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Skutel M, Yanovskaya D, Demkina A, Shenfeld A, Musharova O, Severinov K, Isaev A. RecA-dependent or independent recombination of plasmid DNA generates a conflict with the host EcoKI immunity by launching restriction alleviation. Nucleic Acids Res 2024; 52:5195-5208. [PMID: 38567730 PMCID: PMC11109961 DOI: 10.1093/nar/gkae243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 03/17/2024] [Accepted: 03/22/2024] [Indexed: 05/23/2024] Open
Abstract
Bacterial defence systems are tightly regulated to avoid autoimmunity. In Type I restriction-modification (R-M) systems, a specific mechanism called restriction alleviation (RA) controls the activity of the restriction module. In the case of the Escherichia coli Type I R-M system EcoKI, RA proceeds through ClpXP-mediated proteolysis of restriction complexes bound to non-methylated sites that appear after replication or reparation of host DNA. Here, we show that RA is also induced in the presence of plasmids carrying EcoKI recognition sites, a phenomenon we refer to as plasmid-induced RA. Further, we show that the anti-restriction behavior of plasmid-borne non-conjugative transposons such as Tn5053, previously attributed to their ardD loci, is due to plasmid-induced RA. Plasmids carrying both EcoKI and Chi sites induce RA in RecA- and RecBCD-dependent manner. However, inactivation of both RecA and RecBCD restores RA, indicating that there exists an alternative, RecA-independent, homologous recombination pathway that is blocked in the presence of RecBCD. Indeed, plasmid-induced RA in a RecBCD-deficient background does not depend on the presence of Chi sites. We propose that processing of random dsDNA breaks in plasmid DNA via homologous recombination generates non-methylated EcoKI sites, which attract EcoKI restriction complexes channeling them for ClpXP-mediated proteolysis.
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Affiliation(s)
- Mikhail Skutel
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Daria Yanovskaya
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | - Alina Demkina
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Olga Musharova
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute of Molecular Genetics, National Research Center Kurchatov Institute, Moscow, Russia
| | - Konstantin Severinov
- Waksman Institute of Microbiology, Piscataway, USA
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Artem Isaev
- Skolkovo Institute of Science and Technology, Moscow, Russia
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2
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Gupta P, Hiller A, Chowdhury J, Lim D, Lim DY, Saeij JPJ, Babaian A, Rodriguez F, Pereira L, Morales-Tapia A. A parasite odyssey: An RNA virus concealed in Toxoplasma gondii. Virus Evol 2024; 10:veae040. [PMID: 38817668 PMCID: PMC11137675 DOI: 10.1093/ve/veae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 03/05/2024] [Accepted: 05/10/2024] [Indexed: 06/01/2024] Open
Abstract
We are entering a 'Platinum Age of Virus Discovery', an era marked by exponential growth in the discovery of virus biodiversity, and driven by advances in metagenomics and computational analysis. In the ecosystem of a human (or any animal) there are more species of viruses than simply those directly infecting the animal cells. Viruses can infect all organisms constituting the microbiome, including bacteria, fungi, and unicellular parasites. Thus the complexity of possible interactions between host, microbe, and viruses is unfathomable. To understand this interaction network we must employ computationally assisted virology as a means of analyzing and interpreting the millions of available samples to make inferences about the ways in which viruses may intersect human health. From a computational viral screen of human neuronal datasets, we identified a novel narnavirus Apocryptovirus odysseus (Ao) which likely infects the neurotropic parasite Toxoplasma gondii. Previously, several parasitic protozoan viruses (PPVs) have been mechanistically established as triggers of host innate responses, and here we present in silico evidence that Ao is a plausible pro-inflammatory factor in human and mouse cells infected by T. gondii. T. gondii infects billions of people worldwide, yet the prognosis of toxoplasmosis disease is highly variable, and PPVs like Ao could function as a hitherto undescribed hypervirulence factor. In a broader screen of over 7.6 million samples, we explored phylogenetically proximal viruses to Ao and discovered nineteen Apocryptovirus species, all found in libraries annotated as vertebrate transcriptome or metatranscriptomes. While samples containing this genus of narnaviruses are derived from sheep, goat, bat, rabbit, chicken, and pigeon samples, the presence of virus is strongly predictive of parasitic Apicomplexa nucleic acid co-occurrence, supporting the fact that Apocryptovirus is a genus of parasite-infecting viruses. This is a computational proof-of-concept study in which we rapidly analyze millions of datasets from which we distilled a mechanistically, ecologically, and phylogenetically refined hypothesis. We predict that this highly diverged Ao RNA virus is biologically a T. gondii infection, and that Ao, and other viruses like it, will modulate this disease which afflicts billions worldwide.
