1
|
Kudryavtseva AA, Cséfalvay E, Gnuchikh EY, Yanovskaya DD, Skutel MA, Isaev AB, Bazhenov SV, Utkina AA, Manukhov IV. Broadness and specificity: ArdB, ArdA, and Ocr against various restriction-modification systems. Front Microbiol 2023; 14:1133144. [PMID: 37138625 PMCID: PMC10149784 DOI: 10.3389/fmicb.2023.1133144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 03/10/2023] [Indexed: 05/05/2023] Open
Abstract
ArdB, ArdA, and Ocr proteins inhibit the endonuclease activity of the type I restriction-modification enzymes (RMI). In this study, we evaluated the ability of ArdB, ArdA, and Ocr to inhibit different subtypes of Escherichia coli RMI systems (IA, IB, and IC) as well as two Bacillus licheniformis RMI systems. Furthermore we explored, the antirestriction activity of ArdA, ArdB, and Ocr against a type III restriction-modification system (RMIII) EcoPI and BREX. We found that DNA-mimic proteins, ArdA and Ocr exhibit different inhibition activity, depending on which RM system tested. This effect might be linked to the DNA mimicry nature of these proteins. In theory, DNA-mimic might competitively inhibit any DNA-binding proteins; however, the efficiency of inhibition depend on the ability to imitate the recognition site in DNA or its preferred conformation. In contrast, ArdB protein with an undescribed mechanism of action, demonstrated greater versatility against various RMI systems and provided similar antirestriction efficiency regardless of the recognition site. However, ArdB protein could not affect restriction systems that are radically different from the RMI such as BREX or RMIII. Thus, we assume that the structure of DNA-mimic proteins allows for selective inhibition of any DNA-binding proteins depending on the recognition site. In contrast, ArdB-like proteins inhibit RMI systems independently of the DNA recognition site.
Collapse
Affiliation(s)
- Anna A. Kudryavtseva
- Laboratory for Molecular Genetics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- *Correspondence: Anna A. Kudryavtseva
| | - Eva Cséfalvay
- Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology, Academy of Sciences of the Czech Republic, Nové Hrady, Czechia
| | - Evgeniy Yu Gnuchikh
- Kurchatov Genomic Center, National Research Center Kurchatov Institute, Moscow, Russia
| | - Darya D. Yanovskaya
- Center of Cellular and Molecular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Mikhail A. Skutel
- Center of Cellular and Molecular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Artem B. Isaev
- Center of Cellular and Molecular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Sergey V. Bazhenov
- Laboratory for Molecular Genetics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Laboratory for Microbiology, BIOTECH University, Moscow, Russia
- Faculty of Physics, HSE University, Moscow, Russia
| | - Anna A. Utkina
- Laboratory for Molecular Genetics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ilya V. Manukhov
- Laboratory for Molecular Genetics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Laboratory for Microbiology, BIOTECH University, Moscow, Russia
- Faculty of Physics, HSE University, Moscow, Russia
| |
Collapse
|
2
|
Shen Z, Tang CM, Liu GY. Towards a better understanding of antimicrobial resistance dissemination: what can be learnt from studying model conjugative plasmids? Mil Med Res 2022; 9:3. [PMID: 35012680 PMCID: PMC8744291 DOI: 10.1186/s40779-021-00362-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/26/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteria can evolve rapidly by acquiring new traits such as virulence, metabolic properties, and most importantly, antimicrobial resistance, through horizontal gene transfer (HGT). Multidrug resistance in bacteria, especially in Gram-negative organisms, has become a global public health threat often through the spread of mobile genetic elements. Conjugation represents a major form of HGT and involves the transfer of DNA from a donor bacterium to a recipient by direct contact. Conjugative plasmids, a major vehicle for the dissemination of antimicrobial resistance, are selfish elements capable of mediating their own transmission through conjugation. To spread to and survive in a new bacterial host, conjugative plasmids have evolved mechanisms to circumvent both host defense systems and compete with co-resident plasmids. Such mechanisms have mostly been studied in model plasmids such as the F plasmid, rather than in conjugative plasmids that confer antimicrobial resistance (AMR) in important human pathogens. A better understanding of these mechanisms is crucial for predicting the flow of antimicrobial resistance-conferring conjugative plasmids among bacterial populations and guiding the rational design of strategies to halt the spread of antimicrobial resistance. Here, we review mechanisms employed by conjugative plasmids that promote their transmission and establishment in Gram-negative bacteria, by following the life cycle of conjugative plasmids.
Collapse
Affiliation(s)
- Zhen Shen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.,Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Guang-Yu Liu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.
| |
Collapse
|
3
|
Melkina OE, Zavilgelsky GB. N-Domain of ArdA Antirestriction Proteins Inhibits the Repression Activity of the Histone-Like H-NS Protein. Mol Biol 2021. [DOI: 10.1134/s0026893321020266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
4
|
Ben-Assa N, Coyne MJ, Fomenkov A, Livny J, Robins WP, Muniesa M, Carey V, Carasso S, Gefen T, Jofre J, Roberts RJ, Comstock LE, Geva-Zatorsky N. Analysis of a phase-variable restriction modification system of the human gut symbiont Bacteroides fragilis. Nucleic Acids Res 2020; 48:11040-11053. [PMID: 33045731 PMCID: PMC7641763 DOI: 10.1093/nar/gkaa824] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 09/10/2020] [Accepted: 10/06/2020] [Indexed: 11/28/2022] Open
Abstract
The genomes of gut Bacteroidales contain numerous invertible regions, many of which contain promoters that dictate phase-variable synthesis of surface molecules such as polysaccharides, fimbriae, and outer surface proteins. Here, we characterize a different type of phase-variable system of Bacteroides fragilis, a Type I restriction modification system (R-M). We show that reversible DNA inversions within this R-M locus leads to the generation of eight specificity proteins with distinct recognition sites. In vitro grown bacteria have a different proportion of specificity gene combinations at the expression locus than bacteria isolated from the mammalian gut. By creating mutants, each able to produce only one specificity protein from this region, we identified the R-M recognition sites of four of these S-proteins using SMRT sequencing. Transcriptome analysis revealed that the locked specificity mutants, whether grown in vitro or isolated from the mammalian gut, have distinct transcriptional profiles, likely creating different phenotypes, one of which was confirmed. Genomic analyses of diverse strains of Bacteroidetes from both host-associated and environmental sources reveal the ubiquity of phase-variable R-M systems in this phylum.
