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de Crécy-Lagard V, Hutinet G, Cediel-Becerra JDD, Yuan Y, Zallot R, Chevrette MG, Ratnayake RMMN, Jaroch M, Quaiyum S, Bruner S. Biosynthesis and function of 7-deazaguanine derivatives in bacteria and phages. Microbiol Mol Biol Rev 2024; 88:e0019923. [PMID: 38421302 PMCID: PMC10966956 DOI: 10.1128/mmbr.00199-23] [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] [Indexed: 03/02/2024] Open
Abstract
SUMMARYDeazaguanine modifications play multifaceted roles in the molecular biology of DNA and tRNA, shaping diverse yet essential biological processes, including the nuanced fine-tuning of translation efficiency and the intricate modulation of codon-anticodon interactions. Beyond their roles in translation, deazaguanine modifications contribute to cellular stress resistance, self-nonself discrimination mechanisms, and host evasion defenses, directly modulating the adaptability of living organisms. Deazaguanine moieties extend beyond nucleic acid modifications, manifesting in the structural diversity of biologically active natural products. Their roles in fundamental cellular processes and their presence in biologically active natural products underscore their versatility and pivotal contributions to the intricate web of molecular interactions within living organisms. Here, we discuss the current understanding of the biosynthesis and multifaceted functions of deazaguanines, shedding light on their diverse and dynamic roles in the molecular landscape of life.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
- University of Florida Genetics Institute, Gainesville, Florida, USA
| | - Geoffrey Hutinet
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | | | - Yifeng Yuan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Rémi Zallot
- Department of Life Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - Marc G. Chevrette
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | | | - Marshall Jaroch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Samia Quaiyum
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Steven Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
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2
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Patel PH, Taylor VL, Zhang C, Getz LJ, Fitzpatrick AD, Davidson AR, Maxwell KL. Anti-phage defence through inhibition of virion assembly. Nat Commun 2024; 15:1644. [PMID: 38388474 PMCID: PMC10884400 DOI: 10.1038/s41467-024-45892-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: 11/21/2023] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
Bacteria have evolved diverse antiviral defence mechanisms to protect themselves against phage infection. Phages integrated into bacterial chromosomes, known as prophages, also encode defences that protect the bacterial hosts in which they reside. Here, we identify a type of anti-phage defence that interferes with the virion assembly pathway of invading phages. The protein that mediates this defence, which we call Tab (for 'Tail assembly blocker'), is constitutively expressed from a Pseudomonas aeruginosa prophage. Tab allows the invading phage replication cycle to proceed, but blocks assembly of the phage tail, thus preventing formation of infectious virions. While the infected cell dies through the activity of the replicating phage lysis proteins, there is no release of infectious phage progeny, and the bacterial community is thereby protected from a phage epidemic. Prophages expressing Tab are not inhibited during their own lytic cycle because they express a counter-defence protein that interferes with Tab function. Thus, our work reveals an anti-phage defence that operates by blocking virion assembly, thereby both preventing formation of phage progeny and allowing destruction of the infected cell due to expression of phage lysis genes.
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Affiliation(s)
| | | | - Chi Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Landon J Getz
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | | | - Alan R Davidson
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Karen L Maxwell
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
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3
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Liu K, Wang C, Zhou X, Guo X, Yang Y, Liu W, Zhao R, Song H. Bacteriophage therapy for drug-resistant Staphylococcus aureus infections. Front Cell Infect Microbiol 2024; 14:1336821. [PMID: 38357445 PMCID: PMC10864608 DOI: 10.3389/fcimb.2024.1336821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024] Open
Abstract
Drug-resistant Staphylococcus aureus stands as a prominent pathogen in nosocomial and community-acquired infections, capable of inciting various infections at different sites in patients. This includes Staphylococcus aureus bacteremia (SaB), which exhibits a severe infection frequently associated with significant mortality rate of approximately 25%. In the absence of better alternative therapies, antibiotics is still the main approach for treating infections. However, excessive use of antibiotics has, in turn, led to an increase in antimicrobial resistance. Hence, it is imperative that new strategies are developed to control drug-resistant S. aureus infections. Bacteriophages are viruses with the ability to infect bacteria. Bacteriophages, were used to treat bacterial infections before the advent of antibiotics, but were subsequently replaced by antibiotics due to limited theoretical understanding and inefficient preparation processes at the time. Recently, phages have attracted the attention of many researchers again because of the serious problem of antibiotic resistance. This article provides a comprehensive overview of phage biology, animal models, diverse clinical case treatments, and clinical trials in the context of drug-resistant S. aureus phage therapy. It also assesses the strengths and limitations of phage therapy and outlines the future prospects and research directions. This review is expected to offer valuable insights for researchers engaged in phage-based treatments for drug-resistant S. aureus infections.
