1
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Lu L, Zhao Y, Li M, Wang X, Zhu J, Liao L, Wang J. Contemporary strategies and approaches for characterizing composition and enhancing biofilm penetration targeting bacterial extracellular polymeric substances. J Pharm Anal 2024; 14:100906. [PMID: 38634060 PMCID: PMC11022105 DOI: 10.1016/j.jpha.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/08/2023] [Accepted: 11/26/2023] [Indexed: 04/19/2024] Open
Abstract
Extracellular polymeric substances (EPS) constitutes crucial elements within bacterial biofilms, facilitating accelerated antimicrobial resistance and conferring defense against the host's immune cells. Developing precise and effective antibiofilm approaches and strategies, tailored to the specific characteristics of EPS composition, can offer valuable insights for the creation of novel antimicrobial drugs. This, in turn, holds the potential to mitigate the alarming issue of bacterial drug resistance. Current analysis of EPS compositions relies heavily on colorimetric approaches with a significant bias, which is likely due to the selection of a standard compound and the cross-interference of various EPS compounds. Considering the pivotal role of EPS in biofilm functionality, it is imperative for EPS research to delve deeper into the analysis of intricate compositions, moving beyond the current focus on polymeric materials. This necessitates a shift from heavy reliance on colorimetric analytic methods to more comprehensive and nuanced analytical approaches. In this study, we have provided a comprehensive summary of existing analytical methods utilized in the characterization of EPS compositions. Additionally, novel strategies aimed at targeting EPS to enhance biofilm penetration were explored, with a specific focus on highlighting the limitations associated with colorimetric methods. Furthermore, we have outlined the challenges faced in identifying additional components of EPS and propose a prospective research plan to address these challenges. This review has the potential to guide future researchers in the search for novel compounds capable of suppressing EPS, thereby inhibiting biofilm formation. This insight opens up a new avenue for exploration within this research domain.
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Affiliation(s)
- Lan Lu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
| | - Yuting Zhao
- Meishan Pharmaceutical Vocational College, School of Pharmacy, Meishan, Sichuan, 620200, China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Xiaobo Wang
- Hepatobiliary Surgery, Langzhong People's Hospital, Langzhong, Sichuan, 646000, China
| | - Jie Zhu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
| | - Li Liao
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
| | - Jingya Wang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
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2
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Guler P, Bendori SO, Borenstein T, Aframian N, Kessel A, Eldar A. Arbitrium communication controls phage lysogeny through non-lethal modulation of a host toxin-antitoxin defence system. Nat Microbiol 2024; 9:150-160. [PMID: 38177304 DOI: 10.1038/s41564-023-01551-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 11/07/2023] [Indexed: 01/06/2024]
Abstract
Temperate Bacillus phages often utilize arbitrium communication to control lysis/lysogeny decisions, but the mechanisms by which this control is exerted remains largely unknown. Here we find that the arbitrium system of Bacillus subtilis phage ϕ3T modulates the host-encoded MazEF toxin-antitoxin system to this aim. Upon infection, the MazF ribonuclease is activated by three phage genes. At low arbitrium signal concentrations, MazF is inactivated by two phage-encoded MazE homologues: the arbitrium-controlled AimX and the later-expressed YosL proteins. At high signal, MazF remains active, promoting lysogeny without harming the bacterial host. MazF cleavage sites are enriched on transcripts of phage lytic genes but absent from the phage repressor in ϕ3T and other Spβ-like phages. Combined with low activation levels of MazF during infections, this pattern explains the phage-specific effect. Our results show how a bacterial toxin-antitoxin system has been co-opted by a phage to control lysis/lysogeny decisions without compromising host viability.
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Affiliation(s)
- Polina Guler
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Shira Omer Bendori
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Tom Borenstein
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Nitzan Aframian
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Amit Kessel
- Department of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Avigdor Eldar
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel.
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3
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Kohm K, Jalomo-Khayrova E, Krüger A, Basu S, Steinchen W, Bange G, Frunzke J, Hertel R, Commichau F, Czech L. Structural and functional characterization of MrpR, the master repressor of the Bacillus subtilis prophage SPβ. Nucleic Acids Res 2023; 51:9452-9474. [PMID: 37602373 PMCID: PMC10516654 DOI: 10.1093/nar/gkad675] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/11/2023] [Accepted: 08/09/2023] [Indexed: 08/22/2023] Open
Abstract
Prophages control their lifestyle to either be maintained within the host genome or enter the lytic cycle. Bacillus subtilis contains the SPβ prophage whose lysogenic state depends on the MrpR (YopR) protein, a key component of the lysis-lysogeny decision system. Using a historic B. subtilis strain harboring the heat-sensitive SPβ c2 mutant, we demonstrate that the lytic cycle of SPβ c2 can be induced by heat due to a single nucleotide exchange in the mrpR gene, rendering the encoded MrpRG136E protein temperature-sensitive. Structural characterization revealed that MrpR is a DNA-binding protein resembling the overall fold of tyrosine recombinases. MrpR has lost its recombinase function and the G136E exchange impairs its higher-order structure and DNA binding activity. Genome-wide profiling of MrpR binding revealed its association with the previously identified SPbeta repeated element (SPBRE) in the SPβ genome. MrpR functions as a master repressor of SPβ that binds to this conserved element to maintain lysogeny. The heat-inducible excision of the SPβ c2 mutant remains reliant on the serine recombinase SprA. A suppressor mutant analysis identified a previously unknown component of the lysis-lysogeny management system that is crucial for the induction of the lytic cycle of SPβ.