Collapse
Affiliation(s)
- Nadav Ben-Assa
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Technion Integrated Cancer Center (TICC), Haifa, 3525422 Israel
| | - Michael J Coyne
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Jonathan Livny
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - William P Robins
- Department of Microbiology, Harvard Medical School, Boston, 02115, MA, USA
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, Avda. Diagonal 643 08028 Barcelona Spain
| | - Vincent Carey
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shaqed Carasso
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Technion Integrated Cancer Center (TICC), Haifa, 3525422 Israel
| | - Tal Gefen
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Technion Integrated Cancer Center (TICC), Haifa, 3525422 Israel
| | - Juan Jofre
- Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, Avda. Diagonal 643 08028 Barcelona Spain
| | | | - Laurie E Comstock
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Naama Geva-Zatorsky
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Technion Integrated Cancer Center (TICC), Haifa, 3525422 Israel.,Canadian Institute for Advanced Research (CIFAR) Azrieli Global Scholar, MaRS Centre, West Tower 661 University Ave., Suite 505 Toronto, ON M5G 1M1, Canada
| |
Collapse
|
5
|
Liang W, Tang Y, Li G, Shen P, Tian Y, Jiang H, Jiang X, Lu Y. KlcA HS genes are ubiquitous in clinical, bla KPC-2-positive, Klebsiella pneumoniae isolates. INFECTION GENETICS AND EVOLUTION 2019; 70:84-89. [PMID: 30807842 DOI: 10.1016/j.meegid.2019.02.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 02/14/2019] [Accepted: 02/18/2019] [Indexed: 01/28/2023]
Abstract
Carbapenemase-producing Klebsiella pneumoniae has emerged and spread widely throughout the world. The mechanisms involved remain unclear. To provide insight, five plasmids were obtained from carbapenemase-producing K. pneumoniae clinical isolates. The five sequences were acquired, aligned and analyzed. In addition to the blaKPC-2 gene, which encodes beta lactamase, essentially all the plasmids contained a putative anti-restriction protein-encoding gene, KlcAHS. The KlcAHS gene was found in 98.2% of the blaKPC-2-positive, imipenem-resistant K. pneumoniae clinical isolates and in <1% of the blaKPC-2-negative control group. A searched of the GenBank database indicated that KlcAHS was mainly submitted by Chinese investigators beginning in 2010. Seventeen different KlcA amino acid sequences were found in the database using the restricting words: KlcA and Klebsiella pneumoniae. These sequences were used to generate a phylogenetic tree via MEGA6 software, revealing a distant evolutionary relationship between KlcAHS and other KlcAs. The secondary structure of KlcAHS, predicted with PROMALS3D software, exhibited highly conserved α-helices and β-strands. KlcAHS expressed anti-restriction activity in vivo. In summary, KlcAHS genes are ubiquitous in blaKPC-2-positive Klebsiella pneumoniae clinical isolates collected at Huashan Hospital, China. The KlcAHS protein possesses a secondary structure similar to that exhibited by anti-restriction proteins and displays anti-restriction activity. As such, KlcAHS is a probable factor in the accelerated spread of blaKPC-2 and carbapenem-resistance among clinical, K. pneumoniae isolates.
Collapse
Affiliation(s)
- Wei Liang
- Department of Laboratory Medicine, the Second People's Hospital of Lianyungang City, Jiangsu Province, China
| | - Yu Tang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Gang Li
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Pinghua Shen
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yueru Tian
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Haoqin Jiang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaofei Jiang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Yuan Lu
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
| |
Collapse
|
6
|
Kudryavtseva AA, Osetrova MS, Livinyuk VY, Manukhov IV, Zavilgelsky GB. The importance of C-terminal aspartic acid residue (D141) to the antirestriction activity of the ArdB (R64) protein. Mol Biol 2017. [DOI: 10.1134/s0026893317050119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
7
|
Melkina OE, Goryanin II, Zavilgelsky GB. Histone-like protein H-NS as a negative regulator of quorum sensing systems in gram-negative bacteria. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417020065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
8
|
Melkina OE, Goryanin II, Zavilgelsky GB. The DNA-mimic antirestriction proteins ArdA ColIB-P9, Arn T4, and Ocr T7 as activators of H-NS-dependent gene transcription. Microbiol Res 2016; 192:283-291. [PMID: 27664747 DOI: 10.1016/j.micres.2016.07.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/16/2016] [Accepted: 07/28/2016] [Indexed: 11/16/2022]
Abstract
The antirestriction proteins ArdA ColIb-P9, Arn T4 and Ocr T7 specifically inhibit type I and type IV restriction enzymes and belong to the family of DNA-mimic proteins because their three-dimensional structure is similar to the double-helical B-form DNA. It is proposed that the DNA-mimic proteins are able to bind nucleoid protein H-NS and alleviate H-NS-silencing of the transcription of bacterial genes. Escherichia coli lux biosensors were constructed by inserting H-NS-dependent promoters into a vector, thereby placing each fragment upstream of the promoterless Photorhabdus luminescens luxCDABE operon. It was demonstrated that the DNA-mimic proteins ArdA, Arn and Ocr activate the transcription of H-NS-dependent promoters of the lux operon of marine luminescent bacteria (mesophilic Aliivibrio fischeri and psychrophilic Aliivibrio logei), and the dps gene from E. coli. It was also demonstrated that the ArdA antirestriction protein, the genes of which are located on transmissive plasmids ColIb-P9, R64, PK101, decreases levels of H-NS silencing of the PluxC promoter during conjugation in the recipient bacteria.