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Affiliation(s)
- Purav Gupta
- The Woodlands Secondary School, 3225 Erindale Station Rd,Mississauga, ON L5C 1Y5, Canada
- Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- The Donnelly Centre for Cellular + Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
- The Woodlands Secondary School, 3225 Erindale Station Rd, Mississauga, ON L5C 1Y5, Canada
| | - Aiden Hiller
- Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- The Donnelly Centre for Cellular + Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
- The Woodlands Secondary School, 3225 Erindale Station Rd, Mississauga, ON L5C 1Y5, Canada
| | - Jawad Chowdhury
- Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- The Donnelly Centre for Cellular + Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
- The Woodlands Secondary School, 3225 Erindale Station Rd, Mississauga, ON L5C 1Y5, Canada
| | - Declan Lim
- Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- The Donnelly Centre for Cellular + Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
- The Woodlands Secondary School, 3225 Erindale Station Rd, Mississauga, ON L5C 1Y5, Canada
| | - Dillon Yee Lim
- The Woodlands Secondary School, 3225 Erindale Station Rd, Mississauga, ON L5C 1Y5, Canada
- Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Building, Sherrington Road, Oxford, Oxfordshire, OX1 3PT, UK
| | - Jeroen P J Saeij
- The Woodlands Secondary School, 3225 Erindale Station Rd, Mississauga, ON L5C 1Y5, Canada
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, 1 Shields Ave, Davis, CA 95616, USA
| | - Artem Babaian
- Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- The Donnelly Centre for Cellular + Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
- The Woodlands Secondary School, 3225 Erindale Station Rd, Mississauga, ON L5C 1Y5, Canada
| | - Felipe Rodriguez
- The Woodlands Secondary School, 3225 Erindale Station Rd, Mississauga, ON L5C 1Y5, Canada
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, 1 Shields Ave, Davis, CA 95616, USA
| | - Luke Pereira
- Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- The Donnelly Centre for Cellular + Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
- The Woodlands Secondary School, 3225 Erindale Station Rd, Mississauga, ON L5C 1Y5, Canada
| | - Alejandro Morales-Tapia
- Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- The Donnelly Centre for Cellular + Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
- The Woodlands Secondary School, 3225 Erindale Station Rd, Mississauga, ON L5C 1Y5, Canada
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3
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Agapov A, Baker KS, Bedekar P, Bhatia RP, Blower TR, Brockhurst MA, Brown C, Chong CE, Fothergill JL, Graham S, Hall JP, Maestri A, McQuarrie S, Olina A, Pagliara S, Recker M, Richmond A, Shaw SJ, Szczelkun MD, Taylor TB, van Houte S, Went SC, Westra ER, White MF, Wright R. Multi-layered genome defences in bacteria. Curr Opin Microbiol 2024; 78:102436. [PMID: 38368839 DOI: 10.1016/j.mib.2024.102436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/20/2024]
Abstract
Bacteria have evolved a variety of defence mechanisms to protect against mobile genetic elements, including restriction-modification systems and CRISPR-Cas. In recent years, dozens of previously unknown defence systems (DSs) have been discovered. Notably, diverse DSs often coexist within the same genome, and some co-occur at frequencies significantly higher than would be expected by chance, implying potential synergistic interactions. Recent studies have provided evidence of defence mechanisms that enhance or complement one another. Here, we review the interactions between DSs at the mechanistic, regulatory, ecological and evolutionary levels.
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Affiliation(s)
- Aleksei Agapov
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Kate S Baker
- Department of Genetics, University of Cambridge, CB2 3EH, UK
| | - Paritosh Bedekar
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Rama P Bhatia
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Tim R Blower
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Michael A Brockhurst
- Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Dover Street, Manchester M13 9PT, UK
| | - Cooper Brown
- School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | | | - Joanne L Fothergill
- Dept of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK
| | - Shirley Graham
- School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - James Pj Hall
- Dept of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L69 7ZB, UK
| | - Alice Maestri
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Stuart McQuarrie
- School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Anna Olina
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | | | - Mario Recker
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Anna Richmond
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Steven J Shaw
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS6 7YB, UK
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS6 7YB, UK
| | - Tiffany B Taylor
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | | | - Sam C Went
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Edze R Westra
- ESI, Centre for Ecology and Conservation, University of Exeter, UK.
| | - Malcolm F White
- School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Rosanna Wright
- Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Dover Street, Manchester M13 9PT, UK
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4
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Kamat A, Tran NT, Sharda M, Sontakke N, Le TBK, Badrinarayanan A. Widespread prevalence of a methylation-dependent switch to activate an essential DNA damage response in bacteria. PLoS Biol 2024; 22:e3002540. [PMID: 38466718 PMCID: PMC10957082 DOI: 10.1371/journal.pbio.3002540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/21/2024] [Accepted: 02/06/2024] [Indexed: 03/13/2024] Open
Abstract
DNA methylation plays central roles in diverse cellular processes, ranging from error-correction during replication to regulation of bacterial defense mechanisms. Nevertheless, certain aberrant methylation modifications can have lethal consequences. The mechanisms by which bacteria detect and respond to such damage remain incompletely understood. Here, we discover a highly conserved but previously uncharacterized transcription factor (Cada2), which orchestrates a methylation-dependent adaptive response in Caulobacter. This response operates independently of the SOS response, governs the expression of genes crucial for direct repair, and is essential for surviving methylation-induced damage. Our molecular investigation of Cada2 reveals a cysteine methylation-dependent posttranslational modification (PTM) and mode of action distinct from its Escherichia coli counterpart, a trait conserved across all bacteria harboring a Cada2-like homolog instead. Extending across the bacterial kingdom, our findings support the notion of divergence and coevolution of adaptive response transcription factors and their corresponding sequence-specific DNA motifs. Despite this diversity, the ubiquitous prevalence of adaptive response regulators underscores the significance of a transcriptional switch, mediated by methylation PTM, in driving a specific and essential bacterial DNA damage response.