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Affiliation(s)
- Kaixin Liu
- College of Public Health, Zhengzhou University, Zhengzhou, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Chao Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Xudong Zhou
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- College of Public Health, China Medical University, Shenyang, China
| | - Xudong Guo
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yi Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Wanying Liu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Rongtao Zhao
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hongbin Song
- College of Public Health, Zhengzhou University, Zhengzhou, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- College of Public Health, China Medical University, Shenyang, China
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4
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López-Pérez J, Otero J, Sánchez-Osuna M, Erill I, Cortés P, Llagostera M. Impact of mutagenesis and lateral gene transfer processes in bacterial susceptibility to phage in food biocontrol and phage therapy. Front Cell Infect Microbiol 2023; 13:1266685. [PMID: 37842006 PMCID: PMC10569123 DOI: 10.3389/fcimb.2023.1266685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction The emergence of resistance and interference mechanisms to phage infection can hinder the success of bacteriophage-based applications, but the significance of these mechanisms in phage therapy has not been determined. This work studies the emergence of Salmonella isolates with reduced susceptibility to a cocktail of three phages under three scenarios: i) Salmonella cultures (LAB), ii) biocontrol of cooked ham slices as a model of food safety (FOOD), and iii) oral phage therapy in broilers (PT). Methods S. Typhimurium ATCC 14028 RifR variants with reduced phage susceptibility were isolated from the three scenarios and conventional and molecular microbiology techniques were applied to study them. Results and discussion In LAB, 92% of Salmonella isolates lost susceptibility to all three phages 24 h after phage infection. This percentage was lower in FOOD, with 4.3% of isolates not susceptible to at least two of the three phages after seven days at 4°C following phage treatment. In PT, 9.7% and 3.3 % of isolates from untreated and treated broilers, respectively, displayed some mechanism of interference with the life cycle of some of the phages. In LAB and FOOD scenarios, resistant variants carrying mutations in rfc and rfaJ genes involved in lipopolysaccharide synthesis (phage receptor) were identified. However, in PT, the significant decrease of EOP, ECOI, and burst size observed in isolates was prompted by lateral gene transfer of large IncI1 plasmids, which may encode phage defense mechanisms. These data indicate that the acquisition of specific conjugative plasmids has a stronger impact than mutagenesis on the emergence of reduced phage-susceptibility bacteria in certain environments. In spite of this, neither mechanism seems to significantly impair the success of Salmonella biocontrol and oral phage therapy.
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Affiliation(s)
- Júlia López-Pérez
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Jennifer Otero
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- SK8 Biotech, Parc Científic de Barcelona, Barcelona, Spain
| | - Miquel Sánchez-Osuna
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ivan Erill
- Department of Biological Sciences, University of Maryland, Baltimore, MD, United States
- Departament Enginyeria de la Informació i de les Comunicacions, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Montserrat Llagostera
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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5
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Macdonald E, Wright R, Connolly JPR, Strahl H, Brockhurst M, van Houte S, Blower TR, Palmer T, Mariano G. The novel anti-phage system Shield co-opts an RmuC domain to mediate phage defense across Pseudomonas species. PLoS Genet 2023; 19:e1010784. [PMID: 37276233 DOI: 10.1371/journal.pgen.1010784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/12/2023] [Indexed: 06/07/2023] Open
Abstract
Competitive bacteria-bacteriophage interactions have resulted in the evolution of a plethora of bacterial defense systems preventing phage propagation. In recent years, computational and bioinformatic approaches have underpinned the discovery of numerous novel bacterial defense systems. Anti-phage systems are frequently encoded together in genomic loci termed defense islands. Here we report the identification and characterisation of a novel anti-phage system, that we have termed Shield, which forms part of the Pseudomonas defensive arsenal. The Shield system comprises the core component ShdA, a membrane-bound protein harboring an RmuC domain. Heterologous production of ShdA alone is sufficient to mediate bacterial immunity against several phages. We demonstrate that Shield and ShdA confer population-level immunity and that they can also decrease transformation efficiency. We further show that ShdA homologues can degrade DNA in vitro and, when expressed in a heterologous host, can alter the organisation of the host chromosomal DNA. Use of comparative genomic approaches identified how Shield can be divided into four subtypes, three of which contain additional components that in some cases can negatively affect the activity of ShdA and/or provide additional lines of phage defense. Collectively, our results identify a new player within the Pseudomonas bacterial immunity arsenal that displays a novel mechanism of protection, and reveals a role for RmuC domains in phage defense.
