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Vogelgsang L, Nisar A, Scharf SA, Rommerskirchen A, Belick D, Dilthey A, Henrich B. Characterisation of Type II DNA Methyltransferases of Metamycoplasma hominis. Microorganisms 2023; 11:1591. [PMID: 37375093 DOI: 10.3390/microorganisms11061591] [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: 03/27/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Bacterial virulence, persistence and defence are affected by epigenetic modifications, including DNA methylation. Solitary DNA methyltransferases modulate a variety of cellular processes and influence bacterial virulence; as part of a restriction-modification (RM) system, they act as a primitive immune system in methylating the own DNA, while unmethylated foreign DNA is restricted. We identified a large family of type II DNA methyltransferases in Metamycoplasma hominis, comprising six solitary methyltransferases and four RM systems. Motif-specific 5mC and 6mA methylations were identified with a tailored Tombo analysis on Nanopore reads. Selected motifs with methylation scores >0.5 fit with the gene presence of DAM1 and DAM2, DCM2, DCM3, and DCM6, but not for DCM1, whose activity was strain-dependent. The activity of DCM1 for CmCWGG and of both DAM1 and DAM2 for GmATC was proven in methylation-sensitive restriction and finally for recombinant rDCM1 and rDAM2 against a dam-, dcm-negative background. A hitherto unknown dcm8/dam3 gene fusion containing a (TA) repeat region of varying length was characterized within a single strain, suggesting the expression of DCM8/DAM3 phase variants. The combination of genetic, bioinformatics, and enzymatic approaches enabled the detection of a huge family of type II DNA MTases in M. hominis, whose involvement in virulence and defence can now be characterized in future work.
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Affiliation(s)
- Lars Vogelgsang
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty of the Heinrich-Heine-University Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany
| | - Azlan Nisar
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty of the Heinrich-Heine-University Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany
| | - Sebastian Alexander Scharf
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty of the Heinrich-Heine-University Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany
| | - Anna Rommerskirchen
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty of the Heinrich-Heine-University Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany
| | - Dana Belick
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty of the Heinrich-Heine-University Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany
| | - Alexander Dilthey
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty of the Heinrich-Heine-University Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany
| | - Birgit Henrich
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty of the Heinrich-Heine-University Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany
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2
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Kirillov A, Morozova N, Kozlova S, Polinovskaya V, Smirnov S, Khodorkovskii M, Zeng L, Ispolatov Y, Severinov K. Cells with stochastically increased methyltransferase to restriction endonuclease ratio provide an entry for bacteriophage into protected cell population. Nucleic Acids Res 2022; 50:12355-12368. [PMID: 36477901 PMCID: PMC9757035 DOI: 10.1093/nar/gkac1124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 10/29/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
The action of Type II restriction-modification (RM) systems depends on restriction endonuclease (REase), which cleaves foreign DNA at specific sites, and methyltransferase (MTase), which protects host genome from restriction by methylating the same sites. We here show that protection from phage infection increases as the copy number of plasmids carrying the Type II RM Esp1396I system is increased. However, since increased plasmid copy number leads to both increased absolute intracellular RM enzyme levels and to a decreased MTase/REase ratio, it is impossible to determine which factor determines resistance/susceptibility to infection. By controlled expression of individual Esp1396I MTase or REase genes in cells carrying the Esp1396I system, we show that a shift in the MTase to REase ratio caused by overproduction of MTase or REase leads, respectively, to decreased or increased protection from infection. Consistently, due to stochastic variation of MTase and REase amount in individual cells, bacterial cells that are productively infected by bacteriophage have significantly higher MTase to REase ratios than cells that ward off the infection. Our results suggest that cells with transiently increased MTase to REase ratio at the time of infection serve as entry points for unmodified phage DNA into protected bacterial populations.
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Affiliation(s)
- Alexander Kirillov
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow 121205, Russia,Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Natalia Morozova
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow 121205, Russia,Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Svetlana Kozlova
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow 121205, Russia
| | - Vasilisa Polinovskaya
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow 121205, Russia
| | - Sergey Smirnov
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow 121205, Russia
| | - Mikhail Khodorkovskii
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Lanying Zeng
- Texas A&M University, Department of Biochemistry and Biophysics, Center for Phage Technology, College Station, TX 77843, USA
| | - Yaroslav Ispolatov
- University of Santiago of Chile (USACH), Physics Department, Av. Víctor Jara 3493, Santiago, Chile
| | - Konstantin Severinov
- To whom correspondence should be addressed. Tel: +7 9854570284; Fax: +1 848 445 5735;
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3
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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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4
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Park S, Jung D, O'Brien B, Ruffini J, Dussault F, Dube-Duquette A, Demontier É, Lucier JF, Malouin F, Dufour S, Ronholm J. Comparative genomic analysis of Staphylococcus aureus isolates associated with either bovine intramammary infections or human infections demonstrates the importance of restriction-modification systems in host adaptation. Microb Genom 2022; 8. [PMID: 35179459 PMCID: PMC8942034 DOI: 10.1099/mgen.0.000779] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Staphylococcus aureus is a major etiological agent of clinical and subclinical bovine mastitis. The versatile and adaptative evolutionary strategies of this bacterium have challenged mastitis control and prevention globally, and the high incidence of S. aureus mastitis increases concerns about antimicrobial resistance (AMR) and zoonosis. This study aims to describe the evolutionary relationship between bovine intramammary infection (IMI)-associated S. aureus and human pathogenic S. aureus and further elucidate the specific genetic composition that leads to the emergence of successful bovine IMI-associated S. aureus lineages. We performed a phylogenomic analysis of 187 S. aureus isolates that originated from either dairy cattle or humans. Our results revealed that bovine IMI-associated S. aureus isolates showed distinct clades compared to human-originated S. aureus isolates. From a pan-genome analysis, 2070 core genes were identified. Host-specific genes and clonal complex (CC)-specific genes were also identified in bovine S. aureus isolates, mostly located in mobile genetic elements (MGEs). Additionally, the genome sequences of three apparent human-adapted isolates (two from CC97 and one from CC8), isolated from bovine mastitis samples, may provide an snapshot of the genomic characteristics in early host spillover events. Virulence and AMR genes were not conserved among bovine IMI-associated S. aureus isolates. Restriction-modification (R-M) genes in bovine IMI-associated S. aureus demonstrated that the Type I R-M system was lineage-specific and Type II R-M system was sequence type (ST)-specific. The distribution of exclusive, virulence, and AMR genes were closely correlated with the presence of R-M systems in S. aureus, suggesting that R-M systems may contribute to shaping clonal diversification by providing a genetic barrier to the horizontal gene transfer (HGT). Our findings indicate that the CC or ST lineage-specific R-M systems may limit genetic exchange between bovine-adapted S. aureus isolates from different lineages.
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Affiliation(s)
- Soyoun Park
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Québec, Canada.,Mastitis Network, Saint-Hyacinthe, Québec, Canada.,Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada
| | - Dongyun Jung
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Québec, Canada.,Mastitis Network, Saint-Hyacinthe, Québec, Canada.,Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada
| | - Bridget O'Brien
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Québec, Canada
| | - Janina Ruffini
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Québec, Canada
| | | | - Alexis Dube-Duquette
- Mastitis Network, Saint-Hyacinthe, Québec, Canada.,Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada.,Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Élodie Demontier
- Mastitis Network, Saint-Hyacinthe, Québec, Canada.,Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada.,Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Jean-François Lucier
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - François Malouin
- Mastitis Network, Saint-Hyacinthe, Québec, Canada.,Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada.,Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Simon Dufour
- Mastitis Network, Saint-Hyacinthe, Québec, Canada.,Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada.,Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
| | - Jennifer Ronholm
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Québec, Canada.,Mastitis Network, Saint-Hyacinthe, Québec, Canada.,Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada
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5
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Ramsay JP, Bastholm TR, Verdonk CJ, Tambalo DD, Sullivan JT, Harold LK, Panganiban BA, Colombi E, Perry BJ, Jowsey W, Morris C, Hynes MF, Bond CS, Cameron ADS, Yost CK, Ronson CW. An epigenetic switch activates bacterial quorum sensing and horizontal transfer of an integrative and conjugative element. Nucleic Acids Res 2021; 50:975-988. [PMID: 34904658 PMCID: PMC8789080 DOI: 10.1093/nar/gkab1217] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
Horizontal transfer of the integrative and conjugative element ICEMlSymR7A converts non-symbiotic Mesorhizobium spp. into nitrogen-fixing legume symbionts. Here, we discover subpopulations of Mesorhizobium japonicum R7A become epigenetically primed for quorum-sensing (QS) and QS-activated horizontal transfer. Isolated populations in this state termed R7A* maintained these phenotypes in laboratory culture but did not transfer the R7A* state to recipients of ICEMlSymR7A following conjugation. We previously demonstrated ICEMlSymR7A transfer and QS are repressed by the antiactivator QseM in R7A populations and that the adjacently-coded DNA-binding protein QseC represses qseM transcription. Here RNA-sequencing revealed qseM expression was repressed in R7A* cells and that RNA antisense to qseC was abundant in R7A but not R7A*. Deletion of the antisense-qseC promoter converted cells into an R7A*-like state. An adjacently coded QseC2 protein bound two operator sites and repressed antisense-qseC transcription. Plasmid overexpression of QseC2 stimulated the R7A* state, which persisted following curing of this plasmid. The epigenetic maintenance of the R7A* state required ICEMlSymR7A-encoded copies of both qseC and qseC2. Therefore, QseC and QseC2, together with their DNA-binding sites and overlapping promoters, form a stable epigenetic switch that establishes binary control over qseM transcription and primes a subpopulation of R7A cells for QS and horizontal transfer.