Collapse
Affiliation(s)
- Olga E Melkina
- Laboratory of Bacterial Genetics, State Research Institute of Genetics and Selection of Industrial Microorganisms (GosNIIgenetika), 1-st Dorozhniy Pr., 1, Moscow 117545, Russia
| | - Ignatiy I Goryanin
- Laboratory of Bacterial Genetics, State Research Institute of Genetics and Selection of Industrial Microorganisms (GosNIIgenetika), 1-st Dorozhniy Pr., 1, Moscow 117545, Russia; Laboratory of Molecular Genetics, Moscow Institute of Physics and Technology, 9 Instituitsky per., Dolgoprudny, Moscow Region 141700, Russia
| | - Gennadii B Zavilgelsky
- Laboratory of Bacterial Genetics, State Research Institute of Genetics and Selection of Industrial Microorganisms (GosNIIgenetika), 1-st Dorozhniy Pr., 1, Moscow 117545, Russia.
| |
Collapse
|
9
|
Zavilgelsky GB, Kotova VY, Melkina OE, Balabanov VP, Mindlin SZ. Proteolytic control of the antirestriction activity of Tn21, Tn5053, Tn5045, Tn501, and Tn402 non-conjugative transposons. Mol Biol 2015. [DOI: 10.1134/s0026893315020168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
10
|
Zavilgelsky GB, Kotova VY, Melkina OE, Pustovoit KS. Antirestriction activity of the mercury resistance nonconjugative transposon Tn5053 is controlled by the protease ClpXP. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414090166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
11
|
Balabanov VP, Kotova VY, Kholodii GY, Mindlin SZ, Zavilgelsky GB. A novel gene, ardD, determines antirestriction activity of the non-conjugative transposon Tn5053 and is located antisense within the tniA gene. FEMS Microbiol Lett 2012; 337:55-60. [PMID: 22967207 PMCID: PMC3533173 DOI: 10.1111/1574-6968.12005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 09/05/2012] [Accepted: 09/05/2012] [Indexed: 12/03/2022] Open
Abstract
The mercury-resistance transposon Tn5053 inhibits restriction activity of the type I restriction-modification endonuclease EcoKI in Escherichia coli K12 cells. This is the first report of antirestriction activity of a non-conjugative transposon. The gene (ardD) coding for the antirestriction protein has been cloned. The ardD gene is located within the tniA gene, coding for transposase, on the complementary strand. The direction of transcription is opposite to transcription of the tniA gene.
Collapse
Affiliation(s)
- Vladimir P Balabanov
- State Research Institute of Genetics and Selection of Industrial Microorganisms (GosNIIgenetika), Moscow, Russia
| | | | | | | | | |
Collapse
|
12
|
Balabanov VP, Pustovoit KS, Zavilgelsky GB. Comparative analysis of antirestriction activity of the ArdA and ArdB proteins encoded by genes of the R64 transmissible plasmid (IncI1). Mol Biol 2012. [DOI: 10.1134/s0026893312010025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
13
|
Johnson TJ, Shepard SM, Rivet B, Danzeisen JL, Carattoli A. Comparative genomics and phylogeny of the IncI1 plasmids: A common plasmid type among porcine enterotoxigenic Escherichia coli. Plasmid 2011; 66:144-51. [DOI: 10.1016/j.plasmid.2011.07.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 07/17/2011] [Accepted: 07/19/2011] [Indexed: 11/25/2022]
|
14
|
Garcillán-Barcia MP, Alvarado A, de la Cruz F. Identification of bacterial plasmids based on mobility and plasmid population biology. FEMS Microbiol Rev 2011; 35:936-56. [PMID: 21711366 DOI: 10.1111/j.1574-6976.2011.00291.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Plasmids contain a backbone of core genes that remains relatively stable for long evolutionary periods, making sense to speak about plasmid species. The identification and characterization of the core genes of a plasmid species has a special relevance in the study of its epidemiology and modes of transmission. Besides, this knowledge will help to unveil the main routes that genes, for example antibiotic resistance (AbR) genes, use to travel from environmental reservoirs to human pathogens. Global dissemination of multiple antibiotic resistances and virulence traits by plasmids is an increasing threat for the treatment of many bacterial infectious diseases. To follow the dissemination of virulence and AbR genes, we need to identify the causative plasmids and follow their path from reservoirs to pathogens. In this review, we discuss how the existing diversity in plasmid genetic structures gives rise to a large diversity in propagation strategies. We would like to propose that, using an identification methodology based on plasmid mobility types, we can follow the propagation routes of most plasmids in Gammaproteobacteria, as well as their cargo genes, in complex ecosystems. Once the dissemination routes are known, designing antidissemination drugs and testing their efficacy will become feasible. We discuss in this review how the existing diversity in plasmid genetic structures gives rise to a large diversity in propagation strategies. We would like to propose that, by using an identification methodology based on plasmid mobility types, we can follow the propagation routes of most plasmids in ?-proteobacteria, as well as their cargo genes, in complex ecosystems.