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Affiliation(s)
- Elliot Macdonald
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Rosanna Wright
- Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - James P R Connolly
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Henrik Strahl
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael Brockhurst
- Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Stineke van Houte
- Environment and Sustainability Institute, University of Exeter, Penryn Campus, Penryn, Cornwall, United Kingdom
| | - Tim R Blower
- Department of Biosciences, Durham University, Stockton Road, Durham, United Kingdom
| | - Tracy Palmer
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Giuseppina Mariano
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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6
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Chen Y, Zeng Z, She Q, Han W. The abortive infection functions of CRISPR-Cas and Argonaute. Trends Microbiol 2023; 31:405-418. [PMID: 36463018 DOI: 10.1016/j.tim.2022.11.005] [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: 09/15/2022] [Revised: 11/08/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022]
Abstract
CRISPR-Cas and prokaryotic Argonaute (pAgo) are nucleic acid (NA)-guided defense systems that protect prokaryotes against the invasion of mobile genetic elements. Previous studies established that they are directed by NA fragments (guides) to recognize invading complementary NA (targets), and that they cleave the targets to silence the invaders. Nevertheless, growing evidence indicates that many CRISPR-Cas and pAgo systems exploit the abortive infection (Abi) strategy to confer immunity. The CRISPR-Cas and pAgo Abi systems typically sense invaders using the NA recognition ability and activate various toxic effectors to kill the infected cells to prevent the invaders from spreading. This review summarizes the diverse mechanisms of these CRISPR-Cas and pAgo systems, and highlights their critical roles in the arms race between microbes and invaders.
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Affiliation(s)
- Yu Chen
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China
| | - Zhifeng Zeng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Jimo, 266237, Qingdao, China
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China.
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7
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Type III CRISPR-Cas provides resistance against nucleus-forming jumbo phages via abortive infection. Mol Cell 2022; 82:4471-4486.e9. [PMID: 36395770 DOI: 10.1016/j.molcel.2022.10.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/13/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022]
Abstract
Bacteria have diverse defenses against phages. In response, jumbo phages evade multiple DNA-targeting defenses by protecting their DNA inside a nucleus-like structure. We previously demonstrated that RNA-targeting type III CRISPR-Cas systems provide jumbo phage immunity by recognizing viral mRNA exported from the nucleus for translation. Here, we demonstrate that recognition of phage mRNA by the type III system activates a cyclic triadenylate-dependent accessory nuclease, NucC. Although unable to access phage DNA in the nucleus, NucC degrades the bacterial chromosome, triggers cell death, and disrupts phage replication and maturation. Hence, type-III-mediated jumbo phage immunity occurs via abortive infection, with suppression of the viral epidemic protecting the population. We further show that type III systems targeting jumbo phages have diverse accessory nucleases, including RNases that provide immunity. Our study demonstrates how type III CRISPR-Cas systems overcome the inaccessibility of jumbo phage DNA to provide robust immunity.
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8
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Wirth J, Young M. Viruses in Subsurface Environments. Annu Rev Virol 2022; 9:99-119. [PMID: 36173700 DOI: 10.1146/annurev-virology-093020-015957] [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: 11/09/2022]
Abstract
Over the past 20 years, our knowledge of virus diversity and abundance in subsurface environments has expanded dramatically through application of quantitative metagenomic approaches. In most subsurface environments, viral diversity and abundance rival viral diversity and abundance observed in surface environments. Most of these viruses are uncharacterized in terms of their hosts and replication cycles. Analysis of accessory metabolic genes encoded by subsurface viruses indicates that they evolved to replicate within the unique features of their environments. The key question remains: What role do these viruses play in the ecology and evolution of the environments in which they replicate? Undoubtedly, as more virologists examine the role of viruses in subsurface environments, new insights will emerge.