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Affiliation(s)
- Katharina Kohm
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
- FG Molecular Microbiology, Institute for Biology, University of Hohenheim, Stuttgart, Germany
| | - Ekaterina Jalomo-Khayrova
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Phillips-University Marburg, Marburg, Germany
| | - Aileen Krüger
- Institute of Bio- and Geosciences, iBG-1: Biotechnology, FZ Jülich, Germany
| | - Syamantak Basu
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | - Wieland Steinchen
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Phillips-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Phillips-University Marburg, Marburg, Germany
- Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Julia Frunzke
- Institute of Bio- and Geosciences, iBG-1: Biotechnology, FZ Jülich, Germany
| | - Robert Hertel
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Fabian M Commichau
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
- FG Molecular Microbiology, Institute for Biology, University of Hohenheim, Stuttgart, Germany
| | - Laura Czech
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Phillips-University Marburg, Marburg, Germany
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4
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Wang Y, Osire T, Sokolova OS. In vitro Biofilm Formation by Bacillus subtilis and AR9 Phage Infection: SEM Study. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1133-1134. [PMID: 37613496 DOI: 10.1093/micmic/ozad067.579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Yueqi Wang
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Tolbert Osire
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Olga S Sokolova
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, China
- Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
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5
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W B Jr M, A S R, P M, F B. Cellular and Natural Viral Engineering in Cognition-Based Evolution. Commun Integr Biol 2023; 16:2196145. [PMID: 37153718 PMCID: PMC10155641 DOI: 10.1080/19420889.2023.2196145] [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] [Indexed: 05/10/2023] Open
Abstract
Neo-Darwinism conceptualizes evolution as the continuous succession of predominately random genetic variations disciplined by natural selection. In that frame, the primary interaction between cells and the virome is relegated to host-parasite dynamics governed by selective influences. Cognition-Based Evolution regards biological and evolutionary development as a reciprocating cognition-based informational interactome for the protection of self-referential cells. To sustain cellular homeorhesis, cognitive cells collaborate to assess the validity of ambiguous biological information. That collective interaction involves coordinate measurement, communication, and active deployment of resources as Natural Cellular Engineering. These coordinated activities drive multicellularity, biological development, and evolutionary change. The virome participates as the vital intercessory among the cellular domains to ensure their shared permanent perpetuation. The interactions between the virome and the cellular domains represent active virocellular cross-communications for the continual exchange of resources. Modular genetic transfers between viruses and cells carry bioactive potentials. Those exchanges are deployed as nonrandom flexible tools among the domains in their continuous confrontation with environmental stresses. This alternative framework fundamentally shifts our perspective on viral-cellular interactions, strengthening established principles of viral symbiogenesis. Pathogenesis can now be properly appraised as one expression of a range of outcomes between cells and viruses within a larger conceptual framework of Natural Viral Engineering as a co-engineering participant with cells. It is proposed that Natural Viral Engineering should be viewed as a co-existent facet of Natural Cellular Engineering within Cognition-Based Evolution.
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Affiliation(s)
- Miller W B Jr
- Banner Health Systems - Medicine, Paradise Valley, Arizona, AZ, USA
- CONTACT Miller W B Jr Paradise Valley, Arizona, AZ85253, USA
| | - Reber A S
- Department of Psychology, University of British Columbia, Vancouver, BC, Canada
| | - Marshall P
- Department of Engineering, Evolution 2.0, Oak Park, IL, USA
| | - Baluška F
- Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
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6
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Identification of Novel Viruses and Their Microbial Hosts from Soils with Long-Term Nitrogen Fertilization and Cover Cropping Management. mSystems 2022; 7:e0057122. [PMID: 36445691 PMCID: PMC9765229 DOI: 10.1128/msystems.00571-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Soils are the largest organic carbon reservoir and are key to global biogeochemical cycling, and microbes are the major drivers of carbon and nitrogen transformations in the soil systems. Thus, virus infection-induced microbial mortality could impact soil microbial structure and functions. In this study, we recovered 260 viral operational taxonomic units (vOTUs) in samples collected from soil taken from four nitrogen fertilization (N-fertilization) and cover-cropping practices at an experimental site under continuous cotton production evaluating conservation agricultural management systems for more than 40 years. Only ~6% of the vOTUs identified were clustered with known viruses in the RefSeq database using a gene-sharing network. We found that 14% of 260 vOTUs could be linked to microbial hosts that cover key carbon and nitrogen cycling taxa, including Acidobacteriota, Proteobacteria, Verrucomicrobiota, Firmicutes, and ammonia-oxidizing archaea, i.e., Nitrososphaeria (phylum Thermoproteota). Viral diversity, community structure, and the positive correlation between abundance of a virus and its host indicate that viruses and microbes are more sensitive to N-fertilization than cover-cropping treatment. Viruses may influence key carbon and nitrogen cycling through control of microbial function and host populations (e.g., Chthoniobacterales and Nitrososphaerales). These findings provide an initial view of soil viral ecology and how it is influenced by long-term conservation agricultural management. IMPORTANCE Bacterial viruses are extremely small and abundant particles that can control the microbial abundance and community composition through infection, which gradually showed their vital roles in the ecological process to influence the nutrient flow. Compared to the substrate control, less is known about the influence of soil viruses on microbial community function, and even less is known about microbial and viral diversity in the soil system. To obtain a more complete knowledge of microbial function dynamics, the interaction between microbes and viruses cannot be ignored. To fully understand this process, it is fundamental to get insight into the correlation between the diversity of viral communities and bacteria which could induce these changes.
