1
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Funnell BE. Coordinating plasmid partition with bacterial chromosome segregation. Proc Natl Acad Sci U S A 2024; 121:e2407081121. [PMID: 38722814 PMCID: PMC11127044 DOI: 10.1073/pnas.2407081121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2024] Open
Affiliation(s)
- Barbara E. Funnell
- Department of Molecular Genetics, University of Toronto, Toronto, ONM5G 1M1, Canada
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2
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Murányi G, Szabó M, Acsai K, Kiss J. Two birds with one stone: SGI1 can stabilize itself and expel the IncC helper by hijacking the plasmid parABS system. Nucleic Acids Res 2024; 52:2498-2518. [PMID: 38300764 PMCID: PMC10954446 DOI: 10.1093/nar/gkae050] [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: 07/21/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 02/03/2024] Open
Abstract
The SGI1 family integrative mobilizable elements, which are efficient agents in distribution of multidrug resistance in Gammaproteobacteria, have a complex, parasitic relationship with their IncC conjugative helper plasmids. Besides exploiting the transfer apparatus, SGI1 also hijacks IncC plasmid control mechanisms to time its own excision, replication and expression of self-encoded T4SS components, which provides advantages for SGI1 over its helpers in conjugal transfer and stable maintenance. Furthermore, SGI1 destabilizes its helpers in an unknown, replication-dependent way when they are concomitantly present in the same host. Here we report how SGI1 exploits the helper plasmid partitioning system to displace the plasmid and simultaneously increase its own stability. We show that SGI1 carries two copies of sequences mimicking the parS sites of IncC plasmids. These parS-like elements bind the ParB protein encoded by the plasmid and increase SGI1 stability by utilizing the parABS system of the plasmid for its own partitioning, through which SGI1 also destabilizes the helper plasmid. Furthermore, SGI1 expresses a small protein, Sci, which significantly strengthens this plasmid-destabilizing effect, as well as SGI1 maintenance. The plasmid-induced replication of SGI1 results in an increased copy-number of parS-like sequences and Sci expression leading to strong incompatibility with the helper plasmid.
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Affiliation(s)
- Gábor Murányi
- Department of Microbiology and Applied Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, H2100 Hungary
| | - Mónika Szabó
- Department of Microbiology and Applied Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, H2100 Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Gödöllő, H2100 Hungary
| | - Károly Acsai
- Ceva Animal Health, Ceva-Phylaxia, Budapest, H1107 Hungary
| | - János Kiss
- Department of Microbiology and Applied Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, H2100 Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Gödöllő, H2100 Hungary
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3
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Yu MK, Fogarty EC, Eren AM. Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess. Nat Microbiol 2024; 9:830-847. [PMID: 38443576 PMCID: PMC10914615 DOI: 10.1038/s41564-024-01610-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 01/17/2024] [Indexed: 03/07/2024]
Abstract
Plasmids alter microbial evolution and lifestyles by mobilizing genes that often confer fitness in changing environments across clades. Yet our ecological and evolutionary understanding of naturally occurring plasmids is far from complete. Here we developed a machine-learning model, PlasX, which identified 68,350 non-redundant plasmids across human gut metagenomes and organized them into 1,169 evolutionarily cohesive 'plasmid systems' using our sequence containment-aware network-partitioning algorithm, MobMess. Individual plasmids were often country specific, yet most plasmid systems spanned across geographically distinct human populations. Cargo genes in plasmid systems included well-known determinants of fitness, such as antibiotic resistance, but also many others including enzymes involved in the biosynthesis of essential nutrients and modification of transfer RNAs, revealing a wide repertoire of likely fitness determinants in complex environments. Our study introduces computational tools to recognize and organize plasmids, and uncovers the ecological and evolutionary patterns of diverse plasmids in naturally occurring habitats through plasmid systems.
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Affiliation(s)
- Michael K Yu
- Toyota Technological Institute at Chicago, Chicago, IL, USA.
| | - Emily C Fogarty
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Committee On Microbiology, University of Chicago, Chicago, IL, USA
| | - A Murat Eren
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA.
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany.
- Marine 'Omics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.
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4
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Cornet F, Blanchais C, Dusfour-Castan R, Meunier A, Quebre V, Sekkouri Alaoui H, Boudsoq F, Campos M, Crozat E, Guynet C, Pasta F, Rousseau P, Ton Hoang B, Bouet JY. DNA Segregation in Enterobacteria. EcoSal Plus 2023; 11:eesp00382020. [PMID: 37220081 PMCID: PMC10729935 DOI: 10.1128/ecosalplus.esp-0038-2020] [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: 11/24/2022] [Accepted: 04/13/2023] [Indexed: 01/28/2024]
Abstract
DNA segregation ensures that cell offspring receive at least one copy of each DNA molecule, or replicon, after their replication. This important cellular process includes different phases leading to the physical separation of the replicons and their movement toward the future daughter cells. Here, we review these phases and processes in enterobacteria with emphasis on the molecular mechanisms at play and their controls.
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Affiliation(s)
- François Cornet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Corentin Blanchais
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Romane Dusfour-Castan
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Alix Meunier
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Valentin Quebre
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Hicham Sekkouri Alaoui
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - François Boudsoq
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Manuel Campos
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Estelle Crozat
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Catherine Guynet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Franck Pasta
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Philippe Rousseau
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Bao Ton Hoang
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Jean-Yves Bouet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
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5
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Rozwandowicz M, Kant A, Wagenaar J, Mevius D, Hordijk J, Brouwer M. Understanding the genetic basis of the incompatibility of IncK1 and IncK2 plasmids. OPEN RESEARCH EUROPE 2023; 3:53. [PMID: 38106640 PMCID: PMC10724649 DOI: 10.12688/openreseurope.15121.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 10/23/2023] [Indexed: 12/19/2023]
Abstract
Antimicrobial resistance is a persistent challenge in human and veterinary medicine, which is often encoded on plasmids which are transmissible between bacterial cells. Incompatibility is the inability of two plasmids to be stably maintained in one cell which is caused by the presence of identical or closely related shared determinants between two plasmids originating from partition or replication mechanisms. For I-complex plasmids in Enterobacteriacae, replication- based incompatibility is caused by the small antisense RNA stem-loop structure called RNAI. The I-complex plasmid group IncK consists of two compatible subgroups, IncK1 and IncK2, for which the RNAI differs only by five nucleotides. In this study we focussed on the interaction of the IncK1 and IncK2 RNAI structures by constructing minireplicons containing the replication region of IncK1 or IncK2 plasmids coupled with a kanamycin resistance marker. Using minireplicons excludes involvement of incompatibility mechanisms other than RNAI. Additionally, we performed single nucleotide mutagenesis targeting the five nucleotides that differ between the IncK1 and IncK2 RNAI sequences of these minireplicons. The obtained results show that a single nucleotide change in the RNAI structure is responsible for the compatible phenotype of IncK1 with IncK2 plasmids. Only nucleotides in the RNAI top loop and interior loop have an effect on minireplicon incompatibility with wild type plasmids, while mutations in the stem of the RNAI structure had no significant effect on incompatibility. Understanding the molecular basis of incompatibility is relevant for future in silico predictions of plasmid incompatibility.
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Affiliation(s)
- Marta Rozwandowicz
- National Institute for Public Health and the Environment, Bilthoven, 3721 MA, The Netherlands
| | - Arie Kant
- Wageningen Bioveterinary Research, Lelystd, 8221 RA, The Netherlands
| | - Jaap Wagenaar
- Utrecht University, Utrecht, 3584 CS, The Netherlands
| | - Dik Mevius
- Wageningen Bioveterinary Research, Lelystd, 8221 RA, The Netherlands
| | - Joost Hordijk
- National Institute for Public Health and the Environment, Bilthoven, 3721 MA, The Netherlands
| | - Michael Brouwer
- Wageningen Bioveterinary Research, Lelystd, 8221 RA, The Netherlands
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6
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Connolley L, Schnabel L, Thanbichler M, Murray SM. Partition complex structure can arise from sliding and bridging of ParB dimers. Nat Commun 2023; 14:4567. [PMID: 37516778 PMCID: PMC10387095 DOI: 10.1038/s41467-023-40320-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 07/20/2023] [Indexed: 07/31/2023] Open
Abstract
In many bacteria, chromosome segregation requires the association of ParB to the parS-containing centromeric region to form the partition complex. However, the structure and formation of this complex have been unclear. Recently, studies have revealed that CTP binding enables ParB dimers to slide along DNA and condense the centromeric region through the formation of DNA bridges. Using semi-flexible polymer simulations, we demonstrate that these properties can explain partition complex formation. Transient ParB bridges organize DNA into globular states or hairpins and helical structures, depending on bridge lifetime, while separate simulations show that ParB sliding reproduces the multi-peaked binding profile observed in Caulobacter crescentus. Combining sliding and bridging into a unified model, we find that short-lived ParB bridges do not impede sliding and can reproduce both the binding profile and condensation of the nucleoprotein complex. Overall, our model elucidates the mechanism of partition complex formation and predicts its fine structure.
