molecules and their relationships to B. subtilis subpopulations of cells.
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Chang JD, Vaughan EE, Liu CG, Jelinski JW, Terwilliger AL, Maresso AW. Metabolic profiling reveals nutrient preferences during carbon utilization in Bacillus species. Sci Rep 2021; 11:23917. [PMID: 34903830 PMCID: PMC8669014 DOI: 10.1038/s41598-021-03420-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 11/29/2021] [Indexed: 11/18/2022] Open
Abstract
The genus Bacillus includes species with diverse natural histories, including free-living nonpathogenic heterotrophs such as B. subtilis and host-dependent pathogens such as B. anthracis (the etiological agent of the disease anthrax) and B. cereus, a cause of food poisoning. Although highly similar genotypically, the ecological niches of these three species are mutually exclusive, which raises the untested hypothesis that their metabolism has speciated along a nutritional tract. Here, we developed a pipeline for quantitative total assessment of the use of diverse sources of carbon for general metabolism to better appreciate the "culinary preferences" of three distinct Bacillus species, as well as related Staphylococcus aureus. We show that each species has widely varying metabolic ability to utilize diverse sources of carbon that correlated to their ecological niches. This approach was applied to the growth and survival of B. anthracis in a blood-like environment and find metabolism shifts from sugar to amino acids as the preferred source of energy. Finally, various nutrients in broth and host-like environments are identified that may promote or interfere with bacterial metabolism during infection.
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Affiliation(s)
- James D Chang
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Ellen E Vaughan
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Carmen Gu Liu
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Joseph W Jelinski
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Austen L Terwilliger
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Anthony W Maresso
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
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Effects of konjac glucomannan with different molecular weights on gut microflora with antibiotic perturbance in in vitro fecal fermentation. Carbohydr Polym 2021; 273:118546. [PMID: 34560958 DOI: 10.1016/j.carbpol.2021.118546] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 08/08/2021] [Accepted: 08/08/2021] [Indexed: 02/08/2023]
Abstract
This study investigated the effect of konjac glucomannan (KGM) of different molecular weight on fecal microflora against antibiotic disturbance. KGM (~1.8 × 107 Da) was partially hydrolysed with trifluoroacetic acid (TFA) for 10 and 60 min to KGM1 (~2.1 × 104 Da) and KGM2 (7413 Da), respectively. The acid treatment caused significant reduction of intrinsic viscosity, average molecular weight (MW) and particle size of KGM, but brought limited change to the molecular structure. Low-MW KGM2 showed the most significant effect on fecal microflora in the presence of two common antibiotics (ampicillin and clindamycin), by increasing the relative abundance of Bifidobacteriaceae while decreasing the proportion of Enterobacteriaceae. Additionally, both the native and acid-treated KGM counteracted the adverse influence of antibiotics on the production of short chain fatty acids. The results have demonstrated the effect of KGM on gut microbiota with antibiotic disturbance.
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Integrating transcriptomics and metabolomics analysis on kojic acid combating Acinetobacter baumannii biofilm and its potential roles. Microbiol Res 2021; 254:126911. [PMID: 34763140 DOI: 10.1016/j.micres.2021.126911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/20/2022]
Abstract
As a major secondary metabolite derived from a dominant marine filamentous fungus A7, kojic acid might confer the strain a competitive advantage in natural colonization. The bioactivities of kojic acid against bacterial growth and biofilm formation were investigated against Acinetobacter baumannii (A. baumannii) ATCC 19606. Then, transcriptomics and metabolomics were integrated to characterize the underlying mechanisms. It turned out that kojic acid exhibited a significantly suppressive impact against biofilm but a weak bacteriostatic activity. Meanwhile, a variety of transcriptional and metabolomic profiles were altered within biofilm formation as a result of kojic acid exposure. The alterations highlighted the mechanisms underlying biofilm formation, comprising of quorum sensing, fimbria assembly, bacterial virulence and metabolic plasticity, which could somewhat be hampered by kojic acid. The present study comprehensively elucidated multifactorial schemes for kojic acid combating biofilm formation of A. baumannii, which might provide mechanistic insights into the development of therapeutic strategies against this notorious pathogen. Meanwhile, our observations might shed new light on the ecological roles of kojic acid, e.g., serving as chemical deterrents for host adaptation to marine niches, which, however, awaits further validation.