Collapse
Affiliation(s)
- Maria Pilar Garcillán-Barcia
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC-IDICAN, C. Herrera Oria s/n, Santander, Spain
| | | | | |
Collapse
|
15
|
Zavilgelsky GB, Kotova VY, Rastorguev SM. Antimodification activity of the ArdA and Ocr proteins. RUSS J GENET+ 2011. [DOI: 10.1134/s1022795410081034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
16
|
Zavilgelsky GB, Rastorguev SM. Antirestriction proteins ArdA and Ocr as efficient inhibitors of type I restriction-modification enzymes. Mol Biol 2009. [DOI: 10.1134/s0026893309020071] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
17
|
Zavilgelsky GB, Rastorguev SM. DNA mimicry by proteins as effective mechanism for regulation of activity of DNA-dependent enzymes. BIOCHEMISTRY (MOSCOW) 2007; 72:913-9, 4 p. following 982. [DOI: 10.1134/s0006297907090015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
18
|
Nekrasov SV, Agafonova OV, Belogurova NG, Delver EP, Belogurov AA. Plasmid-encoded antirestriction protein ArdA can discriminate between type I methyltransferase and complete restriction-modification system. J Mol Biol 2006; 365:284-97. [PMID: 17069852 DOI: 10.1016/j.jmb.2006.09.087] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2006] [Revised: 09/25/2006] [Accepted: 09/27/2006] [Indexed: 10/24/2022]
Abstract
Many promiscuous plasmids encode the antirestriction proteins ArdA (alleviation of restriction of DNA) that specifically affect the restriction activity of heterooligomeric type I restriction-modification (R-M) systems in Escherichia coli cells. In addition, a lot of the putative ardA genes encoded by plasmids and bacterial chromosomes are found as a result of sequencing of complete genomic sequences, suggesting that ArdA proteins and type I R-M systems that seem to be widespread among bacteria may be involved in the regulation of gene transfer among bacterial genomes. Here, the mechanism of antirestriction action of ArdA encoded by IncI plasmid ColIb-P9 has been investigated in comparison with that of well-studied T7 phage-encoded antirestriction protein Ocr using the mutational analysis, retardation assay and His-tag affinity chromatography. Like Ocr, ArdA protein was shown to be able to efficiently interact with EcoKI R-M complex and affect its in vivo and in vitro restriction activity by preventing its interaction with specific DNA. However, unlike Ocr, ArdA protein has a low binding affinity to EcoKI Mtase and the additional C-terminal tail region (VF-motif) is needed for ArdA to efficiently interact with the type I R-M enzymes. It seems likely that this ArdA feature is a basis for its ability to discriminate between activities of EcoKI Mtase (modification) and complete R-M system (restriction) which may interact with unmodified DNA in the cells independently. These findings suggest that ArdA may provide a very effective and delicate control for the restriction and modification activities of type I systems and its ability to discriminate against DNA restriction in favour of the specific modification of DNA may give some advantage for efficient transmission of the ardA-encoding promiscuous plasmids among different bacterial populations.
Collapse
Affiliation(s)
- Sergei V Nekrasov
- Department of Genetic Engineering, National Cardiology Research and Development Center, Moscow 121552, Russia
| | | | | | | | | |
Collapse
|
19
|
Zavilgelsky GB, Letuchaya TA, Rastorguev SM. Antirestriction and antimodification activities of the ArdA protein encoded by the IncI1 transmissive plasmids R-64 and ColIb-P9. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406030045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
20
|
Moreira LM, De Souza RF, Digiampietri LA, Da Silva ACR, Setubal JC. Comparative analyses of Xanthomonas and Xylella complete genomes. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2005; 9:43-76. [PMID: 15805778 DOI: 10.1089/omi.2005.9.43] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Computational analyses of four bacterial genomes of the Xanthomonadaceae family reveal new unique genes that may be involved in adaptation, pathogenicity, and host specificity. The Xanthomonas genus presents 3636 unique genes distributed in 1470 families, while Xylella genus presents 1026 unique genes distributed in 375 families. Among Xanthomonas-specific genes, we highlight a large number of cell wall degrading enzymes, proteases, and iron receptors, a set of energy metabolism genes, second copy of the type II secretion system, type III secretion system, flagella and chemotactic machinery, and the xanthomonadin synthesis gene cluster. Important genes unique to the Xylella genus are an additional copy of a type IV pili gene cluster and the complete machinery of colicin V synthesis and secretion. Intersections of gene sets from both genera reveal a cluster of genes homologous to Salmonella's SPI-7 island in Xanthomonas axonopodis pv citri and Xylella fastidiosa 9a5c, which might be involved in host specificity. Each genome also presents important unique genes, such as an HMS cluster, the kdgT gene, and O-antigen in Xanthomonas axonopodis pv citri; a number of avrBS genes and a distinct O-antigen in Xanthomonas campestris pv campestris, a type I restriction-modification system and a nickase gene in Xylella fastidiosa 9a5c, and a type II restriction-modification system and two genes related to peptidoglycan biosynthesis in Xylella fastidiosa temecula 1. All these differences imply a considerable number of gene gains and losses during the divergence of the four lineages, and are associated with structural genome modifications that may have a direct relation with the mode of transmission, adaptation to specific environments and pathogenicity of each organism.