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Affiliation(s)
- Joshua P Ramsay
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Tahlia R Bastholm
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Callum J Verdonk
- School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia.,Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Dinah D Tambalo
- Biology Department, University of Regina, Regina, SK S4S 0A2, Canada
| | - John T Sullivan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Liam K Harold
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Beatrice A Panganiban
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Elena Colombi
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Benjamin J Perry
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - William Jowsey
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Calum Morris
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Michael F Hynes
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 4V8, Canada
| | - Charles S Bond
- School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia
| | | | | | - Clive W Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
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6
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Ren J, Lee HM, Shen J, Na D. Advanced biotechnology using methyltransferase and its applications in bacteria: a mini review. Biotechnol Lett 2021; 44:33-44. [PMID: 34820721 DOI: 10.1007/s10529-021-03208-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/12/2021] [Indexed: 11/26/2022]
Abstract
Since prokaryotic restriction-modification (RM) systems protect the host by cleaving foreign DNA by restriction endonucleases, it is difficult to introduce engineered plasmid DNAs into newly isolated microorganisms whose RM system is not discovered. The prokaryotes also possess methyltransferases to protect their own DNA from the endonucleases. As those methyltransferases can be utilized to methylate engineered plasmid DNAs before transformation and to enhance the stability within the cells, the study on methyltransferases in newly isolated bacteria is essential for genetic engineering. Here, we introduce the mechanism of the RM system, specifically the methyltransferases and their biotechnological applications. These biotechnological strategies could facilitate plasmid DNA-based genetic engineering in bacteria strains that strongly defend against foreign DNA.
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Affiliation(s)
- Jun Ren
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyang-Mi Lee
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - JunHao Shen
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea.
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7
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Negri A, Werbowy O, Wons E, Dersch S, Hinrichs R, Graumann PL, Mruk I. Regulator-dependent temporal dynamics of a restriction-modification system's gene expression upon entering new host cells: single-cell and population studies. Nucleic Acids Res 2021; 49:3826-3840. [PMID: 33744971 PMCID: PMC8053105 DOI: 10.1093/nar/gkab183] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 01/05/2023] Open
Abstract
Restriction-modification (R-M) systems represent a first line of defense against invasive DNAs, such as bacteriophage DNAs, and are widespread among bacteria and archaea. By acquiring a Type II R-M system via horizontal gene transfer, the new hosts generally become more resistant to phage infection, through the action of a restriction endonuclease (REase), which cleaves DNA at or near specific sequences. A modification methyltransferase (MTase) serves to protect the host genome against its cognate REase activity. The production of R-M system components upon entering a new host cell must be finely tuned to confer protective methylation before the REase acts, to avoid host genome damage. Some type II R-M systems rely on a third component, the controller (C) protein, which is a transcription factor that regulates the production of REase and/or MTase. Previous studies have suggested C protein effects on the dynamics of expression of an R-M system during its establishment in a new host cell. Here, we directly examine these effects. By fluorescently labelling REase and MTase, we demonstrate that lack of a C protein reduces the delay of REase production, to the point of being simultaneous with, or even preceding, production of the MTase. Single molecule tracking suggests that a REase and a MTase employ different strategies for their target search within host cells, with the MTase spending much more time diffusing in proximity to the nucleoid than does the REase. This difference may partially ameliorate the toxic effects of premature REase expression.
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Affiliation(s)
- Alessandro Negri
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Olesia Werbowy
- 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
| | - Simon Dersch
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany.,Department of Chemistry, Philipps Universität Marburg, Hans-Meerwein-Strasse 6, 35032 Marburg, Germany
| | - Rebecca Hinrichs
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany.,Department of Chemistry, Philipps Universität Marburg, Hans-Meerwein-Strasse 6, 35032 Marburg, Germany
| | - Peter L Graumann
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, 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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8
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Antibiotic Resistance and Epigenetics: More to It than Meets the Eye. Antimicrob Agents Chemother 2020; 64:AAC.02225-19. [PMID: 31740560 DOI: 10.1128/aac.02225-19] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The discovery of antibiotics in the last century is considered one of the most important achievements in the history of medicine. Antibiotic usage has significantly reduced morbidity and mortality associated with bacterial infections. However, inappropriate use of antibiotics has led to emergence of antibiotic resistance at an alarming rate. Antibiotic resistance is regarded as a major health care challenge of this century. Despite extensive research, well-documented biochemical mechanisms and genetic changes fail to fully explain mechanisms underlying antibiotic resistance. Several recent reports suggest a key role for epigenetics in the development of antibiotic resistance in bacteria. The intrinsic heterogeneity as well as transient nature of epigenetic inheritance provides a plausible backdrop for high-paced emergence of drug resistance in bacteria. The methylation of adenines and cytosines can influence mutation rates in bacterial genomes, thus modulating antibiotic susceptibility. In this review, we discuss a plethora of recently discovered epigenetic mechanisms and their emerging roles in antibiotic resistance. We also highlight specific epigenetic mechanisms that merit further investigation for their role in antibiotic resistance.
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9
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Negri A, Jąkalski M, Szczuka A, Pryszcz LP, Mruk I. Transcriptome analyses of cells carrying the Type II Csp231I restriction-modification system reveal cross-talk between two unrelated transcription factors: C protein and the Rac prophage repressor. Nucleic Acids Res 2019; 47:9542-9556. [PMID: 31372643 PMCID: PMC6765115 DOI: 10.1093/nar/gkz665] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 07/16/2019] [Accepted: 07/23/2019] [Indexed: 12/27/2022] Open
Abstract
Restriction-modification (R–M) systems represent an effective mechanism of defence against invading bacteriophages, and are widely spread among bacteria and archaea. In acquiring a Type II R–M system via horizontal gene transfer, the new hosts become more resistant to phage infection, through the action of a restriction endonuclease (REase), which recognizes and cleaves specific target DNAs. To protect the host cell's DNA, there is also a methyltransferase (MTase), which prevents DNA cleavage by the cognate REase. In some R–M systems, the host also accepts a cis-acting transcription factor (C protein), which regulates the counteracting activities of REase and MTase to avoid host self-restriction. Our study characterized the unexpected phenotype of Escherichia coli cells, which manifested as extensive cell filamentation triggered by acquiring the Csp231I R–M system from Citrobacter sp. Surprisingly, we found that the cell morphology defect was solely dependent on the C regulator. Our transcriptome analysis supported by in vivo and in vitro assays showed that C protein directly silenced the expression of the RacR repressor to affect the Rac prophage-related genes. The rac locus ydaST genes, when derepressed, exerted a toxicity indicated by cell filamentation through an unknown mechanism. These results provide an apparent example of transcription factor cross-talk, which can have significant consequences for the host, and may represent a constraint on lateral gene transfer.
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Affiliation(s)
- Alessandro Negri
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Marcin Jąkalski
- Department of Plant Taxonomy and Nature Conservation, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Aleksandra Szczuka
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Leszek P Pryszcz
- Laboratory of Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology, Warsaw, ul. Trojdena 4, 02-109 Warsaw, Poland
| | - Iwona Mruk
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
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10
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Natural tuning of restriction endonuclease synthesis by cluster of rare arginine codons. Sci Rep 2019; 9:5808. [PMID: 30967604 PMCID: PMC6456624 DOI: 10.1038/s41598-019-42311-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 03/28/2019] [Indexed: 01/21/2023] Open
Abstract
Restriction–modification (R-M) systems are highly widespread among bacteria and archaea, and they appear to play a pivotal role in modulating horizontal gene transfer, as well as in protecting the host organism against viruses and other invasive DNA particles. Type II R-M systems specify two independent enzymes: a restriction endonuclease (REase) and protective DNA methyltransferase (MTase). If the cell is to survive, the counteracting activities as toxin and antitoxin, must be finely balanced in vivo. The molecular basis of this regulatory process remains unclear and current searches for regulatory elements in R-M modules are focused mainly at the transcription step. In this report, we show new aspects of REase control that are linked to translation. We used the EcoVIII R-M system as a model. Both, the REase and MTase genes for this R-M system contain an unusually high number of rare arginine codons (AGA and AGG) when compared to the rest of the E. coli K-12 genome. Clusters of these codons near the N-terminus of the REase greatly affect the translational efficiency. Changing these to higher frequency codons for E. coli (CGC) improves the REase synthesis, making the R-M system more potent to defend its host against bacteriophages. However, this improved efficiency in synthesis reduces host fitness due to increased autorestriction. We hypothesize that expression of the endonuclease gene can be modulated depending on the host genetic context and we propose a novel post-transcriptional mode of R–M system regulation that alleviates the potential lethal action of the restriction enzyme.
