Microbiology Topic 8 Regulation PDF

lOMoARcPSD|31936866 Topic 8 - Regulation The Role of DNA Replication ○ DNA must be intact, but copied to make new cells Transcription ○ DNA turned into working copies to give instructions for enzymes/structural protein production Not every...

lOMoARcPSD|31936866 Topic 8 - Regulation The Role of DNA Replication ○ DNA must be intact, but copied to make new cells Transcription ○ DNA turned into working copies to give instructions for enzymes/structural protein production Not everything is running at the same time when a cell regulates —> prevents cell death Regulation - turning off unused resources (not needed) Environmental conditions Changes in nutrients and their availability Changes in competition (responding to change) Condition specific responses Substrate specificity Metabolism Sporulation - regulating and turning on certain genes must happen in adequate and correct environment, takes a lot of energy ○ Not turning off certain processes (key cellular enzymes Key cellular enzymes are constitutive Constitutive - stay on at all times, no regulation Eg. Do not turn off (stay on) otherwise cell dies ○ TCA - central metabolism ○ ATP synthesis Constitutive genes are also known as housekeeping genes (always on, not regulated) Cellular activities regulated at multiple levels Central dogma is expensive ○ Production of rna and translating to protein —> expensive Cells do not require all gene products at all times Constitutive genes always have to be on Inducible genes are only needed at certain times Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 Basic control of gene expression Can take place on the level of ○ Transcription ○ Translation ○ Post translation (enzyme activity) Proteins Post translation Regulating protein activity (2 ways) Covalent modification (can alter enzyme conformations) ○ Adding to amino acid sequences of enzymes to produce new enzyme conformations through: Phosphorylation Acetylation Methylation Glycosylation (adding carbohydrate groups) ○ Covalent modifications can increase or decrease activity (depending on the enzyme/modification) by altering active site conformation Allosteric regulation ○ (The other site - not active site) ○ A small non-substrate molecule interaction with the other/allosteric site changes the conformation of the protein/enzymes ○ Results in the active site being changed Active site can be changed to better fit the substrate —> allosteric activation Active site can be changed to not fit the substrate —> allosteric inhibition Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 Often result of multi step pathway which serves as the effector molecule Regulating transcription - energy conserved by controlling enzyme synthesis - Many control mechanisms work to prevent transcription of genes when they are not required The Operon - transcriptional unit with series of structural genes and they transcriptional regulatory elements - Structural genes (code for amino acids) Gene A, B, C etc. (lac Z…) - Regulatory elements Operator, promoter region(where RNA polymerase binds), active site Regulation on the operator ○ Negative control of transcription Regulation on the activator ○ Positive control of transcription Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 Regulating Transcription Positive control ○ Allosteric protein activating/allowing mRNA synthesis Negative control ○ Allosteric protein inhibiting/preventing mRNA synthesis **Negative control of transcription** Operator site in DNA and a regulatory protein that prevents or gets in the way of RNA polymerase transcribing the genes (negative - stopping) Two types of negative control involve repression or induction ○ Both are negative control and involve a repressor protein Repression (-) ○ Inhibit transcription due to a signal ○ Stopping transcription - not wanting any more of the genes being transcribed —> enough has been made Turned off / repressed Binds to allosteric site and serves as corepressor ○ Minority of enzymes are controlled by repression ○ Typically affects anabolic (biosynthetic enzymes) Induction (-) ○ Effector molecule ○ Pathway off, there is a regulatory protein blocking RNA pol ○ An inducer can bind to enable an activator, or bind to disable a repressor ○ Derepression of enzyme in response to signal Inducing transcription through a co inducer molecule binding to allosteric site change in conformation of regulatory protein, allowing transcription to proceed Using a compound of interest (eg, lac operon, when lactose is present, induction by co inducer removes repressor) Only synthesizing enzymes when the substrate is available —> no waste of energy ○ Typically affects catabolic enzymes Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 **Positive control of transcription** Regulatory protein helping protein transcription occur more efficiently - upstream of promoter ○ Genes and operons in positive control - RNA pol. And its sigma factor dont bind very well to the promoter (weak association) ○ Therefore, activator protein helps RNA pol. Be physically associated with the promoter (binding and transcription occur much more efficiently - positive) ○ Regulatory