TY - STD TI - Pingoud A, Wilson GG, Wende W. Type II restriction endonucleases—a historical perspective and more. Nucleic Acids Res. 2014;42(12):7489–527. ID - ref1 ER - TY - STD TI - Mruk I, Kobayashi I. To be or not to be: regulation of restriction–modification systems and other toxin–antitoxin systems. Nucleic Acids Res. 2014;42(1):70-86. ID - ref2 ER - TY - JOUR AU - Gingeras, T. R. AU - Brooks, J. E. PY - 1983 DA - 1983// TI - Cloned restriction/modification system from Pseudomonas aeruginosa JO - Proc Natl Acad Sci VL - 80 UR - https://doi.org/10.1073/pnas.80.2.402 DO - 10.1073/pnas.80.2.402 ID - Gingeras1983 ER - TY - JOUR AU - Kiss, A. AU - Posfai, G. AU - Keller, C. C. AU - Venetianer, P. AU - Roberts, R. J. PY - 1985 DA - 1985// TI - Nudeotide sequence of the BsuRI restriction-modification system JO - Nucleic Acids Res VL - 13 UR - https://doi.org/10.1093/nar/13.18.6403 DO - 10.1093/nar/13.18.6403 ID - Kiss1985 ER - TY - JOUR AU - Semenova, E. AU - Minakhin, L. AU - Bogdanova, E. AU - Nagornykh, M. AU - Vasilov, A. AU - Heyduk, T. AU - Solonin, A. AU - Zakharova, M. AU - Severinov, K. PY - 2005 DA - 2005// TI - Transcription regulation of the EcoRV restriction-modification system JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki998 DO - 10.1093/nar/gki998 ID - Semenova2005 ER - TY - JOUR AU - Bogdanova, E. AU - Djordjevic, M. AU - Papapanagiotou, I. AU - Heyduk, T. AU - Kneale, G. AU - Severinov, K. PY - 2008 DA - 2008// TI - Transcription regulation of the type II restriction-modification system AhdI JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkm1116 DO - 10.1093/nar/gkm1116 ID - Bogdanova2008 ER - TY - JOUR AU - Krüger, D. AU - Bickle, T. A. PY - 1983 DA - 1983// TI - Bacteriophage survival: multiple mechanisms for avoiding the deoxyribonucleic acid restriction systems of their hosts JO - Microbiol Rev VL - 47 ID - Krüger1983 ER - TY - JOUR AU - Tock, M. R. AU - Dryden, D. T. PY - 2005 DA - 2005// TI - The biology of restriction and anti-restriction JO - Curr Opin Microbiol VL - 8 UR - https://doi.org/10.1016/j.mib.2005.06.003 DO - 10.1016/j.mib.2005.06.003 ID - Tock2005 ER - TY - JOUR AU - Korona, R. AU - Korona, B. AU - Levin, B. R. PY - 1993 DA - 1993// TI - Sensitivity of naturally occurring coliphages to type I and type II restriction and modification JO - Microbiology VL - 139 ID - Korona1993 ER - TY - JOUR AU - Makino, O. AU - Saito, H. AU - Ando, T. PY - 1980 DA - 1980// TI - Bacillus subtilis-phage φ1 overcomes host-controlled restriction by producing BamNx inhibitor protein JO - Mol Gen Genet MGG VL - 179 UR - https://doi.org/10.1007/BF00271735 DO - 10.1007/BF00271735 ID - Makino1980 ER - TY - BOOK AU - Takahashi, I. AU - Marmur, J. PY - 1963 DA - 1963// TI - Replacement of thymidylic acid by deoxyuridylic acid in the deoxyribonucleic acid of a transducing phage for Bacillus subtilis ID - Takahashi1963 ER - TY - JOUR AU - Kobayashi, I. PY - 2001 DA - 2001// TI - Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution JO - Nucleic Acids Res VL - 29 UR - https://doi.org/10.1093/nar/29.18.3742 DO - 10.1093/nar/29.18.3742 ID - Kobayashi2001 ER - TY - JOUR AU - Jeltsch, A. AU - Pingoud, A. PY - 1996 DA - 1996// TI - Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction-modification systems JO - J Mol Evol VL - 42 UR - https://doi.org/10.1007/BF02198833 DO - 10.1007/BF02198833 ID - Jeltsch1996 ER - TY - STD TI - 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(2):790–800. ID - ref14 ER - TY - JOUR AU - Nagornykh, M. AU - Bogdanova, E. AU - Protsenko, A. AU - Solonin, A. AU - Zakharova, M. AU - Severinov, K. PY - 2008 DA - 2008// TI - Regulation of gene expression in a type II restriction-modification system JO - Russ J Genet VL - 44 UR - https://doi.org/10.1134/S1022795408050037 DO - 10.1134/S1022795408050037 ID - Nagornykh2008 ER - TY - JOUR AU - Ichige, A. AU - Kobayashi, I. PY - 2005 DA - 2005// TI - Stability of EcoRI restriction-modification enzymes in vivo differentiates the EcoRI restriction-modification system from other postsegregational cell killing systems JO - J Bacteriol VL - 187 UR - https://doi.org/10.1128/JB.187.19.6612-6621.2005 DO - 10.1128/JB.187.19.6612-6621.2005 ID - Ichige2005 ER - TY - JOUR AU - Mruk, I. AU - Blumenthal, R. M. PY - 2008 DA - 2008// TI - Real-time kinetics of restriction–modification gene expression after entry into a new host cell JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkn097 DO - 10.1093/nar/gkn097 ID - Mruk2008 ER - TY - STD TI - Ball NJ, McGeehan J, Streeter S, Thresh S-J, Kneale G. The structural basis of differential DNA sequence recognition by restriction–modification controller proteins. Nucleic acids research 2012;40(20):10532–42. ID - ref18 ER - TY - JOUR AU - McGeehan, J. E. AU - Papapanagiotou, I. AU - Streeter, S. D. AU - Kneale, G. G. PY - 2006 DA - 2006// TI - Cooperative binding of the C.AhdI controller protein to the C/R promoter and its role in endonuclease gene expression JO - J Mol Biol VL - 358 UR - https://doi.org/10.1016/j.jmb.2006.02.003 DO - 10.1016/j.jmb.2006.02.003 ID - McGeehan2006 ER - TY - JOUR AU - Sohail, A. AU - Ives, C. L. AU - Brooks, J. E. PY - 1995 DA - 1995// TI - Purification and characterization of C · BamHI, a regulator of the BamHI restriction-modification system JO - Gene VL - 157 UR - https://doi.org/10.1016/0378-1119(94)00698-R DO - 10.1016/0378-1119(94)00698-R ID - Sohail1995 ER - TY - JOUR AU - Sorokin, V. AU - Severinov, K. AU - Gelfand, M. S. PY - 2009 DA - 2009// TI - Systematic prediction of control proteins and their DNA binding sites JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn931 DO - 10.1093/nar/gkn931 ID - Sorokin2009 ER - TY - JOUR AU - Ives, C. L. AU - Nathan, P. D. AU - Brooks, J. E. PY - 1992 DA - 1992// TI - Regulation of the BamHI restriction-modification system by a small intergenic open reading frame, bamHIC, in both Escherichia coli and Bacillus subtilis JO - J Bacteriol VL - 174 UR - https://doi.org/10.1128/jb.174.22.7194-7201.1992 DO - 10.1128/jb.174.22.7194-7201.1992 ID - Ives1992 ER - TY - JOUR AU - Tao, T. AU - Bourne, J. AU - Blumenthal, R. PY - 1991 DA - 1991// TI - A family of regulatory genes associated with type II restriction-modification systems JO - J Bacteriol VL - 173 UR - https://doi.org/10.1128/jb.173.4.1367-1375.1991 DO - 10.1128/jb.173.4.1367-1375.1991 ID - Tao1991 ER - TY - JOUR AU - Česnavičienė, E. AU - Mitkaitė, G. AU - Stankevičius, K. AU - Janulaitis, A. AU - Lubys, A. PY - 2003 DA - 2003// TI - Esp1396I restriction–modification system: structural organization and mode of regulation JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg135 DO - 10.1093/nar/gkg135 ID - Česnavičienė2003 ER - TY - JOUR AU - Karyagina, A. AU - Shilov, I. AU - Tashlitskii, V. AU - Khodoun, M. AU - Vasil’ev, S. AU - Lau, P. C. AU - Nikolskaya, I. PY - 1997 DA - 1997// TI - Specific binding of SsoII DNA methyltransferase to its promoter region provides the regulation of SsoII restriction-modification gene expression JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.11.2114 DO - 