Plasmid-encoded Antirestriction Protein ArdA Can Discriminate between Type I Methyltransferase and Complete Restriction–Modification System

Journal of Molecular Biology - Tập 365 Số 2 - Trang 284-297 - 2007
Sergei V Nekrasov1, O. V. Agafonova, Nataly G Belogurova, Del'ver Ep, Belogurov Aa
1Department of Genetic Engineering, National Cardiology Research and Development Center, Moscow 121552, Russia.

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Wilkins, 1995, Gene transfer by bacterial conjugation: diversity of systems and functional specializations, 31

Thomas, 2000

Heinemann, 1989, Bacterial conjugative plasmids mobilize Dna transfer between bacteria and yeast, Nature, 340, 205, 10.1038/340205a0

Kado, 1998, Evolution of selfish Ti plasmids of Agrobacterium tumefaciens promoting horizontal gene transfer, 63

Waters, 2001, Conjugation between bacterial and mammalian cell, Nature Genet., 29, 375, 10.1038/ng779

Sonea, 1991, Bacterial evolution without speciation, 95

Amablie-Cuevas, 1992, Bacterial plasmids and gene flux, Cell, 70, 189, 10.1016/0092-8674(92)90095-T

Murray, 2000, Type I restriction systems: sophisticated machines (a legacy of Bertani and Weigle), Microbiol. Mol. Biol. Rev., 64, 412, 10.1128/MMBR.64.2.412-434.2000

Dryden, 2001, Nucleoside triphosphate-dependent restriction enzymes, Nucl. Acids Res., 29, 3728, 10.1093/nar/29.18.3728

Bourniquel, 2002, Complex restriction enzymes: NTP-driven molecular motor, Biochimie, 84, 1047, 10.1016/S0300-9084(02)00020-2

Murray, 2002, Immigration control of DNA in bacteria: self versus non-self, Microbiology, 148, 3, 10.1099/00221287-148-1-3

Endlich, 1985, The DNA restriction endonuclease of Escherichia coli B. Further studies of the structure of DNA intermediates and products, J. Biol. Chem., 260, 5729, 10.1016/S0021-9258(18)89083-4

Price, 1986, A possible role for DNA restriction in bacterial evolution, Microbiol Sci., 3, 296

Kruger, 1983, Bacteriophage survival: multiple mechanism for avoiding the deoxyribonucleic acid restriction systems of their host, Microbiol.Rev., 47, 345, 10.1128/MMBR.47.3.345-360.1983

Bickle, 1993, Biology of DNA restriction, Microbiol. Rev., 57, 434, 10.1128/MMBR.57.2.434-450.1993

Tork, 2005, The biology of restriction and anti-restriction, Curr. Opin. Microbiol., 8, 466, 10.1016/j.mib.2005.06.003

Belogurov, 1985, The novel gene(s) ard of plasmid pKM101: alleviation of EcoK restriction, Mol. Gen. Genet., 198, 509, 10.1007/BF00332948

Delver, 1991, Nucleotide sequence of the gene (ard) encoding the antirestriction protein of plasmid ColIb-P9, J. Bacteriol., 173, 5887, 10.1128/jb.173.18.5887-5892.1991

Read, 1992, Evasion of type I and type II DNA restriction systems by IncI1 plasmid ColIb-P9 during transfer by bacterial conjugation, Mol. Microbiol., 6, 1941, 10.1111/j.1365-2958.1992.tb01366.x

Belogurov, 1992, IncN plasmid pKM101 and IncI1 plasmid ColIb-P9 encode homologous antirestriction proteins in their leading regions, J. Bacteriol., 174, 5079, 10.1128/jb.174.15.5079-5085.1992

Belogurov, 1993, Plasmid pKM101 encodes two nonhomologous antirestriction proteins (ArdA and ArdB) whose expression is controlled by homologous regulatory sequences, J. Bacteriol., 175, 4843, 10.1128/jb.175.15.4843-4850.1993

