>>WELCOME TO THE WEDNESDAY AFTERNOON LECTURE SERIES. I'M GIGI S, A PRINCIPLE INVESTIGATOR AND IT IS MY GREAT PLEASURE TO INTRODUCE TODAY'S SPEAKER ON BEHALF OF THE INTEREST GROUP. SO DR. S. WAS A TOP VOTE GETTER FOR LAMBDA LUNCH FOR SEVERAL YEARS IN A ROW SO WE ARE SO PLEASED THAT HE WAS ABLE TO COME THIS WEEK. HE'S THE INCUMBENT OF THE SYLVIA CHAIR IN THE DEPARTMENT AT THE WEISSMAN INSTITUTE IN ISRAEL. HE RECEIVED A BULK OF THE EDUCATION AT TEL AVIV UNIVERISTY WHERE HE EARNED A MASTER'S DEGREE IN GENETICS AND A PH.D. IN HUMAN GENETICS. I DIDN'T KNOW THAT. HE FOLLOWED UP WITH POST-DOCTORAL FELLOWSHIP AT THE BERKLEY LAB IN CALIFORNIA AND RETURNED TO ISRAEL WHERE HE WENT TO THE WEISSMAN AND HAS BEEN GOING UP THE RANKS, MOVING UP THE RANKS AT THE WEISSMAN. SO HE HAS HAD MANY RECOGNITIONS AND ACCOLADES INCLUDE THE GERMAN NATIONAL ACADEMY OF SCIENCES, THE ANDRE PRIZE FOR SCIENTIFIC RESEARCH. THE RAH PA IMPORTANT PRIZE FOR EXCELLENCE AND ELECTION TO BOTH THE AMERICAN ACADEMY OF MICROBIOLOGY. SO RECOGNITION ALL AROUND THE WORLD. BUT MOST IMPORTANTLY ONTO HIS RESEARCH WHICH COMBINES COMPUTATIONAL GENOMICS, SYSTEMS BIOLOGY, METAGENOMICS, HIGH THROUGHPUT SEQUENCING AND MODERN EXPERIMENTAL APPROACHES AND MICROBIOLOGY AND PHAGE BIOLOGY. AMONG THE MOST SIGNIFICANT RESULTS ARE MULTIPLE DISCOVERS ABOUT THE ARMS RACE BETWEEN BACTERIA AND PHAGE. SO MANY PEOPLE HAVE HEARD ABOUT KRIS PER THAT IS NOT THE WHOLE STORY. AS YOU WILL SEE HERE. EXCITING FINDINGS THAT HAVE COME FROM THE LAB INCLUDE THE DISCOVERY OF AN ASTONISHING NUMBER OF SYSTEMS, DEFENSE SYSTEMS BEYOND CRSPR. THE DISCOVERY THAT PHAGES USE SMALL MOLECULE COMMUNICATION TO COORDINATE THEIR INFECTION DYNAMICS. SMALL RNAS AND SMALL PROTEINS WHICH ARE CLOSE TO MY HEART ARE INVOLVED IN THE PROCESS AND MOST INTRIGUINGLY THE PARALLELS BETWEEN THESE. I THINK SOME OF THESE TOPICS ARE THE FOCUS OF THE TALK TODAY. LET ME STOP THERE AND THANK YOU THEM FOR COMING TO VISIT US IN-PERSON. >>THANK YOU SO MUCH IT'S A GREAT PLEASURE AND HONOR FOR ME TO GIVE A LECTURE IN THIS FORUM AND I THANK THE LAMBDA FORUM FOR THE INVITATION AND FOR HOSTING ME FOR SUCH AN INTERESTING MEETING. THESE LAST TWO DAYS HAVE BEEN FASCINATING. I WILL TALK ABOUT OUR ADVENTURE STUDYING BACTERIA AND WHAT WE LEARNED IN THE BAHS PAST FEW YEARS. BACTERIA ARE VERY RARELY INFECTED BY PHAGES. PHAGES ARE VIRUSES, THEY USE SPECIFIC RECEPTOR ON THE BACTERIUM SURFACE AND WILL INJECT THEIR GENETIC MATERIAL. AND WITH THE PHAGES WE STUDY IN THE LAB, AFTER BETWEEN HALF AN HOUR TO TWO HOURS THEY BURST OPEN THE BACTERIA AND ONE HUNDRED PHAGES WILL EMERGE FROM IT AND SEARCH BY DIFFUSION FOR OTHER BACTERIA TO INFECT AND THESE ARE SUPER ABUNDANT IN THE ENVIRONMENT. MORE ON THE OTHER AND IF YOU WEIGH ALTOGETHER THEY MAY MORE THAN ENTIRETY OF HUMANITY ALTOGETHER. BUT YOU CAN ONLY SEE WHEN YOU LOOK AT THE MICROSCOPE. SO BACTERIA ARE INFECTED AND HENCE THEY NEED TO DEVELOP AND EVOLVE AN IMMUNE SYSTEM AND THE IMMUNE SYSTEM OF BACTERIA WE KNOW OF IT FOR MANY YEARS NOW. WE HAVE TWO, OR AT LEAST WHAT WE KNEW UP TO FOUR OR FIVE YEARS AGO THAT WE HAVE TWO ARMS OF IMMUNITY. ONE IS THE ADAPTIVE IMMUNE SYSTEM CALLED KRIS PER CAS THAT PUTS PIECES IN THE BACTERIAL GENOME AND USES THESE PIECES TO MITIGATE FUTURE INFECTION BY THE SAME PHAGE. WE HAVE RESTRICTION MODIFICATION. THESE ARE BASICALLY RESTRICTION ENZYMES THAT CLEAVE THE INCOMING DNA IN SPECIFIC KNOW TIES. THERE'S ALWAYS GOING TO BE ANOTHER PROTEIN THAT YOU MODIFY THE SAME MOTIFS TO PREVENT AUTOIMMUNITY. PREVENT SELF CLEAVAGE BUT A NUMBER OF YEARS AGO WE STARTED THINKING THAT THERE MIGHT BE OTHER DEFENSE MECHANISMS IN BACTERIA THAT WE ARE NOT AOF YET AND THE REASON WHY WE THOUGHT THERE MAY BE NOT SUCH MECHANISMS IS FIRST OF ALL CRISPER IS ABSENT FROM MOST. AND YOU ASK HOW DO THEY SURVIVE PHAGES AND KRIS PER WAS DISCOVERED SO LATE. DISCOVERED ONLY 1 -- 90 YEARS AFTER THE DISCOVERY OF THE PHAGE AND DURING THIS TIME, FANLS HAVE BEEN THE MAJOR DRIVING FORCE FOR STUDYING MOLECULAR BAY YOOLG. HOW TRANSLATION GOES, GENETIC CODE WAS ALL DISCOVERED UPON INFECTION OF PHAGES IN BACTERIA SINCE E. COLI DOESN'T HAVE A WORKING KRIS PER. SO KRIS PER AND E. COLI IS NOT WORKING VERY WELL SO THAT'S WHY IT WAS NOT DISCOVERED DURING ALL THESE DECADES OF RESEARCH. WE THOUGHT THERE MIGHT BE OTHER MECHANISMS THAT E. COLI DOESN'T HAVE BUT OTHER BACTERIA MAY HAVE AND THESE WE COULD DISCOVER. THE REASON WE WERE SO INTERESTED TO FIND NEW IMMUNE SYSTEMS IS FIRST OF ALL, IF WE WANT TO UNDERSTAND THE EVOLUTION, THE CONFLICT OF THESE PHAGES THE DEFENSE SYSTEMS ARE A MAJOR PART OF THAT CONFLICT. SO WE NEED TO UNDERSTAND HOW THEY OVERCOME THEMSELVES AND AND DEFENSE. FOR A MORE PRACTICAL POINT OF VIEW IT SEEMS TO US THAT IN THE PAST WHEN NEW IMMUNE SYSTEMS HAVE BEEN DISCOVERED AND STUDIED, IT FREQUENTLY LED TO REVOLUTIONS IN BIOLOGY SO THE DISCOVERY OF RESTRICTION ENZYMES ALLOWED THE FIRST GENETIC ENGINEERING, BEFORE THAT PEOPLE DIDN'T KNOW HOW TO DO IT. DISCOVERY OF KRIS PER LEADS TO A REVOLUTION IN GENOME ENGINEERING AND IF YOU THINK ABOUT THE BACTERIA, THE DISCOVERY OF RN IAI WHICH IS AN ANTIVIRAL MACHINE THAT SILENCE EUCARYOTES AND THE WAY WE WORK WITH ANTIBODIES IS ALSO PATHOLOGICALLY, YOU KNOW, VERY RICH TOOL AND THE REASON THEY ARE SO BENEFICIAL IS AN IMMUNE SYSTEM BY DEFINITION IS TO IDENTIFY A SPECIFIC MOLECULAR. IN SELF INFECTING FOREIGN ELEMENT AND THEN DO SOMETHING TO THAT MOLECULE, CLEAVE IT OR REMOVE AND IT THAT'S EXACTLY WHAT WE