protein can also adjust conformation of DNA to help efficiency of biding (reason as to why it can occur many genes upstream) Allosteric regulatory proteins activate binding or RNA pol to DNA ○ Activator proteins bind specifically to the activator binding site of the promoter Example is the carbon source maltose in breakdown / catabolism in E. coli ○ When present, maltose binds as a coactivator (affect or molecule) to activator protein which has conformational change, allowing it to interact RNA pol and its promoter ○ Allosteric protein Effectors / Effector Molecules Collective term for molecules that after protein production in relation to allosteric portion regulators Co-inducer or co-activator ○ Co-inducer - negative control ○ Co-activator - positive control Co-repressor: binds and activates a repressor Effectors interact with DNA binding proteins Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 The Lac Operon Glucose is easier to use than lactose The lac operon is not expressed until all glucose is consumed ○ Diauxic growth (two phase growth) ○ Glucose - monosaccharide ○ Lactose - disaccharide ○ More work to use lactose, so if both are available, glucose will be used first until it runs out ○ Delay in between as e.coli prepares to use lactose Structural genes ○ lacZ, lacY, lacA Promoter, operator, etc LacZ ○ Beta Galactosidase - using lactose, this is what cleaves the disaccharide into monosaccharides ○ Key step of using lactose and bringing it into cells as permease Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 LacA ○ Beta galactosidase transacetylase ○ Function unknown Lac operon cont’d Multiple control elements on both the DNA and accessory proteins Inducible expression ○ Lactose in the lac operon only used if conditions are right, otherwise the glucose available is used System is only turned on when needed (cheaper / easier to use glucose) Components allow use of lactose ** Lactose entrance ** ○ LacY Permease on the membrane shuttles lactose molecules in ○ Once in, lactose must be cleaved by ß-galactosidase Cuts disaccharide in half into 2 monosaccharides Glucose and galactose, usable for metabolism ○ While ß-galactosidase cleaves lactose into monosaccharides, side reaction occurs, produces allolactose (the other lactose) Allolactose acts as the signal/co inducer indicating the presence of lactose around Operon Negative control with allolactose ○ Repressor (LacI) binds to operator, blocks RNA pol and inhibits transcription ○ Effector molecule (allolactose) induces transcription by inhibiting the repressor from binding to the operator ○ There is also an activator binding site, the promoter is not strongly bound to the RNA pol, therefore there is no transcription which can be induced with positive control Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 Operon Positive Control ○ What happens when glucose runs out? cAMP levels go up Serves as coactivator binding to activator that binds to active site Assists RNA pol binding to promoter, transcription occurs Lactose present —> transcription with high efficiency Need low glucose and high lactose to have both regulatory elements working together ○ Activator protein (cAMP receptor protein, CRP) binds and increases transcription rates when effector molecule (cAMP) present (low glucose) ○ Effector molecule indices conformational change in activator protein, which increases affinity for binding site, increasing RNA pol. Affinity for the Lac Operon promoter Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 - there will only be high structural protein transcription and metabolism of lactose when glucose concentration is low and lactose concentration is high - The Operon status in this case: - Cyclic receptor protein (CRP) is bound to DNA, and has a coactivator (cAMP) bound to it - RNA polymerase is bound to the promoter - Allolactose inducer is bound to the repressor protein, inhibiting it from binding to the operator, allowing efficient transcription - The rna polymerase doesn’t fully bind to the promoter when there is high glucose, because when glucose is low, there is more cAMP that binds to CRP, which allows RNA pol to bind to DNA, allowing higher levels of transcription - Low glucose results in cAMP - When lactose is cleaved, you also get some glucose - How does lac become present in the cell when there is no transcription of the lac gene? - Turning off and on of transcription is not 0 or 1 (not all or none) - It’s low or high - Detection of glucose being high or low is based on transport of glucose across a membrane Negative Control (cont’d) effector molecules can also inhibit transcription by binding to the repressor protein and enhancing its ability to bind to the operator (common for anabolic operons) Example here is the tryptophan amino acid synthesis operon ○ Anabolic, makes sense to have repression ○ Tryptophan acts as core press or, binding to repressor regulatory protein to operator —> negative control ○ Tryptophan synthesis operon - stopping transcription, transcription controlled tryptophan operon Transcription regulation requires translation to be happening Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 Attenuation