10.1093/nar/25.11.2114 ID - Karyagina1997 ER - TY - JOUR AU - Zakharova, M. AU - Minakhin, L. AU - Solonin, A. AU - Severinov, K. PY - 2004 DA - 2004// TI - Regulation of RNA polymerase promoter selectivity by covalent modification of DNA JO - J Mol Biol VL - 335 UR - https://doi.org/10.1016/j.jmb.2003.09.081 DO - 10.1016/j.jmb.2003.09.081 ID - Zakharova2004 ER - TY - JOUR AU - Vilar, J. M. AU - Saiz, L. PY - 2013 DA - 2013// TI - Systems biophysics of gene expression JO - Biophys J VL - 104 UR - https://doi.org/10.1016/j.bpj.2013.04.032 DO - 10.1016/j.bpj.2013.04.032 ID - Vilar2013 ER - TY - JOUR AU - Tolkunov, D. AU - Morozov, A. V. PY - 2010 DA - 2010// TI - Genomic studies and computational predictions of nucleosome positions and formation energies JO - Adv Protein Chem Struct Biol VL - 79 UR - https://doi.org/10.1016/S1876-1623(10)79001-5 DO - 10.1016/S1876-1623(10)79001-5 ID - Tolkunov2010 ER - TY - JOUR AU - Gertz, J. AU - Siggia, E. D. AU - Cohen, B. A. PY - 2009 DA - 2009// TI - Analysis of combinatorial cis-regulation in synthetic and genomic promoters JO - Nature VL - 457 UR - https://doi.org/10.1038/nature07521 DO - 10.1038/nature07521 ID - Gertz2009 ER - TY - JOUR AU - Seo, Y. -. J. AU - Chen, S. AU - Nilsen-Hamilton, M. AU - Levine, H. A. PY - 2010 DA - 2010// TI - A mathematical analysis of multiple-target SELEX JO - Bull Math Biol VL - 72 UR - https://doi.org/10.1007/s11538-009-9491-x DO - 10.1007/s11538-009-9491-x ID - Seo2010 ER - TY - STD TI - Aguda B, Friedman A. Models of cellular regulation. New York: Oxford University Press; 2008. ID - ref31 ER - TY - STD TI - Alon U. An introduction to systems biology: design principles of biological circuits. London: CRC press; 2006. ID - ref32 ER - TY - STD TI - Williams K, Savageau MA, Blumenthal RM. A bistable hysteretic switch in an activator–repressor regulated restriction–modification system. Nucleic Acids Res. 2013;41(12);6045–57. ID - ref33 ER - TY - JOUR AU - Djordjevic, M. PY - 2013 DA - 2013// TI - Modeling bacterial immune systems: strategies for expression of toxic - but useful - molecules JO - Biosystems VL - 112 UR - https://doi.org/10.1016/j.biosystems.2013.03.004 DO - 10.1016/j.biosystems.2013.03.004 ID - Djordjevic2013 ER - TY - JOUR AU - O’Donnell, S. M. AU - Janssen, G. R. PY - 2001 DA - 2001// TI - The initiation codon affects ribosome binding and translational efficiency in Escherichia coli of cI mRNA with or without the 5′ untranslated leader JO - J Bacteriol VL - 183 UR - https://doi.org/10.1128/JB.183.4.1277-1283.2001 DO - 10.1128/JB.183.4.1277-1283.2001 ID - O’Donnell2001 ER - TY - JOUR AU - Shell, S. S. AU - Wang, J. AU - Lapierre, P. AU - Mir, M. AU - Chase, M. R. AU - Pyle, M. M. AU - Gawande, R. AU - Ahmad, R. AU - Sarracino, D. A. AU - Ioerger, T. R. PY - 2015 DA - 2015// TI - Leaderless transcripts and small proteins are common features of the mycobacterial translational landscape JO - PLoS Genet VL - 11 UR - https://doi.org/10.1371/journal.pgen.1005641 DO - 10.1371/journal.pgen.1005641 ID - Shell2015 ER - TY - JOUR AU - Beletskaya, I. V. AU - Zakharova, M. V. AU - Shlyapnikov, M. G. AU - Semenova, L. M. AU - Solonin, A. S. PY - 2000 DA - 2000// TI - DNA methylation at the CfrBI site is involved in expression control in the CfrBI restriction–modification system JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.19.3817 DO - 10.1093/nar/28.19.3817 ID - Beletskaya2000 ER - TY - JOUR AU - Shea, M. A. AU - Ackers, G. K. PY - 1985 DA - 1985// TI - The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation JO - J Mol Biol VL - 181 UR - https://doi.org/10.1016/0022-2836(85)90086-5 DO - 10.1016/0022-2836(85)90086-5 ID - Shea1985 ER - TY - JOUR AU - Enikeeva, F. N. AU - Severinov, K. V. AU - Gelfand, M. S. PY - 2010 DA - 2010// TI - Restriction–modification systems and bacteriophage invasion: Who wins? JO - J Theor Biol VL - 266 UR - https://doi.org/10.1016/j.jtbi.2010.07.006 DO - 10.1016/j.jtbi.2010.07.006 ID - Enikeeva2010 ER - TY - JOUR AU - Streeter, S. D. AU - Papapanagiotou, I. AU - McGeehan, J. E. AU - Kneale, G. G. PY - 2004 DA - 2004// TI - DNA footprinting and biophysical characterization of the controller protein C.AhdI suggests the basis of a genetic switch JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh975 DO - 10.1093/nar/gkh975 ID - Streeter2004 ER - TY - JOUR AU - Bogdanova, E. AU - Zakharova, M. AU - Streeter, S. AU - Taylor, J. AU - Heyduk, T. AU - Kneale, G. AU - Severinov, K. PY - 2009 DA - 2009// TI - Transcription regulation of restriction-modification system Esp1396I JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkp210 DO - 10.1093/nar/gkp210 ID - Bogdanova2009 ER - TY - JOUR AU - Vesper, O. AU - Amitai, S. AU - Belitsky, M. AU - Byrgazov, K. AU - Kaberdina, A. C. AU - Engelberg-Kulka, H. AU - Moll, I. PY - 2011 DA - 2011// TI - Selective translation of leaderless mRNAs by specialized ribosomes generated by MazF in Escherichia coli JO - Cell VL - 147 UR - https://doi.org/10.1016/j.cell.2011.07.047 DO - 10.1016/j.cell.2011.07.047 ID - Vesper2011 ER - TY - STD TI - Mruk I, Liu Y, Ge L, Kobayashi I. Antisense RNA associated with biological regulation of a restriction–modification system. Nucleic Acids Res. 2011;39(13):5622–32. ID - ref43 ER - TY - JOUR AU - Nagornykh, M. AU - Zakharova, M. AU - Protsenko, A. AU - Bogdanova, E. AU - Solonin, A. S. AU - Severinov, K. PY - 2011 DA - 2011// TI - Regulation of gene expression in restriction-modification system Eco29kI JO - Nucleic Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkr055 DO - 10.1093/nar/gkr055 ID - Nagornykh2011 ER - TY - JOUR AU - Barrangou, R. AU - Marraffini, L. A. PY - 2014 DA - 2014// TI - CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity JO - Mol Cell VL - 54 UR - https://doi.org/10.1016/j.molcel.2014.03.011 DO - 10.1016/j.molcel.2014.03.011 ID - Barrangou2014 ER - TY - JOUR AU - Al-Attar, S. AU - Westra, E. R. AU - Oost, J. AU - Brouns, S. J. PY - 2011 DA - 2011// TI - Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes JO - Biol Chem VL - 392 UR - https://doi.org/10.1515/bc.2011.042 DO - 10.1515/bc.2011.042 ID - Al-Attar2011 ER - TY - STD TI - Rezulak M, Borsuk I, Mruk I: Natural C-independent expression of restriction endonuclease in a C protein-associated restriction-modification system. Nucleic Acids Res. 2016;44(6):2646–60. ID - ref47 ER - TY - JOUR AU - Lubys, A. AU - Jurenaite, S. AU - Janulaitis, A. PY - 1999 DA - 1999// TI - Structural organization and regulation of the plasmid-borne type II restriction-modification system Kpn2l from Klebsiella pneumoniae RFL2 JO - Nucleic Acids Res VL - 27 UR - https://doi.org/10.1093/nar/27.21.4228 DO - 10.1093/nar/27.21.4228 ID - Lubys1999 ER - TY - JOUR AU - Knowle, D. AU - Lintner, R. E. AU - Touma, Y. M. AU - Blumenthal, R. M. PY - 2005 DA - 2005// TI - Nature of the promoter activated by C. PvuII, an unusual regulatory protein conserved among restriction-modification systems JO - J Bacteriol VL - 187 UR - https://doi.org/10.1128/JB.187.2.488-497.2005 DO - 10.1128/JB.187.2.488-497.2005 ID - Knowle2005 ER -