NEED AS MOLECULAR BIOLOGISTS WE NEED THESE PRECISION TOOLS TO BIND, CLEAVE OR REMOVE OR MOVE AWAY OR DO SOMETHING TO A SPECIFIC MOLECULE. SO WE HOPE THAT IF WE FIND NEW DEFENSE SYSTEMS, NEW IMMUNE SYSTEMS THEY MIGHT OH INVOLVE INTO BECOMING NEW MOLECULAR TOOLS BENEFICIAL FOR HUMANITY. HOW CAN WE FIND NEW IMMUNE SYSTEMS IN A SYSTEMATIC MANNER GIVEN THAT ALL THESE IMMUNE SYSTEMS IN THE PAST WERE DISCOVERED JUST BY CHANCE? PEOPLE STUMBLED UPON THEM AND THEN REALIZED WHAT THEY SEE AND SAW LATER ON SO WE'VE BEEN TRYING TO FIND IMMUNE SYSTEMS THROUGH MULTIPLE DIFFERENT KINDS OF METHODOLOGIES AND WE FAILED IN MOST OF THEM. BUT THE THING THAT EVENTUALLY WORKED FOR US COMES FROM A VERY PECULIAR BEHAVIOR OF DEFENSE SYSTEMS IF WE LOOK AT GENOMES OF BACTERIA. GENOME COLLIE SPEAKING, CLUSTERED AS DEFENSE ISLANDS THESE AREAS ARE RICH IN DEFENSE SYSTEMS. WE CAN SEE THAT IN THE GENOME OF THIS MICRO ORGANISM I'M SHOWING YOU A SMALL PIECE OF THAT GENOME. YOU SEE THE GENES THAT CODE FOR CRISPR ARE CODED NOT FOR FOR THOSE RESTRICTION ENZYMES, THESE ARE THE DIFFERENT SUB UNITS AND THEY ARE ENCODED NOT FAR FROM ANOTHER DEFENSE GENE THAT IS NOKNOWN. SO WE THOUGHT THAT IF WE'RE -- IF WE CAN LOOK FOR GENES OR MORE OFTEN GENE CASSETTE THAT CURRENTLY OCCUR AND ARE ENRICHED NEXT TO THESE DIFFERENT SYSTEMS WE MIGHT FIND NEW IMMUNE SYSTEMS THAT WERE NOT KNOWN YET. AND SO A PH.D. STUDENT FROM MY LAB ANALYZED GENOMES THAT ARE OCCURRING NEXT TO CRISPR AND RESTRICTION ENZYMES AND TO OUR SURPRISE FOUND MANY CASSETTES THAT WERE OF UNKNOWN FUNCTION BACK THEN. SO TO SEE WHETHER THEY'RE INDEED FUNCTIONING IN DEFENSE AGAINST PHAGES WE DEVELOPED THIS EXPERIMENTAL PLATFORM TO TEST THEM SO WHAT WE DO WHEN WE SUSPECT THAT WE FOUND NEW DIFFERENTS DEFENSE SYSTEM WE LOOK IS THE ALL THE GENOMES IN THE DEFENSE DATABASE THAT HAVE THIS OPERA AND WE SELECT THE GENOMES THAT ARE AS CLOSE AS POSSIBLE TO OUR LAB ORDER ORGANISMS AND WE SYNTHESIZE THE DNA AND EXPOSE THIS DE BACTERIA TO A SERIES OF PHAGES. SO SINGLE STRAND DNA, RNA, ET CETERA. AND WE LOOK FOR CASES IN WHICH THE SYSTEM WE CLONE. IF THE BACK TEAR YUM PROTECTED AGAINST THAT PHAGE. AND WHEN WE STARTED DOING THESE EXPERIMENTS, WE WERE HOPING TO FIND ONE OR TWO NEW DEFENSE SYSTEMS WHICH WE THOUGHT WOULD BE SUPER EXCITING BUT WE WERE SUPER, SUPER SURPRISED TO FIND NUMEROUS DEFENSE SYSTEMS IN MICROBIAL GENOMES SO FAR I THINK MY LAB DESCRIBED MORE THAN 40 DIFFERENT DEFENSE SYSTEMS THAT ARE ABANDONED IN MICROBES AND OTHER LABS NOW THAT DID EXPERIMENTS INSPIRED BY US FOUND DOZENS OF DEFENSE SYSTEMS. NOW WE KNOW SINCE 2018 OF, YOU KNOW, ABOUT 100 DIFFERENT KINDS OF IMMUNE SYSTEMS OR DEFENSE SYSTEMS THAT BACTERIA ENCODE IN NATURE AND PROTECT THEM AGAINST PHAGES AND SO WHAT YOU SEE HERE, THIS FIGURE LET ME TRY TO EXPLAIN WHAT YOU SEE. THIS IS A FIGURE FROM OUR 2018 PAPER WHERE WE DESCRIBE 9-10 DIFFERENT DEFENSE SYSTEMS WHAT YOU SEE IS A TWO GENE SYSTEM. THIS GENE IS A DOMAIN OF UNKNOWN FUNCTION AND THEN WE HAVE A CASE DOMAIN THAT MANIPULATES DNA OR RNA AND THE SIZE OF THESE GENES IS ABOUT THE SIZE OF CLASS NINE SO IT'S A PRETTY LARGE PROTEIN. WE CLONE IT. AND WE INFECTED THE BACTERIUM WITH TEN DIFFERENT PHAGES AND WHENEVER YOU SEE A RED COLOR HERE MEANS THAT THE SYSTEM PROTECTED THE BACTERIUM AGAINST THE PHAGE AND THIS COLOR MEANS WE NEEDED TO INFECT THE BACTERIA BY TEN MILLION TIMES MORE PHAGES OR ONE THOUSAND TIMES MORE IN ORDER TO SEE THIS. AND IN THE PAST FOUR OR FIVE YEARS, SINCE THE DISCOVERIES OF THE SYSTEMS WE SHIFTED THE GRAVITY OF THE LABS WORK FROM MOSTLY GENETICS TO MUCH MORE BIOCHEMISTRY IN ORDER TO START SOLVING THE MECHANISMS OF HOW THESE SYSTEMS WORK. ONE THING WE SAW QUITE EARLY ON, WHICH WAS VERY SURPRISING FOR US, IS THIS SYSTEM THAT TO THE OTHER SYSTEM. THIS IS ONE OF THE DEFENSE SYSTEM WE CHARACTERIZE. AND IT INTERESTED US BECAUSE IT HAS PROTEINS WITH TIER DOMAINS AND TIER DOMAINS ARE ALREADY KNOWN TO PARTICIPATE IN IMMUNITY BUT IN OUR OWN IMMUNE SYSTEM. THE IMMUNE SYSTEM OF HUMANS. IT'S WITH THE RECEPTORS AND THESE ARE PIECES OF OUR RECEPTORS THAT PARTICIPATE IN OUR OWN IMMUNITY. SO THIS GAVE US THE NOTION THAT FOR SOME DEFENSE SYSTEMS, THE REASON ANCIENT EVOLUTIONARY LINK BETWEEN BACTERIA AND HUMAN AND MORE ACCURATELY, WE HAVE EVIDENCE THAT SOME IMMUNE SYSTEMS IN BACTERIA GAVE RISE, EVOLUTIONARILY TO COMPETENCE OF OUR OWN IMMUNE SYSTEMS AND WE STARTED ASKING OURSELVES WHETHER THERE MIGHT BE OTHER COMPONENTS OF OUR INNATE IMMUNE SYSTEM THAT EVOLVED FROM BACTERIA DEFENSE MECHANISMS AGAINST PHAGE AND THE ANSWER IS YES, I'M GOING TO SHOW YOU A FEW EXAMPLES FOR SUCH COMPETENCE. SO FIRST OF ALL, LET'S LOOK AT THIS, IT'S CALLED THE PATHWAY, IT'S AN IMMUNE PATHWAY IN ANIMALS THAT ALLOW ANIMAL CELL TO IDENTIFY THAT THEY HAVE BEEN INFECTED. BASICALLY, THIS PATHWAY IS PRESENT IN MANY CELLS. NOT NECESSARILY IMMUNE CELLS BUT MANY CELLS IN OUR BODY AND COMPRISES A PROTEIN CALLED CGAS WHICH IS THE CYTOPLASMIC DNA. WHICH WE KNOW IS NOT SUPPOSED TO BE IN THE CYTOPLASM TO HAVE DNA. IT'S ILLEGAL IN THE SAY TO EXAMPLE. THE DNA IS PERCEIVED AS VIRAL INFECTION. AND THE SENSE FOR THAT IS THE PROTEIN CALLED CGAS AND THE NAME CGAS PRODUCES A UNIQUE SIGNALLING MOLECULE WHICH IS CYCLIC GMP-AMP. THESE ARE TWO NUCLEAR TYPE. WHICH ARE BOUND ONE TO EACH OTHER IN A SICKLY SIZED FORM. AND THE MOLECULE ACCUMULATES IN THE CELL AND BINDS ANOTHER PROTEIN CALLED STING. AN ACRONYM. AND I REALLY ENVY THE ACRONYMS. THEY ARE SUPER COOL AND INFORMATIVE