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Grybchuk‐Ieremenko A, Lipovská K, Kouřilová X, Obruča S, Dvořák P. An Initial Genome Editing Toolset for Caldimonas thermodepolymerans, the First Model of Thermophilic Polyhydroxyalkanoates Producer. Microb Biotechnol 2025; 18:e70103. [PMID: 39980168 PMCID: PMC11842462 DOI: 10.1111/1751-7915.70103] [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: 09/25/2024] [Revised: 01/22/2025] [Accepted: 01/24/2025] [Indexed: 02/22/2025] Open
Abstract
The limited number of well-characterised model bacteria cannot address all the challenges in a circular bioeconomy. Therefore, there is a growing demand for new production strains with enhanced resistance to extreme conditions, versatile metabolic capabilities and the ability to utilise cost-effective renewable resources while efficiently generating attractive biobased products. Particular thermophilic microorganisms fulfil these requirements. Non-virulent Gram-negative Caldimonas thermodepolymerans DSM15344 is one such attractive thermophile that efficiently converts a spectrum of plant biomass sugars into high quantities of polyhydroxyalkanoates (PHA)-a fully biodegradable substitutes for synthetic plastics. However, to enhance its biotechnological potential, the bacterium needs to be 'domesticated'. In this study, we established effective homologous recombination and transposon-based genome editing systems for C. thermodepolymerans. By optimising the electroporation protocol and refining counterselection methods, we achieved significant improvements in genetic manipulation and constructed the AI01 chassis strain with improved transformation efficiency and a ΔphaC mutant that will be used to study the importance of PHA synthesis in Caldimonas. The advances described herein highlight the need for tailored approaches when working with thermophilic bacteria and provide a springboard for further genetic and metabolic engineering of C. thermodepolymerans, which can be considered the first model of thermophilic PHA producer.
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Affiliation(s)
- Anastasiia Grybchuk‐Ieremenko
- Department of Experimental Biology (Section of Microbiology), Faculty of ScienceMasaryk UniversityBrnoCzech Republic
| | - Kristýna Lipovská
- Department of Experimental Biology (Section of Microbiology), Faculty of ScienceMasaryk UniversityBrnoCzech Republic
| | - Xenie Kouřilová
- Faculty of Chemistry, Institute of Food Science and BiotechnologyBrno University of TechnologyBrnoCzech Republic
| | - Stanislav Obruča
- Faculty of Chemistry, Institute of Food Science and BiotechnologyBrno University of TechnologyBrnoCzech Republic
| | - Pavel Dvořák
- Department of Experimental Biology (Section of Microbiology), Faculty of ScienceMasaryk UniversityBrnoCzech Republic
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Zhang Z, Todeschini TC, Wu Y, Kogay R, Naji A, Rodriguez JC, Mondi R, Kaganovich D, Taylor DW, Bravo JPK, Teplova M, Amen T, Koonin EV, Patel DJ, Nobrega FL. Kiwa is a bacterial membrane-embedded defence supercomplex activated by phage-induced membrane changes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2023.02.26.530102. [PMID: 39896579 PMCID: PMC11785009 DOI: 10.1101/2023.02.26.530102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/04/2025]
Abstract
Bacteria and archaea deploy diverse, sophisticated defence systems to counter virus infection, yet many immunity mechanisms remain poorly understood. Here, we characterise the Kiwa defence system as a membrane-associated supercomplex that senses changes in the membrane induced by phage infection and plasmid conjugation. This supercomplex, comprising KwaA tetramers bound to KwaB dimers, as its basic repeating unit, detects structural stress via KwaA, activating KwaB, which binds ejected phage DNA through its DUF4868 domain, stalling phage DNA replication forks and thus disrupting replication and late transcription. We show that phage-encoded DNA mimic protein Gam, which inhibits RecBCD, also targets Kiwa through KwaB recognition. However, Gam binding to one defence system precludes its inhibition of the other. These findings reveal a distinct mechanism of bacterial immune coordination, where sensing of membrane disruptions and inhibitor partitioning enhance protection against phages and plasmids.