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7
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Cui Y, Su X, Wang C, Xu H, Hu D, Wang J, Pei K, Sun M, Zou T. Bacterial MazF/MazE toxin-antitoxin suppresses lytic propagation of arbitrium-containing phages. Cell Rep 2022; 41:111752. [PMID: 36476854 DOI: 10.1016/j.celrep.2022.111752] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 05/18/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022] Open
Abstract
Temperate phages dynamically switch between lysis and lysogeny in their full life cycle. Some Bacillus-infecting phages utilize a quorum-sensing-like intercellular communication system, the "arbitrium," to mediate lysis-lysogeny decisions. However, whether additional factors participate in the arbitrium signaling pathway remains largely elusive. Here, we find that the arbitrium signal induces the expression of a functionally conserved operon downstream of the arbitrium module in SPbeta-like phages. SPbeta yopM and yopR (as well as phi3T phi3T_93 and phi3T_97) in the operon play roles in suppressing phage lytic propagation and promoting lysogeny, respectively. We further focus on phi3T_93 and demonstrate that it directly binds antitoxin MazE in the host MazF/MazE toxin-antitoxin (TA) module and facilitates the activation of MazF's toxicity, which is required for phage suppression. These findings show events regulated by the arbitrium system and shed light on how the interplay between phages and the host TA module affects phage-host co-survival.
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Affiliation(s)
- Yongqing Cui
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiang Su
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Chen Wang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Han Xu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Delei Hu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Wang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Kai Pei
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingting Zou
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
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8
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Zhang X, Wang R, Xie X, Hu Y, Wang J, Sun Q, Feng X, Lin W, Tong S, Yan W, Wen H, Wang M, Zhai S, Sun C, Wang F, Niu Q, Kropinski A, Cui Y, Jiang X, Peng S, Li S, Tong Y. Mining bacterial NGS data vastly expands the complete genomes of temperate phages. NAR Genom Bioinform 2022; 4:lqac057. [PMID: 35937545 PMCID: PMC9346568 DOI: 10.1093/nargab/lqac057] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 06/13/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Temperate phages (active prophages induced from bacteria) help control pathogenicity, modulate community structure, and maintain gut homeostasis. Complete phage genome sequences are indispensable for understanding phage biology. Traditional plaque techniques are inapplicable to temperate phages due to their lysogenicity, curbing their identification and characterization. Existing bioinformatics tools for prophage prediction usually fail to detect accurate and complete temperate phage genomes. This study proposes a novel computational temperate phage detection method (TemPhD) mining both the integrated active prophages and their spontaneously induced forms (temperate phages) from next-generation sequencing raw data. Applying the method to the available dataset resulted in 192 326 complete temperate phage genomes with different host species, expanding the existing number of complete temperate phage genomes by more than 100-fold. The wet-lab experiments demonstrated that TemPhD can accurately determine the complete genome sequences of the temperate phages, with exact flanking sites, outperforming other state-of-the-art prophage prediction methods. Our analysis indicates that temperate phages are likely to function in the microbial evolution by (i) cross-infecting different bacterial host species; (ii) transferring antibiotic resistance and virulence genes and (iii) interacting with hosts through restriction-modification and CRISPR/anti-CRISPR systems. This work provides a comprehensively complete temperate phage genome database and relevant information, which can serve as a valuable resource for phage research.
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Affiliation(s)
- Xianglilan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing 100071, People's Republic of China
| | - Ruohan Wang
- Department of Computer Science, City University of Hong Kong , Hong Kong 999077, People's Republic of China
| | - Xiangcheng Xie
- College of Computer, National University of Defense Technology , Changsha 410073, People's Republic of China
| | - Yunjia Hu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, People's Republic of China
- School of Medicine, Shanghai University , Shanghai 200444, People's Republic of China
| | - Jianping Wang
- Department of Computer Science, City University of Hong Kong , Hong Kong 999077, People's Republic of China
| | - Qiang Sun
- The 964th Hospital , Changchun 130021, People's Republic of China
| | - Xikang Feng
- School of Software, Northwestern Polytechnical University , Xi’an 710072, People's Republic of China
| | - Wei Lin
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, People's Republic of China
| | - Shanwei Tong
- Bioinformatics Graduate Program, University of British Columbia , Vancouver BC V6T 1Z4, Canada
- Faculty of Health Sciences, Simon Fraser University , Burnaby , BC V5A 1S6, Canada
| | - Wei Yan
- National Library of Medicine, National Institutes of Health , Bethesda , MD 20894, USA
| | - Huiqi Wen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing 100071, People's Republic of China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, People's Republic of China
| | - Mengyao Wang
- Department of Computer Science, City University of Hong Kong , Hong Kong 999077, People's Republic of China
| | - Shixiang Zhai
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences , Yantai 264003, People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049, People's Republic of China
- Center for Ocean Mega-Science, Chinese Academy of Sciences , Qingdao 266071, People's Republic of China
| | - Cheng Sun
- School of Computer Science and Electronic Engineering, Hunan University , Changsha 410082, People's Republic of China
| | - Fangyi Wang
- Department of Statistics, the Ohio State University , Columbus, OH 43210, USA