BECAUSE WHAT IT DOES IS IT ACTIVATES AN ESCAPE THAT EXPRESSES INTERFERON AND OTHER INTERFERON RELATED GENES SO THIS PATHWAY WAS DESCRIBED ABOUT TEN YEARS AGO. 2013. IN SEMINAL PAPERS. BUT AROUND THE SAME TIME, THE LAB IN HARVARD FOUND THAT SOME BACTERIA CAN ALSO PRODUCE THE SAME MOLECULE, CYC CYCLIC GMP-AMP L IN QUITE RECENTLY THE BIOLOGICAL ROLE WAS COMPLETELY UNKNOWN. AND THE REASON I'M SHOWING YOU THIS IS BECAUSE WHEN WE LOOK AT THE PROTEIN, THE BACTERIAL PROTEIN, AND WE LOOK AT THE BACTERIAL SIGNALS WE SEE IT IS FOUND NEXT TO CRISPR SO IN THIS IT'S FOUND NEXT TO A CRISPR AND IN THIS IT'S FOUND NEXT TO A RESTRICTION ENZYME AND IN ANOTHER BACTERIA, THE GENE IS FOUND NEXT TO OTHER DEFENSE SYSTEMS THAT WE CHARACTERIZE RECENTLY AND THIS CHARACTERIZATION WAS DONE BY DEMINIMUM FROM MY LAB AND MOREOVER YOU CAN SEE THAT THE CGAS IS PRESENT. ONE I WILL TALK ABOUT THIS, GENE, SHORTLY. AND SO THE REASON -- I MEAN, THE FACT THAT THIS OPERATING SO FREQUENTLY BEING PRESENT NEXT TO CRISPR AND RESTRICTION LED US TO THINK THAT IT MIGHT HAVE AN ANTIVIRAL ACTIVITY AND AN ANTIVIRAL SYSTEM IN THE BACTERIAL CODE. AS I TOLD YOU, WHAT WE DO WHEN WE EXPECT IT TO FUNCTION IN AN ANTIVIRAL SYSTEM WE TAKE IT FROM ITS ORIGIN AND CLONED IT TO E. COLI THAT DOESN'T ENCODE IT. AND THEN WE INFECT THE E. COLI BY PHAGES AND THIS IS A TYPICAL EXPERIMENT DONE IN MY LAB EVERYDAY I GUESS. WHAT YOU SEE HERE, THE LIGHTER PARTS ARE LONG OF BACTERIA AND GROWING ON A PETRI DISH AND WE PUT THE FEW PHAGES HERE, TEN TIMES MORE PHAGES, A HUNDRED TIMES, A THOUSAND TIMES MORE AND MORE PHAGES IN EACH SERIAL DILUTION. WHEN ONE PHAGE TOUCHES ONE BACTERIUM ON THAT PLATE. ONE HUNDRED WILL EMERGE AND INFECT CELLS AND WE SEE THIS AREA OF CLEARANCE WHICH ARE THE PLAQUES. REGIONS WHERE THE SINGLE PHAGE HAS BEEN AND KILL THE BACTERIA. WHAT YOU SEE HERE IS WHEN THE BACTERIA ENCODES THE SYSTEM NOW WE NEED TO INFECT THE BACTERIA WITH MORE PHAGES BUT MORE PHAGES MEANING THAT THE SYSTEM PROTECTS THE BACTERIA AGAINST THE PHAGE. AND THIS OBSERVATION THAT WAS DONE BY SARAH IN MY LAB LED US TO, YOU KNOW, YOU KNOW, STARTED ADVENTURE WHICH INVOLVED GENETICS AND BIOCHEMISTRY AND EVENTUALLY WE REALIZED OUT THE SYSTEM WORKS OR AT LEAST HOW THE MAJOR PARTS OF IT WORKS. SO WE UNDERSTAND NOW THAT THE BACTERIAL CGAS ENZYME IS EXPRESSED MORE MATERIALLY. PHAGE ACTIVATION ACTIVATES THIS PROTEIN. BUT IT'S NOT THE DNA OF THE PHAGES THAT ACTIVATES. IT'S SOMETHING ELSE WITHIN THE PHAGE INFECTION. THE DNA IS NOT A GOOD ACTY VA DOOR FOR SENSING DNA WOULD BE FUTILE. IT'S SOMETHING ELSE THAT ACTIVATES THE PROTEIN. WE EXPECT IT IS PART OF THE CAPSID OF THE PHAGE AND WHEN THE PROTEINS ACTIVATED IT PRODUCES CYCLIC GMP-AMP THAT BIND AND ACTIVATE IT. AND THIS ACTIVE PHOSPHOLIPASE, EACH INNER MEMBRANE OF THE CELL AND KILLS IT. AND THE CELL DIES BEFORE THE PHAGE REPLICATION IS COMPLETE AND I KNOW THAT FOR SOME PEOPLE IT SOUNDS WEIRD THAT BACTERIA WOULD KILL THEMSELVES BEING SINGLE CELLED ORGANISMS. WHY WOULD BACTERIA KILL THEMSELVES AS PART OF THEIR DEFENSIVE MEASURE. SO BASICALLY, VERY FREQUENTLY IN NATURE BACTERIA LIVE IN COLONIES EITHER IN SOLID SURFACES OR IN LIQUID CULTURE AND THESE COLONIES ARE NEARLY SAY AYE SEW GENERALIC MEANING THEY START FROM ONE BACTERIA THAT REPLICATED AND THEN WE HAVE A SMALL COLONY OF BACTERIA. AND PHAGES DON'T HAVE A WAY TO BE MOBILE. SO THE INFECTION USUALLY STARTS BY INFUSION OF A SINGLE PHAGE IN THAT COLONY AND THIS PHAGE REPLICATES WITHIN THAT BACTERIUM AND THEN AFTER AWHILE, PHAGE PARTICLES EMERGE FROM THE BACTERIUM AND EVENTUALLY, THE ENTIRE COLONY WILL DEMISE, BUT IF THE BACTERIA HAVE AN ABILITY TO SENSE THAT THEY HAVE BEEN INFECTED, AND THEN KILL THEMSELVES THE SINGLE CELL THAT IS INFECTED WOULD KILL ITSELF BEFORE THE CYCLE IS COMPLETE THEN ONLY ONE CELL IS LOST AND THE COLONY SURVIVES SO BASICALLY GENETICALLY SPEAK, EVOLUTION PREFERS THAT. AND WE -- NOW UNDERSTAND THAT MOST BACTERIA IN NATURE HAVE AT LEAST ONE DEFENSE SYSTEM THAT WORKS THIS WAY. MEANING THAT WE'LL SENSE THE PHASE INFECTION AND THEN KILL THE CELL. THERE ARE MULTIPLE PRINCIPLES THAT GOVERN DEFENSE -- THAT WORKS THIS WAY. ONE OF THEM IS THAT THESE SYSTEMS USUALLY BECOME ACTIVE RELATIVELY LATE IN THE INFECTION CYCLE OF THE PHAGE SO THAT DEFENSE SYSTEMS THAT CAN OVERCOME THE PHAGE WITHOUT KILLING THE CELL COULD WORK FIRST LIKE CRISPR SHOULD BE ABLE TO WORK FIRST. IF THEY DON'T WORK ONLY THEN THE OTHER DEFENSE SYSTEMS THAT KILL THE CELL COME INTO ACTION. SO WE SEE THAT VERY FREQUENTLY. SO AROUND THE SAME TIME WE DISCOVER THESE CGAS SYSTEM IN BACTERIA. PHILLIP AND AARON FROM HARVARD MEDICAL SCHOOL, THEY FOUND THAT THE BACTERIA CGAS IS JUST ONE REPRESENTATION OF A LARGER FAMILY OF PROTEINS THAT PRODUCE THIS PROTOTYPE. SO WHAT THEY FOUND IS THAT THIS REPRESENTS THE FAMILY TREE. THE TREE OF THIS FAMILY OF ENZYMES, THE CGAS-LIKE ENZYMES. SOME OF THEM PRODUCE CYCLIC GMP BUT OTHER PRODUCE OTHER MOLECULES LIKE CYCLIC AMP OR CYCLIC UU OR CYCLIC TRINUCLEOTIDES AND IN MY LAB LOOKED AT WHETHER THESE FAMILIES OF PROTEINS FREQUENTLY OCCUR NEXT TO KNOWN DEFENSE SYSTEMS SO IN 64% OF THE CASES, GENES THAT PRODUCE PROTEINS THAT PRODUCE GMP-AMP, THE GENES WERE NEXT TO SYSTEMS BUT THIS WAS ALSO TRUE FOR OTHER PROTEINS FROM THIS FAMILY. AND THIS LED US TO REALIZE THAT ALL THESE PROTEINS PARTICIPATE IN DEFENSE AGAINST PHAGE AND THAT WHAT WE ACTUALLY SEE AND THIS IS -- FOUND IN -- BETWEEN 13-15% OF THOSE IN THE GENENOMAS WE NOW UNDERSTAND THAT