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Affiliation(s)
- Zhiying Zhang
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Shared first authors
| | - Thomas C. Todeschini
- School of Biological Sciences, University of Southampton, SO17 1BJ Southampton, UK
- Shared first authors
- Current address: RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Yi Wu
- School of Biological Sciences, University of Southampton, SO17 1BJ Southampton, UK
- Shared first authors
| | - Roman Kogay
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Ameena Naji
- School of Biological Sciences, University of Southampton, SO17 1BJ Southampton, UK
- Current address: School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | | | - Rupavidhya Mondi
- School of Biological Sciences, University of Southampton, SO17 1BJ Southampton, UK
- Current address: The William Harvey Research Institute, Barts and The London School of Medicine, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Daniel Kaganovich
- School of Biological Sciences, University of Southampton, SO17 1BJ Southampton, UK
| | - David W. Taylor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Interdisciplinary Life Sciences Graduate Programs, Austin, TX 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA
- LIVESTRONG Cancer Institutes, Dell Medical School, Austin, TX, 78712, USA
| | - Jack P. K. Bravo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Current address: Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Marianna Teplova
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Triana Amen
- School of Biological Sciences, University of Southampton, SO17 1BJ Southampton, UK
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Dinshaw J. Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Franklin L. Nobrega
- School of Biological Sciences, University of Southampton, SO17 1BJ Southampton, UK
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de Andrade FCC, Carvalho MF, Figueiredo AMS. Survival Strategies of Staphylococcus aureus: Adaptive Regulation of the Anti-Restriction Gene ardA-H1 Under Stress Conditions. Antibiotics (Basel) 2024; 13:1131. [PMID: 39766521 PMCID: PMC11672565 DOI: 10.3390/antibiotics13121131] [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: 10/25/2024] [Revised: 11/19/2024] [Accepted: 11/23/2024] [Indexed: 01/11/2025] Open
Abstract
Background/Objective: The anti-restriction protein ArdA-H1, found in multiresistant Staphylococcus aureus (MRSA) strains from the ST239-SCCmecIII lineage, inhibits restriction-modification systems, fostering horizontal gene transfer (HGT) and supporting genetic adaptability and resistance. This study investigates the regulatory mechanisms controlling ardA-H1 expression in S. aureus under various stress conditions, including acidic pH, iron limitation, and vancomycin exposure, and explores the roles of the Agr quorum sensing system. Methods: The expression of ardA-H1 was analyzed in S. aureus strains exposed to environmental stressors using real-time quantitative reverse transcription PCR. Comparisons were made between Agr-functional and Agr-deficient strains. In addition, Agr inhibition was achieved using a heterologous Agr autoinducing peptide. Results: The Agr system upregulated ardA-H1 expression in acidic and iron-limited conditions. However, vancomycin induced ardA-H1 activation specifically in the Agr-deficient strain GV69, indicating that an alternative regulatory pathway controls ardA-H1 expression in the absence of agr. The vancomycin response in GV69 suggests that diminished quorum sensing may offer a survival advantage by promoting persistence and HGT-related adaptability. Conclusion: Overall, our findings provide new insights into the intricate relationships between quorum-sensing, stress responses, bacterial virulence, and genetic plasticity, enhancing our understanding of S. aureus adaptability in challenging environments.
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Affiliation(s)
- Flavia Costa Carvalho de Andrade
- Departamento de Microbiologia Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (F.C.C.d.A.); (M.F.C.)
| | - Mariana Fernandes Carvalho
- Departamento de Microbiologia Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (F.C.C.d.A.); (M.F.C.)
| | - Agnes Marie Sá Figueiredo
- Departamento de Microbiologia Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (F.C.C.d.A.); (M.F.C.)
- Programa de Pós-Graduação em Patologia, Faculdade de Medicina, Universidade Federal Fluminense, Niterói 24033-900, Brazil
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Siedentop B, Losa Mediavilla C, Kouyos RD, Bonhoeffer S, Chabas H. Assessing the Role of Bacterial Innate and Adaptive Immunity as Barriers to Conjugative Plasmids. Mol Biol Evol 2024; 41:msae207. [PMID: 39382385 PMCID: PMC11525042 DOI: 10.1093/molbev/msae207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 09/23/2024] [Accepted: 10/02/2024] [Indexed: 10/10/2024] Open
Abstract
Plasmids are ubiquitous mobile genetic elements, that can be either costly or beneficial for their bacterial host. In response to constant viral threat, bacteria have evolved various immune systems, such as the prevalent restriction modification (innate immunity) and CRISPR-Cas systems (adaptive immunity). At the molecular level, both systems also target plasmids, but the consequences of these interactions for plasmid spread are unclear. Using a modeling approach, we show that restriction modification and CRISPR-Cas are effective as barriers against the spread of costly plasmids, but not against beneficial ones. Consequently, bacteria can profit from the selective advantages that beneficial plasmids confer even in the presence of bacterial immunity. While plasmids that are costly for bacteria may persist in the bacterial population for a certain period, restriction modification and CRISPR-Cas can eventually drive them to extinction. Finally, we demonstrate that the selection pressure imposed by bacterial immunity on costly plasmids can be circumvented through a diversity of escape mechanisms and highlight how plasmid carriage might be common despite bacterial immunity. In summary, the population-level outcome of interactions between plasmids and defense systems in a bacterial population is closely tied to plasmid cost: Beneficial plasmids can persist at high prevalence in bacterial populations despite defense systems, while costly plasmids may face extinction.