Collapse
Affiliation(s)
- Leandro M Moreira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | | |
Collapse
|
21
|
Thomas AT, Brammar WJ, Wilkins BM. Plasmid R16 ArdA protein preferentially targets restriction activity of the type I restriction-modification system EcoKI. J Bacteriol 2003; 185:2022-5. [PMID: 12618468 PMCID: PMC150139 DOI: 10.1128/jb.185.6.2022-2025.2003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ArdA antirestriction protein of the IncB plasmid R16 selectively inhibited the restriction activity of EcoKI, leaving significant levels of modification activity under conditions in which restriction was almost completely prevented. The results are consistent with the hypothesis that ArdA functions in bacterial conjugation to allow an unmodified plasmid to evade restriction in the recipient bacterium and yet acquire cognate modification.
Collapse
Affiliation(s)
- Angela T Thomas
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
| | | | | |
Collapse
|
22
|
Affiliation(s)
- Brian M Wilkins
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK.
| |
Collapse
|
23
|
|
24
|
Belogurov AA, Delver EP, Agafonova OV, Belogurova NG, Lee LY, Kado CI. Antirestriction protein Ard (Type C) encoded by IncW plasmid pSa has a high similarity to the "protein transport" domain of TraC1 primase of promiscuous plasmid RP4. J Mol Biol 2000; 296:969-77. [PMID: 10686096 DOI: 10.1006/jmbi.1999.3493] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The IncW plasmid pSa contains the gene ard encoding an antirestriction function that is specific for type I restriction and modification systems. The nucleotide sequence of ard was determined and an appropriate polypeptide of about 33 kDa was identified in Escherichia coli T7 expression system. Analysis of deduced amino acid sequence of Ard encoded by pSa revealed that this protein has no significant similarities with the known Ard proteins (ArdA and ArdB types) except the "antirestriction" motif (14 amino acid residues in length) conserved for all known Ard proteins. This finding suggests that pSa Ard may be classified as a new type of Ard proteins which we designated ArdC. The remarkable feature of ArdC is that it has a high degree of similarity (about 38 % identity) to the N-terminal region of RP4 TraC1 primase which includes about 300 amino acid residues and seems to be essential for binding to the single-stranded DNA and TraC1 protein transport to the recipient cells during the conjugal transfer of plasmid DNA. ArdC also binds to single-stranded DNA. In addition, this protein is able in vitro to protect the single-stranded but not double-stranded plasmid DNA against the activity of type II restriction endonuclease HhaI that cleaves both single and double-stranded DNA. We suggest that like TraC1, ArdC would be transported as a result of their interaction with the single-stranded DNA of transferred plasmid strand during conjugative passage through the cell envelope to the recipient bacterium. Such properties of ArdC protein might be useful to protect immediately the incoming single-stranded DNA from the host endonucleases.
Collapse
Affiliation(s)
- A A Belogurov
- Department of Genetic Engineering, National Cardiological Research and Development Center, Moscow, 121552, Russia.
| | | | | | | | | | | |
Collapse
|
25
|
Szpirer C, Top E, Couturier M, Mergeay M. Retrotransfer or gene capture: a feature of conjugative plasmids, with ecological and evolutionary significance. MICROBIOLOGY (READING, ENGLAND) 1999; 145 ( Pt 12):3321-3329. [PMID: 10627031 DOI: 10.1099/00221287-145-12-3321] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Cedric Szpirer
- Laboratoire de Génétique des Prokaryotes, Université Libre de Bruxelles, IBMM, B-6041-Gosselies, Belgium1
| | - Eva Top
- Laboratory for Microbial Ecology and Technology, University of Gent, B-9000 Gent, Belgium2
| | - Martine Couturier
- Laboratoire de Génétique des Prokaryotes, Université Libre de Bruxelles, IBMM, B-6041-Gosselies, Belgium1
| | - Max Mergeay
- Laboratory of Microbiology, Radioactive Waste & Clean-up Division, Center of Studies for Nuclear Energy, SCK/CEN, B-2400 Mol, Belgium4
- Environmental Technology, Flemish Institute for Technological Research, VITO, B-2400 Mol, Belgium3
- Laboratoire de Génétique des Prokaryotes, Université Libre de Bruxelles, IBMM, B-6041-Gosselies, Belgium1
| |
Collapse
|
26
|
Abstract
The entire nucleotide sequence of the first DNA segment of the conjugative F plasmid to enter the recipient cell, the leading region, is described. Analysis of the sequence provides further evidence that products encoded within the 13.2-kb leading region are likely to be expressed and perform functions associated with the transferred strand in the recipient cell.
Collapse
Affiliation(s)
- N P Manwaring
- School of Biological Sciences, University of Sydney, New South Wales, 2006, Australia
| | | | | |
Collapse
|
27
|
Althorpe NJ, Chilley PM, Thomas AT, Brammar WJ, Wilkins BM. Transient transcriptional activation of the Incl1 plasmid anti-restriction gene (ardA) and SOS inhibition gene (psiB) early in conjugating recipient bacteria. Mol Microbiol 1999; 31:133-42. [PMID: 9987116 DOI: 10.1046/j.1365-2958.1999.01153.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The ardA gene of the enterobacterial plasmid CollbP-9 acts to alleviate restriction of DNA by type I systems, while psiB inhibits induction of the bacterial SOS response. Both genes are transferred early in a round of bacterial conjugation as part of the plasmid leading region. We report here that ardA and psiB are transcribed transiently after their conjugative transport into the recipient cell. Transcript levels, monitored by competitive reverse transcription-polymerase chain reaction (RT-PCR) amplification of RNA templates, started to increase about 5 min after the initiation of conjugation in a cell population and probably before the first round of plasmid transfer was completed. Genetic evidence is given that the expression of ardA and psiB is activated when the genes enter the recipient cell on the transferring plasmid strand. It is proposed that these and other leading region genes function to promote the establishment of the immigrant plasmid in the new host and are expressed by transcription from promoters active only in single-stranded DNA.