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Affiliation(s)
- Lara Connolley
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology, 35043, Marburg, Germany
| | - Lucas Schnabel
- Department of Biology, University of Marburg, 35043, Marburg, Germany
| | - Martin Thanbichler
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology, 35043, Marburg, Germany
- Department of Biology, University of Marburg, 35043, Marburg, Germany
| | - Seán M Murray
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology, 35043, Marburg, Germany.
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7
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Alav I, Buckner MMC. Non-antibiotic compounds associated with humans and the environment can promote horizontal transfer of antimicrobial resistance genes. Crit Rev Microbiol 2023:1-18. [PMID: 37462915 DOI: 10.1080/1040841x.2023.2233603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/23/2023] [Accepted: 06/30/2023] [Indexed: 02/15/2024]
Abstract
Horizontal gene transfer plays a key role in the global dissemination of antimicrobial resistance (AMR). AMR genes are often carried on self-transmissible plasmids, which are shared amongst bacteria primarily by conjugation. Antibiotic use has been a well-established driver of the emergence and spread of AMR. However, the impact of commonly used non-antibiotic compounds and environmental pollutants on AMR spread has been largely overlooked. Recent studies found common prescription and over-the-counter drugs, artificial sweeteners, food preservatives, and environmental pollutants, can increase the conjugative transfer of AMR plasmids. The potential mechanisms by which these compounds promote plasmid transmission include increased membrane permeability, upregulation of plasmid transfer genes, formation of reactive oxygen species, and SOS response gene induction. Many questions remain around the impact of most non-antibiotic compounds on AMR plasmid conjugation in clinical isolates and the long-term impact on AMR dissemination. By elucidating the role of routinely used pharmaceuticals, food additives, and pollutants in the dissemination of AMR, action can be taken to mitigate their impact by closely monitoring use and disposal. This review will discuss recent progress on understanding the influence of non-antibiotic compounds on plasmid transmission, the mechanisms by which they promote transfer, and the level of risk they pose.
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Affiliation(s)
- Ilyas Alav
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Michelle M C Buckner
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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8
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Siguier P, Campos M, Cornet F, Bouet JY, Guynet C. Atypical low-copy number plasmid segregation systems, all in one? Plasmid 2023; 127:102694. [PMID: 37301314 DOI: 10.1016/j.plasmid.2023.102694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023]
Abstract
Plasmid families harbor different maintenances functions, depending on their size and copy number. Low copy number plasmids rely on active partition systems, organizing a partition complex at specific centromere sites that is actively positioned using NTPase proteins. Some low copy number plasmids lack an active partition system, but carry atypical intracellular positioning systems using a single protein that binds to the centromere site but without an associated NTPase. These systems have been studied in the case of the Escherichia coli R388 and of the Staphylococcus aureus pSK1 plasmids. Here we review these two systems, which appear to be unrelated but share common features, such as their distribution on plasmids of medium size and copy number, certain activities of their centromere-binding proteins, StbA and Par, respectively, as well as their mode of action, which may involve dynamic interactions with the nucleoid-packed chromosome of their hosts.
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Affiliation(s)
- Patricia Siguier
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse F-31000, France
| | - Manuel Campos
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse F-31000, France
| | - François Cornet
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse F-31000, France
| | - Jean-Yves Bouet
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse F-31000, France
| | - Catherine Guynet
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse F-31000, France.
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9
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Couturier A, Virolle C, Goldlust K, Berne-Dedieu A, Reuter A, Nolivos S, Yamaichi Y, Bigot S, Lesterlin C. Real-time visualisation of the intracellular dynamics of conjugative plasmid transfer. Nat Commun 2023; 14:294. [PMID: 36653393 PMCID: PMC9849209 DOI: 10.1038/s41467-023-35978-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
Conjugation is a contact-dependent mechanism for the transfer of plasmid DNA between bacterial cells, which contributes to the dissemination of antibiotic resistance. Here, we use live-cell microscopy to visualise the intracellular dynamics of conjugative transfer of F-plasmid in E. coli, in real time. We show that the transfer of plasmid in single-stranded form (ssDNA) and its subsequent conversion into double-stranded DNA (dsDNA) are fast and efficient processes that occur with specific timing and subcellular localisation. Notably, the ssDNA-to-dsDNA conversion determines the timing of plasmid-encoded protein production. The leading region that first enters the recipient cell carries single-stranded promoters that allow the early and transient synthesis of leading proteins immediately upon entry of the ssDNA plasmid. The subsequent conversion into dsDNA turns off leading gene expression, and activates the expression of other plasmid genes under the control of conventional double-stranded promoters. This molecular strategy allows for the timely production of factors sequentially involved in establishing, maintaining and disseminating the plasmid.
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Affiliation(s)
- Agathe Couturier
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Chloé Virolle
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Kelly Goldlust
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Annick Berne-Dedieu
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Audrey Reuter
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Sophie Nolivos
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Yoshiharu Yamaichi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Sarah Bigot
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France.
| | - Christian Lesterlin
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France.
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10
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Wisniewska A, Wons E, Potrykus K, Hinrichs R, Gucwa K, Graumann PL, Mruk I. Molecular basis for lethal cross-talk between two unrelated bacterial transcription factors - the regulatory protein of a restriction-modification system and the repressor of a defective prophage. Nucleic Acids Res 2022; 50:10964-10980. [PMID: 36271797 DOI: 10.1093/nar/gkac914] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/29/2022] [Accepted: 10/06/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial gene expression depends on the efficient functioning of global transcriptional networks, however their interconnectivity and orchestration rely mainly on the action of individual DNA binding proteins called transcription factors (TFs). TFs interact not only with their specific target sites, but also with secondary (off-target) sites, and vary in their promiscuity. It is not clear yet what mechanisms govern the interactions with secondary sites, and how such rewiring affects the overall regulatory network, but this could clearly constrain horizontal gene transfer. Here, we show the molecular mechanism of one such off-target interaction between two unrelated TFs in Escherichia coli: the C regulatory protein of a Type II restriction-modification system, and the RacR repressor of a defective prophage. We reveal that the C protein interferes with RacR repressor expression, resulting in derepression of the toxic YdaT protein. These results also provide novel insights into regulation of the racR-ydaST operon. We mapped the C regulator interaction to a specific off-target site, and also visualized C protein dynamics, revealing intriguing differences in single molecule dynamics in different genetic contexts. Our results demonstrate an apparent example of horizontal gene transfer leading to adventitious TF cross-talk with negative effects on the recipient's viability. More broadly, this study represents an experimentally-accessible model of a regulatory constraint on horizontal gene transfer.