| | - Qi Niu
- School of Computer Science and Electronic Engineering, Hunan University , Changsha 410082, People's Republic of China
| | - Andrew M Kropinski
- Departments of Food Science, and Pathobiology, University of Guelph , Guelph , ON N1G 2W1 , Canada
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing 100071, People's Republic of China
| | - Xiaofang Jiang
- National Library of Medicine, National Institutes of Health , Bethesda , MD 20894, USA
| | - Shaoliang Peng
- School of Computer Science and Electronic Engineering, Hunan University , Changsha 410082, People's Republic of China
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong , Hong Kong 999077, People's Republic of China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, People's Republic of China
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9
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Gallego Del Sol F, Quiles-Puchalt N, Brady A, Penadés JR, Marina A. Insights into the mechanism of action of the arbitrium communication system in SPbeta phages. Nat Commun 2022; 13:3627. [PMID: 35750663 PMCID: PMC9232636 DOI: 10.1038/s41467-022-31144-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/01/2022] [Indexed: 11/09/2022] Open
Abstract
The arbitrium system is employed by phages of the SPbeta family to communicate with their progeny during infection to decide either to follow the lytic or the lysogenic cycle. The system is controlled by a peptide, AimP, that binds to the regulator AimR, inhibiting its DNA-binding activity and expression of aimX. Although the structure of AimR has been elucidated for phages SPβ and phi3T, there is still controversy regarding the molecular mechanism of AimR function, with two different proposed models for SPβ. In this study, we deepen our understanding of the system by solving the structure of an additional AimR that shows chimerical characteristics with the SPβ receptor. The crystal structures of this AimR (apo, AimP-bound and DNA-bound) together with in vitro and in vivo analyses confirm a mechanism of action by AimP-induced conformational restriction, shedding light on peptide specificity and cross regulation with relevant biological implications.
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Affiliation(s)
- Francisca Gallego Del Sol
- Instituto de Biomedicina de Valencia (IBV), CSIC and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Nuria Quiles-Puchalt
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Aisling Brady
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - José R Penadés
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK.
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV), CSIC and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain.
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10
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Liu S, Lu H, Zhang S, Shi Y, Chen Q. Phages against Pathogenic Bacterial Biofilms and Biofilm-Based Infections: A Review. Pharmaceutics 2022; 14:pharmaceutics14020427. [PMID: 35214158 PMCID: PMC8875263 DOI: 10.3390/pharmaceutics14020427] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 02/01/2023] Open
Abstract
Bacterial biofilms formed by pathogens are known to be hundreds of times more resistant to antimicrobial agents than planktonic cells, making it extremely difficult to cure biofilm-based infections despite the use of antibiotics, which poses a serious threat to human health. Therefore, there is an urgent need to develop promising alternative antimicrobial therapies to reduce the burden of drug-resistant bacterial infections caused by biofilms. As natural enemies of bacteria, bacteriophages (phages) have the advantages of high specificity, safety and non-toxicity, and possess great potential in the defense and removal of pathogenic bacterial biofilms, which are considered to be alternatives to treat bacterial diseases. This work mainly reviews the composition, structure and formation process of bacterial biofilms, briefly discusses the interaction between phages and biofilms, and summarizes several strategies based on phages and their derivatives against biofilms and drug-resistant bacterial infections caused by biofilms, serving the purpose of developing novel, safe and effective treatment methods against biofilm-based infections and promoting the application of phages in maintaining human health.
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Affiliation(s)
| | | | | | - Ying Shi
- Correspondence: (Y.S.); (Q.C.); Tel.: +86-139-6717-1522 (Y.S.)
| | - Qihe Chen
- Correspondence: (Y.S.); (Q.C.); Tel.: +86-139-6717-1522 (Y.S.)
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11
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Aframian N, Omer Bendori S, Kabel S, Guler P, Stokar-Avihail A, Manor E, Msaeed K, Lipsman V, Grinberg I, Mahagna A, Eldar A. Dormant phages communicate via arbitrium to control exit from lysogeny. Nat Microbiol 2021; 7:145-153. [PMID: 34887546 DOI: 10.1038/s41564-021-01008-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/26/2021] [Indexed: 01/23/2023]
Abstract
Temperate bacterial viruses (phages) can transition between lysis-replicating and killing the host-and lysogeny, that is, existing as dormant prophages while keeping the host viable. Recent research showed that on invading a naïve cell, some phages communicate using a peptide signal, termed arbitrium, to control the decision of entering lysogeny. Whether communication can also serve to regulate exit from lysogeny (known as phage induction) is unclear. Here we show that arbitrium-coding prophages continue to communicate from the lysogenic state by secreting and sensing the arbitrium signal. Signalling represses DNA damage-dependent phage induction, enabling prophages to reduce the induction rate when surrounded by other lysogens. We show that in certain phages, DNA damage and communication converge to regulate the expression of the arbitrium-responsive gene aimX, while in others integration of DNA damage and communication occurs downstream of aimX expression. Additionally, signalling by prophages tilts the decision of nearby infecting phages towards lysogeny. Altogether, we find that phages use small-molecule communication throughout their entire life cycle to sense the abundance of lysogens in the population, thus avoiding lysis when they are likely to encounter established lysogens rather than permissive uninfected hosts.