THERE IS A LARGE DIVERSITY OF ANTIPHAGE SIGNALLING SYSTEMS IN THESE GENOMES AND THESE HAVE A UNIFYING PRINCIPLE OF ACTIVITY. THERE'S ALWAYS A PROTEIN FROM THE CGAS FAMILY THAT RECOGNIZES PHAGE INFECTION AND PRODUCES A SIGNALLING MOLECULE. THE SIGNALLING MOLECULE COULD BE CYCLIC GMP-AMP THAT CAN BE ANOTHER KIND OF SIGNALLING MOLECULE AND BINDS AN INFECTOR THAT KILLS THE CELL THAT COULD BE A PHOSPHOLIPASE BUT COULD ALSO BE A DNA AND THE NUCLEASE THAT DEGRADES THE BACTERIUM AND OF THE PHAGE TO KILL BOTH OF THEM DURING INFECTION. AND COULD ALSO BE THE PROTEINS THAT DEPOLARIZE THE MEMBRANE AND WE NOW HAVE PAPER COMING OUT SHOWING THAT SOME EFFECTORS DEGRADE THE ATP POOL FROM THE CELL DURING INFECTION TO ABORT THE REPLICATION OF THE PHAGE AND WE CALL THIS FAMILY OF SIGNALLING SYSTEM, WE CALL THEM IN THE UNIFYING NAME, CALLED CBAS WHICH IS THE ACRONYM OF THE NUCLEAR BASE ANTIPHAGING SYSTEMS. SO AGAIN TO PUT -- TO PUT THE PRINCIPLE OF CBASS INTO WITHIN -- BLUE COLLARED FIG INSTEAD OF THE RED COLORS. THE UNIFYING PRINCIPLE IS THERE'S AN ENZYME THAT RECOGNIZES PHAGE. PRODUCES A SIGNALLING MOLECULE THAT BINDS AN EFFECTOR THAT KILLS THE CELLS. WE IDENTIFIED CBASS WHICH IS FOUND WITHIN 13-15% OF GENOMES BUT LATER ON WE FOUND THAT THERE ARE ADDITIONAL FAMILIES OF IMMUNE SYSTEMS THAT WORK ACCORDING TO THE SAME PRINCIPLE. SO ONE OF THEM WE CALL PIXAR AND THIS IS A STUDY DONE WITH PHILLIP FROM HIS LAB AND PH.D. STUDENT FROM MY LAB AND WE FOUND THIS FAMILY PRODUCE CYCLIC CMP OR SO MONO NUCLEOTIDE THAT ACTIVATE AN EFFECTOR PROTEIN AND THEN WE FOUND ANOTHER FAMILY OF IMMUNE SYSTEMS THAT WORK IN THE SAME PRINCIPLE. THIS IS A TWO AREA SYSTEM IN WHICH TWO MAIN PROTEINS PRODUCE CYCLIC ATP RIBOSE ISOMER WHICH WE WILL NOT TALK MUCH ABOUT HERE. SO ALTOGETHER, MORE THAN 20% OF ALL BACTERIA IN NATURE OR AT LEAST ALL THE BACTERIA FOR WHICH WE HAVE THE GENOME SEQUENCES HAVE AT LEAST ONE OF THESE DEFENSE SYSTEMS. VERY ABUNDANT DEFENSE SYSTEMS IN MICROBIAL GENES. HOW CAN PHAGES OVERCOME THAT? CAN PHAGES DEFEND BACTERIA AND APPARENTLY THEY DON'T STUDYINGS FROM OUR COLLEAGUE, AS YOU CAN SEE WE HAVE A VERY DEEP DEEP UNDERSTANDING WITH PHILLIP. THE LAB HAS DISCOVERED ENZYMES THAT SOME PHAGES BRING THAT CLEAVE THE SIGNALLING MOLECULE AND INACTIVATE THEM ESCAPING DEFENSE BY PHAGES AND A SIMILAR KIND OF CLEAVING ENZYMES WERE FOUND ALSO IN VIRUSES THAT INFECT US. SOME WILL HAVE AN ENZYME THAT CLEAVES THE MOLECULE OF HUMANS. SOMETHING THAT WAS ALSO DISCOVERED BY PHILLIP AND IN A MORE RECENT STUDY TOGETHER WITH PHILLIP LED BY SOMEONE FROM MY LAB AND ALAN FROM PHILLIP'S LAB WE FOUND THAT OTHER ANTIDEFENSE PROTEINS, PHAGES L BIND THE SIGNALLING MOLECULE VERY TIGHTLY AND SEQUESTER IT AND THEREBY, AGAIN, NOT ALLOWING THE SIGNALLING MOLECULE TO BIND THE EFFECTOR PROTEIN AND SAVING THE PHAGE FROM THE DEFENSE SYSTEM. ALL RIGHT SO LET'S GO BACK TO THE CELL AUTONOMOUS IMMUNE SYSTEM THAT OUR OWN BODY HAS. CELLS IN OUR BODY HAVE THE ABILITY TO SENSE THAT THEY HAVE BEEN INFECTED AND I'M NOT TALKING ABOUT IMMUNE CELLS OR T CELLS OR B CELLS BUT ANY KIND OF CELL IN OUR BODY HAS A CELL AUTONOMOUS INNATE IMMUNE SYSTEM THAT ALLOW THE CELL TO IDENTIFY THAT IT HAS BEEN INFECTED AND THEN THROUGH SOME KIND OF SIGNALLING CASCADE TO ACTIVATE FIRST OF ALL SECRETION OF INTERFERON AND SECOND OF ALL THE PRODUCTION OF EFFECTORS WITHIN THE CELL THAT ALLOW THE CELL TO FIGHT AGAINST THE INFECTION OR AT LEAST THE CELL TRIES TO FIGHT AGAINST THE INFECTION BEFORE IT SPREADS. AS I TOLD YOU, SOME OF THE SENSORS ARE CONSERVED BETWEEN BACTERIA AND HUMAN AND THIS IS NOT THE ONLY THING CONSERVED IN THE INNATE IMMUNE SYSTEM OF HUMANS. AM GOING TO SHOW YOU ANOTHER STORY OF A PROTEIN CALLED VIE WRITTEN WHICH IS PRODUCED BY INFECTED CELLS AFTER THEY SENSE THEY HAVE BEEN INFECTED AND HAS ANTIVIRAL CAPACITY. SO IT WAS KNOWN FOR MANY YEARS I THINK MAYBE TWO OR THREE DECADES THAT THE VIPER RIN PROTEIN. IT'S ANOTHER CALL ACRONYM VIRUS INHIBITOR PROTEIN SOMETHING SOMETHING. NICE ACRONYM. AND IT WAS KNOWN THAT IT PROTECTS CELLS FROM INFECTION, IF YOU OVER EXPRESS IT CELLS ARE LESS INCLINED TO BE INFECTED BY SEVERAL DIFFERENT FAMILIES OF VIRUS BUT ONLY ABOUT FIVE YEARS AGO THE MECHANISM OF ACTION WAS DISCOVERED BY A GR GROUP -- A CLEVER GROUP IN MOUNT SINAI I THINK AND WHAT THEY FOUND IS THAT THE VIPER RIN IS AN ENZYME THAT TAKES THE NUCLEOTIDE AND MODIFIES IT BY REMOVING THE THREE PRIME OH AND INSTALLING A DOUBLE BOND INSTEAD AND NOW INSTEAD OF A REGULAR NUCLEOTIDE, THIS MODIFIED NUCLEOTIDE IS A POISON FOR THE VIRUS REPLICATION AND THE REASON IT FORMS A POISON WHICH S WHEN THE VIRUS TAKES THE NUCLEOTIDE TO POLYMERIZE ITS NASCENT CHAIN YOU TAKE THE STRAND AND PUT IT AGAINST THE TEMPLATE STRAND. YOU REMOVE THE TWO PHOSPHATES AND THE LAST PHOSPHATES YOU ATTACH IT TO THE PREVIOUS NUCLEOTIDE SO IF THE VIRUS HAS TAKEN THE MODIFIED NUCLEOTIDE THERE'S NOW NONE. AND THE VIRUS CANNOT CONTINUE TO REPLICATE ITS GENOME AND THIS NUCLEOTIDE IS NON TOIKSIC TO HUMAN CELLS MOST PROBABLY BECAUSE THE IT DOESN'T NEED TO WORK AS FAST AS THE POLYMERASE OF THE VIRUS AND IT CAN BE MODIFIED. THE REASON I'M TELLING YOU THIS IS BECAUSE WE FOUND THIS PROTEIN IN BACTERIA. THIS WAS FOUND BY A POSTDOC IN MY LAB. SHE HAS HER OWN LAB, A VERY SUCCESSFUL LAB AT AN INSTITUTE NOW AND WHAT SHE FOUND IS THAT THERE ARE LOADS OF THE VIPER RIN. THESE ARE FOUND. AND THESE ARE VERY, VERY FREQUENTLY FOUND NEXT TO CRISPR AND ENZYMES. WE THOUGHT AS YOU KNOW NOW, THIS TELLS