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Affiliation(s)
- Aleksandra Wisniewska
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ewa Wons
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Katarzyna Potrykus
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Rebecca Hinrichs
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Philipps Universität Marburg, Germany.,Department of Chemistry, Philipps Universität Marburg, Hans-Meerwein-Strasse 6, 35032 Marburg, Germany
| | - Katarzyna Gucwa
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Peter L Graumann
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Philipps Universität Marburg, Germany.,Department of Chemistry, Philipps Universität Marburg, Hans-Meerwein-Strasse 6, 35032 Marburg, Germany
| | - Iwona Mruk
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
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11
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Balbuena-Alonso MG, Cortés-Cortés G, Kim JW, Lozano-Zarain P, Camps M, Del Carmen Rocha-Gracia R. Genomic analysis of plasmid content in food isolates of E. coli strongly supports its role as a reservoir for the horizontal transfer of virulence and antibiotic resistance genes. Plasmid 2022; 123-124:102650. [PMID: 36130651 PMCID: PMC10896638 DOI: 10.1016/j.plasmid.2022.102650] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 09/08/2022] [Accepted: 09/15/2022] [Indexed: 11/19/2022]
Abstract
The link between E. coli strains contaminating foods and human disease is unclear, with some reports supporting a direct transmission of pathogenic strains via food and others highlighting their role as reservoirs for resistance and virulence genes. Here we take a genomics approach, analyzing a large set of fully-assembled genomic sequences from E. coli available in GenBank. Most of the strains isolated in food are more closely related to each other than to clinical strains, arguing against a frequent direct transmission of pathogenic strains from food to the clinic. We also provide strong evidence of genetic exchanges between food and clinical strains that are facilitated by plasmids. This is based on an overlapped representation of virulence and resistance genes in plasmids isolated from these two sources. We identify clusters of phylogenetically-related plasmids that are largely responsible for the observed overlap and see evidence of specialization, with some food plasmid clusters preferentially transferring virulence factors over resistance genes. Consistent with these observations, food plasmids have a high mobilization potential based on their plasmid taxonomic unit classification and on an analysis of mobilization gene content. We report antibiotic resistance genes of high clinical relevance and their specific incompatibility group associations. Finally, we also report a striking enrichment for adhesins in food plasmids and their association with specific IncF replicon subtypes. The identification of food plasmids with specific markers (Inc and PTU combinations) as mediators of horizontal transfer between food and clinical strains opens new research avenues and should assist with the design of surveillance strategies.
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Affiliation(s)
- María G Balbuena-Alonso
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de Puebla. Ciudad Universitaria, San Manuel, Puebla 72570, Mexico
| | - Gerardo Cortés-Cortés
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de Puebla. Ciudad Universitaria, San Manuel, Puebla 72570, Mexico; Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jay W Kim
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - Patricia Lozano-Zarain
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de Puebla. Ciudad Universitaria, San Manuel, Puebla 72570, Mexico
| | - Manel Camps
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.
| | - Rosa Del Carmen Rocha-Gracia
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de Puebla. Ciudad Universitaria, San Manuel, Puebla 72570, Mexico.
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12
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Al Mamun AAM, Kissoon K, Kishida K, Shropshire WC, Hanson B, Christie PJ. IncFV plasmid pED208: Sequence analysis and evidence for translocation of maintenance/leading region proteins through diverse type IV secretion systems. Plasmid 2022; 123-124:102652. [PMID: 36228885 PMCID: PMC10018792 DOI: 10.1016/j.plasmid.2022.102652] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/02/2022] [Accepted: 10/04/2022] [Indexed: 12/04/2022]
Abstract
Two phylogenetically distantly-related IncF plasmids, F and pED208, serve as important models for mechanistic and structural studies of F-like type IV secretion systems (T4SSFs) and F pili. Here, we present the pED208 sequence and compare it to F and pUMNF18, the closest match to pED208 in the NCBI database. As expected, gene content of the three cargo regions varies extensively, although the maintenance/leading regions (MLRs) and transfer (Tra) regions also carry novel genes or motifs with predicted modulatory effects on plasmid stability, dissemination and host range. By use of a Cre recombinase assay for translocation (CRAfT), we recently reported that pED208-carrying donors translocate several products of the MLR (ParA, ParB1, ParB2, SSB, PsiB, PsiA) intercellularly through the T4SSF. Here, we extend these findings by reporting that pED208-carrying donors translocate 10 additional MLR proteins during conjugation. In contrast, two F plasmid-encoded toxin components of toxin-antitoxin (TA) modules, CcdB and SrnB, were not translocated at detectable levels through the T4SSF. Remarkably, most or all of the pED208-encoded MLR proteins and CcdB and SrnB were translocated through heterologous T4SSs encoded by IncN and IncP plasmids pKM101 and RP4, respectively. Together, our sequence analyses underscore the genomic diversity of the F plasmid superfamily, and our experimental data demonstrate the promiscuous nature of conjugation machines for protein translocation. Our findings raise intriguing questions about the nature of T4SS translocation signals and of the biological and evolutionary consequences of conjugative protein transfer.
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Affiliation(s)
- Abu Amar M Al Mamun
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Fannin St, Houston, TX 77030, United States of America.
| | - Kimberly Kissoon
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Fannin St, Houston, TX 77030, United States of America
| | - Kouhei Kishida
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Fannin St, Houston, TX 77030, United States of America
| | - William C Shropshire
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA; Center for Infectious Diseases, University of Texas Health Science Center, School of Public Health, Houston, TX, USA
| | - Blake Hanson
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA; Center for Infectious Diseases, University of Texas Health Science Center, School of Public Health, Houston, TX, USA
| | - Peter J Christie
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Fannin St, Houston, TX 77030, United States of America.
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13
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Characterization of the DNA Binding Domain of StbA, A Key Protein of A New Type of DNA Segregation System. J Mol Biol 2022; 434:167752. [PMID: 35868361 DOI: 10.1016/j.jmb.2022.167752] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 11/21/2022]
Abstract
Low-copy-number plasmids require sophisticated genetic devices to achieve efficient segregation of plasmid copies during cell division. Plasmid R388 uses a unique segregation mechanism, based on StbA, a small multifunctional protein. StbA is the key protein in a segregation system not involving a plasmid-encoded NTPase partner, it regulates the expression of several plasmid operons, and it is the main regulator of plasmid conjugation. The mechanisms by which StbA, together with the centromere-like sequence stbS, achieves segregation, is largely uncharacterized. To better understand the molecular basis of R388 segregation, we determined the crystal structure of the conserved N-terminal domain of StbA to 1.9 Å resolution. It folds into an HTH DNA-binding domain, structurally related to that of the PadR subfamily II of transcriptional regulators. StbA is organized in two domains. Its N-terminal domain carries the specific stbS DNA binding activity. A truncated version of StbA, deleted of its C-terminal domain, displays only partial activities in vivo, indicating that the non-conserved C-terminal domain is required for efficient segregation and subcellular plasmid positioning. The structure of StbA DNA-binding domain also provides some insight into how StbA monomers cooperate to repress transcription by binding to the stbDR and to form the segregation complex with stbS.
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14
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The Specificity of ParR Binding Determines the Incompatibility of Conjugative Plasmids in Clostridium perfringens. mBio 2022; 13:e0135622. [PMID: 35726914 PMCID: PMC9426499 DOI: 10.1128/mbio.01356-22] [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] [Indexed: 12/04/2022] Open
Abstract
Plasmids that encode the same replication machinery are generally unable to coexist in the same bacterial cell. However, Clostridium perfringens strains often carry multiple conjugative toxin or antibiotic resistance plasmids that are closely related and encode similar Rep proteins. In many bacteria, plasmid partitioning upon cell division involves a ParMRC system; in C. perfringens plasmids, there are approximately 10 different ParMRC families, with significant differences in amino acid sequences between each ParM family (15% to 54% identity). Since plasmids carrying genes belonging to the same ParMRC family are not observed in the same strain, these families appear to represent the basis for plasmid compatibility in C. perfringens. To understand this process, we examined the key recognition steps between ParR DNA-binding proteins and their parC binding sites. The ParR proteins bound to sequences within a parC site from the same ParMRC family but could not interact with a parC site from a different ParMRC family. These data provide evidence that compatibility of the conjugative toxin plasmids of C. perfringens is mediated by their parMRC-like partitioning systems. This process provides a selective advantage by enabling the host bacterium to maintain separate plasmids that encode toxins that are specific for different host targets.