Interruption of transcription after initiation but before termination Attenuate - to quench a signal Transcription in Bacteria - RNA pol transcription, RNA from DNA - Starts, moves along genes, then stops - Stops in two ways: rho-dependent: ○ rho protein follows RNA pol and removes it from the DNA when it reaches a termination sequence rho-independent: ○ RNA hairpin loop forms, causing RNA pol to dissociate from the DNA ○ RNA folds back on itself, creating a necessary hairpin loop ○ Folding back catches RNA pol behind it and stalls it on a weak point of association and causes it to fall off DNA template strand Tryptophan synthesis operon and regulatory region of mRNA Structural genes: trpE, D ,C, B, A etc. ○ These genes required to make tryptophan must be stopped if there is enough tryptophan P - promoter O - operator (negative control) Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 trpL region (left to right) ○ RNA pol will produce an mRNA strand ○ Transcription starts, immediately behind the mRNA producing transcripted RNA, a ribosome will follow and make a peptide wherever it is coded to make one ○ Eg. at structural genes or the small gene ‘trpL’ TrpL doesn’t code for anything but is critical for regulation ○ Ribosome makes the small peptide, but the issue is tRNA (transfer RNA) charges with amino acids ○ Ribosomes will demand methionine, lysine, adenine, etc. ○ Ribosome will build the peptide, though further along in the leader peptide, two tryptophans will be demanded in a row ○ Will there be enough tryptophan for ribosome? If there is a lot of tryptophan abundant, the ribosome will have no problem making peptide If there is not enough tryptophan for the ribosome to make the peptide, it will stall and wait for a transfer RNA charged with tryptophan ○ This results in slow progress of the ribosome ^^ basis of regulation Below will be the RNA secondary structures ○ Hairpin structures forming ○ Regions that can make hairpins —> 3 & 4 Attenuator sequence Complementary, anneal to each other Produced as RNA ○ Region 3 can also bind to region 2 Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 Attenuation on transcription by high vs low levels of tryptophan High: Enough tryptophan - no need to transcribe structural genes —> trp not made ○ Lots of trp around ○ RNA pol makes mRNA, ribosome follows, making leader peptide ○ Ribosome will move quickly through the peptide, will occupy space close to region 2 / occupies region 2 (overlapping) ○ Region 2 will not bind with region 3 as it is occupied by ribosome ○ Region 3 and 4 one together to make a hairpin Rho-independent terminator loop forms Because 3 & 4 anneal to each other and make the terminator loop The loop catches RNA pol and stops / terminates transcription RNA pol detached from a point of weak association A and T, double hydrogen bonds - weak Low: not enough tryptophan - transcription of structural genes desired —> trp will be made ○ RNA pol will produce mRNA strand ○ ribosome will come in and make the leader peptide till before region two, where it will wait for tryptophan as there is not enough ○ The ribosome is not fast - slow progress ○ Region 2 is not obstructed, and will quickly bind to region 3 as soon as region 3 is formed ○ When region 2 and 3 bind it looks like a loop ***not a terminator loop*** Is just occupies region 2 and 3 no term loop forms RNA pol continues unobstructed, transcribing the rest of the genes, they get translated an tryptophan is produced Attenuation cont’d control of transcription by mRNA secondary structure ○ Folding on itself in two dimensions an interaction between translation (ribosome) and transcription (RNA pol) processes Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 ○ if ribosome quickly follows RNA polymerase, rho- independent terminator hairpin RNA loops are formed in the leader sequence and the polymerase detaches ○ “stalling out” of ribosome in mRNA leader sequence (i.e., not enough of that amino acid loaded in tRNA) allows transcription to continue This process cannot occur in eukaryotes: why not? Because there is no transcription and translation in the same place at the same time, a nucleus separates the two processes Quorum Sensing Quorum: numbers of a group that must be present for business or function to be carried out / conducted A chemical signaling system that allows microbes to communicate with each other - count each other Regulation of gene expression based on population density Cells release autoinducer molecules into the environment as the population density increases ○ The release of the autoinducer is regulatory, this is the mechanism by which quorum sensing works Detecting changed in autoinducer levels causes regulation of gene expression ○ The ability to count and check on the autoinducer level is what lets gene expression be regulated In summary, quorum sensing allows ○ Regulation of gene expression based on population density ○ Positive feedback ○ Paid induction ○ Linking behavior to population density ○ Coordinating expensive additive processes ○ Roles in interactions with eukaryotes Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 Hawaiian bobtail squid bioluminescence - aka aliivibrio The squid counterilluminates the backlight using the light organ Lux is a prototypical quorum sensing system found in vibrio fischeri ○ V. fischeri live freely or in symbiosis with the bobtail squid ○ Cells only emit light when in the light organ of the squid ○ The v. fischeri are only used in the night, Hereford when the squid sleeps in the daytime, it flushes out the v. fischeri ○ While sleeping, new v. fischeri grow and are used to hunt in the night ○ It takes a lot of ATP to make light, regulation is key to saving energy and only making light when necessary when grown to high density, the cells produce lots of N-acyl-homoserine lactone (AHL), which stimulates luminescence ○ AHL governs a lot of bacterial behaviors ○ Can be modified Lux protein catalyzes AHL synthesis examination of how cells detect levels of AHL has been an area of active research How does it work ○ Lux, a regulator transcriptional activator, interacts with AHL when it reaches a high enough concentration ○ binds the "lux box" DNA regulatory site (activator binding site ○ leads to transcription of luciferase protein genes and lux, which creates positive feedback loop forming more AHL Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 No Quorum - lux genes for production of light with luciferase enzyme - Not much made in the day - Enzyme luxI that makes AHL produces molecules during the day in little amounts - Not much transcription happening because RNA pol that would transcribe all the regions doesn’t bind very well to its promoter - Activator will be necessary (luxR regulatory protein) - LuxR is the activator / regulatory protein that will bind to the activator binding site - Wen made in little amounts, AHL will diffuse outwards, not much coming back in (no quorum, light not made) - *transcription in not binary, not all or none, there will always be some AHL (low concentration) Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 With Quorum - it is at night time when all the millions of cells will be producing AHL - They diffuse out and also come pouring back in - Many cells make AHLs - When diffusing back, AHL bind to allosteric site of luxR protein - Changes conformation of luxR protein - AHL acts as a coactivator - Now there is very efficient transcription - Activator binding site with luxR associated w coactivator - Transcription of lux gene occurs - Luciferase production —> uses ATP, which uses oxygen - ATP and O2 required for light - expensive - Energy dependant process, occurs at night time - Rapid induction, positive feedback When grown to high density, the cells produce lots of N-acyl-homoserine lactose (AHL), which stimulates luminescence LuxI protein catalyzes AHL synthesis examination of how cells detect levels of AHL has been an area of active research luxR, a regulator transcriptional activator, interacts with AHL when it reaches a high enough concentration binds the “lux box” DNA regulatory site (activator binding site) leads to transcription of luciferase protein genes and luxI, which creates positive feedback loop forming more AHL Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 Quorum sensing is widespread broad range of microbes possess quorum sensing systems mechanisms controlled include: ○ motility ○ conjugation ○ biofilm formation ○ pathogenesis autoinducers may even play a role in competition interrupting or inhibiting a control pathway in other microorganisms in the environment Two-Component Regulatory System - chemotaxis is a modified two-component regulatory system Can use one protein as a sensor and other to control transcription ○ Genes are turned on or off depending on what is happening outside of the cell Allows for response to changes in the environment Signal transduction induced inside the cell alters the cell to respond appropriately ○ The passing along of information/communication by chemical means between proteins is known as signal transduction Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 Two component regulatory systems often involve: (1) Sensors kinase (HPK eg.) —> detects the environmental stimulus ○ Histidine protein kinases - histidine phosphate interactions ○ A kinase is a protein that adds a phosphate group to proteins ○ Knows as histidine protein kinases, as phosphate groups are added to the histidine residue in the proteins ○ Phosphate group is added when something is sensed outside and phosphate group is transferred as signal transduction occurs ○ Phosphate is transferred to component 2 (response regulator) (2) Response regulator (RR eg.) —> regulates transcription ○ Response appropriate to the environmental signal ○ Once the phosphate group is transferred through signal transduction th the regulator kinase, is is phosphorylated and the conformation is changed (covalent modification) ○ When this occurs, the response regulator becomes the regulatory protein on the operator / operon (activators, repressor, etc) ○ Covalent modification causes regulatory protein to changed and have the interaction with the operator This interaction must be short lived and temporary Not just turned on and permanently on, it is a response to what is outside Response