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Affiliation(s)
- Nitzan Aframian
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Shira Omer Bendori
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Stav Kabel
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Polina Guler
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | | | - Erica Manor
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Kholod Msaeed
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Valeria Lipsman
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel.,Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Grinberg
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Alaa Mahagna
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Avigdor Eldar
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel.
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12
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Pei K, Zhang J, Zou T, Liu Z. AimR Adopts Preexisting Dimer Conformations for Specific Target Recognition in Lysis-Lysogeny Decisions of Bacillus Phage phi3T. Biomolecules 2021; 11:biom11091321. [PMID: 34572534 PMCID: PMC8464984 DOI: 10.3390/biom11091321] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/30/2021] [Accepted: 09/05/2021] [Indexed: 12/04/2022] Open
Abstract
A bacteriophage switches between lytic and lysogenic life cycles. The AimR-AimP-AimX communication system is responsible for phage lysis-lysogeny decisions during the infection of Bacillus subtilis. AimX is a regulator biasing phage lysis, AimR is a transcription factor activating AimX expression, and AimP is an arbitrium peptide that determines phage lysogeny by deactivating AimR. A strain-specific mechanism for the lysis-lysogeny decisions is proposed in SPbeta and phi3T phages. That is, the arbitrium peptide of the SPbeta phage stabilizes the SPbeta AimR (spAimR) dimer, whereas the phi3T-derived peptide disassembles the phi3T AimR (phAimR) dimer into a monomer. Here, we find that phAimR does not undergo dimer-to-monomer conversion upon arbitrium peptide binding. Gel-filtration, static light scattering (SLS) and analytical ultracentrifugation (AUC) results show that phAimR is dimeric regardless of the presence of arbitrium peptide. Small-angle X-ray scattering (SAXS) reveals that the arbitrium peptide binding makes an extended dimeric conformation. Single-molecule fluorescence resonance energy transfer (smFRET) analysis reveals that the phAimR dimer fluctuates among two distinct conformational states, and each preexisting state is selectively recognized by the arbitrium peptide or the target DNA, respectively. Collectively, our biophysical characterization of the phAimR dynamics underlying specific target recognition provides new mechanistic insights into understanding lysis-lysogeny decisions in Bacillus phage phi3T.
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13
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Niu NN, Lu L, Peng PP, Fu ZJ, Miao D, Zhou M, Noy D, Zhao KH. The phycobilisome core-membrane linkers from Synechocystis sp. PCC 6803 and red-algae assemble in the same topology. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1420-1431. [PMID: 34171163 DOI: 10.1111/tpj.15389] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 06/06/2021] [Accepted: 06/19/2021] [Indexed: 06/13/2023]
Abstract
The phycobilisomes (PBSs) of cyanobacteria and red-algae are unique megadaltons light-harvesting protein-pigment complexes that utilize bilin derivatives for light absorption and energy transfer. Recently, the high-resolution molecular structures of red-algal PBSs revealed how the multi-domain core-membrane linker (LCM ) specifically organizes the allophycocyanin subunits in the PBS's core. But, the topology of LCM in these structures was different than that suggested for cyanobacterial PBSs based on lower-resolution structures. Particularly, the model for cyanobacteria assumed that the Arm2 domain of LCM connects the two basal allophycocyanin cylinders, whereas the red-algal PBS structures revealed that Arm2 is partly buried in the core of one basal cylinder and connects it to the top cylinder. Here, we show by biochemical analysis of mutations in the apcE gene that encodes LCM , that the cyanobacterial and red-algal LCM topologies are actually the same. We found that removing the top cylinder linker domain in LCM splits the PBS core longitudinally into two separate basal cylinders. Deleting either all or part of the helix-loop-helix domain at the N-terminal end of Arm2, disassembled the basal cylinders and resulted in degradation of the part containing the terminal emitter, ApcD. Deleting the following 30 amino-acids loop severely affected the assembly of the basal cylinders, but further deletion of the amino-acids at the C-terminal half of Arm2 had only minor effects on this assembly. Altogether, the biochemical data are consistent with the red-algal LCM topology, suggesting that the PBS cores in cyanobacteria and red-algae assemble in the same way.