Chilley, 1995, Distribution of the ardA family of antirestriction genes on conjugative plasmids, Microbiology, 141, 2157, 10.1099/13500872-141-9-2157

Belogurov, 2000, 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., 296, 969, 10.1006/jmbi.1999.3493

Belogurov, 1995, 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, Nucl. Acids Res., 23, 785, 10.1093/nar/23.5.785

Wilkins, 2002, Plasmid promiscuity: meteeng the challenge of DNA immigration control, Envir. Microbiol., 4, 495, 10.1046/j.1462-2920.2002.00332.x

Finn, 2006, Pfam: clans, web tools and services, Nucl. Acids Res., 34, D247, 10.1093/nar/gkj149

Thomson, 1997, The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucl. Acids Res., 24, 4876, 10.1093/nar/25.24.4876

Dunn, 1981, Amino acid sequence of the gene 0.3 protein of bacteriophage T7 and nucleotide sequence of its mRNA, J. Biol. Chem., 256, 2579, 10.1016/S0021-9258(19)69822-4

Bandyopadhyay, 1985, Inhibition of type I restriction-modification enzymes EcoB and EcoK by the gene 0.3 protein of bacteriophage T7, J. Mol. Biol., 182, 567, 10.1016/0022-2836(85)90242-6

Spoerel, 1979, A novel bacteriophage defence mechanism: the anti-restriction protein, Nature, 278, 30, 10.1038/278030a0

Kruger, 1985, DNA methylation of bacterial viruses T3 and T7 by different DNA methylases in Escherichia coli K12 cells, Eur. J. Biochem., 150, 323, 10.1111/j.1432-1033.1985.tb09024.x

Atanasiu, 2001, Haracterization of the structure of ocr, the gene 0.3 protein of bacteriophage T7, Nucl. Acids Res., 29, 3059, 10.1093/nar/29.14.3059

Walkinshaw, 2002, Structure of ocr from bacteriophage T7, a protein that mimics B-form DNA, Mol. Cell, 9, 187, 10.1016/S1097-2765(02)00435-5

Atanasiu, 2002, Interaction of the ocr gene 0.3 protein of bacteriophage T7 with EcoKI restriction/modification enzyme, Nucl. Acids Res., 30, 3936, 10.1093/nar/gkf518

Dryden, 1993, Purification and characterization of the methyltransferase from the type I restriction and modification system of Escherichia coli K12, J. Biol. Chem., 268, 13228, 10.1016/S0021-9258(19)38641-7

Dryden, 1997, The in vitro assembly of the EcoKI type DNA restriction/modification enzyme and its in vivo implications, Biochemistry, 36, 1065, 10.1021/bi9619435

Weiserova, 1993, Cloning, production and characterization of wild type and mutant forms of the R.EcoK endonuclease, Nucl. Acids Res., 21, 373, 10.1093/nar/21.3.373

Thomas, 2003, Plasmid R16 ArdA protein preferentially targets restriction activity of the type I restriction-modification system EcoKI, J. Bacteriol., 185, 2022, 10.1128/JB.185.6.2022-2025.2003

Zavilgelsky, 2004, Antirestriction activity of ArdA encoded by the IncI1 transmissive plasmid R64 Mol, Biol. (Moscow), 38, 901

Studier, 1988, Model for how type I restriction enzymes select cleavage sites in DNA, Proc. Natl Acad. Sci. USA, 80, 2310

Loenen, 1987, Organization and sequence of the hsd genes of Escherichia coli K-12, J. Mol. Biol., 198, 159, 10.1016/0022-2836(87)90303-2

Prakash-Cheng, 1993, The expression and regulation of hsdK genes after conjugative transfer, Mol. Gen. Genet., 241, 491, 10.1007/BF00279890

Kulik, 1996, Regulation of the activity of the type IC EcoR124I restriction enzyme, J. Mol. Biol., 264, 891, 10.1006/jmbi.1996.0685

Delver, 1997, Organization of the leading region of IncN plasmid pKM101 (R46): a regulation controlled by CUP sequence elements, J. Mol. Biol., 271, 13, 10.1006/jmbi.1997.1124