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Affiliation(s)
- Jennifer Wirth
- Department of Plant Science and Plant Pathology and Thermal Biology Institute, Montana State University, Bozeman, Montana, USA;
| | - Mark Young
- Department of Plant Science and Plant Pathology and Thermal Biology Institute, Montana State University, Bozeman, Montana, USA;
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9
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Gostimskaya I. CRISPR-Cas9: A History of Its Discovery and Ethical Considerations of Its Use in Genome Editing. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:777-788. [PMID: 36171658 PMCID: PMC9377665 DOI: 10.1134/s0006297922080090] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/07/2022] [Accepted: 07/19/2022] [Indexed: 06/16/2023]
Abstract
The development of a method for genome editing based on CRISPR-Cas9 technology was awarded The Nobel Prize in Chemistry in 2020, less than a decade after the discovery of all principal molecular components of the system. For the first time in history a Nobel prize was awarded to two women, Emmanuelle Charpentier and Jennifer Doudna, who made key discoveries in the field of DNA manipulation with the CRISPR-Cas9 system, so-called "genetic scissors". It is difficult to overestimate the importance of the technique as it enables one not only to manipulate genomes of model organisms in scientific experiments, and modify characteristics of important crops and animals, but also has the potential of introducing revolutionary changes in medicine, especially in treatment of genetic diseases. The original biological function of CRISPR-Cas9 system is the protection of prokaryotes from mobile genetic elements, in particular viruses. Currently, CRISPR-Cas9 and related technologies have been successfully used to cure life-threatening diseases, make coronavirus detection tests, and even to modify human embryo cells with the consequent birth of babies carrying the introduced modifications. This intervention with human germplasm cells resulted in wide disapproval in the scientific community due to ethical concerns, and calls for a moratorium on inheritable genomic manipulations. This review focuses on the history of the discovery of the CRISPR-Cas9 system with some aspects of its current applications, including ethical concerns about its use in humans.
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10
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Ongenae V, Mabrouk AS, Crooijmans M, Rozen D, Briegel A, Claessen D. Reversible bacteriophage resistance by shedding the bacterial cell wall. Open Biol 2022; 12:210379. [PMID: 35673854 PMCID: PMC9174709 DOI: 10.1098/rsob.210379] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Phages are highly abundant in the environment and pose a major threat for bacteria. Therefore, bacteria have evolved sophisticated defence systems to withstand phage attacks. Here, we describe a previously unknown mechanism by which mono- and diderm bacteria survive infection with diverse lytic phages. Phage exposure leads to a rapid and near-complete conversion of walled cells to a cell-wall-deficient state, which remains viable in osmoprotective conditions and can revert to the walled state. While shedding the cell wall dramatically reduces the number of progeny phages produced by the host, it does not always preclude phage infection. Altogether, these results show that the formation of cell-wall-deficient cells prevents complete eradication of the bacterial population and suggest that cell wall deficiency may potentially limit the efficacy of phage therapy, especially in highly osmotic environments or when used together with antibiotics that target the cell wall.
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Affiliation(s)
- Véronique Ongenae
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands,Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Adam Sidi Mabrouk
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands,Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Marjolein Crooijmans
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands,Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Daniel Rozen
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Ariane Briegel
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands,Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Dennis Claessen
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands,Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
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11
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Mestre MR, Gao LA, Shah SA, López-Beltrán A, González-Delgado A, Martínez-Abarca F, Iranzo J, Redrejo-Rodríguez M, Zhang F, Toro N. UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions. Nucleic Acids Res 2022; 50:6084-6101. [PMID: 35648479 PMCID: PMC9226505 DOI: 10.1093/nar/gkac467] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/11/2022] [Accepted: 05/17/2022] [Indexed: 11/20/2022] Open
Abstract
Reverse transcriptases (RTs) are enzymes capable of synthesizing DNA using RNA as a template. Within the last few years, a burst of research has led to the discovery of novel prokaryotic RTs with diverse antiviral properties, such as DRTs (Defense-associated RTs), which belong to the so-called group of unknown RTs (UG) and are closely related to the Abortive Infection system (Abi) RTs. In this work, we performed a systematic analysis of UG and Abi RTs, increasing the number of UG/Abi members up to 42 highly diverse groups, most of which are predicted to be functionally associated with other gene(s) or domain(s). Based on this information, we classified these systems into three major classes. In addition, we reveal that most of these groups are associated with defense functions and/or mobile genetic elements, and demonstrate the antiphage role of four novel groups. Besides, we highlight the presence of one of these systems in novel families of human gut viruses infecting members of the Bacteroidetes and Firmicutes phyla. This work lays the foundation for a comprehensive and unified understanding of these highly diverse RTs with enormous biotechnological potential.