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Affiliation(s)
- Berit Siedentop
- Institute for Integrative Biology, ETH Zürich, Zürich, Switzerland
| | | | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Hélène Chabas
- Institute for Integrative Biology, ETH Zürich, Zürich, Switzerland
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Gladysheva-Azgari M, Sharko F, Evteeva M, Kuvyrchenkova A, Boulygina E, Tsygankova S, Slobodova N, Pustovoit K, Melkina O, Nedoluzhko A, Korzhenkov A, Kudryavtseva A, Utkina A, Manukhov I, Rastorguev S, Zavilgelsky G. ArdA genes from pKM101 and from B. bifidum chromosome have a different range of regulated genes. Heliyon 2023; 9:e22986. [PMID: 38144267 PMCID: PMC10746416 DOI: 10.1016/j.heliyon.2023.e22986] [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: 04/17/2023] [Revised: 09/18/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023] Open
Abstract
The ardA genes are present in a wide variety of conjugative plasmids and play an important role in overcoming the restriction barrier. To date, there is no information on the chromosomal ardA genes. It is still unclear whether they keep their antirestriction activity and why bacterial chromosomes contain these genes. In the present study, we confirmed the antirestriction function of the ardA gene from the Bifidobacterium bifidum chromosome. Transcriptome analysis in Escherichia coli showed that the range of regulated genes varies significantly for ardA from conjugative plasmid pKM101 and from the B. bifidum chromosome. Moreover, if the targets for both ardA genes match, they often show an opposite effect on regulated gene expression. The results obtained indicate two seemingly mutually exclusive conclusions. On the one hand, the pleiotropic effect of ardA genes was shown not only on restriction-modification system, but also on expression of a number of other genes. On the other hand, the range of affected genes varies significally for ardA genes from different sources, which indicates the specificity of ardA to inhibited targets. Author Summary. Conjugative plasmids, bacteriophages, as well as transposons, are capable to transfer various genes, including antibiotic resistance genes, among bacterial cells. However, many of those genes pose a threat to the bacterial cells, therefore bacterial cells have special restriction systems that limit such transfer. Antirestriction genes have previously been described as a part of conjugative plasmids, and bacteriophages and transposons. Those plasmids are able to overcome bacterial cell protection in the presence of antirestriction genes, which inhibit bacterial restriction systems. This work unveils the antirestriction mechanisms, which play an important role in the bacterial life cycle. Here, we clearly show that antirestriction genes, which are able to inhibit cell protection, exist not only in plasmids but also in the bacterial chromosomes themselves. Moreover, antirestrictases have not only an inhibitory function but also participate in the regulation of other bacterial genes. The regulatory function of plasmid antirestriction genes also helps them to overcome the bacterial cell protection against gene transfer, whereas the regulatory function of genomic antirestrictases has no such effect.
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Affiliation(s)
| | - F.S. Sharko
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - M.A. Evteeva
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
| | | | - E.S. Boulygina
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
| | - S.V. Tsygankova
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
| | - N.V. Slobodova
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
| | - K.S. Pustovoit
- State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center “Kurchatov Institute”, Moscow, Russia, 115454
| | - O.E. Melkina
- State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center “Kurchatov Institute”, Moscow, Russia, 115454
| | - A.V. Nedoluzhko
- European University at Saint Petersburg, 191187, Saint-Petersburg, Russia
| | - A.A. Korzhenkov
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
| | - A.A. Kudryavtseva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - A.A. Utkina
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - I.V. Manukhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
- Faculty of Physics, HSE University, 109028, Moscow, Russia
- Laboratory for Microbiology, BIOTECH University, 125080, Moscow, Russia
| | - S.M. Rastorguev
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
- Pirogov Russian National Research Medical University, Ostrovityanova Str. 1, Moscow, 117997, Russia
| | - G.B. Zavilgelsky
- State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center “Kurchatov Institute”, Moscow, Russia, 115454
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