Althorpe, 1999, Transient transcriptional activation of the IncI1 plasmid anti-restriction gene (ardA) and SOS inhibition gene (psiB) early in conjugating recipient bacteria, Mol. Microbiol., 31, 133, 10.1046/j.1365-2958.1999.01153.x

Bates, 1999, Expression of leading region genes on IncI1 plasmid ColIb-P9: genetic evidence for single-stranded DNA transcription, Microbiology, 145, 2655, 10.1099/00221287-145-10-2655

Nasim, 2004, The activity of a single-stranded promoter of plasmid ColIb-P9 depends on its secondary structure, Mol. Microbiol., 53, 405, 10.1111/j.1365-2958.2004.04114.x

Makovets, 1999, Regulation of endonuclease activity by proteolysis prevents breakage of unmodified bacterial chromosomes by type I restriction enzymes, Proc. Natl Acad. Sci. USA, 96, 9757, 10.1073/pnas.96.17.9757

Bertani, 1953, Host-controlled variation in bacterial viruses, J. Bacteriol., 65, 113, 10.1128/JB.65.2.113-121.1953

Day, 1977, UV-induced alleviation of K-specific restriction of bacteriophage lambda, J. Virol., 21, 1249, 10.1128/JVI.21.3.1249-1251.1977

Thoms, 1982, UV-induced alleviation of lambda restriction in Escherichia coli K12: kinetics of induction and specificity of this SOS function, Mol. Gen. Genet., 186, 111, 10.1007/BF00422921

Efimova, 1988, 2-Aminopurine and 5-bromouracil induce alleviation of type I restriction in Escherichia coli: mismatches function as inducing signals?, Mol. Gen. Genet., 214, 317, 10.1007/BF00337728

Fuller-Pace, 1984, Murray N.E. Genetic recombination can generate altered restriction specificity, Proc. Natl Acad. Sci. USA, 81, 6095, 10.1073/pnas.81.19.6095

Gann, 1987, Reassortment of DNA recognition domains and the evolution of new specificities, Mol. Microbiol., 1, 13, 10.1111/j.1365-2958.1987.tb00521.x

Price, 1989, Basis for changes in DNA recognition by the EcoR124 and EcoR124/3 type I DNA restriction and modification enzymes, J. Mol. Biol., 205, 115, 10.1016/0022-2836(89)90369-0

Arber, 2000, Genetic variation: molecular mechanisms and impact on microbial evolution, FEMS Microbiol. Rev., 24, 1, 10.1111/j.1574-6976.2000.tb00529.x

Yanisch-Perron, 1985, Improved M13 phage cloning vectors and host strains: nucleotide sequences of M13mp18 and pUC19 vectors, Gene, 33, 103, 10.1016/0378-1119(85)90120-9

Studier, 1991, Use of T7 RNA polymerase to direct expression of cloned genes, Methods Enzimol., 185, 60, 10.1016/0076-6879(90)85008-C

Bachmann, 1987, Derivations and genotypes of some mutant derivatives of Escherichia coli K-12, 1190

Brosius, 1984, Plasmid vector for selection of promoters, Gene, 27, 151, 10.1016/0378-1119(84)90136-7

Sain, 1980, The hsd (host specificity) genes of E. coli K-12, Mol. Gen. Genet., 180, 35, 10.1007/BF00267350

Sambrook, 1989

Webb, 1996, Restriction by EcoKI is enhanced by co-operative interactions between target sequences and is dependent on DEAD box motifs, EMBO J., 15, 2003, 10.1002/j.1460-2075.1996.tb00551.x

Sanger, 1977, DNA sequencing with chain-terminating inhibitor, Proc. Natl Acad. Sci. USA, 74, 5463, 10.1073/pnas.74.12.5463

Show, 1975, Chloramphenicol acethyltransferase from chloramphenicol-resistant bacteria, Meth. Enzymol., 43, 737, 10.1016/0076-6879(75)43141-X