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Affiliation(s)
- Mario Rodríguez Mestre
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Madrid, Spain
| | - Linyi Alex Gao
- Howard Hughes Medical Institute, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA, USA.,McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Society of Fellows, Harvard University, Cambridge, MA 02138, USA
| | - Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Ledreborg Allé 34, DK-2820 Gentofte, Denmark
| | - Adrián López-Beltrán
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Alejandro González-Delgado
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Spain
| | - Francisco Martínez-Abarca
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Spain
| | - Jaime Iranzo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain.,Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain
| | - Modesto Redrejo-Rodríguez
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Madrid, Spain
| | - Feng Zhang
- Howard Hughes Medical Institute, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA, USA.,McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicolás Toro
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Spain
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12
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Payne LJ, Meaden S, Mestre MR, Palmer C, Toro N, Fineran PC, Jackson SA. PADLOC: a web server for the identification of antiviral defence systems in microbial genomes. Nucleic Acids Res 2022; 50:W541-W550. [PMID: 35639517 PMCID: PMC9252829 DOI: 10.1093/nar/gkac400] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 04/24/2022] [Accepted: 05/05/2022] [Indexed: 12/16/2022] Open
Abstract
Most bacteria and archaea possess multiple antiviral defence systems that protect against infection by phages, archaeal viruses and mobile genetic elements. Our understanding of the diversity of defence systems has increased greatly in the last few years, and many more systems likely await discovery. To identify defence-related genes, we recently developed the Prokaryotic Antiviral Defence LOCator (PADLOC) bioinformatics tool. To increase the accessibility of PADLOC, we describe here the PADLOC web server (freely available at https://padloc.otago.ac.nz), allowing users to analyse whole genomes, metagenomic contigs, plasmids, phages and archaeal viruses. The web server includes a more than 5-fold increase in defence system types detected (since the first release) and expanded functionality enabling detection of CRISPR arrays and retron ncRNAs. Here, we provide user information such as input options, description of the multiple outputs, limitations and considerations for interpretation of the results, and guidance for subsequent analyses. The PADLOC web server also houses a precomputed database of the defence systems in > 230,000 RefSeq genomes. These data reveal two taxa, Campylobacterota and Spriochaetota, with unusual defence system diversity and abundance. Overall, the PADLOC web server provides a convenient and accessible resource for the detection of antiviral defence systems.
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Affiliation(s)
- Leighton J Payne
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Sean Meaden
- Biosciences, University of Exeter, Penryn, UK
| | | | - Chris Palmer
- Information Technology Services Research and Teaching Group, University of Otago, Dunedin, New Zealand
| | - Nicolás Toro
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Granada, Spain
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.,Genetics Otago, University of Otago, Dunedin, New Zealand.,Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Simon A Jackson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.,Genetics Otago, University of Otago, Dunedin, New Zealand.,Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
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13
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Zeng Z, Chen Y, Pinilla-Redondo R, Shah SA, Zhao F, Wang C, Hu Z, Wu C, Zhang C, Whitaker RJ, She Q, Han W. A short prokaryotic Argonaute activates membrane effector to confer antiviral defense. Cell Host Microbe 2022; 30:930-943.e6. [PMID: 35594868 DOI: 10.1016/j.chom.2022.04.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/25/2022] [Accepted: 04/26/2022] [Indexed: 11/03/2022]
Abstract
Argonaute (Ago) proteins are widespread nucleic-acid-guided enzymes that recognize targets through complementary base pairing. Although, in eukaryotes, Agos are involved in RNA silencing, the functions of prokaryotic Agos (pAgos) remain largely unknown. In particular, a clade of truncated and catalytically inactive pAgos (short pAgos) lacks characterization. Here, we reveal that a short pAgo protein in the archaeon Sulfolobus islandicus, together with its two genetically associated proteins, Aga1 and Aga2, provide robust antiviral protection via abortive infection. Aga2 is a toxic transmembrane effector that binds anionic phospholipids via a basic pocket, resulting in membrane depolarization and cell killing. Ago and Aga1 form a stable complex that exhibits nucleic-acid-directed nucleic-acid-recognition ability and directly interacts with Aga2, pointing to an immune sensing mechanism. Together, our results highlight the cooperation between pAgos and their widespread associated proteins, suggesting an uncharted diversity of pAgo-derived immune systems.