Collapse
Affiliation(s)
- N J Althorpe
- Department of Genetics, University of Leicester, UK
| | | | | | | | | |
Collapse
|
28
|
Rastorguev SM, Zavilgelsky GB, Tchurikov NA. IncI1 plasmid R64 encodes the ArsR protein that alleviates type I restriction. FEBS Lett 1998; 426:21-3. [PMID: 9598970 DOI: 10.1016/s0014-5793(98)00285-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The host-controlled EcoK restriction of unmodified phage lambda was five-fold alleviated in the wild-type Escherichia coli strain K12 carrying the R64 plasmid of the incompatibility group I1. The relevant gene was mapped between the origin of vegetative replication (rep, oriV) and the tet(r) gene about 60 kbp downstream from the origin of transfer, oriT. We cloned this gene inside the 613 bp long EcoRI-PstI fragment and sequenced it. Only one 351 bp long open reading frame (ORF) starting at 124 bp from the beginning of the insert was found in the sequence. Computer search in the current databases revealed that the putative protein is identical to the ArsR protein specified by the IncFI plasmid R773. ArsR is a repressor of the arsenical resistance (ars) operon, arsRDABC. There are no arsABC genes in the R64 plasmid since plasmid R64- (or pSR8)-mediated resistance of E. coli K12 cells to the arsenicals arsenate and arsenite was not detected. The gene arsR and the antirestriction genes ard (ardA and ardB) are non-homologous. However, comparison of the deduced amino acid sequence of ArsR with the ArdA and ArdB sequences revealed only one small region of similarity, a 9 amino acid motif found in different antirestriction proteins that is hypothesized to be an interaction site for antirestriction proteins with restriction endonucleases.
Collapse
Affiliation(s)
- S M Rastorguev
- State Scientific Centre of Russian Federation GNIIGENETIKA, Moscow
| | | | | |
Collapse
|
29
|
Delver EP, Belogurov AA. Organization of the leading region of IncN plasmid pKM101 (R46): a regulation controlled by CUP sequence elements. J Mol Biol 1997; 271:13-30. [PMID: 9300052 DOI: 10.1006/jmbi.1997.1124] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Analysis of the nucleotide sequence of the 13.8 kb leading region of the IncN plasmid pKM101 (a deletion derivative of R46) revealed eight copies of highly conserved repetitive elements, CUP (Conserved UPstream), and at least nine novel open reading frames (ORFs). Appropriate protein products were identified for eight ORFs and the analysis of their deduced amino acid sequences revealed similarities with some well-known proteins (KorA of RK2/RP4, RecX and PsiB) that may play a role in the adaptation of promiscuous plasmids to the new host. Comparison of CUP elements revealed that the CUP core is 417 nucleotides long and consists of two portions that markedly differ in GC content. The larger portion (307 nucleotides) of the core is about 74% GC and contains at least one NotI site, while the other (110 nucleotides) is only about 40% GC. The remarkable features of CUP elements is that five of them are oriented in the same direction and fused in a similar mode to the open reading frames (ORFs) that are able to encode unrelated proteins. The spacings between the right boundary of the CUP core and the potential ATG start codons of these ORFs are slightly different in length (16 to 18 bp), highly divergent in sequence but in all cases contain the conserved hexamer 5'-AGGAGT-3' at the position that is typical for the ribosome binding site of Escherichia coli. The A+T-rich portion of the CUP sequences contains the strong negatively regulated promoter and appears to function as a genetic switch that coordinately controls the expression of CUP-fused genes during the conjugal transfer. These findings suggest that seven plasmid genes fused to the CUP elements including repA and two ard genes encoding positively acting replication protein and antirestriction proteins, respectively, may be members of one regulatory network based on the CUP elements and two plasmid-encoded regulatory proteins ArdK and ArdR. At least, the ArdK protein may act as a typical repressor by binding to the promoter region of the CUP sequence. Most of the structural and functional features of organization of the CUP-controlled regulatory network are associated with the idea that the CUP elements may be involved in the natural genetic engineering process of organizing various functionally related genes in one regulon.
Collapse
Affiliation(s)
- E P Delver
- Department of Genetic Engineering, Cardiology Research Center, Moscow, Russia
| | | |
Collapse
|
30
|
Blázquez J, Navas A, Gonzalo P, MartÃnez J, Baquero F. Spread and evolution of natural plasmids harboring transposon Tn5. FEMS Microbiol Ecol 1996. [DOI: 10.1111/j.1574-6941.1996.tb00199.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
31
|
Clewell DB, Flannagan SE, Jaworski DD. Unconstrained bacterial promiscuity: the Tn916-Tn1545 family of conjugative transposons. Trends Microbiol 1995; 3:229-36. [PMID: 7648031 DOI: 10.1016/s0966-842x(00)88930-1] [Citation(s) in RCA: 266] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Conjugative transposons are highly ubiquitous elements found throughout the bacterial world. Members of the Tn916-Tn1545 family carry the widely disseminated tetracycline-resistance determinant Tet M, as well as additional resistance genes. They have been found naturally in, or been introduced into, over 50 different species and 24 genera of bacteria. Recent investigations have led to insights into the molecular basis of movement of these interesting mobile elements.