regulators must be dephosphorylated by proteins that come along and remove the phosphate groups - short lived response Or protein can remove the phosphate group itself ○ Signals must remain outside to keep adding phosphates after they are removed ○ Response regulators can bind to activor sites ○ The signal is transduced by phosphorylation Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 Eg of two component regulatory system Crown-gall tumors in willow trees DNA was transferred from agrobacterium ○ Opines come out afterwards ○ Response to plant damage ○ That damage is what agrobacterium needs to sense on the outside - that is the signal Virulence of A. Tumefaciens - two components for agrobacterium to detect plant damage - Sugars and phenol / compounds released from plant binding to sensor kinase virA - Results in phosphate group coming from ATP - now virA is phosphorylated and phosphate is transferred to signal transduction - Component 2, response regulator Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 - response regulator changes conformation of protein, binding to activator - positive control of transcription - What is being transcribed? - All the virulence genes - The genes launch an attack to make the tumor form and transfer DNA in response to plant damage Vir genes found on the Ti plasmid are only expressed under conditions similar to a plant wound site VirA/virG are required for expression of the other virulence genes Chemotaxis - Modified two-component regulatory system - Not transcriptional regulation, thing still a way that a cell responds to its environment based on external signals - Chemotaxis is a way in which bacteria can tell differences in chemical signals - Motility, bacteria typically do not steer, but they get to point A to point B - Sophisticated movement - Studying mutants reveals a lot about movement A complex bacterial behavior modulated by shift in protein activity Chemotactic bacteria sense changes in chemical gradients over time Changes induce altered direction and duration of flagellar rotation, leading to directed movement over time Extra comment: this is a modified two-component regulatory system Study of Chemotaxis Using Mutants - mutants that cannot carry out chemotaxis properly are important - When a system is broken, look at what broke inside of the cell - Figuring out what gene was changed or broken can help find what that gene does and what it codes for and what it does to make it work in cells that don't have them broken - Mutants are high value ways of studying processes - that’s how we know how all genes work, by collecting mutants Isolated using a capillary tube filled with nutrients Microbes with normal chemotaxis will move into tube Those with mutations in chemotactic proteins will remain outside the tube Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 mutants are in the flask, not capillary tube The capillary tube: —> ○ Good carbon source available in semi-solid agar ○ Cells can swim in migrate into agar ○ If they can carry out chemotaxis with motility, they will enter into the tube ○ Normal cells in tube ○ Mutants outside in the flask, they have problems with motility and chemotaxis We can study them and figure out why they couldn’t get into the tube and what genes were affected Regulation of chemotaxis Step 1 : response to signal Step 2 : control of flagellar rotation Step 3 : adaption Step 1 : response to signal - detecting on the outside - Ecoli and most bacteria have methyl accepting chemotaxis proteins surrounding the membrane that bind the chemicals - If fervent MCPs bund to different chemical (some to repellents and some to attractants) - They are on the outside sensing the environment - Not kinases, need another protein for that, CheA - will be phosphorylated (sensor kinase) - Works with modular methyl-accepting chemotaxis proteins - Response to signal: bind to attractant/ repellent, then respond accordingly by signal transduction with phosphorylation coming from ATP - Response of signal initiates signal transduction Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 Bound to repellent - tumble phosphorylation ○ Bad, undesired ○ MCPs sense specific attractants / repellents Methyl-accepting chemotaxis proteins Initiates signal transduction Step 2 : controlling flagella rotation - Eg. when tumbling (bad) occurs, phosphorylation of CheA, occurs - Phosphate group is transduced to CheY - When CheY is phosphorylated, it interacts with flagella motor proteins and changes their direction, results in tumbling - Phosphorylated CheY interacting with motor proteins - Flagella rotation is con trolled ○ CheY protein Phosphorylated by CheA-P Che Y-P initiates flagellar reversal: tumbling (Step 1&2 summary) - phosphate group transferred to CheY interacts with motor proteins results in tumble, flagellar rotation controlled in a ‘bad’ situation with repellants bound - If you don't have attractant bound, there will still be phosphorylation and tumble still occurs - Repellent or not attractant bound tumble will happen - CheA transfers phosphate group to CheY —> tumble Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 - Only lasts for a short period