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Affiliation(s)
- Nan-Nan Niu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Lu Lu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Pan-Pan Peng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Zhi-Juan Fu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Dan Miao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Ming Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Dror Noy
- MIGAL-Galilee Research Institute, S. Industrial Zone, Kiryat Shmona, Israel
- Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee, Israel
| | - Kai-Hong Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
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14
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Brady A, Felipe-Ruiz A, Gallego Del Sol F, Marina A, Quiles-Puchalt N, Penadés JR. Molecular Basis of Lysis-Lysogeny Decisions in Gram-Positive Phages. Annu Rev Microbiol 2021; 75:563-581. [PMID: 34343015 DOI: 10.1146/annurev-micro-033121-020757] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Temperate bacteriophages (phages) are viruses of bacteria. Upon infection of a susceptible host, a temperate phage can establish either a lytic cycle that kills the host or a lysogenic cycle as a stable prophage. The life cycle pursued by an infecting temperate phage can have a significant impact not only on the individual host bacterium at the cellular level but also on bacterial communities and evolution in the ecosystem. Thus, understanding the decision processes of temperate phages is crucial. This review delves into the molecular mechanisms behind lysis-lysogeny decision-making in Gram-positive phages. We discuss a variety of molecular mechanisms and the genetic organization of these well-understood systems. By elucidating the strategies used by phages to make lysis-lysogeny decisions, we can improve our understanding of phage-host interactions, which is crucial for a variety of studies including bacterial evolution, community and ecosystem diversification, and phage therapeutics. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Aisling Brady
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom;
| | - Alonso Felipe-Ruiz
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 46010 Valencia, Spain;
| | - Francisca Gallego Del Sol
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 46010 Valencia, Spain;
| | - Alberto Marina
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 46010 Valencia, Spain;
| | - Nuria Quiles-Puchalt
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom;
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom; .,MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom;
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15
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Abstract
Bacteriophages are the most diverse and abundant biological entities on the Earth and require host bacteria to replicate. Because of this obligate relationship, in addition to the challenging conditions of surrounding environments, phages must integrate information about extrinsic and intrinsic factors when infecting their host. This integration helps to determine whether the infection becomes lytic or lysogenic, which likely influences phage spreading and long-term survival. Although a variety of environmental and physiological clues are known to modulate lysis-lysogeny decisions, the social interplay among phages and host populations has been overlooked until recently. A growing body of evidence indicates that cell-cell communication in bacteria and, more recently, peptide-based communication among phage-phage populations, affect phage-host interactions by controlling phage lysis-lysogeny decisions and phage counter-defensive strategies in bacteria. Here, we explore and discuss the role of signal molecules as well as quorum sensing and quenching factors that mediate phage-host interactions. Our aim is to provide an overview of population-dependent mechanisms that influence phage replication, and how social communication may affect the dynamics and evolution of microbial communities, including their implications in phage therapy.
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16
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Gu Y, Zhi SX, Yang N, Yang WS. Understanding the mechanism of asymmetric gene regulation determined by the VqmA of vibriophage. Biochem Biophys Res Commun 2021; 558:51-56. [PMID: 33895551 DOI: 10.1016/j.bbrc.2021.04.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 11/16/2022]
Abstract
The quorum-sensing (QS) system between the phages and their hosts is important for the phage lysis-lysogeny decision. In Vibrio cholerae, the QS system consists of a LuxR-type receptor VqmA (VqmAVc) and an autoinducer molecule 3,5-dimethylpyrazin-2-ol (DPO). A VqmA homolog encoded by vibriophage VP882 (VqmAPhage) can intervene the host QS system via binding to both the host-produced DPO and its cognate promoter (Pqtip) to induce the phage lysogeny-to-lysis transition, whereas VqmAVc cannot influence the VqmAPhage-induced pathway, suggesting an asymmetry regulation. In this study, we report the crystal structure of VqmAPhage-DPO complex at 2.65 Å and reveal that the mechanism of DPO recognition is conserved in VqmA homologs. Besides, we identify a non-classical palindrome sequence in Pqtip, which can be effectively recognized by VqmAPhage but not VqmAVc. The sequence contains an interval longer than that in the vqmR promoter recognized by VqmAVc. In addition, the two DBD regions in the VqmAPhage dimer exhibit more relaxed architecture than that of the reported VqmAVc, which is likely to be in the conformation that may easily bind to target promoter containing a longer interval. In summary, our findings provide a structural and biochemical basis for the DBD-dependent DNA recognition in different promoter regions in the phage lysogeny-to-lysis decision communication system, and provide clues for developing phage therapies against Vibrio cholerae infection.
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Affiliation(s)
- Yue Gu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, 300353, Tianjin, China
| | - Shu-Xin Zhi
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, 300353, Tianjin, China
| | - Na Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, 300353, Tianjin, China.
| | - Wen-Si Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
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17
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Horiuk Y, Horiuk V, Kukhtyn M, Tsvihun A, Kernychnyi S. Characterization of lytic activity of Phage SAvB14 on Staphylococcus aureus variant bovis. J Adv Vet Anim Res 2020; 7:509-513. [PMID: 33005677 PMCID: PMC7521818 DOI: 10.5455/javar.2020.g447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/02/2020] [Accepted: 04/08/2020] [Indexed: 12/18/2022] Open
Abstract
Objective The objective of this study was to investigate the intensity of phage infection caused by Phage SAvB14, which was isolated from dairy farms, depending on the initial number of Staphylococcus aureus cells in the medium. Material and methods To evaluate the impact of the viable bacteria S. aureus var. bovis on the intensity of phage infection caused by Phage SAvB14, 1 mg of phagolysate (phage titer 105 CFU/ ml) was introduced in 9 ml of nutrient broth with an appropriate amount of daily culture of S. aureus var. bovis under study. The number of viable staphylococci was determined by total viable count/ml. Results In this experiment, we found that the intensity of phages lytic activity was dependent on the number of sensitive bacterial cells in the volume of the culture medium. Effective phage therapy requires a high concentration of phages in the medium (inflammation foci) for rapid contact of the virus with bacteria. Conclusion When developing a phage drug to treat subclinical mastitis, it is necessary to increase the phage titer in the drug or its dosage compared to the clinical form, as there is a lower probability of phage contact with a susceptible microbial cell. Besides, at a high concentration of bacteria, there is a gradual decrease in nutrients in the medium, resulting in phages going back to the condition of lysogeny.