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11
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Djordjevic M, Rodic A, Graovac S. From biophysics to 'omics and systems biology. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:413-424. [PMID: 30972433 DOI: 10.1007/s00249-019-01366-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 02/12/2019] [Accepted: 04/03/2019] [Indexed: 01/03/2023]
Abstract
Recent decades brought a revolution to biology, driven mainly by exponentially increasing amounts of data coming from "'omics" sciences. To handle these data, bioinformatics often has to combine biologically heterogeneous signals, for which methods from statistics and engineering (e.g. machine learning) are often used. While such an approach is sometimes necessary, it effectively treats the underlying biological processes as a black box. Similarly, systems biology deals with inherently complex systems, characterized by a large number of degrees of freedom, and interactions that are highly non-linear. To deal with this complexity, the underlying physical interactions are often (over)simplified, such as in Boolean modelling of network dynamics. In this review, we argue for the utility of applying a biophysical approach in bioinformatics and systems biology, including discussion of two examples from our research which address sequence analysis and understanding intracellular gene expression dynamics.
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Affiliation(s)
- Marko Djordjevic
- Faculty of Biology, Institute of Physiology and Biochemistry, University of Belgrade, Belgrade, Serbia.
| | - Andjela Rodic
- Faculty of Biology, Institute of Physiology and Biochemistry, University of Belgrade, Belgrade, Serbia.,Interdisciplinary PhD Program in Biophysics, University of Belgrade, Belgrade, Serbia
| | - Stefan Graovac
- Faculty of Biology, Institute of Physiology and Biochemistry, University of Belgrade, Belgrade, Serbia.,Interdisciplinary PhD Program in Biophysics, University of Belgrade, Belgrade, Serbia
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12
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Graovac S, Rodic A, Djordjevic M, Severinov K, Djordjevic M. Effects of Population Dynamics on Establishment of a Restriction-Modification System in a Bacterial Host. Molecules 2019; 24:E198. [PMID: 30621083 PMCID: PMC6337176 DOI: 10.3390/molecules24010198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/28/2018] [Accepted: 01/03/2019] [Indexed: 12/16/2022] Open
Abstract
In vivo dynamics of protein levels in bacterial cells depend on both intracellular regulation and relevant population dynamics. Such population dynamics effects, e.g., interplay between cell and plasmid division rates, are, however, often neglected in modeling gene expression regulation. Including them in a model introduces additional parameters shared by the dynamical equations, which can significantly increase dimensionality of the parameter inference. We here analyse the importance of these effects, on a case of bacterial restriction-modification (R-M) system. We redevelop our earlier minimal model of this system gene expression regulation, based on a thermodynamic and dynamic system modeling framework, to include the population dynamics effects. To resolve the problem of effective coupling of the dynamical equations, we propose a "mean-field-like" procedure, which allows determining only part of the parameters at a time, by separately fitting them to expression dynamics data of individual molecular species. We show that including the interplay between kinetics of cell division and plasmid replication is necessary to explain the experimental measurements. Moreover, neglecting population dynamics effects can lead to falsely identifying non-existent regulatory mechanisms. Our results call for advanced methods to reverse-engineer intracellular regulation from dynamical data, which would also take into account the population dynamics effects.
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Affiliation(s)
- Stefan Graovac
- Faculty of Biology, University of Belgrade, 11000 Belgrade, Serbia.
- Multidisciplinary PhD program in Biophysics, University of Belgrade, 11000 Belgrade, Serbia.
| | - Andjela Rodic
- Faculty of Biology, University of Belgrade, 11000 Belgrade, Serbia.
- Multidisciplinary PhD program in Biophysics, University of Belgrade, 11000 Belgrade, Serbia.
| | | | - Konstantin Severinov
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854, USA.
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143026, Russia.
| | - Marko Djordjevic
- Faculty of Biology, University of Belgrade, 11000 Belgrade, Serbia.
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13
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Klimuk E, Bogdanova E, Nagornykh M, Rodic A, Djordjevic M, Medvedeva S, Pavlova O, Severinov K. Controller protein of restriction-modification system Kpn2I affects transcription of its gene by acting as a transcription elongation roadblock. Nucleic Acids Res 2018; 46:10810-10826. [PMID: 30295835 PMCID: PMC6237814 DOI: 10.1093/nar/gky880] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/13/2018] [Accepted: 09/18/2018] [Indexed: 12/21/2022] Open
Abstract
C-proteins control restriction-modification (R-M) systems' genes transcription to ensure sufficient levels of restriction endonuclease to allow protection from foreign DNA while avoiding its modification by excess methyltransferase. Here, we characterize transcription regulation in C-protein dependent R-M system Kpn2I. The Kpn2I restriction endonuclease gene is transcribed from a constitutive, weak promoter, which, atypically, is C-protein independent. Kpn2I C-protein (C.Kpn2I) binds upstream of the strong methyltransferase gene promoter and inhibits it, likely by preventing the interaction of the RNA polymerase sigma subunit with the -35 consensus element. Diminished transcription from the methyltransferase promoter increases transcription from overlapping divergent C-protein gene promoters. All known C-proteins affect transcription initiation from R-M genes promoters. Uniquely, the C.Kpn2I binding site is located within the coding region of its gene. C.Kpn2I acts as a roadblock stalling elongating RNA polymerase and decreasing production of full-length C.Kpn2I mRNA. Mathematical modeling shows that this unusual mode of regulation leads to the same dynamics of accumulation of R-M gene transcripts as observed in systems where C-proteins act at transcription initiation stage only. Bioinformatics analyses suggest that transcription regulation through binding of C.Kpn2I-like proteins within the coding regions of their genes may be widespread.
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Affiliation(s)
- Evgeny Klimuk
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | | | - Max Nagornykh
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Puschino, Russia
| | - Andjela Rodic
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | | | - Sofia Medvedeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Olga Pavlova
- Waksman Institute of Microbiology, Piscataway, NJ 08854, USA
| | - Konstantin Severinov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
- Waksman Institute of Microbiology, Piscataway, NJ 08854, USA
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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14
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Rodic A, Blagojevic B, Djordjevic M, Severinov K, Djordjevic M. Features of CRISPR-Cas Regulation Key to Highly Efficient and Temporally-Specific crRNA Production. Front Microbiol 2017; 8:2139. [PMID: 29163425 PMCID: PMC5675862 DOI: 10.3389/fmicb.2017.02139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 10/19/2017] [Indexed: 12/15/2022] Open
Abstract
Bacterial immune systems, such as CRISPR-Cas or restriction-modification (R-M) systems, affect bacterial pathogenicity and antibiotic resistance by modulating horizontal gene flow. A model system for CRISPR-Cas regulation, the Type I-E system from Escherichia coli, is silent under standard laboratory conditions and experimentally observing the dynamics of CRISPR-Cas activation is challenging. Two characteristic features of CRISPR-Cas regulation in E. coli are cooperative transcription repression of cas gene and CRISPR array promoters, and fast non-specific degradation of full length CRISPR transcripts (pre-crRNA). In this work, we use computational modeling to understand how these features affect the system expression dynamics. Signaling which leads to CRISPR-Cas activation is currently unknown, so to bypass this step, we here propose a conceptual setup for cas expression activation, where cas genes are put under transcription control typical for a restriction-modification (R-M) system and then introduced into a cell. Known transcription regulation of an R-M system is used as a proxy for currently unknown CRISPR-Cas transcription control, as both systems are characterized by high cooperativity, which is likely related to similar dynamical constraints of their function. We find that the two characteristic CRISPR-Cas control features are responsible for its temporally-specific dynamical response, so that the system makes a steep (switch-like) transition from OFF to ON state with a time-delay controlled by pre-crRNA degradation rate. We furthermore find that cooperative transcription regulation qualitatively leads to a cross-over to a regime where, at higher pre-crRNA processing rates, crRNA generation approaches the limit of an infinitely abrupt system induction. We propose that these dynamical properties are associated with rapid expression of CRISPR-Cas components and efficient protection of bacterial cells against foreign DNA. In terms of synthetic applications, the setup proposed here should allow highly efficient expression of small RNAs in a narrow time interval, with a specified time-delay with respect to the signal onset.