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15
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Optimizing Efficiency and Motility of a Polyvalent Molecular Motor. MICROMACHINES 2022; 13:mi13060914. [PMID: 35744528 PMCID: PMC9228586 DOI: 10.3390/mi13060914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 02/04/2023]
Abstract
Molecular motors play a vital role in the transport of material within the cell. A family of motors of growing interest are burnt bridge ratchets (BBRs). BBRs rectify spatial fluctuations into directed motion by creating and destroying motor-substrate bonds. It has been shown that the motility of a BBR can be optimized as a function of the system parameters. However, the amount of energy input required to generate such motion and the resulting efficiency has been less well characterized. Here, using a deterministic model, we calculate the efficiency of a particular type of BBR, namely a polyvalent hub interacting with a surface of substrate. We find that there is an optimal burn rate and substrate concentration that leads to optimal efficiency. Additionally, the substrate turnover rate has important implications on motor efficiency. We also consider the effects of force-dependent unbinding on the efficiency and find that under certain conditions the motor works more efficiently when bond breaking is included. Our results provide guidance for how to optimize the efficiency of BBRs.
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16
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Bell PJL. Eukaryogenesis: The Rise of an Emergent Superorganism. Front Microbiol 2022; 13:858064. [PMID: 35633668 PMCID: PMC9130767 DOI: 10.3389/fmicb.2022.858064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/15/2022] [Indexed: 12/11/2022] Open
Abstract
Although it is widely taught that all modern life descended via modification from a last universal common ancestor (LUCA), this dominant paradigm is yet to provide a generally accepted explanation for the chasm in design between prokaryotic and eukaryotic cells. Counter to this dominant paradigm, the viral eukaryogenesis (VE) hypothesis proposes that the eukaryotes originated as an emergent superorganism and thus did not evolve from LUCA via descent with incremental modification. According to the VE hypothesis, the eukaryotic nucleus descends from a viral factory, the mitochondrion descends from an enslaved alpha-proteobacteria and the cytoplasm and plasma membrane descend from an archaeal host. A virus initiated the eukaryogenesis process by colonising an archaeal host to create a virocell that had its metabolism reprogrammed to support the viral factory. Subsequently, viral processes facilitated the entry of a bacterium into the archaeal cytoplasm which was also eventually reprogrammed to support the viral factory. As the viral factory increased control of the consortium, the archaeal genome was lost, the bacterial genome was greatly reduced and the viral factory eventually evolved into the nucleus. It is proposed that the interaction between these three simple components generated a superorganism whose emergent properties allowed the evolution of eukaryotic complexity. If the radical tenets of the VE hypothesis are ultimately accepted, current biological paradigms regarding viruses, cell theory, LUCA and the universal Tree of Life (ToL) should be fundamentally altered or completely abandoned.
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17
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Possoz C, Yamaichi Y, Galli E, Ferat JL, Barre FX. Vibrio cholerae Chromosome Partitioning without Polar Anchoring by HubP. Genes (Basel) 2022; 13:genes13050877. [PMID: 35627261 PMCID: PMC9140986 DOI: 10.3390/genes13050877] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/02/2022] Open
Abstract
Partition systems are widespread among bacterial chromosomes. They are composed of two effectors, ParA and ParB, and cis acting sites, parS, located close to the replication origin of the chromosome (oriC). ParABS participate in chromosome segregation, at least in part because they serve to properly position sister copies of oriC. A fourth element, located at cell poles, is also involved in some cases, such as HubP for the ParABS1 system of Vibrio cholerae chromosome 1 (ch1). The polar anchoring of oriC of ch1 (oriC1) is lost when HubP or ParABS1 are inactivated. Here, we report that in the absence of HubP, ParABS1 actively maintains oriC1 at mid-cell, leading to the subcellular separation of the two ch1 replication arms. We further show that parS1 sites ectopically inserted in chromosome 2 (ch2) stabilize the inheritance of this replicon in the absence of its endogenous partition system, even without HubP. We also observe the positioning interference between oriC1 and oriC of ch2 regions when their positionings are both driven by ParABS1. Altogether, these data indicate that ParABS1 remains functional in the absence of HubP, which raises questions about the role of the polar anchoring of oriC1 in the cell cycle.
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18
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Examination of Rickettsial Host Range for Shuttle Vectors Based on dnaA and parA Genes from the pRM Plasmid of Rickettsia monacensis. Appl Environ Microbiol 2022; 88:e0021022. [PMID: 35323021 PMCID: PMC9004397 DOI: 10.1128/aem.00210-22] [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] [Indexed: 12/02/2022] Open
Abstract
The genus Rickettsia encompasses a diverse group of obligate intracellular bacteria that are highly virulent disease agents of mankind as well as symbionts of arthropods. Native plasmids of Rickettsia amblyommatis (AaR/SC) have been used as models to construct shuttle vectors for genetic manipulation of several Rickettsia species. Here, we report on the isolation of the complete plasmid (pRM658B) from Rickettsia monacensis IrR/Munich mutant Rmona658B and the construction of shuttle vectors based on pRM. To identify regions essential for replication, we made vectors containing the dnaA and parA genes of pRM with various portions of the region surrounding these genes and a selection reporter cassette conferring resistance to spectinomycin and expression of green fluorescent protein. Rickettsia amblyommatis (AaR/SC), R. monacensis (IrR/Munich), Rickettsia bellii (RML 369-C), Rickettsia parkeri (Tate’s Hell), and Rickettsia montanensis (M5/6) were successfully transformed with shuttle vectors containing pRM parA and dnaA. PCR assays targeting pRM regions not included in the vectors revealed that native pRM was retained in R. monacensis transformants. Determination of native pRM copy number using a plasmid-carried gene (RM_p5) in comparison to chromosomally carried gltA indicated reduced copy numbers in R. monacensis transformants. In transformed R. monacensis strains, native pRM and shuttle vectors with homologous parA and dnaA formed native plasmid-shuttle vector complexes. These studies provide insight on the maintenance of plasmids and shuttle vectors in rickettsiae. IMPORTANCERickettsia spp. are found in a diverse array of organisms, from ticks, mites, and fleas to leeches and insects. Many are not pathogenic, but others, such as Rickettsia rickettsii and Rickettsia prowazeckii, can cause severe illness or death. Plasmids are found in a large percentage of nonpathogenic rickettsiae, but not in species that cause severe disease. Studying these plasmids can reveal their role in the biology of these bacteria, as well as the molecular mechanism whereby they are maintained and replicate in rickettsiae. Here, we describe a new series of shuttle plasmids for the transformation of rickettsiae based on parA and dnaA sequences of plasmid pRM from Rickettsia monacensis. These shuttle vectors support transformation of diverse rickettsiae, including the native host of pRM, and are useful for investigating genetic determinants that govern rickettsial virulence or their ability to function as symbionts.
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19
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Igler C, Huisman JS, Siedentop B, Bonhoeffer S, Lehtinen S. Plasmid co-infection: linking biological mechanisms to ecological and evolutionary dynamics. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200478. [PMID: 34839701 PMCID: PMC8628072 DOI: 10.1098/rstb.2020.0478] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/09/2021] [Indexed: 12/27/2022] Open
Abstract
As infectious agents of bacteria and vehicles of horizontal gene transfer, plasmids play a key role in bacterial ecology and evolution. Plasmid dynamics are shaped not only by plasmid-host interactions but also by ecological interactions between plasmid variants. These interactions are complex: plasmids can co-infect the same cell and the consequences for the co-resident plasmid can be either beneficial or detrimental. Many of the biological processes that govern plasmid co-infection-from systems that exclude infection by other plasmids to interactions in the regulation of plasmid copy number-are well characterized at a mechanistic level. Modelling plays a central role in translating such mechanistic insights into predictions about plasmid dynamics and the impact of these dynamics on bacterial evolution. Theoretical work in evolutionary epidemiology has shown that formulating models of co-infection is not trivial, as some modelling choices can introduce unintended ecological assumptions. Here, we review how the biological processes that govern co-infection can be represented in a mathematical model, discuss potential modelling pitfalls, and analyse this model to provide general insights into how co-infection impacts ecological and evolutionary outcomes. In particular, we demonstrate how beneficial and detrimental effects of co-infection give rise to frequency-dependent selection on plasmid variants. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.