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Affiliation(s)
- Yulia Horiuk
- Faculty of Veterinary Medicine and Technologies in Livestock, Department of Infectious and Parasitic Diseases, State Agrarian and Engineering University in Podilya, Kamianets-Podilskyi, Ukraine
| | - Victor Horiuk
- Faculty of Veterinary Medicine and Technologies in Livestock, Department of Veterinary Obstetrics, Pathology and Surgery, State Agrarian and Engineering University in Podilya, Kamianets-Podilskyi, Ukraine
| | - Mykola Kukhtyn
- Faculty of Engineering of Machines, Structures and Technologies, Department of Food Biotechnology and Chemistry, Ternopil Ivan Pului National Technical University, Ternopil, Ukraine
| | - Anatoliy Tsvihun
- Faculty of Veterinary Medicine and Technologies in Livestock, Department of Animal Feeding, Breeding and Feed Technology, State Agrarian and Engineering University in Podilya, Kamianets-Podilskyi, Ukraine
| | - Sergiy Kernychnyi
- Faculty of Veterinary Medicine and Technologies in Livestock, Department of Veterinary Obstetrics, Pathology and Surgery, State Agrarian and Engineering University in Podilya, Kamianets-Podilskyi, Ukraine
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18
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Liang X, Wagner RE, Li B, Zhang N, Radosevich M. Quorum Sensing Signals Alter in vitro Soil Virus Abundance and Bacterial Community Composition. Front Microbiol 2020; 11:1287. [PMID: 32587586 PMCID: PMC7298970 DOI: 10.3389/fmicb.2020.01287] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/20/2020] [Indexed: 12/18/2022] Open
Abstract
Cell-density dependent quorum sensing (QS) is fundamental for many coordinated behaviors among bacteria. Most recently several studies have revealed a role for bacterial QS communication in bacteriophage (phage) reproductive decisions. However, QS based phage-host interactions remain largely unknown, with the mechanistic details revealed for only a few phage-host pairs and a dearth of information available at the microbial community level. Here we report on the specific action of eight different individual QS signals (acyl-homoserine lactones; AHLs varying in acyl-chain length from four to 14 carbon atoms) on prophage induction in soil microbial communities. We show QS autoinducers, triggered prophage induction in soil bacteria and the response was significant enough to alter bacterial community composition in vitro. AHL treatment significantly decreased the bacterial diversity (Shannon Index) but did not significantly impact species richness. Exposure to short chain-length AHLs resulted in a decrease in the abundance of different taxa than exposure to higher molecular weight AHLs. Each AHL targeted a different subset of bacterial taxa. Our observations indicate that individual AHLs may trigger prophage induction in different bacterial taxa leading to changes in microbial community structure. The findings also have implications for the role of phage-host interactions in ecologically significant processes such as biogeochemical cycles, and phage mediated transfer of host genes, e.g., photosynthesis and heavy metal/antibiotic resistance.
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Affiliation(s)
- Xiaolong Liang
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Regan E Wagner
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Bingxue Li
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
| | - Ning Zhang
- College of Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Mark Radosevich
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
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19
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Zhen X, Zhou H, Ding W, Zhou B, Xu X, Perčulija V, Chen CJ, Chang MX, Choudhary MI, Ouyang S. Structural basis of AimP signaling molecule recognition by AimR in Spbeta group of bacteriophages. Protein Cell 2020; 10:131-136. [PMID: 30421358 PMCID: PMC6340889 DOI: 10.1007/s13238-018-0588-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Affiliation(s)
- Xiangkai Zhen
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.,Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Huan Zhou
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Wei Ding
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Biao Zhou
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.,Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Xiaolong Xu
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.,Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Vanja Perčulija
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.,Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Chun-Jung Chen
- Institute of Biotechnology, National Cheng Kung University, Tainan, 701, China
| | - Ming-Xian Chang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Muhammad Iqbal Choudhary
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China. .,Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China. .,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
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20
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Stokar-Avihail A, Tal N, Erez Z, Lopatina A, Sorek R. Widespread Utilization of Peptide Communication in Phages Infecting Soil and Pathogenic Bacteria. Cell Host Microbe 2019; 25:746-755.e5. [PMID: 31071296 DOI: 10.1016/j.chom.2019.03.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/04/2019] [Accepted: 03/25/2019] [Indexed: 11/27/2022]
Abstract
Temperate phages can adopt either a lytic or lysogenic lifestyle within their host bacteria. It was recently shown that Bacillus-subtilis-infecting phages of the SPbeta group utilize a peptide-based communication system called arbitrium to coordinate the lysogeny decision. The occurrence of peptide-based communication systems among phages more broadly remains to be explored. Here, we uncover a wide array of peptide-based communication systems utilized by phages for lysogeny decisions. These arbitrium-like systems show diverse peptide codes and can be detected in numerous genetically distant phage types and conjugative elements. The pathogens Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis are commonly infected by arbitrium-carrying mobile elements, which often carry toxins essential for pathogenicity. Experiments with phages containing these arbitrium-like systems demonstrate their involvement in lysogeny decisions. Finally, our results suggest that the peptide-based decision is executed by an antisense RNA that controls the regulator of the lysogenic state.