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Woroszyło M, Ciecholewska-Juśko D, Junka A, Pruss A, Kwiatkowski P, Wardach M, Fijałkowski K. The Impact of Intraspecies Variability on Growth Rate and Cellular Metabolic Activity of Bacteria Exposed to Rotating Magnetic Field. Pathogens 2021; 10:1427. [PMID: 34832583 PMCID: PMC8624435 DOI: 10.3390/pathogens10111427] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 12/02/2022] Open
Abstract
Majority of research on the influence of magnetic fields on microorganisms has been carried out with the use of different species or different groups of microorganisms, but not with the use of different strains belonging to one species. The purpose of the present study was to assess the effect of rotating magnetic fields (RMF) of 5 and 50 Hz on the growth and cellular metabolic activity of eight species of bacteria: Staphylococcus aureus, Pseudomonas aeruginosa, Proteus mirabilis, Klebsiella pneumoniae, Enterococcus faecalis, Enterobacter cloacae, Moraxella catarrhalis, and Bacillus cereus. However, contrary to the research conducted so far, each species was represented by at least four different strains. Moreover, an additional group of S. aureus belonging to a single clonal type but representing different biotypes was also included in the experiment. The results showed a varied influence of RMF on growth dynamics and cellular metabolic activity, diversified to the greatest extent in dependence on the bacterial strain exposed to the RMF and to a lesser extent in dependence on the frequency of the generated magnetic field. It was found that, with regard to the exposed strain of the same species, the effect exerted by the RMF may be positive (i.e., manifests as the increase in the growth rate or/and cellular metabolic activity) or negative (i.e., manifests as a reduction of both aforementioned features) or none. Even when one clonal type of S. aureus was used, the results of RMF exposure also varied (although the degree of differentiation was lower than for strains representing different clones). Therefore, the research has proven that, apart from the previously described factors related primarily to the physical parameters of the magnetic field, one of the key parameters affecting the final result of its influence is the bacterial intraspecies variability.
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Affiliation(s)
- Marta Woroszyło
- Department of Microbiology and Biotechnology, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, Piastów 45, 70-311 Szczecin, Poland; (M.W.); (D.C.-J.)
| | - Daria Ciecholewska-Juśko
- Department of Microbiology and Biotechnology, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, Piastów 45, 70-311 Szczecin, Poland; (M.W.); (D.C.-J.)
| | - Adam Junka
- Department of Pharmaceutical Microbiology and Parasitology, Faculty of Pharmacy, Medical University of Wroclaw, Borowska 211a, 50-534 Wrocław, Poland
- Laboratory of Microbiology, Łukasiewicz Research Network-PORT Polish Center for Technology Development, 54-066 Wrocław, Poland
| | - Agata Pruss
- Department of Laboratory Medicine, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich 72, 70-111 Szczecin, Poland;
| | - Paweł Kwiatkowski
- Department of Diagnostic Immunology, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich 72, 70-111 Szczecin, Poland;
| | - Marcin Wardach
- Faculty of Electrical Engineering, West Pomeranian University of Technology in Szczecin, Sikorskiego 37, 70-313 Szczecin, Poland;
| | - Karol Fijałkowski
- Department of Microbiology and Biotechnology, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, Piastów 45, 70-311 Szczecin, Poland; (M.W.); (D.C.-J.)
