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рватски српски srpski türkçe українська 中文 edit links article talk english read edit view history tools tools move to sidebar hide actions read edit view history general what links here related changes upload file permanent link page information cite this page get shortened url switch to legacy parser print export download as pdf printable version in other projects wikidata item appearance move to sidebar hide from wikipedia the free encyclopedia defense system in bacteria and archaea restriction enzyme ecorv bound to cleaved dna substrate the restriction modification system rm system is found in bacteria and archaea and provides a defense against foreign dna such as that borne by bacteriophages bacteria have restriction enzymes also called restriction endonucleases which cleave double stranded dna at specific points into fragments which are then degraded further by other endonucleases this prevents infection by effectively destroying the foreign dna introduced by an infectious agent such as a bacteriophage approximately one quarter of known bacteria possess rm systems and of those about one half have more than one type of system as the sequences recognized by the restriction enzymes are very short the bacterium itself will almost certainly contain some within its genome in order to prevent destruction of its own dna by the restriction enzymes methyl groups are added these modifications must not interfere with the dna base pairing and therefore usually only a few specific bases are modified on each strand endonucleases cleave internal non terminal phosphodiester bonds they do so only after recognising specific sequences in dna which are usually 4 6 base pairs long and often palindromic history edit the rm system was first discovered by salvatore luria and mary human in 1952 and 1953 1 2 they found that a bacteriophage growing within an infected bacterium could be modified so that upon their release and re infection of a related bacterium the bacteriophage s growth is restricted inhibited also described by luria in his autobiography on pages 45 and 99 in 1984 3 in 1953 jean weigle and giuseppe bertani reported similar examples of host controlled modification using different bacteriophage system 4 later work by daisy roulland dussoix and werner arber in 1962 5 and many other subsequent workers led to the understanding that restriction was due to attack and breakdown of the modified bacteriophage s dna by specific enzymes of the recipient bacteria further work by hamilton o smith isolated hin dii the first of the class of enzymes now known as restriction enzymes while daniel nathans showed that it can be used for restriction mapping 6 when these enzymes were isolated in the laboratory they could be used for controlled manipulation of dna thus providing the foundation for the development of genetic engineering werner arber daniel nathans and hamilton smith were awarded the nobel prize in physiology or medicine in 1978 for their work on restriction modification citation needed types edit further information restriction enzyme types there are four categories of restriction modification systems type i type ii type iii and type iv 7 all have restriction enzyme activity and a methylase activity except for type iv that has no methylase activity they were named in the order of discovery although the type ii system is the most common 7 type i systems are the most complex consisting of three polypeptides r restriction m modification and s specificity the resulting complex can both cleave and methylate dna both reactions require atp and cleavage often occurs a considerable distance from the recognition site the s subunit determines the specificity of both restriction and methylation cleavage occurs at variable distances from the recognition sequence so discrete bands are not easily visualized by gel electrophoresis citation needed type ii systems are the simplest and the most prevalent 8 instead of working as a complex the methyltransferase and endonuclease are encoded as two separate proteins and act independently there is no specificity protein both proteins recognize the same recognition site and therefore compete for activity the methyltransferase acts as a monomer methylating the duplex one strand at a time the endonuclease acts as a homodimer which facilitates the cleavage of both strands cleavage occurs at a defined position close to or within the recognition sequence thus producing discrete fragments during gel electrophoresis for this reason type ii systems are used in labs for dna analysis and gene cloning citation needed type iii systems have r res and m mod proteins that form a complex of modification and cleavage the m protein however can methylate on its own methylation also only occurs on one strand of the dna unlike most other known mechanisms the heterodimer formed by the r and m proteins competes with itself by modifying and restricting the same