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Affiliation(s)
- Zhifeng Zeng
- State Key Laboratory of Agricultural Microbiology and College of Life Sciences and Technology, Huazhong Agricultural University, 430070 Wuhan, China; Hubei Hongshan Laboratory, 430070 Wuhan, China
| | - Yu Chen
- State Key Laboratory of Agricultural Microbiology and College of Life Sciences and Technology, Huazhong Agricultural University, 430070 Wuhan, China; Hubei Hongshan Laboratory, 430070 Wuhan, China
| | - Rafael Pinilla-Redondo
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
| | - Fen Zhao
- Hubei Hongshan Laboratory, 430070 Wuhan, China; National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, 430070 Wuhan, China
| | - Chen Wang
- Hubei Hongshan Laboratory, 430070 Wuhan, China; National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, 430070 Wuhan, China
| | - Zeyu Hu
- State Key Laboratory of Agricultural Microbiology and College of Life Sciences and Technology, Huazhong Agricultural University, 430070 Wuhan, China; Hubei Hongshan Laboratory, 430070 Wuhan, China
| | - Chang Wu
- State Key Laboratory of Agricultural Microbiology and College of Life Sciences and Technology, Huazhong Agricultural University, 430070 Wuhan, China; Hubei Hongshan Laboratory, 430070 Wuhan, China
| | - Changyi Zhang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - Rachel J Whitaker
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Jimo, 266237 Qingdao, China
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology and College of Life Sciences and Technology, Huazhong Agricultural University, 430070 Wuhan, China; Hubei Hongshan Laboratory, 430070 Wuhan, China.
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14
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Zaworski J, Dagva O, Brandt J, Baum C, Ettwiller L, Fomenkov A, Raleigh EA. Reassembling a cannon in the DNA defense arsenal: Genetics of StySA, a BREX phage exclusion system in Salmonella lab strains. PLoS Genet 2022; 18:e1009943. [PMID: 35377874 PMCID: PMC9009780 DOI: 10.1371/journal.pgen.1009943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 04/14/2022] [Accepted: 03/01/2022] [Indexed: 11/18/2022] Open
Abstract
Understanding mechanisms that shape horizontal exchange in prokaryotes is a key problem in biology. A major limit on DNA entry is imposed by restriction-modification (RM) processes that depend on the pattern of DNA modification at host-specified sites. In classical RM, endonucleolytic DNA cleavage follows detection of unprotected sites on entering DNA. Recent investigation has uncovered BREX (BacteRiophage EXclusion) systems. These RM-like activities employ host protection by DNA modification, but immediate replication arrest occurs without evident of nuclease action on unmodified phage DNA. Here we show that the historical stySA RM locus of Salmonella enterica sv Typhimurium is a variant BREX system. A laboratory strain disabled for both the restriction and methylation activity of StySA nevertheless has wild type sequence in pglX, the modification gene homolog. Instead, flanking genes pglZ and brxC each carry multiple mutations (μ) in their C-terminal domains. We further investigate this system in situ, replacing the mutated pglZμ and brxCμ genes with the WT counterpart. PglZ-WT supports methylation in the presence of either BrxCμ or BrxC-WT but not in the presence of a deletion/insertion allele, ΔbrxC::cat. Restriction requires both BrxC-WT and PglZ-WT, implicating the BrxC C-terminus specifically in restriction activity. These results suggests that while BrxC, PglZ and PglX are principal components of the BREX modification activity, BrxL is required for restriction only. Furthermore, we show that a partial disruption of brxL disrupts transcription globally. Horizontal gene transfer is a major driver of evolution and adaptation in bacteria. Genes from outside may be beneficial or dangerous to the receiving cell. Benefits include new food sources such as sugars, or new homes by adhesion, or new resistances, as to antibiotics. Dangers are posed by bacteriophages--viruses that take over the cell machinery, multiply, and release progeny to kill sister cells. Host-dependent restriction-modification systems enable defense that distinguishes relatives from strangers: using a modification pattern (M) carried by DNA bases added by the host cell to prevent restriction (R). Sisters and cousin cells will have the same protective pattern on DNA, while DNA of foreign origin will have the wrong M pattern and be restricted (R, rejected). Typically, restriction involves nuclease digestion. Here we address the enigmatic StySA RM system, one of the earliest to be genetically characterized. It is a variant of the newly recognized defense mechanism, BREX. BREX systems also track DNA history via modification pattern, but restrict by a novel, uncharacterized mechanism. Like other BREX family systems, StySA-BREX modification requires multiple components. When StySA-BREX transcription is unbalanced, we find global disruption of gene transcription. The disruption pattern does not suggest SOS-inducing damage to DNA.