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Affiliation(s)
- Andjela Rodic
- Faculty of Biology, Institute of Physiology and Biochemistry, University of Belgrade, Belgrade, Serbia.,Multidisciplinary PhD Program in Biophysics, University of Belgrade, Belgrade, Serbia
| | - Bojana Blagojevic
- Institute of Physics Belgrade, University of Belgrade, Belgrade, Serbia
| | | | - Konstantin Severinov
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, United States.,Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Marko Djordjevic
- Faculty of Biology, Institute of Physiology and Biochemistry, University of Belgrade, Belgrade, Serbia
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15
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Rodic A, Blagojevic B, Zdobnov E, Djordjevic M, Djordjevic M. Understanding key features of bacterial restriction-modification systems through quantitative modeling. BMC SYSTEMS BIOLOGY 2017; 11:377. [PMID: 28466789 PMCID: PMC5333194 DOI: 10.1186/s12918-016-0377-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Background Restriction-modification (R-M) systems are rudimentary bacterial immune systems. The main components include restriction enzyme (R), which cuts specific unmethylated DNA sequences, and the methyltransferase (M), which protects the same DNA sequences. The expression of R-M system components is considered to be tightly regulated, to ensure successful establishment in a naïve bacterial host. R-M systems are organized in different architectures (convergent or divergent) and are characterized by different features, i.e. binding cooperativities, dissociation constants of dimerization, translation rates, which ensure this tight regulation. It has been proposed that R-M systems should exhibit certain dynamical properties during the system establishment, such as: i) a delayed expression of R with respect to M, ii) fast transition of R from “OFF” to “ON” state, iii) increased stability of the toxic molecule (R) steady-state levels. It is however unclear how different R-M system features and architectures ensure these dynamical properties, particularly since it is hard to address this question experimentally. Results To understand design of different R-M systems, we computationally analyze two R-M systems, representative of the subset controlled by small regulators called ‘C proteins’, and differing in having convergent or divergent promoter architecture. We show that, in the convergent system, abolishing any of the characteristic system features adversely affects the dynamical properties outlined above. Moreover, an extreme binding cooperativity, accompanied by a very high dissociation constant of dimerization, observed in the convergent system, but absent from other R-M systems, can be explained in terms of the same properties. Furthermore, we develop the first theoretical model for dynamics of a divergent R-M system, which does not share any of the convergent system features, but has overlapping promoters. We show that i) the system dynamics exhibits the same three dynamical properties, ii) introducing any of the convergent system features to the divergent system actually diminishes these properties. Conclusions Our results suggest that different R-M architectures and features may be understood in terms of constraints imposed by few simple dynamical properties of the system, providing a unifying framework for understanding these seemingly diverse systems. We also provided predictions for the perturbed R-M systems dynamics, which may in future be tested through increasingly available experimental techniques, such as re-engineering R-M systems and single-cell experiments. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0377-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andjela Rodic
- Institute of Physiology and Biochemistry, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000, Belgrade, Serbia.,Multidisciplinary PhD program in Biophysics, University of Belgrade, Belgrade, Serbia
| | - Bojana Blagojevic
- Institute of Physics Belgrade, University of Belgrade, Belgrade, Serbia
| | - Evgeny Zdobnov
- Department of Genetic Medicine and Development, University of Geneva and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | | | - Marko Djordjevic
- Institute of Physiology and Biochemistry, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000, Belgrade, Serbia.
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16
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Fisunov GY, Evsyutina DV, Manuvera VA, Govorun VM. Binding site of restriction-modification system controller protein in Mollicutes. BMC Microbiol 2017; 17:26. [PMID: 28143392 PMCID: PMC5282649 DOI: 10.1186/s12866-017-0935-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/17/2017] [Indexed: 12/23/2022] Open
Abstract
Background Bacteria of the class Mollicutes underwent extreme reduction of genomes and gene expression control systems. Only a few regulators are known to date. In this work, we describe a novel group of transcriptional regulators that are distributed within different Mollicutes and control the expression of restriction-modification systems (RM-systems). Results We performed cross-species search of putative regulators of RM-systems (C-proteins) and respective binding sites in Mollicutes. We identified a set of novel putative C-protein binding motifs distributed within Mollicutes. We studied the most frequent motif and respective C-protein on the model of Mycoplasma gallisepticum S6. We confirmed our prediction and identified key nucleotides important for C-protein binding. Further we identified novel target promoters of C-protein in M. gallisepticum. Conclusions We found that C-protein of M. gallisepticum binds predicted conserved direct repeats of the (GTGTTAN5)2 motif. Apart from its own operon promoter, HsdC can bind to the promoters of the clpB chaperone gene and a tRNA cluster. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-0935-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gleb Y Fisunov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119992, Russia.
| | - Daria V Evsyutina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119992, Russia.,Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory, GSP-1, 73, Moscow, 119234, Russia
| | - Valentin A Manuvera
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119992, Russia
| | - Vadim M Govorun
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119992, Russia
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17
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Morozova N, Sabantsev A, Bogdanova E, Fedorova Y, Maikova A, Vedyaykin A, Rodic A, Djordjevic M, Khodorkovskii M, Severinov K. Temporal dynamics of methyltransferase and restriction endonuclease accumulation in individual cells after introducing a restriction-modification system. Nucleic Acids Res 2016; 44:790-800. [PMID: 26687717 PMCID: PMC4737168 DOI: 10.1093/nar/gkv1490] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/08/2015] [Accepted: 12/08/2015] [Indexed: 11/14/2022] Open
Abstract
Type II restriction-modification (R-M) systems encode a restriction endonuclease that cleaves DNA at specific sites, and a methyltransferase that modifies same sites protecting them from restriction endonuclease cleavage. Type II R-M systems benefit bacteria by protecting them from bacteriophages. Many type II R-M systems are plasmid-based and thus capable of horizontal transfer. Upon the entry of such plasmids into a naïve host with unmodified genomic recognition sites, methyltransferase should be synthesized first and given sufficient time to methylate recognition sites in the bacterial genome before the toxic restriction endonuclease activity appears. Here, we directly demonstrate a delay in restriction endonuclease synthesis after transformation of Escherichia coli cells with a plasmid carrying the Esp1396I type II R-M system, using single-cell microscopy. We further demonstrate that before the appearance of the Esp1396I restriction endonuclease the intracellular concentration of Esp1396I methyltransferase undergoes a sharp peak, which should allow rapid methylation of host genome recognition sites. A mathematical model that satisfactorily describes the observed dynamics of both Esp1396I enzymes is presented. The results reported here were obtained using a functional Esp1396I type II R-M system encoding both enzymes fused to fluorescent proteins. Similar approaches should be applicable to the studies of other R-M systems at single-cell level.
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Affiliation(s)
- Natalia Morozova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - Anton Sabantsev
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - Ekaterina Bogdanova
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yana Fedorova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia Skolkovo Institute of Science and Technology, Skolkovo, 143026, Russia
| | - Anna Maikova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia Skolkovo Institute of Science and Technology, Skolkovo, 143026, Russia
| | - Alexey Vedyaykin
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - Andjela Rodic
- Faculty of Biology, University of Belgrade, 11000 Belgrade, Serbia
| | - Marko Djordjevic
- Faculty of Biology, University of Belgrade, 11000 Belgrade, Serbia
| | - Mikhail Khodorkovskii
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - Konstantin Severinov
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
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18
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Rezulak M, Borsuk I, Mruk I. Natural C-independent expression of restriction endonuclease in a C protein-associated restriction-modification system. Nucleic Acids Res 2015; 44:2646-60. [PMID: 26656489 PMCID: PMC4824078 DOI: 10.1093/nar/gkv1331] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 11/13/2015] [Indexed: 12/24/2022] Open
Abstract
Restriction-modification (R-M) systems are highly prevalent among bacteria and archaea, and appear to play crucial roles in modulating horizontal gene transfer and protection against phage. There is much to learn about these diverse enzymes systems, especially their regulation. Type II R-M systems specify two independent enzymes: a restriction endonuclease (REase) and protective DNA methyltransferase (MTase). Their activities need to be finely balanced in vivo Some R-M systems rely on specialized transcription factors called C (controller) proteins. These proteins play a vital role in the temporal regulation of R-M gene expression, and function to indirectly modulate the horizontal transfer of their genes across the species. We report novel regulation of a C-responsive R-M system that involves a C protein of a poorly-studied structural class - C.Csp231I. Here, the C and REase genes share a bicistronic transcript, and some of the transcriptional auto-control features seen in other C-regulated R-M systems are conserved. However, separate tandem promoters drive most transcription of the REase gene, a distinctive property not seen in other tested C-linked R-M systems. Further, C protein only partially controls REase expression, yet plays a role in system stability and propagation. Consequently, high REase activity was observed after deletion of the entire C gene, and cells bearing the ΔC R-M system were outcompeted in mixed culture assays by those with the WT R-M system. Overall, our data reveal unexpected regulatory variation among R-M systems.
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Affiliation(s)
- Monika Rezulak
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Izabela Borsuk
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Iwona Mruk
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
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19
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Shevtsov MB, Streeter SD, Thresh SJ, Swiderska A, McGeehan JE, Kneale GG. Structural analysis of DNA binding by C.Csp231I, a member of a novel class of R-M controller proteins regulating gene expression. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:398-407. [PMID: 25664751 PMCID: PMC4321490 DOI: 10.1107/s139900471402690x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 12/08/2014] [Indexed: 01/03/2023]
Abstract
In a wide variety of bacterial restriction-modification systems, a regulatory `controller' protein (or C-protein) is required for effective transcription of its own gene and for transcription of the endonuclease gene found on the same operon. We have recently turned our attention to a new class of controller proteins (exemplified by C.Csp231I) that have quite novel features, including a much larger DNA-binding site with an 18 bp (∼60 Å) spacer between the two palindromic DNA-binding sequences and a very different recognition sequence from the canonical GACT/AGTC. Using X-ray crystallography, the structure of the protein in complex with its 21 bp DNA-recognition sequence was solved to 1.8 Å resolution, and the molecular basis of sequence recognition in this class of proteins was elucidated. An unusual aspect of the promoter sequence is the extended spacer between the dimer binding sites, suggesting a novel interaction between the two C-protein dimers when bound to both recognition sites correctly spaced on the DNA. A U-bend model is proposed for this tetrameric complex, based on the results of gel-mobility assays, hydrodynamic analysis and the observation of key contacts at the interface between dimers in the crystal.