reaction this results in incomplete digestion 9 10 type iv systems are not true rm systems because they only contain a restriction enzyme and not a methylase unlike the other types type iv restriction enzymes recognize and cut only modified dna 11 function edit neisseria meningitidis has multiple type ii restriction endonuclease systems that are employed in natural genetic transformation natural genetic transformation is a process by which a recipient bacterial cell can take up dna from a neighboring donor bacterial cell and integrate this dna into its genome by recombination although early work on restriction modification systems focused on the benefit to bacteria of protecting themselves against invading bacteriophage dna or other foreign dna it is now known that these systems can also be used to restrict dna introduced by natural transformation from other members of the same or related species citation needed in the pathogenic bacterium neisseria meningitidis meningococci competence for transformation is a highly evolved and complex process where multiple proteins at the bacterial surface in the membranes and in the cytoplasm interact with the incoming transforming dna restriction modification systems are abundant in the genus neisseria n meningitidis has multiple type ii restriction endonuclease systems 12 the restriction modification systems in n meningitidis vary in specificity between different clades 12 13 this specificity provides an efficient barrier against dna exchange between clades 12 luria on page 99 of his autobiography 3 referred to such a restriction behavior as an extreme instance of unfriendliness restriction modification appears to be a major driver of sexual isolation and speciation in the meningococci 14 caugant and maiden 15 suggested that restriction modification systems in meningococci may act to allow genetic exchange among very close relatives while reducing but not completely preventing genetic exchange among meningococci belonging to different clonal complexes and related species citation needed rm systems can also act as selfish genetic elements forcing their maintenance on the cell through postsegregational cell killing 16 some viruses have evolved ways of subverting the restriction modification system usually by modifying their own dna by adding methyl or glycosyl groups to it thus blocking the restriction enzymes other viruses such as bacteriophages t3 and t7 encode proteins that inhibit the restriction enzymes citation needed to counteract these viruses some bacteria have evolved restriction systems which only recognize and cleave modified dna but do not act upon the host s unmodified dna some prokaryotes have developed multiple types of restriction modification systems citation needed r m systems are more abundant in promiscuous species wherein they establish preferential paths of genetic exchange within and between lineages with cognate r m systems 17 because the repertoire and or specificity of r m systems in bacterial lineages vary quickly the preferential fluxes of genetic transfer within species are expected to constantly change producing time dependent networks of gene transfer citation needed applications edit molecular biology edit a cloning rm systems can be cloned into plasmids and selected because of the resistance provided by the methylation enzyme once the plasmid begins to replicate the methylation enzyme will be produced and methylate the plasmid dna protecting it from a specific restriction enzyme citation needed b restriction fragment length polymorphisms restriction enzymes are also used to analyse the composition of dna in regard to presence or absence of mutations that affect the rease cleavage specificity when wild type and mutants are analysed by digestion with different reases the gel electrophoretic products vary in length largely because mutant genes will not be cleaved in a similar pattern as wild type for presence of mutations that render the reases non specific to the mutant sequence citation needed gene therapy edit the bacteria r m system has been proposed as a model for devising human anti viral gene or genomic vaccines and therapies since the rm system serves an innate defense role in bacteria by restricting tropism of bacteriophages 18 research is on reases and zfn that can cleave the dna of various human viruses including hsv 2 high risk hpvs and hiv 1 with the ultimate goal of inducing target mutagenesis and aberrations of human infecting viruses 19 20 21 the human genome already contains remnants of retroviral genomes that have been inactivated and harnessed for self gain indeed the mechanisms for silencing active l1 genomic retroelements by the three prime repair exonuclease 1 trex1 and excision repair cross complementing 1 ercc appear to mimic the action of rm systems in bacteria and the non homologous end joining nhej that follows the use of zfn without a repair template 22 23 a major advance is the creation of artificial