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Affiliation(s)
- Julie Zaworski
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Oyut Dagva
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Julius Brandt
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Chloé Baum
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Laurence Ettwiller
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Alexey Fomenkov
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Elisabeth A. Raleigh
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
- * E-mail:
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15
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Miroshnikov KA, Evseev PV, Lukianova AA, Ignatov AN. Tailed Lytic Bacteriophages of Soft Rot Pectobacteriaceae. Microorganisms 2021; 9:1819. [PMID: 34576713 PMCID: PMC8472413 DOI: 10.3390/microorganisms9091819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
The study of the ecological and evolutionary traits of Soft Rot Pectobacteriaceae (SRP) comprising genera Pectobacterium and Dickeya often involves bacterial viruses (bacteriophages). Bacteriophages are considered to be a prospective tool for the ecologically safe and highly specific protection of plants and harvests from bacterial diseases. Information concerning bacteriophages has been growing rapidly in recent years, and this has included new genomics-based principles of taxonomic distribution. In this review, we summarise the data on phages infecting Pectobacterium and Dickeya that are available in publications and genomic databases. The analysis highlights not only major genomic properties that assign phages to taxonomic families and genera, but also the features that make them potentially suitable for phage control applications. Specifically, there is a discussion of the molecular mechanisms of receptor recognition by the phages and problems concerning the evolution of phage-resistant mutants.
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Affiliation(s)
- Konstantin A Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
| | - Peter V Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Anna A Lukianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, bldg. 12, 119234 Moscow, Russia
| | - Alexander N Ignatov
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str., 6, 117198 Moscow, Russia
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16
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A Bacterial Dynamin-Like Protein Confers a Novel Phage Resistance Strategy on the Population Level in Bacillus subtilis. mBio 2021; 13:e0375321. [PMID: 35164550 PMCID: PMC8844932 DOI: 10.1128/mbio.03753-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Bacillus subtilis DynA is a member of the dynamin superfamily, involved in membrane remodeling processes. DynA was shown to catalyze full membrane fusion and it plays a role in membrane surveillance against antibiotics. We show here that DynA also provides a novel resistance mechanism against phage infection. Cells lacking DynA are efficiently lysed after phage infection and virus replication. DynA does not prevent phage infection and replication in individual cells, but significantly delays host cell lysis, thereby slowing down the release of phage progeny from the host cells. During the process, DynA forms large, almost immobile clusters on the cell membrane that seem to support membrane integrity. Single-molecule tracking revealed a shift of freely diffusive molecules within the cytosol toward extended, confined motion at the cell membrane following phage induction. Thus, the bacterial dynamins are the first anti-phage system reported to delay host cell lysis and the last line of defense of a multilayered antiviral defense. DynA is therefore providing protective effects on the population, but not on single cell level. IMPORTANCE Bacteria have to cope with myriads of phages in their natural environments. Consequently, they have evolved sophisticated systems to prevent phage infection or epidemic spreading of the infection in the population. We show here that a bacterial dynamin-like protein is involved in phage resistance. The Bacillus subtilis DynA protein delays lysis of infected bacteria and reduces spreading of the phage particles. Thus, the dynamin mediated protection is not at the level of the individual cell, but on the population level. The bacterial DynA is the last line of defense to reduce the deleterious effect of a phage infection in a bacterial community. Interestingly, dynamin-like proteins such as Mx proteins are also involved in antiviral activities in Eukaryotes. Thus, the interaction of dynamin-like proteins and viruses seem to be an evolutionary ancient process.
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