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Affiliation(s)
- Claudia Igler
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
| | - Jana S. Huisman
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Berit Siedentop
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
| | - Sebastian Bonhoeffer
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
| | - Sonja Lehtinen
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
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20
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Baquero F, Martínez JL, F. Lanza V, Rodríguez-Beltrán J, Galán JC, San Millán A, Cantón R, Coque TM. Evolutionary Pathways and Trajectories in Antibiotic Resistance. Clin Microbiol Rev 2021; 34:e0005019. [PMID: 34190572 PMCID: PMC8404696 DOI: 10.1128/cmr.00050-19] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Evolution is the hallmark of life. Descriptions of the evolution of microorganisms have provided a wealth of information, but knowledge regarding "what happened" has precluded a deeper understanding of "how" evolution has proceeded, as in the case of antimicrobial resistance. The difficulty in answering the "how" question lies in the multihierarchical dimensions of evolutionary processes, nested in complex networks, encompassing all units of selection, from genes to communities and ecosystems. At the simplest ontological level (as resistance genes), evolution proceeds by random (mutation and drift) and directional (natural selection) processes; however, sequential pathways of adaptive variation can occasionally be observed, and under fixed circumstances (particular fitness landscapes), evolution is predictable. At the highest level (such as that of plasmids, clones, species, microbiotas), the systems' degrees of freedom increase dramatically, related to the variable dispersal, fragmentation, relatedness, or coalescence of bacterial populations, depending on heterogeneous and changing niches and selective gradients in complex environments. Evolutionary trajectories of antibiotic resistance find their way in these changing landscapes subjected to random variations, becoming highly entropic and therefore unpredictable. However, experimental, phylogenetic, and ecogenetic analyses reveal preferential frequented paths (highways) where antibiotic resistance flows and propagates, allowing some understanding of evolutionary dynamics, modeling and designing interventions. Studies on antibiotic resistance have an applied aspect in improving individual health, One Health, and Global Health, as well as an academic value for understanding evolution. Most importantly, they have a heuristic significance as a model to reduce the negative influence of anthropogenic effects on the environment.
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Affiliation(s)
- F. Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. L. Martínez
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - V. F. Lanza
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Central Bioinformatics Unit, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - J. Rodríguez-Beltrán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. C. Galán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - A. San Millán
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - R. Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - T. M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
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21
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Hu L, Rech J, Bouet JY, Liu J. Spatial control over near-critical-point operation ensures fidelity of ParABS-mediated DNA partition. Biophys J 2021; 120:3911-3924. [PMID: 34418367 PMCID: PMC8511131 DOI: 10.1016/j.bpj.2021.08.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/26/2021] [Accepted: 08/13/2021] [Indexed: 01/20/2023] Open
Abstract
In bacteria, most low-copy-number plasmid and chromosomally encoded partition systems belong to the tripartite ParABS partition machinery. Despite the importance in genetic inheritance, the mechanisms of ParABS-mediated genome partition are not well understood. Combining theory and experiment, we provided evidence that the ParABS system-DNA partitioning in vivo via the ParA-gradient-based Brownian ratcheting-operates near a transition point in parameter space (i.e., a critical point), across which the system displays qualitatively different motile behaviors. This near-critical-point operation adapts the segregation distance of replicated plasmids to the half length of the elongating nucleoid, ensuring both cell halves to inherit one copy of the plasmids. Further, we demonstrated that the plasmid localizes the cytoplasmic ParA to buffer the partition fidelity against the large cell-to-cell fluctuations in ParA level. The spatial control over the near-critical-point operation not only ensures both sensitive adaptation and robust execution of partitioning but also sheds light on the fundamental question in cell biology: how do cells faithfully measure cellular-scale distance by only using molecular-scale interactions?
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Affiliation(s)
- Longhua Hu
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jérôme Rech
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative, Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse, France
| | - Jean-Yves Bouet
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative, Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse, France.
| | - Jian Liu
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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22
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Mori K, Verrone V, Amatsu R, Fukui K, Meijer WJJ, Ishikawa S, Wipat A, Yoshida KI. Assessment of Bacillus subtilis Plasmid pLS20 Conjugation in the Absence of Quorum Sensing Repression. Microorganisms 2021; 9:microorganisms9091931. [PMID: 34576826 PMCID: PMC8470214 DOI: 10.3390/microorganisms9091931] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 12/21/2022] Open
Abstract
Bacillus subtilis conjugative plasmid pLS20 uses a quorum-sensing mechanism to control expression levels of its conjugation genes, involving the repressor RcopLS20, the anti-repressor RappLS20, and the signaling peptide Phr*pLS20. In previous studies, artificial overexpression of rappLS20 in the donor cells was shown to enhance conjugation efficiency. However, we found that the overexpression of rappLS20 led to various phenotypic traits, including cell aggregation and death, which might have affected the correct determination of the conjugation efficiency when determined by colony formation assay. In the current study, conjugation efficiencies were determined under different conditions using a two-color fluorescence-activated flow cytometry method and measuring a single-round of pLS20-mediated transfer of a mobilizable plasmid. Under standard conditions, the conjugation efficiency obtained by fluorescence-activated flow cytometry was 23-fold higher than that obtained by colony formation. Furthermore, the efficiency difference increased to 45-fold when rappLS20 was overexpressed.
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Affiliation(s)
- Kotaro Mori
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (K.M.); (R.A.); (K.F.); (S.I.)
| | - Valeria Verrone
- School of Computing, Newcastle University, 1 Science Square, Science Central, Newcastle upon Tyne NE4 5TG, UK; (V.V.); (A.W.)
| | - Ryotaro Amatsu
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (K.M.); (R.A.); (K.F.); (S.I.)
| | - Kaho Fukui
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (K.M.); (R.A.); (K.F.); (S.I.)
| | - Wilfried J. J. Meijer
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain;
| | - Shu Ishikawa
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (K.M.); (R.A.); (K.F.); (S.I.)
| | - Anil Wipat
- School of Computing, Newcastle University, 1 Science Square, Science Central, Newcastle upon Tyne NE4 5TG, UK; (V.V.); (A.W.)
| | - Ken-ichi Yoshida
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (K.M.); (R.A.); (K.F.); (S.I.)
- Correspondence: ; Tel.: +81-78-803-5891
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23
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Boudsocq F, Salhi M, Barbe S, Bouet JY. Three ParA Dimers Cooperatively Assemble on Type Ia Partition Promoters. Genes (Basel) 2021; 12:genes12091345. [PMID: 34573327 PMCID: PMC8465637 DOI: 10.3390/genes12091345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 02/03/2023] Open
Abstract
Accurate DNA segregation is essential for faithful inheritance of genetic material. In bacteria, this process is mainly ensured by partition systems composed of two proteins, ParA and ParB, and a centromere site. Auto-regulation of Par operon expression is important for efficient partitioning and is primarily mediated by ParA for type Ia plasmid partition systems. For the F-plasmid, four ParAF monomers were proposed to bind to four repeated sequences in the promoter region. By contrast, using quantitative surface-plasmon-resonance, we showed that three ParAF dimers bind to this region. We uncovered that one perfect inverted repeat (IR) motif, consisting of two hexamer sequences spaced by 28-bp, constitutes the primary ParAF DNA binding site. A similar but degenerated motif overlaps the former. ParAF binding to these motifs is well supported by biochemical and modeling analyses. Molecular dynamics simulations predict that the winged-HTH domain displays high flexibility, which may favor the cooperative ParA binding to the promoter. We propose that three ParAF dimers bind cooperatively to overlapping motifs, thus covering the promoter region. A similar organization is found on closely related and distant plasmid partition systems, suggesting that such promoter organization for auto-regulated Par operons is widespread and may have evolved from a common ancestor.
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Affiliation(s)
- François Boudsocq
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062 Toulouse, France; (M.S.); (J.-Y.B.)
- Correspondence:
| | - Maya Salhi
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062 Toulouse, France; (M.S.); (J.-Y.B.)
| | - Sophie Barbe
- CNRS, Toulouse Biotechnology Institute (TBI), Université de Toulouse, INRAE, INSA, F-31077 Toulouse, France;
| | - Jean-Yves Bouet
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062 Toulouse, France; (M.S.); (J.-Y.B.)
