Modification-dependent restriction systems (MDRs) recognize and cleave modified foreign DNA. These proteins are thought to play a role in establishing the epigenetic landscape of bacterial genomes and are especially important in protecting against predatory bacteriophage viruses, many of which incorporate modifiedbasesintotheirDNAtoevadedetectionbyotherdefensesystems.WhileMDRscanbefoundin mostantibiotic-resistantbacteriaincludingmethicillin-resistantStaphylococcusaureus(MRSA),Clostridium difficile,andcarbapenem-resistantenterobacteriaceaelikeKlebsiellapneumoniae,noeukaryotichomologs exist,makingthempromisingtargetsfordrugdesign.Inhibitingthesesystemshasthepotentialtoenhance the efficacy of phage-mediated bacterial killing, thus providing new therapeutic strategies to combat persistent, antibiotic resistant microbial infections. It is our long-term goal to study the basic biology and mechanismsofMDRsandusethisknowledgetoimprovecurrentphagetherapyapproaches.Thisproposal examines the structure and function of the McrBC restriction system, a two-component MDR that targets DNA containing methylated cytosines. E. coli McrB contains an N-terminal DNA binding domain and a C- terminal AAA+ motor domain that hydrolyzes GTP and mediates nucleotide-dependent oligomerization. McrB?sbasalGTPaseactivityisstimulatedviainteractionwithitspartnerendonucleaseMcrC.Biochemical studies suggest a model for DNA cleavage in which McrB and McrC assemble together at two distant methylated sites and translocate in a manner dependent on stimulated GTP hydrolysis. Collision of these McrBC assemblies triggers cleavage of both DNA strands. Despite this model, the molecular and mechanisticdetailsunderlyingMcrBCfunctionremainpoorlydefined.
In Aim1, wewilldissectthespecies- specific determinants of DNA binding in different McrB homologs using X-ray crystallography and biochemistry. We will also generate chimeras that exchange the DNA binding domains between different McrB homologs to test the hypothesis that the core hydrolysis and cleavage machineries in McrBC are conservedandhaveadaptedtodifferentevolutionarypressuresviaamodulardesign.
In Aim2, wewilluse mutagenesisandkineticassaystoidentifythecriticalcatalyticcomponentsresponsibleforMcrC-stimulated GTPase activity.
In Aim 3, we will determine the structure and architectural organization of the McrBC restriction complex at atomic resolution by X-ray crystallography and cryo-electron microscopy. These effortswillprovidenewinsightsintohowMcrBCcomplexesbindDNA,assemble,andhydrolyzeGTP.
McrBC is a conserved bacterial defense system that cleaves modified DNA. Our research objective is to understand the structure, function and regulation of McrBC at the molecular level, which may lead to new therapeutictoolsandapproachestocombatmultidrugresistantbacterialinfections.
|Hosford, Christopher J; Chappie, Joshua S (2018) The crystal structure of the Helicobacter pylori LlaJI.R1 N-terminal domain provides a model for site-specific DNA binding. J Biol Chem 293:11758-11771|