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Affiliation(s)
- M. B. Shevtsov
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, England
| | - S. D. Streeter
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, England
| | - S.-J. Thresh
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, England
| | - A. Swiderska
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, England
| | - J. E. McGeehan
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, England
| | - G. G. Kneale
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, England
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20
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Pingoud A, Wilson GG, Wende W. Type II restriction endonucleases--a historical perspective and more. Nucleic Acids Res 2014; 42:7489-527. [PMID: 24878924 PMCID: PMC4081073 DOI: 10.1093/nar/gku447] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 05/02/2014] [Accepted: 05/07/2014] [Indexed: 12/17/2022] Open
Abstract
This article continues the series of Surveys and Summaries on restriction endonucleases (REases) begun this year in Nucleic Acids Research. Here we discuss 'Type II' REases, the kind used for DNA analysis and cloning. We focus on their biochemistry: what they are, what they do, and how they do it. Type II REases are produced by prokaryotes to combat bacteriophages. With extreme accuracy, each recognizes a particular sequence in double-stranded DNA and cleaves at a fixed position within or nearby. The discoveries of these enzymes in the 1970s, and of the uses to which they could be put, have since impacted every corner of the life sciences. They became the enabling tools of molecular biology, genetics and biotechnology, and made analysis at the most fundamental levels routine. Hundreds of different REases have been discovered and are available commercially. Their genes have been cloned, sequenced and overexpressed. Most have been characterized to some extent, but few have been studied in depth. Here, we describe the original discoveries in this field, and the properties of the first Type II REases investigated. We discuss the mechanisms of sequence recognition and catalysis, and the varied oligomeric modes in which Type II REases act. We describe the surprising heterogeneity revealed by comparisons of their sequences and structures.
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Affiliation(s)
- Alfred Pingoud
- Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
| | - Geoffrey G Wilson
- New England Biolabs Inc., 240 County Road, Ipswich, MA 01938-2723, USA
| | - Wolfgang Wende
- Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
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21
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Structural and mutagenic analysis of the RM controller protein C.Esp1396I. PLoS One 2014; 9:e98365. [PMID: 24887147 PMCID: PMC4041747 DOI: 10.1371/journal.pone.0098365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 05/01/2014] [Indexed: 12/01/2022] Open
Abstract
Bacterial restriction-modification (RM) systems are comprised of two complementary enzymatic activities that prevent the establishment of foreign DNA in a bacterial cell: DNA methylation and DNA restriction. These two activities are tightly regulated to prevent over-methylation or auto-restriction. Many Type II RM systems employ a controller (C) protein as a transcriptional regulator for the endonuclease gene (and in some cases, the methyltransferase gene also). All high-resolution structures of C-protein/DNA-protein complexes solved to date relate to C.Esp1396I, from which the interactions of specific amino acid residues with DNA bases and/or the phosphate backbone could be observed. Here we present both structural and DNA binding data for a series of mutations to the key DNA binding residues of C.Esp1396I. Our results indicate that mutations to the backbone binding residues (Y37, S52) had a lesser affect on DNA binding affinity than mutations to those residues that bind directly to the bases (T36, R46), and the contributions of each side chain to the binding energies are compared. High-resolution X-ray crystal structures of the mutant and native proteins showed that the fold of the proteins was unaffected by the mutations, but also revealed variation in the flexible loop conformations associated with DNA sequence recognition. Since the tyrosine residue Y37 contributes to DNA bending in the native complex, we have solved the structure of the Y37F mutant protein/DNA complex by X-ray crystallography to allow us to directly compare the structure of the DNA in the mutant and native complexes.
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22
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Liu B, Shadrin A, Sheppard C, Mekler V, Xu Y, Severinov K, Matthews S, Wigneshweraraj S. A bacteriophage transcription regulator inhibits bacterial transcription initiation by σ-factor displacement. Nucleic Acids Res 2014; 42:4294-305. [PMID: 24482445 PMCID: PMC3985653 DOI: 10.1093/nar/gku080] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bacteriophages (phages) appropriate essential processes of bacterial hosts to benefit their own development. The multisubunit bacterial RNA polymerase (RNAp) enzyme, which catalyses DNA transcription, is targeted by phage-encoded transcription regulators that selectively modulate its activity. Here, we describe the structural and mechanistic basis for the inhibition of bacterial RNAp by the transcription regulator P7 encoded by Xanthomonas oryzae phage Xp10. We reveal that P7 uses a two-step mechanism to simultaneously interact with the catalytic β and β' subunits of the bacterial RNAp and inhibits transcription initiation by inducing the displacement of the σ(70)-factor on initial engagement of RNAp with promoter DNA. The new mode of interaction with and inhibition mechanism of bacterial RNAp by P7 underscore the remarkable variety of mechanisms evolved by phages to interfere with host transcription.
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Affiliation(s)
- Bing Liu
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, London SW7 2AZ, UK, Waksman Institute for Microbiology and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ USA and St. Petersburg State Polytechnical University, St. Petersburg, Russia
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23
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Loenen WAM, Dryden DTF, Raleigh EA, Wilson GG, Murray NE. Highlights of the DNA cutters: a short history of the restriction enzymes. Nucleic Acids Res 2014; 42:3-19. [PMID: 24141096 PMCID: PMC3874209 DOI: 10.1093/nar/gkt990] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/24/2013] [Accepted: 10/02/2013] [Indexed: 11/16/2022] Open
Abstract
In the early 1950's, 'host-controlled variation in bacterial viruses' was reported as a non-hereditary phenomenon: one cycle of viral growth on certain bacterial hosts affected the ability of progeny virus to grow on other hosts by either restricting or enlarging their host range. Unlike mutation, this change was reversible, and one cycle of growth in the previous host returned the virus to its original form. These simple observations heralded the discovery of the endonuclease and methyltransferase activities of what are now termed Type I, II, III and IV DNA restriction-modification systems. The Type II restriction enzymes (e.g. EcoRI) gave rise to recombinant DNA technology that has transformed molecular biology and medicine. This review traces the discovery of restriction enzymes and their continuing impact on molecular biology and medicine.
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Affiliation(s)
- Wil A. M. Loenen
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - David T. F. Dryden
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Elisabeth A. Raleigh
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Geoffrey G. Wilson
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
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24
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Liang J, Blumenthal RM. Naturally-occurring, dually-functional fusions between restriction endonucleases and regulatory proteins. BMC Evol Biol 2013; 13:218. [PMID: 24083337 PMCID: PMC3850674 DOI: 10.1186/1471-2148-13-218] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 10/01/2013] [Indexed: 01/03/2023] Open
Abstract
Background Restriction-modification (RM) systems appear to play key roles in modulating gene flow among bacteria and archaea. Because the restriction endonuclease (REase) is potentially lethal to unmethylated new host cells, regulation to ensure pre-expression of the protective DNA methyltransferase (MTase) is essential to the spread of RM genes. This is particularly true for Type IIP RM systems, in which the REase and MTase are separate, independently-active proteins. A substantial subset of Type IIP RM systems are controlled by an activator-repressor called C protein. In these systems, C controls the promoter for its own gene, and for the downstream REase gene that lacks its own promoter. Thus MTase is expressed immediately after the RM genes enter a new cell, while expression of REase is delayed until sufficient C protein accumulates. To study the variation in and evolution of this regulatory mechanism, we searched for RM systems closely related to the well-studied C protein-dependent PvuII RM system. Unexpectedly, among those found were several in which the C protein and REase genes were fused. Results The gene for CR.NsoJS138I fusion protein (nsoJS138ICR, from the bacterium Niabella soli) was cloned, and the fusion protein produced and partially purified. Western blots provided no evidence that, under the conditions tested, anything other than full-length fusion protein is produced. This protein had REase activity in vitro and, as expected from the sequence similarity, its specificity was indistinguishable from that for PvuII REase, though the optimal reaction conditions were different. Furthermore, the fusion was active as a C protein, as revealed by in vivo activation of a lacZ reporter fusion to the promoter region for the nsoJS138ICR gene. Conclusions Fusions between C proteins and REases have not previously been characterized, though other fusions have (such as between REases and MTases). These results reinforce the evidence for impressive modularity among RM system proteins, and raise important questions about the implications of the C-REase fusions on expression kinetics of these RM systems.
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Affiliation(s)
- Jixiao Liang
- Department of Medical Microbiology & Immunology, College of Medicine and Life Sciences, University of Toledo, 3100 Transverse Drive, Toledo, OH 43614, USA.
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25
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Martin RNA, McGeehan JE, Ball NJ, Streeter SD, Thresh SJ, Kneale GG. Structural analysis of DNA-protein complexes regulating the restriction-modification system Esp1396I. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:962-6. [PMID: 23989141 PMCID: PMC3758141 DOI: 10.1107/s174430911302126x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/30/2013] [Indexed: 11/10/2022]
Abstract
The controller protein of the type II restriction-modification (RM) system Esp1396I binds to three distinct DNA operator sequences upstream of the methyltransferase and endonuclease genes in order to regulate their expression. Previous biophysical and crystallographic studies have shown molecular details of how the controller protein binds to the operator sites with very different affinities. Here, two protein-DNA co-crystal structures containing portions of unbound DNA from native operator sites are reported. The DNA in both complexes shows significant distortion in the region between the conserved symmetric sequences, similar to that of a DNA duplex when bound by the controller protein (C-protein), indicating that the naked DNA has an intrinsic tendency to bend when not bound to the C-protein. Moreover, the width of the major groove of the DNA adjacent to a bound C-protein dimer is observed to be significantly increased, supporting the idea that this DNA distortion contributes to the substantial cooperativity found when a second C-protein dimer binds to the operator to form the tetrameric repression complex.