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24
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Protein Transfer through an F Plasmid-Encoded Type IV Secretion System Suppresses the Mating-Induced SOS Response. mBio 2021; 12:e0162921. [PMID: 34253063 PMCID: PMC8406263 DOI: 10.1128/mbio.01629-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Bacterial type IV secretion systems (T4SSs) mediate the conjugative transfer of mobile genetic elements (MGEs) and their cargoes of antibiotic resistance and virulence genes. Here, we report that the pED208-encoded T4SS (TrapED208) translocates not only this F plasmid but several plasmid-encoded proteins, including ParA, ParB1, single-stranded DNA-binding protein SSB, ParB2, PsiB, and PsiA, to recipient cells. Conjugative protein translocation through the TrapED208 T4SS required engagement of the pED208 relaxosome with the TraD substrate receptor or coupling protein. T4SSs translocate MGEs as single-stranded DNA intermediates (T-strands), which triggers the SOS response in recipient cells. Transfer of pED208 deleted of psiB or ssb, which, respectively, encode the SOS inhibitor protein PsiB and single-stranded DNA-binding protein SSB, elicited a significantly stronger SOS response than pED208 or mutant plasmids deleted of psiA, parA, parB1, or parB2. Conversely, translocation of PsiB or SSB, but not PsiA, through the TrapED208 T4SS suppressed the mating-induced SOS response. Our findings expand the repertoire of known substrates of conjugation systems to include proteins with functions associated with plasmid maintenance. Furthermore, for this and other F-encoded Tra systems, docking of the DNA substrate with the TraD receptor appears to serve as a critical activating signal for protein translocation. Finally, the observed effects of PsiB and SSB on suppression of the mating-induced SOS response establishes a novel biological function for conjugative protein translocation and suggests the potential for interbacterial protein translocation to manifest in diverse outcomes influencing bacterial communication, physiology, and evolution.
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Walter JC, Lepage T, Dorignac J, Geniet F, Parmeggiani A, Palmeri J, Bouet JY, Junier I. Supercoiled DNA and non-equilibrium formation of protein complexes: A quantitative model of the nucleoprotein ParBS partition complex. PLoS Comput Biol 2021; 17:e1008869. [PMID: 33861734 PMCID: PMC8092679 DOI: 10.1371/journal.pcbi.1008869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 05/03/2021] [Accepted: 03/11/2021] [Indexed: 11/18/2022] Open
Abstract
ParABS, the most widespread bacterial DNA segregation system, is composed of a centromeric sequence, parS, and two proteins, the ParA ATPase and the ParB DNA binding proteins. Hundreds of ParB proteins assemble dynamically to form nucleoprotein parS-anchored complexes that serve as substrates for ParA molecules to catalyze positioning and segregation events. The exact nature of this ParBS complex has remained elusive, what we address here by revisiting the Stochastic Binding model (SBM) introduced to explain the non-specific binding profile of ParB in the vicinity of parS. In the SBM, DNA loops stochastically bring loci inside a sharp cluster of ParB. However, previous SBM versions did not include the negative supercoiling of bacterial DNA, leading to use unphysically small DNA persistences to explain the ParB binding profiles. In addition, recent super-resolution microscopy experiments have revealed a ParB cluster that is significantly smaller than previous estimations and suggest that it results from a liquid-liquid like phase separation. Here, by simulating the folding of long (≥ 30 kb) supercoiled DNA molecules calibrated with realistic DNA parameters and by considering different possibilities for the physics of the ParB cluster assembly, we show that the SBM can quantitatively explain the ChIP-seq ParB binding profiles without any fitting parameter, aside from the supercoiling density of DNA, which, remarkably, is in accord with independent measurements. We also predict that ParB assembly results from a non-equilibrium, stationary balance between an influx of produced proteins and an outflux of excess proteins, i.e., ParB clusters behave like liquid-like protein condensates with unconventional “leaky” boundaries. In bacteria, faithful genome inheritance requires the two replicated DNA molecules to be segregated at the opposite halves of the cell. ParABS, the most widespread bacterial DNA segregation system, is composed of a centromere sequence, parS, and two proteins, the ParA ATPase and the ParB DNA binding protein. Hundreds of ParB assemble dynamically to form clusters around parS, which then serve as substrates for ParA molecules to catalyze the positioning and segregation events. The nature of these clusters and their interaction with DNA have remained elusive. Here, we propose a realistic minimal model that captures quantitatively the peculiar DNA binding profile of ParB in the vicinity of parS in Escherichia coli. From the viewpoint of DNA, the only fitting parameter is the in vivo supercoiling density resulting from the removal of DNA helices by toposiomerases, which is in accord with previous independent estimations. From the viewpoint of ParB clusters, we predict that they behave like liquid-like protein condensates with unconventional boundaries. Namely, we predict boundaries to be leaky (i.e. not sharp) as a result of the non-equilibrium protein production, diffusion and dilution. Altogether, our work provides novel insights into bacterial DNA organization and intracellular liquid-liquid phase separation.
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Affiliation(s)
- Jean-Charles Walter
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
- * E-mail: (J-CW); (IJ)
| | | | - Jérôme Dorignac
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
| | - Frédéric Geniet
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
| | - Andrea Parmeggiani
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
- LPHI, Univ. Montpellier, CNRS, Montpellier, France
| | - John Palmeri
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
| | | | - Ivan Junier
- CNRS, Univ. Grenoble Alpes, TIMC, Grenoble, France
- * E-mail: (J-CW); (IJ)
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Meijer WJJ, Boer DR, Ares S, Alfonso C, Rojo F, Luque-Ortega JR, Wu LJ. Multiple Layered Control of the Conjugation Process of the Bacillus subtilis Plasmid pLS20. Front Mol Biosci 2021; 8:648468. [PMID: 33816561 PMCID: PMC8014075 DOI: 10.3389/fmolb.2021.648468] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 02/08/2021] [Indexed: 11/24/2022] Open
Abstract
Bacterial conjugation is the main horizontal gene transfer route responsible for the spread of antibiotic resistance, virulence and toxin genes. During conjugation, DNA is transferred from a donor to a recipient cell via a sophisticated channel connecting the two cells. Conjugation not only affects many different aspects of the plasmid and the host, ranging from the properties of the membrane and the cell surface of the donor, to other developmental processes such as competence, it probably also poses a burden on the donor cell due to the expression of the large number of genes involved in the conjugation process. Therefore, expression of the conjugation genes must be strictly controlled. Over the past decade, the regulation of the conjugation genes present on the conjugative Bacillus subtilis plasmid pLS20 has been studied using a variety of methods including genetic, biochemical, biophysical and structural approaches. This review focuses on the interplay between RcopLS20, RappLS20 and Phr*pLS20, the proteins that control the activity of the main conjugation promoter Pc located upstream of the conjugation operon. Proper expression of the conjugation genes requires the following two fundamental elements. First, conjugation is repressed by default and an intercellular quorum-signaling system is used to sense conditions favorable for conjugation. Second, different layers of regulation act together to repress the Pc promoter in a strict manner but allowing rapid activation. During conjugation, ssDNA is exported from the cell by a membrane-embedded DNA translocation machine. Another membrane-embedded DNA translocation machine imports ssDNA in competent cells. Evidences are reviewed indicating that conjugation and competence are probably mutually exclusive processes. Some of the questions that remain unanswered are discussed.