because CheZ is always looking to dephosphorylate CheY and send it back to native state, no tumble, run Step 3 : Adaption - ***low sensitivity close, high sensitivity far away*** - Has to do with methylation - Methyl-accepting chemotaxis proteins (MCPs) can be methylated at more than one location multiple times, more methyl groups - altered sensitivity of proteins in membrane - Adding / removing methyl groups - increasing / decreasing sensitivity - Moving away from repellent: - sensitivity increases, surrounded by less repellants and concentration is low, no repellants binding to MCPs - Because CheR always adds methyl groups to MCPs, no phosphorylation of CheA,Y,B, no repellants bound - CheB removes methyl groups - Adding methyl groups to MCPs increases sensitivity for repellents - Moving towards repellents (wrong direction) - Phosphorylation increases, methyl groups coming off of MCPs, sensitivity to repellents goes down - Attractants - bind to MCP, no phosphorylation, no tumbles - Methyl groups added - Close to source of attractants - sensitivity is low - Fully methylated MCP is at low sensitivity to attractants - Fully methylated MCP is at high sensitivity to repellents ○ Feedback loop Allows the system to reset itself Allows temporal detection of signal concentration Requires modification of MCPs by methylation Che proteins: a two component regulatory system CheA works as a sensor kinase, becomes phosphorylated (bad thing) CheA then phosphorylated CheY (RR protein) - tumble CheY binds to flagellar motor, changes activity ○ Through adaptation, there will be CheB phosphorylated (bad thing) Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 MCPs also work in chemotaxis systems By interaction with CheW proteins, autophosphorylation of CheA is modulated ○ Attractants decrease phosphorylation ○ Repellants increase phosphorylation Provide for longer sustained runs of directed motion when attractants are present - no attractant bound, CheA phosphorylated, bad thing, CheY phosphorylated, tumble, CheZ resets it Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 - attractants are bound, good thing, only thing happening is continues methylation of MCPs by CheR Methylation of MCPs also regulates attraction during periods of high attractant levels in a process known as “adaptation” - CheR methylating all the time, CheB occasionally demethylating when in a bad situation, sensitivity being adjusted accordingly ○ Highly methylated MCPs will only respond to very high levels of attractant ○ If very high levels are not maintained phosphorylation of CheA/CheB will lead to eventual demethylation of MCP ○ Results in greater sensitivity to the attractant, helping the system “reset” and avoid saturation over time ***watch overview*** Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 Regulons - Two component regulatory systems always involve +/- control, one operon and its function, etc. - Though, some regulatory proteins like repressor proteins can bind to operators for multiple different sets of genes, - Some RNA pol with a sigma factor, can bind to genes throughout the cell that respond to same type of signal - When there are genes and operons that fall under the same regulatory controls, they are regulons - All genes under control of one regulatory element (eg, sigma element, regulatory protein) Regulons are: Sets of genes that are coordinated together responding to the same regulatory systems ○ Catabolite repression: shutdown of several systems that use various carbon sources when glucose is present Shutting other systems off when not used as another available source is present ○ SOS response: multigene system for wide scale DNA repair in response to serious DNA damage Not used unless chances of cell death are high, this responds to widespread DNA damage, turning it on when not necessary can be harmful and fatal ○ Two of the most important regulatory proteins for SOS response: recA (single stranded binding protein) lexA Repressor bound to all the operators on the genes on all the different operons, preventing transcription when things are ok When things are not ok, single stranded DNA (indicating cell damage) gets bound by recA, then cleaves lexA, leaving it unable of binding to operators anymore, resulting in its of transcription of all the genes to fix DNA quickly Downloaded by Mahek Desai ([email protected])  lOMoARcPSD|31936866 When single stranded DNA and recA are available, genes transcribed at high frequency are lexA and recA, to quickly turn everything off after repair No more recA binding, no more cleaving of lexA, lexA can now stop transcription One regulatory control is in charge of all genes that are about to be turned on if DNA is repaired in this way ○ Though the polymerases are error prone, make mistakes but they get the job done, better than nothing Alternative Sigma Factors - different sigma factors help RNA pol to transcribe different types of genes - Sigma-70 is default - Heat response - sigma 32 - General stress - sigma 38 In bacteria, use of different sigma factors directs RNA pol to certain genes Most E. coli promoters are recognized by sigma-70 Downloaded by Mahek Desai ([email protected])