Collapse
Affiliation(s)
- D B Clewell
- Dept of Biologic and Materials Sciences, School of Dentistry, School of Medicine, University of Michigan, Ann Arbor 48109, USA
| | | | | |
Collapse
|
32
|
Belogurov AA, Delver EP. A motif conserved among the type I restriction-modification enzymes and antirestriction proteins: a possible basis for mechanism of action of plasmid-encoded antirestriction functions. Nucleic Acids Res 1995; 23:785-7. [PMID: 7708494 PMCID: PMC306760 DOI: 10.1093/nar/23.5.785] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Antirestriction proteins Ard encoded by some self-transmissible plasmids specifically inhibit restriction by members of all three families of type I restriction-modification (R-M) systems in E.coli. Recently, we have identified the amino acid region, 'antirestriction' domain, that is conserved within different plasmid and phage T7-encoded antirestriction proteins and may be involved in interaction with the type I R-M systems. In this paper we demonstrate that this amino acid sequence shares considerable similarity with a well-known conserved sequence (the Argos repeat) found in the DNA sequence specificity (S) polypeptides of type I systems. We suggest that the presence of these similar motifs in restriction and antirestriction proteins may give a structural basis for their interaction and that the antirestriction action of Ard proteins may be a result of the competition between the 'antirestriction' domains of Ard proteins and the similar conserved domains of the S subunits that are believed to play a role in the subunit assembly of type I R-M systems.
Collapse
Affiliation(s)
- A A Belogurov
- Department of Genetic Engineering, Cardiology Research Center, Moscow, Russia
| | | |
Collapse
|
33
|
Larsen MH, Figurski DH. Structure, expression, and regulation of the kilC operon of promiscuous IncP alpha plasmids. J Bacteriol 1994; 176:5022-32. [PMID: 7519596 PMCID: PMC196341 DOI: 10.1128/jb.176.16.5022-5032.1994] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The kil-kor regulon was first identified on the broad-host-range IncP alpha plasmid RK2 by the presence of multiple kil loci (kilA, kilB, kilC, and recently kilE) that are lethal to Escherichia coli host cells in the absence of regulation by kor functions in various combinations. Whereas the kilB operon is required for mating-pair formation during conjugation, the functions encoded by the other kil loci are not known. They are not essential for replication or conjugal transfer, but their coregulation with replication and transfer genes indicates that they are likely to be important for RK2. In this report, we describe molecular and genetic studies on kilC. We determined the nucleotide sequence of the kilC region, which is located between the origin of vegetative replication (oriV) and transposon Tn1 on RK2. Primer extension analysis identified the transcriptional start site and showed that a sequence corresponding to a strong sigma 70 promoter is functional. The abundance of RNA initiated from the kilC promoter is reduced in the presence of korA and korC, as predicted from genetic analysis of kilC regulation. The first gene of the kilC operon (klcA) is sufficient to express the host-lethal phenotype of the kilC determinant in the absence of korA and korC. By comparing RK2 to the related IncP alpha plasmids pUZ8 and R995, we determined that the Tn1 transposon in RK2 interrupts a gene (klcB) immediately downstream of klcA. Thus, the kilC determinant is normally part of an autoregulated operon of three genes: klcA, klcB, and korC. klcA is predicted to encode a 15,856-Da polypeptide that is related to the ArdB antirestriction protein of the IncN plasmid pKM101, suggesting a role for klcA in the broad host ranges of IncP alpha plasmids. The predicted product of the uninterrupted klcB gene is a polypeptide of 51,133 Da that contains a segment with significant similarity to the RK2 regulatory proteins KorA and TrbA. Located 145 bp upstream of the kilC promoter is a 10th copy of the 17-bp oriV iteron sequence in inverted orientation relative to that of the other nine iterons of oriV. Iteron 10 is identical to the "orphan" iteron 1, and both have identical 6-bp flanking sequences that make them likely to be strong binding sites for the TrfA replication initiator protein. The locations and relative orientation of orphan iterons 10 and 1 raise the possibility that these iterons promote the formation of a DNA loop via protein-protein interactions by bound TrfA and lead us to propose that they demarcate the functional origin of replication. This analysis of the kilC region and our previous studies on the other kil loci of RK2 have revealed that the region between oriV and the korABF operon in wild-type IncP alpha plasmids is saturated by the kilC, kilE, and kilA loci arranged in four kor-regulated operons encoding a total of 12 genes.