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Affiliation(s)
- Wilfried J J Meijer
- Laboratory 402, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | | | - Saúl Ares
- Laboratory 35, C. Grupo Interdisciplinar de Sistemas Complejos and Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Carlos Alfonso
- Laboratory B08, Systems Biochemistry of Bacterial Division Lab, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Fernando Rojo
- Laboratory 216, Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Juan R Luque-Ortega
- Laboratory S07, Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, United Kingdom
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Adamczyk M, Lewicka E, Szatkowska R, Nieznanska H, Ludwiczak J, Jasiński M, Dunin-Horkawicz S, Sitkiewicz E, Swiderska B, Goch G, Jagura-Burdzy G. Revealing biophysical properties of KfrA-type proteins as a novel class of cytoskeletal, coiled-coil plasmid-encoded proteins. BMC Microbiol 2021; 21:32. [PMID: 33482722 PMCID: PMC7821693 DOI: 10.1186/s12866-020-02079-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/20/2020] [Indexed: 01/22/2023] Open
Abstract
Background DNA binding KfrA-type proteins of broad-host-range bacterial plasmids belonging to IncP-1 and IncU incompatibility groups are characterized by globular N-terminal head domains and long alpha-helical coiled-coil tails. They have been shown to act as transcriptional auto-regulators. Results This study was focused on two members of the growing family of KfrA-type proteins encoded by the broad-host-range plasmids, R751 of IncP-1β and RA3 of IncU groups. Comparative in vitro and in silico studies on KfrAR751 and KfrARA3 confirmed their similar biophysical properties despite low conservation of the amino acid sequences. They form a wide range of oligomeric forms in vitro and, in the presence of their cognate DNA binding sites, they polymerize into the higher order filaments visualized as “threads” by negative staining electron microscopy. The studies revealed also temperature-dependent changes in the coiled-coil segment of KfrA proteins that is involved in the stabilization of dimers required for DNA interactions. Conclusion KfrAR751 and KfrARA3 are structural homologues. We postulate that KfrA type proteins have moonlighting activity. They not only act as transcriptional auto-regulators but form cytoskeletal structures, which might facilitate plasmid DNA delivery and positioning in the cells before cell division, involving thermal energy. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-020-02079-w.
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Affiliation(s)
- M Adamczyk
- Warsaw University of Technology, Faculty of Chemistry, Chair of Drug and Cosmetics Biotechnology, Noakowskiego 3, 00-664, Warsaw, Poland.
| | - E Lewicka
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - R Szatkowska
- Warsaw University of Technology, Faculty of Chemistry, Chair of Drug and Cosmetics Biotechnology, Noakowskiego 3, 00-664, Warsaw, Poland
| | - H Nieznanska
- Nencki Institute of Experimental Biology PAS, Laboratory of Electron Microscopy, Pasteura 3, 02-093, Warsaw, Poland
| | - J Ludwiczak
- University of Warsaw, Centre of New Technologies, Laboratory of Structural Bioinformatics, 02-097, Warsaw, Poland.,Nencki Institute of Experimental Biology, Laboratory of Bioinformatics, Pasteura 3, 02-093, Warsaw, Poland
| | - M Jasiński
- University of Warsaw, Centre of New Technologies, Laboratory of Structural Bioinformatics, 02-097, Warsaw, Poland
| | - S Dunin-Horkawicz
- University of Warsaw, Centre of New Technologies, Laboratory of Structural Bioinformatics, 02-097, Warsaw, Poland
| | - E Sitkiewicz
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - B Swiderska
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - G Goch
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - G Jagura-Burdzy
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106, Warsaw, Poland
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Bacteria Broadly-Resistant to Last Resort Antibiotics Detected in Commercial Chicken Farms. Microorganisms 2021; 9:microorganisms9010141. [PMID: 33435450 PMCID: PMC7826917 DOI: 10.3390/microorganisms9010141] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/27/2022] Open
Abstract
Resistance to last resort antibiotics in bacteria is an emerging threat to human and animal health. It is important to identify the source of these antimicrobial resistant (AMR) bacteria that are resistant to clinically important antibiotics and evaluate their potential transfer among bacteria. The objectives of this study were to (i) detect bacteria resistant to colistin, carbapenems, and β-lactams in commercial poultry farms, (ii) characterize phylogenetic and virulence markers of E. coli isolates to potentiate virulence risk, and (iii) assess potential transfer of AMR from these isolates via conjugation. Ceca contents from laying hens from conventional cage (CC) and cage-free (CF) farms at three maturity stages were randomly sampled and screened for extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae, carbapenem-resistant Acinetobacter (CRA), and colistin resistant Escherichia coli (CRE) using CHROMagar™ selective media. We found a wide-spread abundance of CRE in both CC and CF hens across all three maturity stages. Extraintestinal pathogenic Escherichia coli phylogenetic groups B2 and D, as well as plasmidic virulence markers iss and iutA, were widely associated with AMR E. coli isolates. ESBL-producing Enterobacteriaceae were uniquely detected in the early lay period of both CC and CF, while multidrug resistant (MDR) Acinetobacter were found in peak and late lay periods of both CC and CF. CRA was detected in CF hens only. blaCMY
was detected in ESBL-producing E. coli in CC and CF and MDR Acinetobacter spp. in CC. Finally, the blaCMY
was shown to be transferrable via an IncK/B plasmid in CC. The presence of MDR to the last-resort antibiotics that are transferable between bacteria in food-producing animals is alarming and warrants studies to develop strategies for their mitigation in the environment.
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Baxter JC, Waples WG, Funnell BE. Nonspecific DNA binding by P1 ParA determines the distribution of plasmid partition and repressor activities. J Biol Chem 2020; 295:17298-17309. [PMID: 33055234 PMCID: PMC7863886 DOI: 10.1074/jbc.ra120.015642] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/10/2020] [Indexed: 12/13/2022] Open
Abstract
The faithful segregation, or "partition," of many low-copy number bacterial plasmids is driven by plasmid-encoded ATPases that are represented by the P1 plasmid ParA protein. ParA binds to the bacterial nucleoid via an ATP-dependent nonspecific DNA (nsDNA)-binding activity, which is essential for partition. ParA also has a site-specific DNA-binding activity to the par operator (parOP), which requires either ATP or ADP, and which is essential for it to act as a transcriptional repressor but is dispensable for partition. Here we examine how DNA binding by ParA contributes to the relative distribution of its plasmid partition and repressor activities, using a ParA with an alanine substitution at Arg351, a residue previously predicted to participate in site-specific DNA binding. In vivo, the parAR351A allele is compromised for partition, but its repressor activity is dramatically improved so that it behaves as a "super-repressor." In vitro, ParAR351A binds and hydrolyzes ATP, and undergoes a specific conformational change required for nsDNA binding, but its nsDNA-binding activity is significantly damaged. This defect in turn significantly reduces the assembly and stability of partition complexes formed by the interaction of ParA with ParB, the centromere-binding protein, and DNA. In contrast, the R351A change shows only a mild defect in site-specific DNA binding. We conclude that the partition defect is due to altered nsDNA binding kinetics and affinity for the bacterial chromosome. Furthermore, the super-repressor phenotype is explained by an increased pool of non-nucleoid bound ParA that is competent to bind parOP and repress transcription.
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Affiliation(s)
- Jamie C Baxter
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario Canada
| | - William G Waples
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario Canada
| | - Barbara E Funnell
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario Canada.
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Physical Modeling of a Sliding Clamp Mechanism for the Spreading of ParB at Short Genomic Distance from Bacterial Centromere Sites. iScience 2020; 23:101861. [PMID: 33319179 PMCID: PMC7725951 DOI: 10.1016/j.isci.2020.101861] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/16/2020] [Accepted: 11/19/2020] [Indexed: 12/20/2022] Open
Abstract
Bacterial ParB partitioning proteins involved in chromosomes and low-copy-number plasmid segregation are cytosine triphosphate (CTP)-dependent molecular switches. CTP-binding converts ParB dimers to DNA clamps, allowing unidimensional diffusion along the DNA. This sliding property has been proposed to explain the ParB spreading over large distances from parS centromere sites where ParB is specifically loaded. We modeled such a "clamping and sliding" mechanism as a typical reaction-diffusion system, compared it to the F plasmid ParB DNA binding pattern, and found that it can account neither for the long range of ParB binding to DNA nor for the rapid assembly kinetics observed in vivo after parS duplication. Also, it predicts a strong effect on the F plasmid ParB binding pattern from the presence of a roadblock that is not observed in ChIP-sequencing (ChIP-seq). We conclude that although "clamping and sliding" can occur at short distances from parS, another mechanism must apply for ParB recruitment at larger genomic distances.