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Affiliation(s)
| | - Nitzan Tal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Zohar Erez
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Anna Lopatina
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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21
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Ye M, Sun M, Huang D, Zhang Z, Zhang H, Zhang S, Hu F, Jiang X, Jiao W. A review of bacteriophage therapy for pathogenic bacteria inactivation in the soil environment. ENVIRONMENT INTERNATIONAL 2019; 129:488-496. [PMID: 31158595 DOI: 10.1016/j.envint.2019.05.062] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/22/2019] [Accepted: 05/23/2019] [Indexed: 06/09/2023]
Abstract
The emerging contamination of pathogenic bacteria in the soil has caused a serious threat to public health and environmental security. Therefore, effective methods to inactivate pathogenic bacteria and decrease the environmental risks are urgently required. As a century-old technique, bacteriophage (phage) therapy has a high efficiency in targeting and inactivating pathogenic bacteria in different environmental systems. This review provides an update on the status of bacteriophage therapy for the inactivation of pathogenic bacteria in the soil environment. Specifically, the applications of phage therapy in soil-plant and soil-groundwater systems are summarized. In addition, the impact of phage therapy on soil functioning is described, including soil function gene transmission, soil microbial community stability, and soil nutrient cycling. Soil factors, such as soil temperature, pH, clay mineral, water content, and nutrient components, influence the survival and activity of phages in the soil. Finally, the future research prospects of phage therapy in soil environments are described.
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Affiliation(s)
- Mao Ye
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Mingming Sun
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Dan Huang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zhongyun Zhang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Hui Zhang
- Jiangsu Key Laboratory of Food Quality and Safety-State Key Laboratory Cultivation Base of MOST, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Shengtian Zhang
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection of China, Nanjing 210042, China
| | - Feng Hu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Jiang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Wentao Jiao
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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22
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23
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Abstract
Recently members of Bacillus phages were found to utilize a small peptide (6 aa long) to communicate with their descendants, aiding in a complex decision-making process. Proteins involved in this remarkable viral communication phenomenon were further investigated at the structural level for better understanding in this issue of Molecular Cell (Gallego del Sol et al., 2019).
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24
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Guan Z, Pei K, Wang J, Cui Y, Zhu X, Su X, Zhou Y, Zhang D, Tang C, Yin P, Liu Z, Zou T. Structural insights into DNA recognition by AimR of the arbitrium communication system in the SPbeta phage. Cell Discov 2019; 5:29. [PMID: 31149347 PMCID: PMC6536502 DOI: 10.1038/s41421-019-0101-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 04/28/2019] [Accepted: 05/05/2019] [Indexed: 12/11/2022] Open
Abstract
A newly identified arbitrium communication system regulates the lysis-to-lysogeny decision in a Bacillus bacteriophage. This system contains an arbitrium hexapeptide as a signal, the cellular receptor AimR, and the lysogenic negative regulator AimX. AimR specifically targets the downstream DNA to activate aimX gene expression. The arbitrium peptide binds to AimR, inhibiting its DNA-binding to promote phage lysogeny. Recently, we and other groups have elucidated how arbitrium peptide sensed by AimR. However, the molecular mechanisms of DNA recognition by AimR and the regulation of its DNA-binding activity by the peptide remain largely unknown. Here, we report the crystal structure of the AimR–DNA complex at 2.1 Å resolution. The N-terminal HTH motif recognizes the palindromic DNA sequence, buttressed by interactions between positively charged residues and the DNA phosphate groups. The DNA-bound AimR assembles a more closed dimer than the peptide-bound form. Single-molecule FRET and crosslinking assays revealed that the AimR protein samples both open and closed conformations in solution. Arbitrium peptide binding induces a closed-to-open conformational change of AimR, eliminating DNA targeting. Our structural and functional analysis provides new insights into the DNA recognition mechanism of AimR and its regulation by the arbitrium peptide in the context of phage lysis-lysogeny decisions.
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Affiliation(s)
- Zeyuan Guan
- 1National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Kai Pei
- 1National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Jing Wang
- 1National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Yongqing Cui
- 1National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Xiang Zhu
- 1National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Xiang Su
- 1National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Yuanbao Zhou
- 1National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Delin Zhang
- 1National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Chun Tang
- 2CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071 Hubei Province China
| | - Ping Yin
- 1National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Zhu Liu
- 1National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Tingting Zou
- 3College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei China
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Gallego Del Sol F, Penadés JR, Marina A. Deciphering the Molecular Mechanism Underpinning Phage Arbitrium Communication Systems. Mol Cell 2019; 74:59-72.e3. [PMID: 30745087 PMCID: PMC6458997 DOI: 10.1016/j.molcel.2019.01.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/12/2018] [Accepted: 01/15/2019] [Indexed: 10/28/2022]
Abstract
Bacillus phages use a communication system, termed "arbitrium," to coordinate lysis-lysogeny decisions. Arbitrium communication is mediated by the production and secretion of a hexapeptide (AimP) during lytic cycle. Once internalized, AimP reduces the expression of the negative regulator of lysogeny, AimX, by binding to the transcription factor, AimR, promoting lysogeny. We have elucidated the crystal structures of AimR from the Bacillus subtilis SPbeta phage in its apo form, bound to its DNA operator and in complex with AimP. AimR presents intrinsic plasticity, sharing structural features with the RRNPP quorum-sensing family. Remarkably, AimR binds to an unusual operator with a long spacer that interacts nonspecifically with the receptor TPR domain, while the HTH domain canonically recognizes two inverted repeats. AimP stabilizes a compact conformation of AimR that approximates the DNA-recognition helices, preventing AimR binding to the aimX promoter region. Our results establish the molecular basis of the arbitrium communication system.
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Affiliation(s)
- Francisca Gallego Del Sol
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain.
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26
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Structure Regulates Phage Lysis–Lysogeny Decisions. Trends Microbiol 2019; 27:3-4. [DOI: 10.1016/j.tim.2018.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 11/14/2018] [Indexed: 11/19/2022]
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