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Affiliation(s)
- Aditya Kamat
- National Centre for Biological Sciences (TIFR), Bengaluru, India
| | - Ngat T. Tran
- John Innes Centre, Department of Molecular Microbiology, Colney Lane, Norwich, United Kingdom
| | - Mohak Sharda
- National Centre for Biological Sciences (TIFR), Bengaluru, India
| | - Neha Sontakke
- National Centre for Biological Sciences (TIFR), Bengaluru, India
| | - Tung B. K. Le
- John Innes Centre, Department of Molecular Microbiology, Colney Lane, Norwich, United Kingdom
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5
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Schumacher MA, Cannistraci E, Salinas R, Lloyd D, Messner E, Gozzi K. Structure of the WYL-domain containing transcription activator, DriD, in complex with ssDNA effector and DNA target site. Nucleic Acids Res 2024; 52:1435-1449. [PMID: 38142455 PMCID: PMC10853764 DOI: 10.1093/nar/gkad1198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/20/2023] [Accepted: 12/01/2023] [Indexed: 12/26/2023] Open
Abstract
Transcription regulators play central roles in orchestrating responses to changing environmental conditions. Recently the Caulobacter crescentus transcription activator DriD, which belongs to the newly defined WYL-domain family, was shown to regulate DNA damage responses independent of the canonical SOS pathway. However, the molecular mechanisms by which DriD and other WYL-regulators sense environmental signals and recognize DNA are not well understood. We showed DriD DNA-binding is triggered by its interaction with ssDNA, which is produced during DNA damage. Here we describe the structure of the full-length C. crescentus DriD bound to both target DNA and effector ssDNA. DriD consists of an N-terminal winged-HTH (wHTH) domain, linker region, three-helix bundle, WYL-domain and C-terminal WCX-dimer domain. Strikingly, DriD binds DNA using a novel, asymmetric DNA-binding mechanism that results from different conformations adopted by the linker. Although the linker does not touch DNA, our data show that contacts it makes with the wHTH are key for specific DNA binding. The structure indicates how ssDNA-effector binding to the WYL-domain impacts wHTH DNA binding. In conclusion, we present the first structure of a WYL-activator bound to both effector and target DNA. The structure unveils a unique, asymmetric DNA binding mode that is likely conserved among WYL-activators.
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Affiliation(s)
- Maria A Schumacher
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC 27710, USA
| | - Emily Cannistraci
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC 27710, USA
| | - Raul Salinas
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC 27710, USA
| | - Devin Lloyd
- 100 Edwin H Land Blvd, Rowland Institute at Harvard, Harvard University, Cambridge, Cambridge, MA 02142, USA
| | - Ella Messner
- 100 Edwin H Land Blvd, Rowland Institute at Harvard, Harvard University, Cambridge, Cambridge, MA 02142, USA
| | - Kevin Gozzi
- 100 Edwin H Land Blvd, Rowland Institute at Harvard, Harvard University, Cambridge, Cambridge, MA 02142, USA
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6
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Keller LML, Flattich K, Weber-Ban E. Novel WYL domain-containing transcriptional activator acts in response to genotoxic stress in rapidly growing mycobacteria. Commun Biol 2023; 6:1222. [PMID: 38042942 PMCID: PMC10693628 DOI: 10.1038/s42003-023-05592-6] [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: 07/05/2023] [Accepted: 11/15/2023] [Indexed: 12/04/2023] Open
Abstract
The WYL domain is a nucleotide-sensing module that controls the activity of transcription factors involved in the regulation of DNA damage response and phage defense mechanisms in bacteria. In this study, we investigated a WYL domain-containing transcription factor in Mycobacterium smegmatis that we termed stress-involved WYL domain-containing regulator (SiwR). We found that SiwR controls adjacent genes that belong to the DinB/YfiT-like putative metalloenzymes superfamily by upregulating their expression in response to various genotoxic stress conditions, including upon exposure to H2O2 or the natural antibiotic zeocin. We show that SiwR binds different forms of single-stranded DNA (ssDNA) with high affinity, primarily through its characteristic WYL domain. In combination with complementation studies of a M. smegmatis siwR deletion strain, our findings support a role of the WYL domains as signal-sensing activity switches of WYL domain-containing transcription factors (WYL TFs). Our study provides evidence that WYL TFs are involved in the adaptation of bacteria to changing environments and encountered stress conditions.
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Affiliation(s)
| | - Kim Flattich
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093, Zurich, Switzerland
| | - Eilika Weber-Ban
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093, Zurich, Switzerland.
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