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31
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Kim JW, Bugata V, Cortés-Cortés G, Quevedo-Martínez G, Camps M. Mechanisms of Theta Plasmid Replication in Enterobacteria and Implications for Adaptation to Its Host. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0026-2019. [PMID: 33210586 PMCID: PMC7724965 DOI: 10.1128/ecosalplus.esp-0026-2019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Indexed: 11/20/2022]
Abstract
Plasmids are autonomously replicating sequences that help cells adapt to diverse stresses. Theta plasmids are the most frequent plasmid class in enterobacteria. They co-opt two host replication mechanisms: replication at oriC, a DnaA-dependent pathway leading to replisome assembly (theta class A), and replication fork restart, a PriA-dependent pathway leading to primosome assembly through primer extension and D-loop formation (theta classes B, C, and D). To ensure autonomy from the host's replication and to facilitate copy number regulation, theta plasmids have unique mechanisms of replication initiation at the plasmid origin of replication (ori). Tight plasmid copy number regulation is essential because of the major and direct impact plasmid gene dosage has on gene expression. The timing of plasmid replication and segregation are also critical for optimizing plasmid gene expression. Therefore, we propose that plasmid replication needs to be understood in its biological context, where complex origins of replication (redundant origins, mosaic and cointegrated replicons), plasmid segregation, and toxin-antitoxin systems are often present. Highlighting their tight functional integration with ori function, we show that both partition and toxin-antitoxin systems tend to be encoded in close physical proximity to the ori in a large collection of Escherichia coli plasmids. We also propose that adaptation of plasmids to their host optimizes their contribution to the host's fitness while restricting access to broad genetic diversity, and we argue that this trade-off between adaptation to host and access to genetic diversity is likely a determinant factor shaping the distribution of replicons in populations of enterobacteria.
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Affiliation(s)
- Jay W Kim
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, 95064
| | - Vega Bugata
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, 95064
| | - Gerardo Cortés-Cortés
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, 95064
| | - Giselle Quevedo-Martínez
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, 95064
| | - Manel Camps
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, 95064
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Daniel S, Goldlust K, Quebre V, Shen M, Lesterlin C, Bouet JY, Yamaichi Y. Vertical and Horizontal Transmission of ESBL Plasmid from Escherichia coli O104:H4. Genes (Basel) 2020; 11:genes11101207. [PMID: 33081159 PMCID: PMC7602700 DOI: 10.3390/genes11101207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/05/2020] [Accepted: 10/13/2020] [Indexed: 12/16/2022] Open
Abstract
Multidrug resistance (MDR) often results from the acquisition of mobile genetic elements (MGEs) that encode MDR gene(s), such as conjugative plasmids. The spread of MDR plasmids is founded on their ability of horizontal transference, as well as their faithful inheritance in progeny cells. Here, we investigated the genetic factors involved in the prevalence of the IncI conjugative plasmid pESBL, which was isolated from the Escherichia coli O104:H4 outbreak strain in Germany in 2011. Using transposon-insertion sequencing, we identified the pESBL partitioning locus (par). Genetic, biochemical and microscopic approaches allowed pESBL to be characterized as a new member of the Type Ib partitioning system. Inactivation of par caused mis-segregation of pESBL followed by post-segregational killing (PSK), resulting in a great fitness disadvantage but apparent plasmid stability in the population of viable cells. We constructed a variety of pESBL derivatives with different combinations of mutations in par, conjugational transfer (oriT) and pnd toxin-antitoxin (TA) genes. Only the triple mutant exhibited plasmid-free cells in viable cell populations. Time-lapse tracking of plasmid dynamics in microfluidics indicated that inactivation of pnd improved the survival of plasmid-free cells and allowed oriT-dependent re-acquisition of the plasmid. Altogether, the three factors—active partitioning, toxin-antitoxin and conjugational transfer—are all involved in the prevalence of pESBL in the E. coli population.
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Affiliation(s)
- Sandra Daniel
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (S.D.); (M.S.)
| | - Kelly Goldlust
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007 Lyon, France; (K.G.); (C.L.)
| | - Valentin Quebre
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), CBI, CNRS, Université de Toulouse, UPS, 31062 Toulouse, France; (V.Q.); (J.-Y.B.)
| | - Minjia Shen
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (S.D.); (M.S.)
- Graduate School of Structure and Dynamics of Living Systems, Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Christian Lesterlin
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007 Lyon, France; (K.G.); (C.L.)
| | - Jean-Yves Bouet
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), CBI, CNRS, Université de Toulouse, UPS, 31062 Toulouse, France; (V.Q.); (J.-Y.B.)
| | - Yoshiharu Yamaichi
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (S.D.); (M.S.)
- Correspondence:
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Planchenault C, Pons MC, Schiavon C, Siguier P, Rech J, Guynet C, Dauverd-Girault J, Cury J, Rocha EPC, Junier I, Cornet F, Espéli O. Intracellular Positioning Systems Limit the Entropic Eviction of Secondary Replicons Toward the Nucleoid Edges in Bacterial Cells. J Mol Biol 2020; 432:745-761. [PMID: 31931015 DOI: 10.1016/j.jmb.2019.11.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/04/2019] [Accepted: 11/25/2019] [Indexed: 01/16/2023]
Abstract
Bacterial genomes, organized intracellularly as nucleoids, are composed of the main chromosome coexisting with different types of secondary replicons. Secondary replicons are major drivers of bacterial adaptation by gene exchange. They are highly diverse in type and size, ranging from less than 2 to more than 1000 kb, and must integrate with bacterial physiology, including to the nucleoid dynamics, to limit detrimental costs leading to their counter-selection. We show that large DNA circles, whether from a natural plasmid or excised from the chromosome tend to localize in a dynamic manner in a zone separating the nucleoid from the cytoplasm at the edge of the nucleoid. This localization is in good agreement with silico simulations of DNA circles in the nucleoid volume. Subcellular positioning systems counteract this tendency, allowing replicons to enter the nucleoid space. In enterobacteria, these systems are found in replicons above 25 kb, defining the limit with small randomly segregated plasmids. Larger replicons carry at least one of the three described family of systems, ParAB, ParRM, and StbA. Replicons above 180 kb all carry a ParAB system, suggesting this system is specifically required in the cases of large replicons. Simulations demonstrated that replicon size profoundly affects localization, compaction, and dynamics of DNA circles in the nucleoid volume. The present work suggests that presence of partition systems on the larger plasmids or chromids is not only due to selection for accurate segregation but also to counteract their unmixing with the chromosome and consequent exclusion from the nucleoid.
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Affiliation(s)
- Charlène Planchenault
- Center for Interdisciplinary Research in Biology - Collège de France, CNRS UMR7241, INSERM U1050, PSL University, France
| | - Marine C Pons
- Centre de Biologie Intégrative de Toulouse (CBI Toulouse), Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Université de Toulouse, UPS, CNRS, France
| | - Caroline Schiavon
- Centre de Biologie Intégrative de Toulouse (CBI Toulouse), Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Université de Toulouse, UPS, CNRS, France
| | - Patricia Siguier
- Centre de Biologie Intégrative de Toulouse (CBI Toulouse), Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Université de Toulouse, UPS, CNRS, France
| | - Jérôme Rech
- Centre de Biologie Intégrative de Toulouse (CBI Toulouse), Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Université de Toulouse, UPS, CNRS, France
| | - Catherine Guynet
- Centre de Biologie Intégrative de Toulouse (CBI Toulouse), Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Université de Toulouse, UPS, CNRS, France
| | - Julie Dauverd-Girault
- Center for Interdisciplinary Research in Biology - Collège de France, CNRS UMR7241, INSERM U1050, PSL University, France
| | - Jean Cury
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
| | - Ivan Junier
- CNRS, Univ. Grenoble Alpes, TIMC-IMAG, F-38000 Grenoble, France
| | - François Cornet
- Centre de Biologie Intégrative de Toulouse (CBI Toulouse), Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Université de Toulouse, UPS, CNRS, France
| | - Olivier Espéli
- Center for Interdisciplinary Research in Biology - Collège de France, CNRS UMR7241, INSERM U1050, PSL University, France.
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Physical Views on ParABS-Mediated DNA Segregation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1267:45-58. [PMID: 32894476 DOI: 10.1007/978-3-030-46886-6_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
In this chapter, we will focus on ParABS: an apparently simple, three-component system, required for the segregation of bacterial chromosomes and plasmids. We will specifically describe how biophysical measurements combined with physical modeling advanced our understanding of the mechanism of ParABS-mediated complex assembly, segregation and positioning.
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Affiliation(s)
- Barbara E Funnell
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada.
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