US THAT THIS PROTEIN HAS A FUNCTION, HAS AN ANTIVIRAL FUNCTION IN BACTERIA AS WELL SO, AGAIN, WE TOOK A BUNCH OF THESE PROTEINS, WE CLONED THEM IN BACTERIA. IN THIS CASE I'M SHOWING YOU T 7. ONE, TEN, THESE ARE HUGE PLAQUES. T 7 HAS A SHORT CYCLE. THAT'S WHY IT FORMS A HUGE PLAQUE AFTER OVERNIGHT. AND WHAT YOU SEE IS THAT WHEN WE EXPRESS -- THE VIPER RIN WITHIN E. COLI CELLS WE SEE MUCH FEWER PLAQUES. THIS TOOK US TO ADVENTURE THAT INVOLVES A LOT OF CHEMISTRY. AND EVENTUALLY WHAT AUDE FOUND WAS THIS PRODUCED A FAMILY OF MOLECULES. SOME OF THEM ARE THE SAME LIKE THE HUMAN MOLECULE WHILE OTHERS ARE BASED ON A DIFFERENT NUCLEOTNUCLEOTID CASES THE OH FROM THE 3 PRIME END IS DEHYDRATED AND A DOUBLE BOND BECOMES -- IS INSTALLED AND POISONS THE PHAGE REPLICATION. SO WHEN WE TAKE ALL THE BACTERIAL ENZYMES AND PUT THEM ON THE TREE WHAT WE SEE IS THAT EWE SEE MULTIPLE CLAIFS THAT ARE FORMED. SOME OF THEM HAVE MORE TENDENCY TO PRODUCE THE OTHER NUCLEOTIDES AND WHEN WE ADD TO THIS TREE, THE SEQUENCES OF ALL THE YOU KARYOTIC. WE SEE ALL OF THEM CLUSTER ON A SINGLE CLAYED THAT EMERGES FROM THE CLAYED THAT PRODUCES THE CTP AND THAT IS MOSTLY UNREACHED. SO WE THINK WE HAVE PRETTY STRONG REASONS TO BELIEVE NOW THAT THERE HAS BEEN A SINGLE ACQUISITION EVENT IN THE VERY EVOLUTION OF EUKARYOTES WHERE THE EARLY EUCARYOTE ACQUIRED ONE VIPER RIN FROM BACTERIA AND STARTED ON THIS ACQUISITION AND LED TO WHAT WE SEE TODAY IN HUMANS AND OTHER EUKARYOTES. ONE THING THAT REALLY -- AGAIN, THERE ARE MANY SURPRISES IN THIS STORY. THAT WAS ANOTHER SURPRISE THAT BACTERIA CAN PRODUCE ANTIVIRAL MOLECULES. WE'RE USED TO THINKING ABOUT BACTERIA HAS A SOURCE MORE MOLECULES BUT THEY MOUSSE MORE MOLECULES TO PROTECT THEMSELVES FROM PHAGES. THESE OF YOU WHO UNDERSTAND HOW ANTIVIRALS WORK, REALIZE THAT IN MANY CASES, ANTIVIRALS THAT WE USE AGAINST VIRUSES THAT INFECT US ARE ALSO BASED ON MODIFIED NUCLEOTIDES. THIS MOLECULE IN THE MIDDLE IS PART OF THE THREE DRUG COCKTAIL THAT PEOPLE TAKE AGAINST HIV. AND THIS IS A NUCLEOTIDE THAT HAS INSTEAD OF THE THREE PRIME OH HAS THREE NITROGENS. THIS IS THE DRUG THAT PEOPLE TAKE AGAINST HERPES VIRUSES THAT YOU PUT ON YOUR LIPS, THIS OINTMENT WHEN YOU HAVE HERPES, THIS IS A MODIFY NUCLEOTIDE THAT BLOCKS THE BOTTOM PART OF THE VIRALS. THIS WORKS THE SAME WAY. IT TAKES IT IN AND SO WE THINK NOW REALIZING THAT BACTERIA PRODUCE AGAINST PHAGES WE WONDER WHETHER THESE MOLECULES CAN WORK AGAINST VIRUSES THAT INFECT US AND WE ARE TRYING TO SEE WHETHER THEY CAN BE NEW DRUGS IN THE FUTURE. HERE'S ANOTHER DEFENSE SYSTEM THAT IS VERY, VERY -- STUDIED ONE DAY IN HUMANS. SO IN ANIMAL CELLS INCLUDING IN OUR OWN CELLS THERE IS A SYSTEM THAT, OR AN APPARATUS CALLED THE INFLAM MA SOME THAT RECOGNIZES INFECTION AND ONCE THE INFECTION IS RECOGNIZED. PROTEINS CALLED CAS PACES BECOME ACTIVATED. AND THIS CAS PACE IS BY DOING SOME CLEAVAGE EVENT ON A PROTEIN CALLED GAS DER MIN, ONCE IT'S CLEAVED BECOMES ACTIVITY AND MAKES A GIANT PORE IN THE CELL MEMBRANE AND BASICALLY THE CELL LEAKS OUT AND DIES AT THE SAME TIME THAT THE CELL DIES IT SECRETES INTERNAL TO THE SITE OF THE INFECTION AND THAT'S WHY THIS IS CALLED PYRO TO SIS BECAUSE IT'S DEATH THAT CAUSES INFECTION. IN MY LAB, WAS DISCOVERED HOMOLOGS OF THE HUMAN GAS DER MIN AND FOUND THAT IN ALL CASES, THIS HOMO LOGS ARE FOUND NEXT TO A PROTEASE EITHER FROM THE CAS PACE FAMILY OR ANOTHER KIND OF PROTEASE SO WE SUSPECTED AND ALSO THESE ARE FOUND NEXT TO CRISPR SO WE SUSPECTED THIS IS ANOTHER DEFENSE SYSTEM IN BACTERIA. AND TOGETHER WITH OTHERS, THEY SHOWED THAT INDEED DURING INFECTION, THIS IS FROM MY LAB, DURING INFECTION THE CASPASES ARE ACTIVATED. THE CASPASE-LIKE PROTEINS ARE SENSING THE PHAGE AND WE VERIFY THE CLEAVAGE AND THEY MAKE GIANT HOLES IN THE MEMBRANE THAT KILL THE CELL. A SYSTEM THAT KILLS THE CELL BEFORE THE PHAGE IS READY. BEFORE THE PHAGE PARTICLES ARE RIPE WITHIN THE INFECTED CELL LET ME KNOW YOU ANOTHER PECULIAR MODE OF DEFENSE. THIS IS FOUND IN MY LAB BY A PH.D. STUDENT. SOMEONE WHO HAS BEEN VERY SUCCESSFUL IN HER DISCOVERS. THERE ARE FAMILIES OF ENZYMES THAT RECOGNIZE PHAGE INFECTION, MOST PROBABLY THEY RECOGNIZE THE PHASE AS INHIBITED FROM THE TRANSCRIPTION AND ONCE THIS IS SENSED THESE ENZYMES TAKE ONE OF THE NUCLEOTIDES IN THE CELL WHICH ARE THE BUILDING BLOCKS FOR DNA REPLICATION AND BASICALLY DEGRADES THAT NUCLEOTIDE. SO SHE FOUND TWO FAMILIES OF ENZYME ONE IS THAT THE DPASE AND ANOTHER FAMILY OF ENZYMES IS THE AM MIN NICES WHICH REMOVED THE NH FROM THE CTP. BASICALLY THESE ENZYMES HIDE ONE OF THE OXY NUCLEOTIDES AWAY FROM THE PHAGE AND THEY TRY TO REPLICATE THE GENOME AND WITHOUT THE NUCLEOTIDE IT GETS STUCK AND IS NOT REPLICATED. THE REASON I'M SHOWING YOU THE CONTEXT OF THIS IS BECAUSE, WE WERE VERY PROUD OF OURSELVES FOR DISCOVERING A NEW MODE, A NEW STRATEGY TO PROTECT AGAINST INFECTION BUT THEN WE REALIZED THAT A LONG TIME AGO IT WAS ALREADY DISCOVERED IN THE HUMAN IMMUNE SYSTEM AND THIS IS MANIFESTED BY A PROTEIN CALLED H 21. IT IS AN ANTI-HIV FACTOR THAT BLOCKS INFECTION BY DEGRADING THE OXY NTPS INTO THE THREE PHOSPHATES AND SUGAR AND BASE MOIETY BUT IT DOES THAT FOR ALL PROTOTYPES. SO WE NEVER REALIZED THAT MULTIPLE COMPONENTS OF OUR INNATE IMMUNE SYSTEMS HAVE PARALLELS IN THE BACTERIAL IMMUNE SYSTEM AND IN SOME CASES WE HAVE VERY SOLID PROOF THAT THE HUMAN COMPONENT HAS EVOLVED FROM THE BACTERIAL COMPONENT. YOU KNOW, GENETICALLY BASED PROOF. SO WHAT WE THINK HAPPENED IS