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Affiliation(s)
- Richard N. A. Martin
- Institute of Biomedical and Biomolecular Science, University of Portsmouth, King Henry I Street, Portsmouth, Hampshire PO1 2DY, England
| | - John E. McGeehan
- Institute of Biomedical and Biomolecular Science, University of Portsmouth, King Henry I Street, Portsmouth, Hampshire PO1 2DY, England
| | - Neil J. Ball
- Institute of Biomedical and Biomolecular Science, University of Portsmouth, King Henry I Street, Portsmouth, Hampshire PO1 2DY, England
| | - Simon D. Streeter
- Institute of Biomedical and Biomolecular Science, University of Portsmouth, King Henry I Street, Portsmouth, Hampshire PO1 2DY, England
| | - Sarah-Jane Thresh
- Institute of Biomedical and Biomolecular Science, University of Portsmouth, King Henry I Street, Portsmouth, Hampshire PO1 2DY, England
| | - G. G. Kneale
- Institute of Biomedical and Biomolecular Science, University of Portsmouth, King Henry I Street, Portsmouth, Hampshire PO1 2DY, England
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26
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Mruk I, Kobayashi I. To be or not to be: regulation of restriction-modification systems and other toxin-antitoxin systems. Nucleic Acids Res 2013; 42:70-86. [PMID: 23945938 PMCID: PMC3874152 DOI: 10.1093/nar/gkt711] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
One of the simplest classes of genes involved in programmed death is that containing the toxin–antitoxin (TA) systems of prokaryotes. These systems are composed of an intracellular toxin and an antitoxin that neutralizes its effect. These systems, now classified into five types, were initially discovered because some of them allow the stable maintenance of mobile genetic elements in a microbial population through postsegregational killing or the death of cells that have lost these systems. Here, we demonstrate parallels between some TA systems and restriction–modification systems (RM systems). RM systems are composed of a restriction enzyme (toxin) and a modification enzyme (antitoxin) and limit the genetic flux between lineages with different epigenetic identities, as defined by sequence-specific DNA methylation. The similarities between these systems include their postsegregational killing and their effects on global gene expression. Both require the finely regulated expression of a toxin and antitoxin. The antitoxin (modification enzyme) or linked protein may act as a transcriptional regulator. A regulatory antisense RNA recently identified in an RM system can be compared with those RNAs in TA systems. This review is intended to generalize the concept of TA systems in studies of stress responses, programmed death, genetic conflict and epigenetics.
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Affiliation(s)
- Iwona Mruk
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, Gdansk, 80-308, Poland, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan and Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
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27
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Williams K, Savageau MA, Blumenthal RM. A bistable hysteretic switch in an activator-repressor regulated restriction-modification system. Nucleic Acids Res 2013; 41:6045-57. [PMID: 23630319 PMCID: PMC3695507 DOI: 10.1093/nar/gkt324] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Restriction–modification (RM) systems are extremely widespread among bacteria and archaea, and are often specified by mobile genetic elements. In type II RM systems, where the restriction endonuclease (REase) and protective DNA methyltransferase (MTase) are separate proteins, a major regulatory challenge is delaying expression of the REase relative to the MTase after RM genes enter a new host cell. Basic understanding of this regulation is available for few RM systems, and detailed understanding for none. The PvuII RM system is one of a large subset in which the central regulatory role is played by an activator–repressor protein (called C, for controller). REase expression depends upon activation by C, whereas expression of the MTase does not. Thus delay of REase expression depends on the rate of C-protein accumulation. This is a nonlinear process, as C also activates transcription of its own gene. Mathematical modeling of the PvuII system led to the unexpected predictions of responsiveness to a factor not previously studied in RM system control—gene copy number—and of a hysteretic response. In this study, those predictions have been confirmed experimentally. The results may apply to many other C-regulated RM systems, and help explain their ability to spread so widely.
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Affiliation(s)
- Kristen Williams
- Department of Medical Microbiology & Immunology, and Program in Bioinformatics, University of Toledo, Toledo, OH 43614, USA
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28
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Djordjevic M. Modeling bacterial immune systems: strategies for expression of toxic - but useful - molecules. Biosystems 2013; 112:139-44. [PMID: 23499818 DOI: 10.1016/j.biosystems.2013.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Protection of bacterial cells against virus infection requires expression of molecules that are able to destroy the incoming foreign DNA. However, these molecules can also be toxic for the host cell. In both restriction-modification (R-M), and the recently discovered CRISPR/Cas systems, the toxicity is (in part) avoided through rapid transition of the expression of the toxic molecules from "OFF" to "ON" state. In restriction-modification systems the rapid transition is achieved through a large binding cooperativity, and low translation rate of the control protein. On the other hand, CRISPR array expression in CRISPR/Cas systems involves a mechanism where a small decrease of unprocessed RNAs leads to a rapid increase of processed small RNAs. Surprisingly, this rapid amplification crucially depends on fast non-specific degradation of the unprocessed molecules by an unidentified nuclease, rather than on large cooperativity in protein binding. Furthermore, the major control elements that are responsible for fast transition of R-M and CRISPR/Cas systems from "OFF" to "ON" state, are also directly involved in increased stability of the steady states of these systems. We here discuss mechanisms that allow rapid transition of toxic molecules from the unproductive to the productive state in R-M and CRISPR/Cas systems. The main purpose of this discussion is to put relevant theoretical and experimental work in a perspective that points to general similarities in otherwise mechanistically very different bacterial immune systems.
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Affiliation(s)
- Marko Djordjevic
- Institute of Physiology and Biochemistry, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia.
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29
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Ramsay JP, Major AS, Komarovsky VM, Sullivan JT, Dy RL, Hynes MF, Salmond GPC, Ronson CW. A widely conserved molecular switch controls quorum sensing and symbiosis island transfer inMesorhizobium lotithrough expression of a novel antiactivator. Mol Microbiol 2012; 87:1-13. [DOI: 10.1111/mmi.12079] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Joshua P. Ramsay
- Department of Microbiology and Immunology; University of Otago; PO Box 56; Dunedin; New Zealand
| | - Anthony S. Major
- Department of Microbiology and Immunology; University of Otago; PO Box 56; Dunedin; New Zealand
| | - Victor M. Komarovsky
- Department of Microbiology and Immunology; University of Otago; PO Box 56; Dunedin; New Zealand
| | - John T. Sullivan
- Department of Microbiology and Immunology; University of Otago; PO Box 56; Dunedin; New Zealand
| | - Ron L. Dy
- Department of Microbiology and Immunology; University of Otago; PO Box 56; Dunedin; New Zealand
| | - Michael F. Hynes
- Department of Biological Sciences; University of Calgary; Calgary; Canada; T2N 1N4
| | | | - Clive W. Ronson
- Department of Microbiology and Immunology; University of Otago; PO Box 56; Dunedin; New Zealand
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30
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Ball NJ, McGeehan JE, Streeter SD, Thresh SJ, Kneale GG. The structural basis of differential DNA sequence recognition by restriction-modification controller proteins. Nucleic Acids Res 2012; 40:10532-42. [PMID: 22941636 PMCID: PMC3488213 DOI: 10.1093/nar/gks718] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Controller (C) proteins regulate the expression of restriction-modification (RM) genes in a wide variety of RM systems. However, the RM system Esp1396I is of particular interest as the C protein regulates both the restriction endonuclease (R) gene and the methyltransferase (M) gene. The mechanism of this finely tuned genetic switch depends on differential binding affinities for the promoters controlling the R and M genes, which in turn depends on differential DNA sequence recognition and the ability to recognize dual symmetries. We report here the crystal structure of the C protein bound to the M promoter, and compare the binding affinities for each operator sequence by surface plasmon resonance. Comparison of the structure of the transcriptional repression complex at the M promoter with that of the transcriptional activation complex at the R promoter shows how subtle changes in protein-DNA interactions, underpinned by small conformational changes in the protein, can explain the molecular basis of differential regulation of gene expression.
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Affiliation(s)
- N J Ball
- Biomolecular Structure Group, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
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31
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McGeehan JE, Ball NJ, Streeter SD, Thresh SJ, Kneale GG. Recognition of dual symmetry by the controller protein C.Esp1396I based on the structure of the transcriptional activation complex. Nucleic Acids Res 2011; 40:4158-67. [PMID: 22210861 PMCID: PMC3351150 DOI: 10.1093/nar/gkr1250] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The controller protein C.Esp1396I regulates the timing of gene expression of the restriction–modification (RM) genes of the RM system Esp1396I. The molecular recognition of promoter sequences by such transcriptional regulators is poorly understood, in part because the DNA sequence motifs do not conform to a well-defined symmetry. We report here the crystal structure of the controller protein bound to a DNA operator site. The structure reveals how two different symmetries within the operator are simultaneously recognized by the homo-dimeric protein, underpinned by a conformational change in one of the protein subunits. The recognition of two different DNA symmetries through movement of a flexible loop in one of the protein subunits may represent a general mechanism for the recognition of pseudo-symmetric DNA sequences.