Collapse
Affiliation(s)
- M H Larsen
- Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, New York 10032
| | | |
Collapse
|
34
|
Belogurov AA, Delver EP, Rodzevich OV. Plasmid pKM101 encodes two nonhomologous antirestriction proteins (ArdA and ArdB) whose expression is controlled by homologous regulatory sequences. J Bacteriol 1993; 175:4843-50. [PMID: 8393008 PMCID: PMC204937 DOI: 10.1128/jb.175.15.4843-4850.1993] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The IncN plasmid pKM101 (a derivative of R46) encodes the antirestriction protein ArdB (alleviation of restriction of DNA) in addition to another antirestriction protein, ArdA, described previously. The relevant gene, ardB, was located in the leading region of pKM101, about 7 kb from oriT. The nucleotide sequence of ardB was determined, and an appropriate polypeptide was identified in maxicells of Escherichia coli. Like ArdA, ArdB efficiently inhibits restriction by members of the three known families of type I systems of E. coli and only slightly affects the type II enzyme, EcoRI. However, in contrast to ArdA, ArdB is ineffective against the modification activity of the type I (EcoK) system. Comparison of deduced amino acid sequences of ArdA and ArdB revealed only one small region of similarity (nine residues), suggesting that this region may be somehow involved in the interaction with the type I restriction systems. We also found that the expression of both ardA and ardB genes is controlled jointly by two pKM101-encoded proteins, ArdK and ArdR, with molecular weights of about 15,000 and 20,000, respectively. The finding that the sequences immediately upstream of ardA and ardB share about 94% identity over 218 bp suggests that their expression may be controlled by ArdK and ArdR at the transcriptional level. Deletion studies and promoter probe analysis of these sequences revealed the regions responsible for the action of ArdK and ArdR as regulatory proteins. We propose that both types of antirestriction proteins may play a pivotal role in overcoming the host restriction barrier by self-transmissible broad-host-range plasmids. It seems likely that the ardKR-dependent regulatory system serves in this case as a genetic switch that controls the expression of plasmid-encoded antirestriction functions during mating.
Collapse
Affiliation(s)
- A A Belogurov
- Department of Genetic Engineering, National Cardiology Research Center, Moscow, Russia
| | | | | |
Collapse
|
35
|
Abstract
Our understanding of the evolution of DNA restriction and modification systems, the control of the expression of the structural genes for the enzymes, and the importance of DNA restriction in the cellular economy has advanced by leaps and bounds in recent years. This review documents these advances for the three major classes of classical restriction and modification systems, describes the discovery of a new class of restriction systems that specifically cut DNA carrying the modification signature of foreign cells, and deals with the mechanisms developed by phages to avoid the restriction systems of their hosts.
Collapse
Affiliation(s)
- T A Bickle
- Department of Microbiology, Biozentrum, Basel University, Switzerland
| | | |
Collapse
|
36
|
Belogurov AA, Delver EP, Rodzevich OV. IncN plasmid pKM101 and IncI1 plasmid ColIb-P9 encode homologous antirestriction proteins in their leading regions. J Bacteriol 1992; 174:5079-85. [PMID: 1321121 PMCID: PMC206324 DOI: 10.1128/jb.174.15.5079-5085.1992] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The IncN plasmid pKM101 (a derivative of R46), like the IncI1 plasmid ColIb-P9, carries a gene (ardA, for alleviation of restriction of DNA) encoding an antirestriction function. ardA was located about 4 kb from the origin of transfer, in the region transferred early during bacterial conjugation. The nucleotide sequence of ardA was determined, and an appropriate polypeptide with the predicted molecular weight of about 19,500 was identified in maxicells of Escherichia coli. Comparison of the deduced amino acid sequences of the antirestriction proteins of the unrelated plasmids pKM101 and ColIb (ArdA and Ard, respectively) revealed that these proteins have about 60% identity. Like ColIb Ard, pKM101 ArdA specifically inhibits both the restriction and modification activities of five type I systems of E. coli tested and does not influence type III (EcoP1) restriction or the 5-methylcytosine-specific restriction systems McrA and McrB. However, in contrast to ColIb Ard, pKM101 ArdA is effective against the type II enzyme EcoRI. The Ard proteins are believed to overcome the host restriction barrier during bacterial conjugation. We have also identified two other genes of pKM101, ardR and ardK, which seem to control ardA activity and ardA-mediated lethality, respectively. Our findings suggest that ardR may serve as a genetic switch that determines whether the ardA-encoded antirestriction function is induced during mating.
Collapse
Affiliation(s)
- A A Belogurov
- Department of Genetic Engineering, National Cardiology Research Center, Moscow, Russia
| | | | | |
Collapse
|
37
|
Affiliation(s)
- C F Amábile-Cuevas
- Department of Molecular and Cellular Toxicology Harvard School of Public Health, Boston, Massachusetts 02115
| | | |
Collapse
|
38
|
Read TD, Thomas AT, Wilkins BM. Evasion of type I and type II DNA restriction systems by IncI1 plasmid CoIIb-P9 during transfer by bacterial conjugation. Mol Microbiol 1992; 6:1933-41. [PMID: 1508042 DOI: 10.1111/j.1365-2958.1992.tb01366.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Transmission of unmodified plasmid CoIIb-P9 by bacterial conjugation is markedly resistant to restriction compared with transfer by transformation. One process allowing evasion of type I and II restriction systems involves conjugative transfer of multiple copies of the plasmid. A more specialized evasion mechanism requires the Ard (alleviation of restriction of DNA) system encoded by CoIIb. The ard gene is transferred early in conjugation and specifically alleviates DNA restriction by all known families of type I enzyme, including EcoK. CoIIb has no effect on EcoK modification but this activity is impaired by multicopy recombinant plasmids supporting overexpression of ard. Genetic evidence shows that Ard protects CoIIb from EcoK restriction following conjugative transfer and that this protection requires expression of the gene on the immigrant plasmid. It is proposed that carriage of ard facilitates transfer of CoIIb between its natural enterobacterial hosts and that the route of DNA entry is important to the restriction-evasion mechanism.
Collapse
Affiliation(s)
- T D Read
- Department of Genetics, University of Leicester, UK
| | | | | |
Collapse
|
39
|
New nucleotide sequence data on the EMBL File Server. Nucleic Acids Res 1992; 20:627-40. [PMID: 1741309 PMCID: PMC310449 DOI: 10.1093/nar/20.3.627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
|