THAT, I MEAN, WHAT CAN EXPLAIN THAT IS THAT PHAGES, AND THAT'S VERY WELL ACCEPTED. THAT PHAGES HAVE BEEN IN THE WORLD WELL BEFORE EUKARYOTES EVEN WERE HERE. SO PHAGES WERE INFECTING BACTERIA VERY LONG TIME AGO, VERY EARLY ON AFTER THE BACTERIA WAS INVENTED AND DEFENSE SYSTEMS HAVE INVOLVED IN BACTERIA BEFORE EUKARYOTES CAME TO BE AND THESE DEFENSE SYSTEMS HAVE BEEN IN BACTERIA FOR HUNDRED OF YEARS AND AT SOME POINT THE FIRST EUKARYOTE CAME TO BE MOSTLY BY DIFFUSION AND THESE THIS BACTERIUM USED TO HAVE DEFENSE SYSTEMS IN THEM AND THESE DEFENSE SYSTEMS WERE THE BASIS OF THE IMMUNE SYSTEM THAT WE KNOW TODAY SO THIS TEACHES US ABOUT THE EVOLUTION OF OUR OWN IMMUNE SYSTEM BUT CAN ALSO BE BENEFICIAL FOR UNDERSTANDING IMMUNE SYSTEMS OF HUMANS. AND WHAT DO I MEAN? WE ARE GOING TO FIND NOW DEFENSE SYSTEMS THAT WE KNOW EXIST IN HUMAN BUT WE DON'T KNOW HOW THEY WORK AND WE NOW FIND THEM IN BACTERIA. SO THIS IS ONE INTERESTING IMMUNE SYSTEM. IT'S CALLED I 15. IT'S A YOU WICK WE TIN LIKE PROTEIN THAT IS PRODUCED BY INTERFERON. IT'S DEDUCED TOGETHER WITH UBIQUITIN CHARGING ENZYMES THAT ARE SPECIFIC AND PROTECTS OURSELVES AGAINST SOME VIRUSES. AND HAS SOME ROLES IN COVID PROTECTION FROM COVID INFECTION. BUT WE DON'T KNOW HOW IT WORKS. PEOPLE IN IMMUNOLOGY FEEL THEY DON'T KNOW HOW IT WORKS. NOW WE REALIZE THAT SUCH A SYSTEM EXISTS IN BACTERIA. THERE IS AN INTERFERON IN PROTEINS AND THE UBIQUITIN DOMAIN AND WE SHOW IT PROTECTS AGAINST PHAGES. NOW WE'RE TRYING TO FIGURE OUT WHY AND WE HOPE IF WE SOLVE THE MECHANISM IN BACTERIA THIS CAN TRANSLATE INTO UNDERSTANDING HOW THE HUMAN MECHANISMS WORK AS WELL. WE HAVE A BUNCH OF IMMUNE MECHANISMS THAT ARE FOUND BOTH IN HUMANS AND IN BACTERIA BUT WE DON'T KNOW YET HIGH THEY WORK IN HUMAN. WE HOPE TO SOLVE THIS RIDDLE. NOT ALL OF THE DEFENSE SYSTEMS HAVE HOMO LOGS IN HUMANS. FOR EXAMPLE, WE FOUND THIS PROTEIN CALLED RADAR. THIS IS A SYSTEM THAT WAS FOUND. WHICH COMPRISES TWO VERY BIG GENES. ONE OF THEM AS A DOMAIN, THE OTHER HAS AN ATPASE DOMAIN. AND TOGETHER IN THE LAB, THEY SHOWED THAT THESE PROTEINS FORM A GIANT COMPLEX IN THE CELL. THIS GIANT COMPLEX IS BUILT FROM TWELVE MONOMERS OF THIS. THEY FORM LIKE THIS KIND OF A SOCCER BALL. AND THIS PROTEIN FORMS THE HEP TAMIR AND EACH HEP TAMIR SITS ON ONE FACE OF THE SOCCER -- THE DECK KA HER TO FORM A GIANT COMPLEX. THAT IS FOUR TIMES AS HEAVY AS A RIBOSOME SO A VERY BIG COMPLEX AND WHAT WE SHOWED IS THAT THIS COMPLEX CONVERTS MASSIVELY ATP TO ADEKNOW SIGN DURING INFECTION WE DON'T KNOW HOW IT PROTECTS AGAINST PHAGE. BUT THIS CONVERSION, MAYBE IT'S PROTECTION AGAINST PHAGE, WE'RE STILL STUDYING THAT. THE COMPLEX IS SOMETHING LIKE -- WE HAVEN'T SEEN ANYTHING LIKE THAT. IT'S SUCH A GIANT COMPLEX IN ORDER TO MEDIATE THIS ACTIVITY. ANOTHER THING THAT IS VERY INTERESTING TO US WE FOUND IS SOMETHING CALLED LET TRONS. THIS IS A VERY PECULIAR ENTITY IN BACTERIA. IT'S COMPRISING RNA AND THERE ARE REVERSE TRANSCRIPTASE THAT CONVERT INTO CDNA LEAVING IT BOUND. SO THIS IS RNA AND DNA THAT WAS KNOWN IN BACTERIA FOR MANY YEARS IT'S FOUND IN MORE THAN 10% OF ALL BACTERIA AND THE FUNCTION OF THIS WAS NOT KNOWN. WE FOUND THAT IT PARTICIPATES IN DEFENSE AGAINST PHAGES AND WE FOUND THAT ONE OF THESE -- IT'S CALLED A LET TRON. ONE OF THESE LET TRON IS A GUARDIAN OF ANOTHER DEFENSE SYSTEM. SO THERE IS A DEFENSE SYSTEM OR THERE IS A COMPLEX CALLED RECK BCD IN THE CELL THAT ALSO CLEAVES LINEAR DNA. YOU KNOW WHEN THE PHAGE EJECTS THIS FROM THE CELL IT EATS THE DNA VERY RAPIDLY AND FOR THIS REASON MANY PHAGES ARE ALSO BRINGING PROTEINS TO INHIBITORY RECK BCD. WE FOUND THESE GUARD THE REC BCD AND WHEN IT COMES INTO ACTION AND TOGETHER KILLS ANOTHER CELL. IT'S A GUARDIAN OF ANOTHER DEFENSE SYSTEM AND IF THIS OTHER DEFENSE SYSTEM BECOMES INHIBITED BY PHAGE, THIS GUARDIAN KILLS THE CELL. WE DON'T YET UNDERSTAND WHY WE NEED THIS A CHI MARA BETWEEN DNA AND RNA. THERE ARE MANY OPEN QUESTIONS. THIS HAPPENS FAST, THESE DISCOVERS AND WE STILL DON'T UNDERSTAND MUCH. FOR EXAMPLE, FOR MANY SYSTEMS WE KNOW WHAT HAPPENS AFTER THE PHAGE. IN SOME CASES THEY DO SOMETHING ELSE. BUT WE DON'T KNOW WHAT IS BEING RECOGNIZED. HOW THEY RECOGNIZE PHAGE INFECTION. NOW WE HAVE SOMEONE FROM MY LAB, SHE RECENTLY DID A VERY LARGE SCREENING EXPERIMENT. WHERE SHE TOOK ALL THE DEFENSE SYSTEMS THAT WE HAVE. ABOUT 50 DEFENSE SYSTEMS THAT WE HAVE IN THE LAB AND EACH DEFENSE SYSTEM SHE INFECTED THE CELL THAT ENCODES THE SYSTEM WITH A PHAGE THAT IS NORMALLY BLOCKED BY THE SYSTEM AND SHE SEARCHED FOR PHAGE MUTANTS THAT CAN OVERCOME THE DEFENSE SYSTEM THEN SEQUENCED THE PHASE GENOME TO SEE WHAT GOT MUTATED AND IN MANY CASES IT'S THE GENE THAT GETS RECOGNIZED BY THE DEFENSE REALIZED AND SHE REALIZED THEY FREQUENTLY IDENTIFY EITHER THE COMPONENTS OF THE PHAGE. THESE ARE THE PROTEIN THAT FORM THE REPLICATION MACHINERY. THIS IS A VERY RELATIVELY CONSERVATIVE. OTHER SYSTEMS RECOGNIZE STRUCTURAL COMPETENCE OF THE PHAGE. WOULD BE, YOU KNOW, THE PHAGE TWO PROTEIN OR THE CAPSID OR SOMETHING ELSE THIS THE STRUCTURE. AND SO OTHER SYSTEMS RECOGNIZE THE PHAGES TAKING OVER THE CELL. YOU KNOW, SOME OF THEM RECOGNIZE THAT ANOTHER DEFENSE SYSTEM GETS INHIBITED AND SOME OTHERS RECOGNIZED THAT TRANSCRIPTION BECOMES INHIBITED. THIS BECOMES UNIFYING PRINCIPLE IN HOW DEFENSE SYSTEMS ARE RECOGNIZED, INFECTION BY PHAGE. ANOTHER OPEN QUESTION IS, WHAT ARE THOSE DEFENSE ODDS? SO I TOLD YOU THAT WE IDENTIFIED MULTIPLE DEFENSE SYSTEMS BASED ON THE