L6 Microbial Genetics II PDF

L6: Microbial genetics II BIO-440 Feb 4, 2025 By Dr. Anny Cárdenas Assistant Professor, Department of Biology 1 Content Topic 1: Sensing and Signal Transduction Two-Component Regulatory Systems Regulation of Chemotaxis Cell-to-Cell Signaling Topic...

L6: Microbial genetics II BIO-440 Feb 4, 2025 By Dr. Anny Cárdenas Assistant Professor, Department of Biology 1 Content Topic 1: Sensing and Signal Transduction Two-Component Regulatory Systems Regulation of Chemotaxis Cell-to-Cell Signaling Topic 2: Global Control The lac Operon Stringent and General Stress Responses The Phosphate (Pho) Regulon Topic 3: Gene Transfer in Bacteria Genetic Recombination Transformation Transduction Conjugation Preserving Genomic Integrity and CRISPR Sensing and Signal Transduction Two-Component Regulatory Systems: a regulatory system consisting of two proteins: a sensor kinase and a response regulator 1 818 whats Sensor kinase autophosphorylates Response receivy regulator ofgenesoncephosphorylated expression activate Two-Component Regulatory Systems: a regulatory system consisting of two proteins: a sensor kinase and a response regulator Feedback loop Feedback loop is a way to reset the system for another cycle. This feedback loop employs a phosphatase, an enzyme that removes the phosphate from the response regulator at a constant rate (typically slower than kinases). Osmotic sensing by the EnvZ/OmpR in E. coli systemthatdetectsosmgt.IT Sensor kinase: changes in osmotic pressure triggers autophosphorylation Response regulator: Low osmotic pressure activates transcription of the ompF gene. Conversely, high osmotic pressure, represses transcription of ompF and simultaneously activates transcription of ompC iiion  Nitrogen metabolism by the Ntr systemin E. coli Sensor kinase: NRII senses ammonia levels in the cell. It can switch from kinase activity to phosphatase activity depending on the nitrogen status of the cell Response regulator: NRI-P oligomerizes and binds upstream of the promoter for nitrogen assimilation genes, looping the DNA to contact RNA polymerase and sigma factor, activating transcription of nitrogen assimilation genes Regulation of chemotaxis Bacterial chemotaxis uses a modified two-component system. It senses temporal changes in attractants or repellents to regulate flagellar rotation, rather than controlling their gene transcription. Response Sensor regulator kinase Regulation of chemotaxis Sensory proteins called methyl-accepting chemotaxis proteins (MCPs) allow the cell to monitor the concentration of various substances over time Response Sensor regulator kinase Regulation of chemotaxis any that in can Attractant: CheW is inactive and phosphorylation of CheA is inhibited. CheY is inactive and therefore the flagellar switch continues in a counterclockwise (CCW) rotation and cell running toward the attractant occurs. Inactive CheA Sensor kinase Regulation of chemotaxis Repellent: increase in repellent concentration increases the rate of CheA autophosphorylation. Phosphorilated CheY results in clockwise (CW) rotation and cell tumbling. Phosphorylated Response regulator I E Adaptation CheB becomes phosphorylated and CheB-P demethylates the MCPs. CheA-P donates a phosphate group not only to CheY but to CheB as well CheZ, dephosphorylates CheY, returning it to the form that allows runs instead of tumbles Restoration ofsystem Cell-to-cell communication / Quorum sensing A regulatory system that monitors the population density and controls gene expression based on density active only cell unen is density high Basic quorum sensing: How bacteria know who’s around them. (Nidhi Srivaths) Cell-to-cell communication / Quorum sensing Basic quorum sensing: How bacteria know who’s around them. (Nidhi Srivaths) Autoinducer molecules Autoinducer 2 Autoinducer 1 Gram-positive bacteria and archaea often use peptides as autoinducer molecules cyclic furan derivative Autoinducer: small signal molecules that take part in quorum sensing high concentrations into to Quorum Sensing was discovered as the mechanism by which light emission in bioluminescent bacteria is regulated AHL receptor sentor'monecure Aliivibrio fischeri AHL synthase Regulation of the Shiga toxin by E. coli E. coli O157 produces AI-3 while host intestinal cells produce the stress hormones epinephrine and norepinephrine All three signal molecules bind to