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Affiliation(s)
- J E McGeehan
- Biomolecular Structure Group, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth, Hampshire PO1 2DY, UK
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32
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Beierlein FR, Kneale GG, Clark T. Predicting the effects of basepair mutations in DNA-protein complexes by thermodynamic integration. Biophys J 2011; 101:1130-8. [PMID: 21889450 DOI: 10.1016/j.bpj.2011.07.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 06/28/2011] [Accepted: 07/05/2011] [Indexed: 10/17/2022] Open
Abstract
Thermodynamically rigorous free energy methods in principle allow the exact computation of binding free energies in biological systems. Here, we use thermodynamic integration together with molecular dynamics simulations of a DNA-protein complex to compute relative binding free energies of a series of mutants of a protein-binding DNA operator sequence. A guanine-cytosine basepair that interacts strongly with the DNA-binding protein is mutated into adenine-thymine, cytosine-guanine, and thymine-adenine. It is shown that basepair mutations can be performed using a conservative protocol that gives error estimates of ∼10% of the change in free energy of binding. Despite the high CPU-time requirements, this work opens the exciting opportunity of being able to perform basepair scans to investigate protein-DNA binding specificity in great detail computationally.
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Affiliation(s)
- Frank R Beierlein
- Computer-Chemie-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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33
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McGeehan J, Streeter S, Thresh SJ, Taylor J, Shevtsov M, Kneale G. Structural analysis of a novel class of R-M controller proteins: C.Csp231I from Citrobacter sp. RFL231. J Mol Biol 2011; 409:177-88. [PMID: 21440553 PMCID: PMC3115060 DOI: 10.1016/j.jmb.2011.03.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 03/14/2011] [Accepted: 03/16/2011] [Indexed: 11/22/2022]
Abstract
Controller proteins play a key role in the temporal regulation of gene expression in bacterial restriction-modification (R-M) systems and are important mediators of horizontal gene transfer. They form the basis of a highly cooperative, concentration-dependent genetic switch involved in both activation and repression of R-M genes. Here we present biophysical, biochemical, and high-resolution structural analysis of a novel class of controller proteins, exemplified by C.Csp231I. In contrast to all previously solved C-protein structures, each protein subunit has two extra helices at the C-terminus, which play a large part in maintaining the dimer interface. The DNA binding site of the protein is also novel, having largely AAAA tracts between the palindromic recognition half-sites, suggesting tight bending of the DNA. The protein structure shows an unusual positively charged surface that could form the basis for wrapping the DNA completely around the C-protein dimer.
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Affiliation(s)
- J.E. McGeehan
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | | | | | | | | | - G.G. Kneale
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
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34
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Nagornykh M, Zakharova M, Protsenko A, Bogdanova E, Solonin AS, Severinov K. Regulation of gene expression in restriction-modification system Eco29kI. Nucleic Acids Res 2011; 39:4653-63. [PMID: 21310712 PMCID: PMC3113576 DOI: 10.1093/nar/gkr055] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Eco29kI restriction-modification (R-M) system consists of two partially overlapping genes, eco29kIR, encoding a restriction endonuclease and eco29kIM, encoding methyltransferase. The two genes are thought to form an operon with the eco29kIR gene preceding the eco29kIM gene. Such an organization is expected to complicate establishment of plasmids containing this R-M system in naive hosts, since common logic dictates that methyltransferase should be synthesized first to protect the DNA from cleavage by the endonuclease. Here, we characterize the Eco29kI gene transcription. We show that a separate promoter located within the eco29kIR gene is sufficient to synthesize enough methyltransferase to completely modify host DNA. We further show that transcription from two intragenic antisense promoters strongly decreases the levels of eco29kIR gene transcripts. The antisense transcripts act by preventing translation initiation from the bicistronic eco29kIR–eco29kIM mRNA and causing its degradation. Both eco29kIM and antisense promoters are necessary for Eco29kI genes establishment and/or stable maintenance, indicating that they jointly contribute to coordinated expression of Eco29kI genes.
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Affiliation(s)
- Maxim Nagornykh
- Waksman Institute of Microbiology, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
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35
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Abstract
The restriction-modification system is a toxin-antitoxin mechanism of bacterial cells to resist phage attacks. High efficiency comes at a price of high maintenance costs: (1) a host cell dies whenever it loses restriction-modification genes and (2) whenever a plasmid with restriction-modification genes enters a naïve cell, modification enzyme (methylase) has to be expressed prior to the synthesis of the restriction enzyme (restrictase) or the cell dies. These phenomena imply a sophisticated regulatory mechanism. During the evolution several such mechanisms were developed, of which one relies on a special C(control)-protein, a short autoregulatory protein containing an HTH-domain. Given the extreme diversity among restriction-modification systems, one could expect that C-proteins had evolved into several groups that might differ in autoregulatory binding sites architecture. However, only a few C-proteins (and the corresponding binding sites) were known before this study. Bioinformatics studies applied to C-proteins and their binding sites were limited to groups of well-known C-proteins and lacked systematic analysis. In this work, the authors use bioinformatics techniques to discover 201 C-protein genes with predicted autoregulatory binding sites. The systematic analysis of the predicted sites allowed for the discovery of 10 structural classes of binding sites.
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36
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Streeter SD, McGeehan JE, Kneale GG. Overexpression, purification and preliminary X-ray diffraction analysis of the controller protein C.Csp231I from Citrobacter sp. RFL231. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:898-901. [PMID: 19724127 PMCID: PMC2795595 DOI: 10.1107/s1744309109028681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 07/20/2009] [Indexed: 11/12/2022]
Abstract
Restriction-modification controller proteins play an essential role in regulating the temporal expression of restriction-modification genes. The controller protein C.Csp231I represents a new class of controller proteins. The gene was sublconed to allow overexpression in Escherichia coli. The protein was purified to homogeneity and crystallized using the hanging-drop vapour-diffusion method. The crystals diffracted to 2.0 A resolution and belonged to space group P2(1). An electrophoretic mobility-shift assay provided evidence of strong binding of C.Csp231I to a sequence located upstream of the csp231IC start codon.
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Affiliation(s)
- S. D. Streeter
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, England
| | - J. E. McGeehan
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, England
| | - G. G. Kneale
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, England
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37
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Bogdanova E, Zakharova M, Streeter S, Taylor JEN, Heyduk T, Kneale G, Severinov K. Transcription regulation of restriction-modification system Esp1396I. Nucleic Acids Res 2009; 37:3354-66. [PMID: 19336410 PMCID: PMC2691842 DOI: 10.1093/nar/gkp210] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Revised: 03/03/2009] [Accepted: 03/13/2009] [Indexed: 01/12/2023] Open
Abstract
The convergently transcribed restriction (R) and methylase (M) genes of the Restriction-Modification system Esp1396I are tightly regulated by a controller (C) protein that forms part of the CR operon. We have mapped the transcriptional start sites from each promoter and examined the regulatory role of C.Esp1396I in vivo and in vitro. C-protein binding at the CR and M promoters was analyzed by DNA footprinting and a range of biophysical techniques. The distal and proximal C-protein binding sites at the CR promoter are responsible for activation and repression, respectively. In contrast, a C-protein dimer binds to a single site at the M-promoter to repress the gene, with an affinity much greater than for the CR promoter. Thus, during establishment of the system in a naïve host, the activity of the M promoter is turned off early, preventing excessive synthesis of methylase. Mutational analysis of promoter binding sites reveals that the tetranucleotide inverted repeats long believed to be important for C-protein binding to DNA are less significant than previously thought. Instead, symmetry-related elements outside of these repeats appear to be critical for the interaction and are discussed in terms of the recent crystal structure of C.Esp139I bound to the CR promoter.