PRESENCE FREQUENTLY NEXT TO DEFENSE SYSTEMS. AND THIS DEFENSE ISLAND WAS VERY FRUITFUL FOR US WITH THE DISCOVERY OF NEW SYSTEMS BUT THE QUESTION OF WHAT ARE THE DEFENSE ISLANDS BOTHERED US FOR A NUMBER OF YEARS AND A PH STUDENT IN MY LAB FOUND THAT THE DEFENSE SYSTEMS ARE CARRIED USUALLY BY MOBILE GENETIC ELEMENTS. THIS ISN'T STUDYING E. COLI. SHE SHOWED THAT DIFFERENT STRAINS OF E. COLI HAVE DIFFERENT STRAINS THAT ARE CARRIED ON DEDICATED MOBILE GENOMIC ELEMENTS. THIS IS THE LAB STRAIN THAT LACKS MOST OF THE DEFENSE SYSTEMS THAT WE FOUND. AND THESE ARE DIFFERENT STRAINS OF E. COLI. YOU SEE IN EACH OF THESE STRAINS AN ISL ISLAND -- A MOBILE ISLAND HAS INTEGRATED IN THE SAME PLACE. AND SO, IF YOU LOOK AT, WE LOOKED AT ABOUT 1,000 E. COLI GENOMES. WE SEE OUR ABILITY IN THE DEFENSE SYSTEMS IN THESE GENOMES. MOST OF THE SYSTEMS ARE CARRIED BY MOBILE GENETIC ELEMENTS SO HERE, THIS IS THE ELEMENT THAT BRINGS MANY KINDS OF DEFENSE SYSTEMS INTO THE SAME POSITION IN THE E. COLI GENOME BUT IN EACH STRAIN IT'S A DIFFERENT SET OF DEFENSE SYSTEMS FORMING THESE DEFENSE ISLANDS AND THIS PANNED OUT INTO SOMETHING THAT WE DIDN'T EXPECT. IN TERMS OF THE DISTRIBUTION OF DEFENSE SYSTEMS IN MICROBIAL GENOMES. WE SEE THAT THEY ARE VERY SPORADICALLY PRESENT IN MICROBES. WHAT YOU SEE HERE, EACH ROW HERE IS A STRAIN OF E. COLI. AND EACH COLUMN IS THE DEFENSE SYSTEM. SO THIS IS A RESTRICTION ENZYME TYPE ONE, TWO, THREE, FOUR. OTHER DEFENSE SYSTEMS THAT WE DISCOVERED, CRISPR, WHENEVER YOU SEE THE COLORED BOX MEANS THIS STRAIN HAS THE SYSTEM. AND YOU SEE THAT THE SYSTEMS SPORADICALLY OCCUR IN STRAINS. THE FIRST STRAIN HAS THIS SYSTEM AND THE THIRD STRAIN, YOU KNOW, HAS A TYPE FOUR RESTRICTION ENZYME. IT HAS A SYSTEM, ET CETERA. AND SO THESE SYSTEMS ARE SPORADICALLY OCCURRING AND WE CALL THAT THE PAN IMMUNE SYSTEM OF BACTERIA. WE THINK THAT A SINGLE BACTERIUM CANNOT ENCODE ALL THE DEFENSE SYSTEMS AT ONCE BECAUSE THE TIME IT EMERGES AS AUTOIMMUNITY OCCURS TO TOO MUCH TOXICITY BUT ON THE OTHER HAND THE OTHER BACTERIA THAT ENCODE COULD CONTRIBUTE THAT THROUGH HORIZONTAL GENE TRANSFER AND THESE SYSTEMS COULD BE ACQUIRED BY NATURE IF THEY'RE NEEDED. AND SO I WANT TO END, YOU KNOW BY SHOWING THIS POSTER WE WERE ASKED TO PUT WHAT WE KNOW ON DEFENSE SYSTEMS OF BACTERIA ON A SINGLE POSTER. OBVIOUSLY IT'S TOO SMALL FOR YOU TO SEE. WE HAVE RESTRICTION ENZYMES HERE. WHAT FASCINATES ME ABOUT THE POSTER, WE PUBLISHED IT LAST YEAR AND NOW MANY ADDITIONAL SYSTEMS AND MECHANISMS WERE DISCOVERED SINCE THEN. BUT WHAT REALLY FASCINATES ME IS THAT MANY OF THE MECHANISMS THAT ARE DESCRIBED HERE ARE ONLY THE PRODUCT OF STUDIES OF OUR LAB AND MANY OTHER LABS AND THE VERY, YOU KNOW, VERY RECENTLY. MUCH OF THE IMMUNE SYSTEMS WE JUST DIDN'T KNOW AND NOW IT'S LIKE, YOU KNOW, LIFTING, OR DIGGING A GIANT EXCAVATION SITE AND REALIZING THERE HAS BEEN A CITY BELOW AND MOVER WHAT YOU SEE IN THE TINY FONT ARE THE LIST OF NAMES. OF DEFENSE SYSTEMS THAT WE KNOW PROTECT AGAINST PHAGE BUT WE DON'T KNOW YET HOW. VERY LARGE, YOU KNOW, VERY LARGE GROUNDS FOR HAVING, YOU KNOW, MAKING FUN BIOLOGY AND FUTURE DISCOVERIES. AND I WANT TO END BY THANKING MY LAB WHICH ARE VERY TALENTED GROUP OF PEOPLE. VERY GLAD TO HELP WITH THEM TO WORK WITH THEM. AND ALSO OUR DEAR COLLABORATORS PHILLIP AND MANY MEMBERS OF HIS LAB. WE'VE BEEN HAVING A WONDERFUL COLLABORATION OVER A VERY SHORT TIME PERIOD AND MOST OF THIS COLLABORATION WAS DONE UNDER COVID SO WE HAVEN'T MET UNTIL RECENTLY. WE PUBLISHED PAPERS TOGETHER AND ONLY MET ONCE. BUT ON ZOOM. AND THANK YOU VERY MUCH MORE LISTENING. >>(APPLAUSE). >>OF COURSE ANYONE HERE IS FREE TO USE THE MICS AND AS YOU ARE MAKING YOUR WAY OVER THERE I DO HAVE A COUPLE QUESTIONS FROM THE ONLINE. THIS ONE COMES RATHER EARLY IN THE TALK. DOES EXPRESSION OF VIRAL CAPSID PROTEINS LEAD TO CELL DEATH VIA THE CGAS SYSTEM? >>THAT'S A GREAT QUESTION. SO IN SOME CASES, IN SOME DEFENSE SYSTEMS, EXPRESSION OF THE STRUCTURAL COMPONENTS OF THE PHAGE IS DIRECTLY LEADING TO TOXICITY, LEADS TO CELL DEATH IN THE CASE OF CGAS WE COULDN'T FIND -- IN ANOTHER CALLED PYCSAR WHERE WE FOUND IT IN THE CAPSID THERE WAS NO TOXICITY. THE DEFENSE IS GONE. SO WE THINK THAT EITHER THE LARGER CONTEXT OF THE PHAGE THAT'S BEING ASSEMBLED WITHIN THE MATERIAL IS THE TRIGGER FOR THE CGAS ACTIVATION OR YOU NEED MULTIPLE SIGNALS, YOU KNOW, BOTH THE CAPSID AND SOMETHING ELSE THAT WE DON'T KNOW OF YET SO WE DON'T SEE ACTIVATION JUST BY EXPRESSING THE CAPSID FOR THE SPECIFIC CASE. >>YOU MAY HAVE TOUCHED ON THIS RIGHT AT THE END AND I MAY HAVE JUST MISSED IT. DO YOU FIND THE BACTERIA STEALING PIECES OF THE FABL PHAGE AS MAKING A BOARD. OR MAKING SOME UNITS THAT DON'T WORK OR OTHER SORTS OF THINGS? >>WE DON'T FIND EVIDENCE THAT BACTERIA, THAT THE DEFENSE SYSTEMS THAT ARE WITHIN THIS DEFENSE ISLANDS, WE DIDN'T YET FIND EVIDENCE THAT THEY COMPRISE ANCIENT PIECES OF PHAGES. IT DOESN'T MEAN THAT THIS IS NOT A STRATEGY OF BACTERIA. IT COULD BE THAT SOME BACTERIA PROTECTS BY THIS BUT MAYBE THESE PROTEINS ARE NOT TRAVELING ON DEFENSE ISLANDS LIKE THESE SYSTEMS. >>IT WOULD BE A FOLLOW UP WITH A DOUBLE QUESTION ABOUT THE ISLANDS. NO QUESTION IS AN ISLAND I GUESS. ARE DEFENSE ISLANDS TRANSCRIPTIONALLY ORGANIZED WITH THEIR RESPONSE TO PHAGE AND DO DEFENSE ISLANDS DEFEND AGAINST COMPETITOR BIOFILMS, PROTEIN AGGREGATES. >>RIGHT. SO BASED ON THE ORGANIZATION OF THE GENES IN DEFENSE ISLANDS WE DON'T THINK THAT THERE IS ORGANIZATION BY GENE