two separate sensor kinases in the E. coli cytoplasmic membrane, resulting in the phosphorylation and activation of two transcriptional activator proteins Regulation of virulence Staphylococcus aureus grampositive Global control globalregulatorsofgene expression  Catabolite repression: The suppression of alternative catabolic pathways by a preferred source of carbon. activatesorinhibitsgenes Diauxic growth (two exponential phases) of Escherichia coli of onconcentration based glucose on a mixture of glucose and lactose. Eg glucose second lactose Cyclic AMP: a regulatory nucleotide that participates in catabolite repression + cyclic AMP receptor protein (CRP) The lac operon Stringent response: a regulatory mechanism used by bacteria to survive nutrient depravation cell for system alarm Alarmones: Guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp) Stringent response: a regulatory mechanism used by bacteria to survive nutrient depravation RelA is responsible for the synthesis of ppGpp that triggers the synthesis of uncharged tRNAs The Stringent Response and Microbial Ecology The General Stress Response: The RpoS Regulon RpoS regulon comprises over 400 genes including those associated with nutrient limitation, resistance to DNA damage, biofilm formation, and responses to osmotic, oxidative, and acid stresses. The Phosphate (Pho) Regulon gaitis.ae of Gene transfer in bacteria Transduction Transformation Conjugation Transformation: is a genetic transfer process by which free DNA is incorporated into a recipient cell and brings about genetic change Pray aging cells T6SS labeled with a green fluorescent protein Pray DNA uptake proteins cells labeled with a red fluorescent protein i Transformation: is a genetic transfer process by which free DNA is incorporated into a recipient cell and brings about genetic change Membrane- associated DNA-binding protein nucleases Competence specific proteins General mechanism of transformation DNA-binding protein is bound to DNA and nucleases degrade one strand General mechanism of transformation Competence proteins protect single-stranded DNA until RecA binds the complex some integrate General mechanism of transformation Integration in the recipient genome yea Swthe ionosome degraded WE hasno if it to homology chromosome General mechanism of transformation Transformed cell Transduction: a bacterial virus (bacteriophage) transfers DNA from one cell to another. viralinfection Specialized: DNA from a specific region of the host chromosome is integrated directly into the virus genome—usually replacing Generalized: DNA derived some of the virus gene. from virtually any portion of the host genome is packaged Eration inside the mature virion in place of the virus genome. ofgenome Generalized transduction Occasionally, during lytic infection, the enzymes responsible for packaging viral DNA into the bacteriophage sometimes package host DNA accidentally Generalized transduction iii randombatina to cell new viiion Occasionally, during lytic infection, the enzymes responsible for packaging viral DNA into the bacteriophage sometimes package host DNA accidentally Lysogeny and specialized transduction Lysogeny: The phage genome is integrated into the bacterial chromosome at a specific site Normal Rare event event Conjugation: form of HGT that requires cell-to-cell contact Plasmid-encoded mechanism (conjugative plasmids) Depending on the plasmid, DNA transference occurs between closely or distantly related cells Conjugation: form of HGT that requires cell-to-cell contact Insertion sequences in yellow that allow the tra region: contains the plasmid to integrate genes needed for conjugative into the host transfer (e.g., pilus, T4SS) chromosome Replication and segregation: Origin of replication and transfer Transfer of plasmid DNA by conjugation closep.it DNA transfer is triggered by cell-to-cell contact nothe nasplasmid dokiteplasmid One strand of the plasmid is nicked Transfer of plasmid DNA by conjugation Transference of the nicked single strand W always a Simultaneous replication Transfer of plasmid DNA by conjugation Rolling circle replication: A mechanism used by some plasmids and viruses to replicate their genome. Starts by nicking one strand of DNA. Preserving Genomic Integrity chemically iti man form of adaptive immunity analogous to innate immunity Adaptive Immunity and CRISPR O INA “Memory bank”