restriction enzymes created by linking the foki dna cleavage domain with an array of dna binding proteins or zinc finger arrays denoted now as zinc finger nucleases zfn 24 zfns are a powerful tool for host genome editing due to their enhanced sequence specificity zfn work in pairs their dimerization being mediated in situ through the foki domain each zinc finger array zfa is capable of recognizing 9 12 base pairs making for 18 24 for the pair a 5 7 bp spacer between the cleavage sites further enhances the specificity of zfn making them a safe and more precise tool that can be applied in humans a recent phase i clinical trial of zfn for the targeted abolition of the ccr5 co receptor for hiv 1 has been undertaken 25 relation with mobile genetic elements edit r m systems are major players in the co evolutionary interaction between mobile genetic elements mges and their hosts 26 genes encoding r m systems have been reported to move between prokaryotic genomes within mges such as plasmids prophages insertion sequences transposons integrative conjugative elements ices and integrons however it was recently found that there are relatively few r m systems in plasmids some in prophages and practically none in phages on the other hand all these mges encode a large number of solitary r m genes notably mtases 26 in light of this it is likely that r m mobility may be less dependent on mges and more dependent for example on the existence of small genomic integration hotspots it is also possible that r m systems frequently exploit other mechanisms such as natural transformation vesicles nanotubes gene transfer agents or generalized transduction in order to move between genomes citation needed see also edit methylation restriction enzyme references edit luria se human ml 1952 a nonhereditary host induced variation of bacterial viruses j bacteriol 64 4 557 69 doi 10 1128 jb 64 4 557 569 1952 pmc 169391 pmid 12999684 luria se 1953 host induced modifications of viruses cold spring harb symp quant biol 18 237 44 doi 10 1101 sqb 1953 018 01 034 pmid 13168990 1 2 salvator e luria a slot machine a broken test tube an autobiography harper row new york 1984 pp 228 isbn 0 06 015260 5 usa and canada bertani g weigle jj 1953 host controlled variation in bacterial viruses j bacteriol 65 2 113 21 doi 10 1128 jb 65 2 113 121 1953 pmc 169650 pmid 13034700 dussoix d arber w 1962 host specificity of dna produced by escherichia coli ii control over acceptance of dna from infecting phage lambda j mol biol 5 37 49 doi 10 1016 s0022 2836 62 80059 x pmid 13888713 nathans d smith ho 1975 restriction endonucleases in the analysis and restructuring of dna molecules annu rev biochem 44 273 93 doi 10 1146 annurev bi 44 070175 001421 pmid 166604 1 2 loenen wa dryden dt raleigh ea wilson gg murray ne january 2014 highlights of the dna cutters a short history of the restriction enzymes nucleic acids research 42 1 3 19 doi 10 1093 nar gkt990 hdl 20 500 11820 4fce7b9e 56b0 49ff 9c76 8374775b976f pmc 3874209 pmid 24141096 rodic a blagojevic b zdobnov e djordjevic m djordjevic m 24 february 2017 understanding key features of bacterial restriction modification systems through quantitative modeling bmc systems biology 11 suppl 1 377 doi 10 1186 s12918 016 0377 x pmc 5333194 pmid 28466789 wilson g 1991 organization of restriction modification systems nucleic acids research 19 10 2539 2566 doi 10 1093 nar 19 10 2539 pmc 328170 pmid 2041731 wilson g 1991 restriction and modification systems annual review of genetics 25 585 627 doi 10 1146 annurev ge 25 120191 003101 pmid 1812816 loenen wa 2013 the other face of restriction modification dependent enzymes nucleic acids research 42 1 56 69 doi 10 1093 nar gkt747 pmc 3874153 pmid 23990325 1 2 3 budroni s siena e dunning hotopp jc seib kl serruto d nofroni c comanducci m riley dr daugherty sc angiuoli sv covacci a pizza m rappuoli r moxon er tettelin h medini d 2011 neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination proc natl acad sci u s a 108 11 4494 9 bibcode 2011pnas 108 4494b doi 10 1073 pnas 1019751108 pmc 3060241 pmid 21368196 claus h friedrich a frosch m vogel u 2000 differential distribution of novel restriction modification systems in clonal lineages of neisseria meningitidis j bacteriol 182 5 1296 303 doi 10 1128 jb 182 5 1296 1303 2000 pmc 94415 pmid 10671450 ambur oh frye sa nilsen m hovland e tønjum t 2012 restriction and sequence alterations affect dna uptake sequence dependent transformation in neisseria meningitidis plos one 7 7 e39742 bibcode 2012ploso 739742a doi 10 1371 journal pone 0039742 pmc 3388099 pmid 22768309 caugant da maiden mc 2009 meningococcal carriage and disease population biology and evolution vaccine 27 suppl 2 4 b64 70 doi 10 1016 j vaccine 2009 04 061 pmc 2719693 pmid 19464092 kusano k 1995 restriction modification systems as genomic parasites in competition for specific sequences proceedings of the national academy of sciences of the united states of america 92 24 ...