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Schoenborn AA, Yannarell SM, Wallace ED, Clapper H, Weinstein IC, Shank EA. Defining the Expression, Production, and Signaling Roles of Specialized Metabolites during Bacillus subtilis Differentiation. J Bacteriol 2021; 203:e0033721. [PMID: 34460312 PMCID: PMC8544424 DOI: 10.1128/jb.00337-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/11/2021] [Indexed: 11/20/2022] Open
Abstract
Bacterial specialized (or secondary) metabolites are structurally diverse molecules that mediate intra- and interspecies interactions by altering growth and cellular physiology and differentiation. Bacillus subtilis, a Gram-positive model bacterium commonly used to study biofilm formation and sporulation, has the capacity to produce more than 10 specialized metabolites. Some of these B. subtilis specialized metabolites have been investigated for their role in facilitating cellular differentiation, but only rarely has the behavior of multiple metabolites been simultaneously investigated. In this study, we explored the interconnectivity of differentiation (biofilm and sporulation) and specialized metabolites in B. subtilis. Specifically, we interrogated how development influences specialized metabolites and vice versa. Using the sporulation-inducing medium DSM, we found that the majority of the specialized metabolites examined are expressed and produced during biofilm formation and sporulation. Additionally, we found that six of these metabolites (surfactin, ComX, bacillibactin, bacilysin, subtilosin A, and plipastatin) are necessary signaling molecules for proper progression of B. subtilis differentiation. This study further supports the growing body of work demonstrating that specialized metabolites have essential physiological functions as cell-cell communication signals in bacteria. IMPORTANCE Bacterially produced specialized metabolites are frequently studied for their potential use as antibiotics and antifungals. However, a growing body of work has suggested that the antagonistic potential of specialized metabolites is not their only function. Here, using Bacillus subtilis as our model bacterium, we demonstrated that developmental processes such as biofilm formation and sporulation are tightly linked to specialized metabolite gene expression and production. Additionally, under our differentiation-inducing conditions, six out of the nine specialized metabolites investigated behave as intraspecific signals that impact B. subtilis physiology and influence biofilm formation and sporulation. Our work supports the viewpoint that specialized metabolites have a clear role as cell-cell signaling molecules within differentiated populations of bacteria.
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Affiliation(s)
- Alexi A. Schoenborn
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah M. Yannarell
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - E. Diane Wallace
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Haley Clapper
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ilon C. Weinstein
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Elizabeth A. Shank
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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50
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Kolenc Ž, Pirih N, Gretic P, Kunej T. Top Trends in Multiomics Research: Evaluation of 52 Published Studies and New Ways of Thinking Terminology and Visual Displays. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:681-692. [PMID: 34678084 DOI: 10.1089/omi.2021.0160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Multiomics study designs have significantly increased understanding of complex biological systems. The multiomics literature is rapidly expanding and so is their heterogeneity. However, the intricacy and fragmentation of omics data are impeding further research. To examine current trends in multiomics field, we reviewed 52 articles from PubMed and Web of Science, which used an integrated omics approach, published between March 2006 and January 2021. From studies, data regarding investigated loci, species, omics type, and phenotype were extracted, curated, and streamlined according to standardized terminology, and summarized in a previously developed graphical summary. Evaluated studies included 21 omics types or applications of omics technology such as genomics, transcriptomics, metabolomics, epigenomics, environmental omics, and pharmacogenomics, species of various phyla including human, mouse, Arabidopsis thaliana, Saccharomyces cerevisiae, and various phenotypes, including cancer and COVID-19. In the analyzed studies, diverse methods, protocols, results, and terminology were used and accordingly, assessment of the studies was challenging. Adoption of standardized multiomics data presentation in the future will further buttress standardization of terminology and reporting of results in systems science. This shall catalyze, we suggest, innovation in both science communication and laboratory medicine by making available scientific knowledge that is easier to grasp, share, and harness toward medical breakthroughs.
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Affiliation(s)
- Živa Kolenc
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Nina Pirih
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Petra Gretic
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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