EXPRESSION. WE SEE THE DEFENSE SYSTEMS WILL DISCOVER OUR EXPRESS. AND FIND THOSE PROTEINS BEFORE IT INFECTS. THE REASON WE THINK THIS IS ESSENTIAL IS BECAUSE SOME PHAGES ARE QUICKLY KILLING THE CELLS. SOME PHAGES WILL DEGRADE THE INFECTED CELL AFTER FOUR MINUTES. THIS IS SOMETHING IT DOES. AND SO THIS IS NOT ENOUGH TIME TO ACTIVATE EXPRESSION AND THEN DEFENSE. SO USUALLY THE ACTIVATION OF THE SYSTEMS IS DONE IN THE PROTEIN LEVEL. THERE ARE EVIDENCE THAT YOU CAN ELEVATE THE EXPRESSION OF SOME DEFENSE SYSTEMS USING EXTERNAL SIGNALS. MOST OF THEM ARE INVOLVED IN THE DENSITY OF THE CULTURE. AND SOME OF THEM ARE NOT DONE YET. SO THAT'S THE ANSWER FOR THE FIRST QUESTION. THE SECOND QUESTION, DO DEFENSE ISLAND -- >>COMPETITORS LIKE PROTEIN AGGREG AGGREGATES. >>NOT THAT I KNOW OF. WE'VE BEEN STUDYING THE DEFENSE SYSTEMS IN AN ISOLATED MANNER. BASICALLY WHAT WE'VE BEEN DOING IS TAKE A DEFENSE ISLAND AND STORE IT IN ECO LIE. WE'VE TAKEN ONE SYSTEM AND STUDY WHAT IT DOES. WE DON'T KNOW IF THESE ISLANDS DO OTHER STUFF. >>I NOTICED EARLIER IN YOUR TALK WHEN YOU WERE GIVING US SPECIFIC DEFENSE MECHANISMS THAT THE NAMES WERE ACRONYMS BASED ON WHAT THEY DO. BUT AT THE END YOU GAVE US A LIST OF FIFTY NAMES THAT SOUNDED A LOT MORE IMAGINATIVE. WHERE ARE THOSE NAMES COMING FROM? >>THANK YOU FOR THIS QUESTION. YEAH, WE STARTED QUOTING THE DEFENSE SYSTEMS AS THE FIRST SYSTEM WE EVER DISCOVERED WAS CALLED BRICKS. THE SECOND WAS DISARM, WHICH WAS WITH MODIFICATION. AND THEN WE RAN OUT OF ACRONYMS SO WE STARTED CALLING THEM OF PROTECTIVE GODS FROM DIFFERENT MYTHOLOGIES. WE HAVE THE LITHUANIA GOD. WE HAVE A CELTIC GOD OF THE FOREST. WE HAVE AN EGYPTIAN GODDESS. THAT'S THE NAMES. >>ON A MORE SERIOUS NOTE, SINCE A LOT OF THE MECHANISMS KILL BACTERIA, IS THERE AN OBVIOUS WAY AND I'M SURE YOU'VE THOUGHT ABOUT THIS, TO USE THOSE MECHANISMS, TO ACTIVATE THEM AS ANTIBIOTICS? >>THIS IS A GREAT QUESTION. I'M NOT SURE HOW USEFUL WOULD THIS BE BECAUSE THE SYSTEMS ARE SO SPORADICALLY PRESENT IN BACTERIA. SO, YOU KNOW, THE CBASS SYSTEM WHICH IS PRESENT IN ABOUT 15% OF THE GENOMES, YOU CAN IMAGINE THAT IF YOU GIVE THEM THE SIGNAL IN HEIGHT OF CONCENTRATION THAT THE PSYCHLY GMP-AMP, SOME OF THEM WILL FORCE THE CELL TO DIE. SOME OF THEM USED PSYCHLY UMP, TRINUCLEOTIDE SO YOU'D BE ABLE TO ONLY KILL A SMALL NUMBER OF THEM AND SINCE IT'S NOT THAT YOU WILL EVER BE ABLE TO KILL ALL THE E. COLIS. BECAUSE THE M SYSTEMS ARE SPORADICALLY PRESENT. SO YOU'D BE ABLE TO KILL JUST SPECIFIC STRANDS OF THE BACTERIUM AND WILL NOT BE PROFITABLE FOR A DRUG COMPANY TO BE SO SPECIFIC I IMAGINE. >>YES. THERE ARE COLLEAGUE FROM YOURS AND PROBABLY SWITZERLAND FOR THE WEDNESDAY EVENING LECTURE SERIES WE HAVE THERE. LUKE. GREAT TALK, WHY ARE RESTRICTION ENZYMES SO PREVALENT COMPARED TO OTHER INNATE DEFENSE SYSTEMS? >>WELL E RESTRICTION ENZYMES GIVE A VERY GOOD ABILITY TO PROTECT AGAINST THE PHAGE WITHOUT KILLING ITSELF. THAT'S A GOOD REASON TO KEEP THEM THERE. SOME PHAGES BRING ANTIRESTRICTION. THAT IS SOMETHING THAT IS COMMON IN PHAGES. PROTEINS THAT PROHIBIT RESTRICTION ENZYMES IN CASES WHERE YOUR RESTRICTION ENZYMES ARE PROHIBITED I GUESS THE CELL WOULD WANT TO ACTIVATE THE SYSTEM THAT LEADS TO DEATH. >>AND WHAT, FIFTY YEARS AGO ON THE SUBJECT, WHEN THE PHAGE INFECTS E. COLI, THE VERY FIRST THING THAT HAPPENS, AT THIS I DON'T KNOW, BUT IMMEDIATELY INACTIVATES THE POLYMERASE TR TRANSCRIPTION OF THE E. COLI. BECAUSE IT HAS THE SIGMA FACTOR AND ONLY THIS, AS WAS EARLIER STATED, ON THE POLYMERASE. IT CAN TRANSCRIBE THE T4 DNA AND THAT IS HOW THE WHOLE PROCESS PROCEEDS DOWN THE ROAD. SO THAT IS I THINK LONG BACK DISCOVERED. VERY FIRST THING, THE MODIFICATION. VERY IMPORTANT SIGMA FACTOR WHICH IS INVOLVED IN THE INITIATION OF THE TRANSCRIPTION OF RNA AND DNA. >>YEAH. YEAH. >>DO YOU HAVE ANOTHER QUESTION? >>NO. >>SO IT'LL BE ONE LAST QUESTION ONLINE. WE'RE JUST PAST THE HOUR. GIVEN HEMOLOGY BETWEEN BACTERIAL AND EUCARYOTE IMMUNITY, IS THERE ANY EVIDENCE FOR HEMOLOGY BETWEEN ANTIDEFENSE GENES OF PHAGES AND VIRUSES ATTACKING EUKARYOTIC CELLS? >>IT IS A GREAT QUESTION. WE HAVEN'T FOUND -- SO FAR WE DIDN'T DISCOVER TOO MANY PHAGE PROTEINS THAT INHIBIT DEFENSES. MAYBE FOUR OR FIVE SUCH FAMILIES AND WE HAVEN'T FOUND HEMOLOGIES TO PROTEINS AND VIRUSES THAT INFECT HUMANS. SOMETIMES THERE IS ANALOGY. SO AS I TOLD YOU THERE ARE ENZYMES THAT PHAGES BRING THAT CLEAVE THE SIGNALLING MOLECULE TO THE DEFENSE SYSTEM AND THERE ARE ENZYMES THAT CLEAVE THE SAME MOLECULE IN HUMAN BUT THESE ARE NOT THE SAME FAMILY SO THEY EVOLVED SEPARATELY IN THOSE LINEAGES. THERE'S NO STRUCTURAL HEMOLOGY THERE. I IMAGINE THERE MIGHT BE. WE HAVEN'T FOUND THEM YET. >>ONE MORE IF YOU DON'T MIND. >>LAST ONE. >>I PROMISE. DO YOU SEE ANY ROLE FOR MODIFIED NUCLEOTIDES MADE IN BACTERIA IN A MICROBIOME CONTEXT BEING TAKEN UP BY THE SURROUNDING EUKARYOTIC CELLS? ARE THESE ABSOLUTE CONVERSIONS OF THE ENTIRE POOL INSIDE THE CELL? >>WE HAVEN'T LOOKED INTO THAT. GOOD QUESTION, BUT WE HAVEN'T EXPLORED IT. >>OKAY. MY LIPS ARE SEALED. >>ON THAT NOTE, ON BEHALF OF LAMBDA LUNCH I WANT TO THANK YOU FOR SUCH A FASCINATING TALK AND THE AUDIENCE FOR SUCH A GREAT DISCUSSION. I WANT TO INVITE EVERYBODY HERE, LIVE AND PRESENT IN THE AUDIENCE TO RECEPTION. WITH COOKIES AND COFFEE, SPONSORED BY LAMBDA LUNCH. THEY'RE REAL COOKIES AND REAL COFFEE. PLEASE JOIN US OUT THERE TO CONTINUE THE DISCUSSION. SO THANK YOU VERY MUCH. >>THANK YOU VERY MUCH. THANK YOU. >>(APPLAUSE).