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Affiliation(s)
- Ekaterina Bogdanova
- Waksman Institute for Microbiology, Department of
Biochemistry and Molecular Biology, Rutgers, the State University of New Jersey,
Piscataway, NJ 08854 USA, Institute of Biochemistry and Physiology of
Microorganisms, Russian Academy of Sciences, Pushchino, 142292 Russia,
Institute of Biomedical and Biomolecular Sciences, University of
Portsmouth, Portsmouth PO1 2DT, UK, E. A. Doisy Department of
Biochemistry and Molecular Biology, St Louis University Medical School, St Louis, MO
63104, USA and Institutes of Molecular Genetics and Gene Biology,
Russian Academy of Sciences, Moscow, Russia
| | - Marina Zakharova
- Waksman Institute for Microbiology, Department of
Biochemistry and Molecular Biology, Rutgers, the State University of New Jersey,
Piscataway, NJ 08854 USA, Institute of Biochemistry and Physiology of
Microorganisms, Russian Academy of Sciences, Pushchino, 142292 Russia,
Institute of Biomedical and Biomolecular Sciences, University of
Portsmouth, Portsmouth PO1 2DT, UK, E. A. Doisy Department of
Biochemistry and Molecular Biology, St Louis University Medical School, St Louis, MO
63104, USA and Institutes of Molecular Genetics and Gene Biology,
Russian Academy of Sciences, Moscow, Russia
| | - Simon Streeter
- Waksman Institute for Microbiology, Department of
Biochemistry and Molecular Biology, Rutgers, the State University of New Jersey,
Piscataway, NJ 08854 USA, Institute of Biochemistry and Physiology of
Microorganisms, Russian Academy of Sciences, Pushchino, 142292 Russia,
Institute of Biomedical and Biomolecular Sciences, University of
Portsmouth, Portsmouth PO1 2DT, UK, E. A. Doisy Department of
Biochemistry and Molecular Biology, St Louis University Medical School, St Louis, MO
63104, USA and Institutes of Molecular Genetics and Gene Biology,
Russian Academy of Sciences, Moscow, Russia
| | - James E. N. Taylor
- Waksman Institute for Microbiology, Department of
Biochemistry and Molecular Biology, Rutgers, the State University of New Jersey,
Piscataway, NJ 08854 USA, Institute of Biochemistry and Physiology of
Microorganisms, Russian Academy of Sciences, Pushchino, 142292 Russia,
Institute of Biomedical and Biomolecular Sciences, University of
Portsmouth, Portsmouth PO1 2DT, UK, E. A. Doisy Department of
Biochemistry and Molecular Biology, St Louis University Medical School, St Louis, MO
63104, USA and Institutes of Molecular Genetics and Gene Biology,
Russian Academy of Sciences, Moscow, Russia
| | - Tomasz Heyduk
- Waksman Institute for Microbiology, Department of
Biochemistry and Molecular Biology, Rutgers, the State University of New Jersey,
Piscataway, NJ 08854 USA, Institute of Biochemistry and Physiology of
Microorganisms, Russian Academy of Sciences, Pushchino, 142292 Russia,
Institute of Biomedical and Biomolecular Sciences, University of
Portsmouth, Portsmouth PO1 2DT, UK, E. A. Doisy Department of
Biochemistry and Molecular Biology, St Louis University Medical School, St Louis, MO
63104, USA and Institutes of Molecular Genetics and Gene Biology,
Russian Academy of Sciences, Moscow, Russia
| | - Geoff Kneale
- Waksman Institute for Microbiology, Department of
Biochemistry and Molecular Biology, Rutgers, the State University of New Jersey,
Piscataway, NJ 08854 USA, Institute of Biochemistry and Physiology of
Microorganisms, Russian Academy of Sciences, Pushchino, 142292 Russia,
Institute of Biomedical and Biomolecular Sciences, University of
Portsmouth, Portsmouth PO1 2DT, UK, E. A. Doisy Department of
Biochemistry and Molecular Biology, St Louis University Medical School, St Louis, MO
63104, USA and Institutes of Molecular Genetics and Gene Biology,
Russian Academy of Sciences, Moscow, Russia
| | - Konstantin Severinov
- Waksman Institute for Microbiology, Department of
Biochemistry and Molecular Biology, Rutgers, the State University of New Jersey,
Piscataway, NJ 08854 USA, Institute of Biochemistry and Physiology of
Microorganisms, Russian Academy of Sciences, Pushchino, 142292 Russia,
Institute of Biomedical and Biomolecular Sciences, University of
Portsmouth, Portsmouth PO1 2DT, UK, E. A. Doisy Department of
Biochemistry and Molecular Biology, St Louis University Medical School, St Louis, MO
63104, USA and Institutes of Molecular Genetics and Gene Biology,
Russian Academy of Sciences, Moscow, Russia
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38
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Mruk I, Blumenthal RM. Tuning the relative affinities for activating and repressing operators of a temporally regulated restriction-modification system. Nucleic Acids Res 2009; 37:983-98. [PMID: 19126580 PMCID: PMC2647307 DOI: 10.1093/nar/gkn1010] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Most type II restriction-modification (R-M) systems produce separate endonuclease (REase) and methyltransferase (MTase) proteins. After R-M genes enter a new cell, MTase activity must appear before REase or the host chromosome will be cleaved. Temporal control of these genes thus has life-or-death consequences. PvuII and some other R-M systems delay endonuclease expression by cotranscribing the REase gene with the upstream gene for an autogenous activator/repressor (C protein). C.PvuII was previously shown to have low levels early, but positive feedback later boosts transcription of the C and REase genes. The MTase is expressed without delay, and protects the host DNA. C.PvuII binds to two sites upstream of its gene: OL, associated with activation, and OR, associated with repression. Even when symmetry elements of each operator are made identical, C.PvuII binds preferentially to OL. In this study, the intra-operator spacers are shown to modulate relative C.PvuII affinity. In light of a recently reported C.Esp1396I-DNA co-crystal structure, in vitro and in vivo effects of altering OL and OR spacers were determined. The results suggest that the GACTnnnAGTC consensus is the primary determinant of C.PvuII binding affinity, with intra-operator spacers playing a fine-tuning role that affects mobility of this R-M system.
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Affiliation(s)
- Iwona Mruk
- Department of Medical Microbiology and Immunology, University of Toledo Health Sciences Campus, Toledo, OH 43614-2598, USA
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Sorokin V, Severinov K, Gelfand MS. Systematic prediction of control proteins and their DNA binding sites. Nucleic Acids Res 2008; 37:441-51. [PMID: 19056824 PMCID: PMC2632904 DOI: 10.1093/nar/gkn931] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
We present here the results of a systematic bioinformatics analysis of control (C) proteins, a class of DNA-binding regulators that control time-delayed transcription of their own genes as well as restriction endonuclease genes in many type II restriction-modification systems. More than 290 C protein homologs were identified and DNA-binding sites for ∼70% of new and previously known C proteins were predicted by a combination of phylogenetic footprinting and motif searches in DNA upstream of C protein genes. Additional analysis revealed that a large proportion of C protein genes are translated from leaderless RNA, which may contribute to time-delayed nature of genetic switches operated by these proteins. Analysis of genetic contexts of newly identified C protein genes revealed that they are not exclusively associated with restriction-modification genes; numerous instances of associations with genes originating from mobile genetic elements were observed. These instances might be vestiges of ancient horizontal transfers and indicate that during evolution ancestral restriction-modification system genes were the sites of mobile elements insertions.
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Affiliation(s)
- Valeriy Sorokin
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
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40
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McGeehan JE, Streeter SD, Thresh SJ, Ball N, Ravelli RBG, Kneale GG. Structural analysis of the genetic switch that regulates the expression of restriction-modification genes. Nucleic Acids Res 2008; 36:4778-87. [PMID: 18644840 PMCID: PMC2504287 DOI: 10.1093/nar/gkn448] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Controller (C) proteins regulate the timing of the expression of restriction and modification (R–M) genes through a combination of positive and negative feedback circuits. A single dimer bound to the operator switches on transcription of the C-gene and the endonuclease gene; at higher concentrations, a second dimer bound adjacently switches off these genes. Here we report the first structure of a C protein–DNA operator complex, consisting of two C protein dimers bound to the native 35 bp operator sequence of the R–M system Esp1396I. The structure reveals a role for both direct and indirect DNA sequence recognition. The structure of the DNA in the complex is highly distorted, with severe compression of the minor groove resulting in a 50° bend within each operator site, together with a large expansion of the major groove in the centre of the DNA sequence. Cooperative binding between dimers governs the concentration-dependent activation–repression switch and arises, in part, from the interaction of Glu25 and Arg35 side chains at the dimer–dimer interface. Competition between Arg35 and an equivalent residue of the σ70 subunit of RNA polymerase for the Glu25 site underpins the switch from activation to repression of the endonuclease gene.
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Affiliation(s)
- John E McGeehan
- Biophysics Laboratories, School of Biological Sciences, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth PO1 2DT, UK
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41
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Mruk I, Blumenthal RM. Real-time kinetics of restriction-modification gene expression after entry into a new host cell. Nucleic Acids Res 2008; 36:2581-93. [PMID: 18334533 PMCID: PMC2377437 DOI: 10.1093/nar/gkn097] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Most type II restriction-modification (R-M) systems produce separate restriction endonuclease (REase) and methyltransferase (MTase) proteins. After R-M system genes enter a new cell, protective MTase must appear before REase to avoid host chromosome cleavage. The basis for this apparent temporal regulation is not well understood. PvuII and some other R-M systems appear to achieve this delay by cotranscribing the REase gene with the gene for an autogenous transcription activator/repressor (the 'C' protein C.PvuII). To test this model, bacteriophage M13 was used to introduce the PvuII genes into a bacterial population in a relatively synchronous manner. REase mRNA and activity appeared approximately 10 min after those of the MTase, but never rose if there was an inactivating pvuIIC mutation. Infection with recombinant M13pvuII phage had little effect on cell growth, relative to infection with parental M13. However, infection of cells pre-expressing C.PvuII led to cessation of growth. This study presents the first direct demonstration of delayed REase expression, relative to MTase, when type II R-M genes enter a new host cell. Surprisingly, though the C and REase genes are cotranscribed, the pvuIIC portion of the mRNA was more abundant than the pvuIIR portion after stable establishment of the R-M system.
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Affiliation(s)
- Iwona Mruk
- Department of Medical Microbiology and Immunology, University of Toledo Health Sciences Campus, Toledo, OH 43614-2598, USA.
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