Gene Expression Flashcards
(106 cards)
1
Q
What is the difference between a genome, transcriptome and proteome?
A
Genome: all DNA in a given cell
Transcriptome: all RNA at a given moment
Proteome: all proteins in a given cell
2
Q
What are the two ways microbes regulate protein function?
A
1.Control AMOUNT of protein (via transcriptional control and translation control)
- Control ACTIVITY of protein (post-translational regulatory processes)
3
Q
How is the control of amounts of mRNA economical?
A
Genes expressed only when the products are needed and in the amount they are needed. This is due to energy conservation and interference between expressed products.
4
Q
What is the difference between specific and non-specific protein-nucleic acid interactions?
A
Non-Specific: Protein attaches anywhere along the major groove of the nucleic acid
Specific: protein attaches at a specific site on the major groove of the nucleic acid
5
Q
How is the specificity of specific protein-nucleic acid interactions achieved?
A
Interactions between specific AA side chains and chemical groups on nitrogenous bases/sugar phosphate backbone
6
Q
How are DNA binding proteins homodimeric?
A
Protein consists of identical polypeptide subunits divided into regions with specific structure and function called domains (e.g. LacI repressor binds to inverted repeats)
7
Q
What is the helix-turn-helix structure? What are the 3 parts?
A
Most common domain structure formed in DNA-binding proteins.
- 1st alpha helix of protein interacts specifically with DNA
- 2nd helix stabilizes the 1st helix via hydrophobic interactions along the backbone
- The two helices are linked by a “turn” containing 3 amino acids.
8
Q
What types of proteins are involved in regulating gene expression?
A
sigma factors and transcription factors
9
Q
What are the six sigma factors in E. coli?
A
- σS: activates genes that protect cells from starvation, redirect metabolism, and alter cell shape
- σN: regulates expression of genes encoding involved in nitrogen fixation
- σH: regulate expression of genes encoding for proteins aiding in recovery from heat shock
- σE: regulate expression of genes encoding for proteins aiding in recovery from heat shock
- σF: regulates expression of genes encoding proteins involved in chemotaxis
- σD / σ70: most constitutive genes (housekeeping/always turned on) and exponential growth phase genes
10
Q
What is the difference between sigma factors and transcription factors?
A
σ factors: help guide RNA polymerase to specific promoters of certain genes encoding proteins required for certain environments.
transcription factors: control the rate of gene transcription by binding to specific DNA sequences
11
Q
What is the difference between activators and repressors?
A
Activators: positive regulation/inducible expression
Repressor: negative regulation/ repressible expression
12
Q
What is the difference between negative inducible and repressible mechanisms?
A
Negative inducible: repressor actively blocks transcription, but inducer binding to the repressor removes the block
Negative repressible: Repressor is inactive by default allowing transcription to occur, but corepressor binding to repressor activates it and blocks transcription
13
Q
What is the difference between positive inducible and positive repressible mechanisms?
A
Positive Inducible: activator is inactive but when an inducer binds, it becomes active and promotes transcription
Positive repressible: Activator is active by default, but when a repressor binds, it inactivates the activator, stopping transcription.
14
Q
What are regulatory genes?
A
Genes that encode for transcription factors that may affect expression of one gene, few genes, many genes, or involved in autoregulation.
15
Q
What is a regulon?
A
group of genes/operons controlled by a SINGLE regulator
16
Q
What is the difference between constitutive and inducible/repressible proteins?
A
constitutive: protein is always present because gene is always is expressed
inducible/repressible: gene expression is regulated in response to change in environment or if certain enzymes are already present in sufficient amounts.
17
Q
What is the difference between enzyme repression and induction?
A
Induction: enzyme is only made when substrate is present (affects catabolic enzymes)
Repression: enzyme is not made if the product is present in the medium in sufficient amounts
18
Q
What is an example of enzyme repression and induction?
A
repression: Arginine biosynthetic operon
induction: maltose operon
19
Q
What are effectors?
A
Cell metabolites (substrates/end products) affecting activity of repressors and activator regulators associated with the pathways by allosterically binding and activating/inactivating them. Includes inducers and corepressors
20
Q
What is the difference between an inducer and a corepressor?
A
Inducer: substance induces enzyme synthesis by allosterically activating an inducer or inactivating a repressor
Corepressor: substance that represses enzyme synthesis by allosterically activating a repressor
21
Q
What is allosteric regulation?
A
Binding of effectors to a domain (on an enzyme or DNA-binding protein) that changes the conformation of the target to an active or inactive form
22
Q
What is the difference between negative and positive control?
A
Negative: regulatory mechanism where repressor binds to DNA to prevent transcription
Positive: regulatory mechanism where activator binds to DNA to enhance transcription
23
Q
What is the function of the repressor?
A
Repressors interact with the operator downstream of the promoter region and blocks binding of sigma factor/RNA Polymerase, preventing mRNA synthesis (negative control)
24
Q
What are the steps in the mechanism of repression of the arginine biosynthetic operon?
A
- Sigma factor + RNA Polymerase transcribe polycistronic mRNA when ArgR repressor is inactive, producing Arginine
- Arginine product acts as a corepressor and binds to inactive ArgR, activating it via llosteric regulation
- Activated ArgR-Arginine complex binds to the arg Operator downstream of the arg Promoter, blocking transcription
25
What are the steps in the mechanism of De-repression in the lactose operon?
1. Transcription is blocked by active LacI repressor at the lac Operator region, downstream of the lac Promoter
2. After lactose is endocytosed, it is converted to allolactose
3. Allolactose binds to LacI repressor and inactivates it, causing dissociation from the lac operator and transcription to proceed and create lactase.
26
What is the function of an activator?
Begin transcription by recruiting RNA polymerase + sigma factor to the promotor region, interacting with the activator binding site located upstream of the promoter region (positive control)
27
How does the activator reach the promoter based on how upstream the activator binding site is?
if site is PROXIMAL to promoter, it makes contact with RNA pol holoenzyme
if site is DISTAL to promoter, DNA is looped out to make contact with RNA pol holoenzyme
28
What are the steps of activation of maltose operon?
1. MalT activator protein is inactive and transcription does not occur WITHOUT presence of maltose
2. When maltose is endocytosed, maltose acts as an inducer for MalT activator protein, activating it via allosteric activation
3. Activated MalT binds to activator binding site which allows RNA polymerase and sigma factor to be led to the mal Promoter and proceed with transcription.
29
What is an operon?
Two or more genes (polycistronic) of which the expression is controlled by one promoter and one terminator. This ensure encoded products are translated at the same time (e.g. mal and lac operons)
30
What is the difference between an operon and a regulon?
Operon: single promoter, single polycistronic mRNA for multiple genes
Regulon: multiple promoters whose genes are regulated by the same protein
31
What are the parts of the lactose operon?
- Lac permease (LacY): transports lactose into the cell
- Beta galactosidase (LacZ): cleaves lactose into glucose and galactose
- transacetylase (LacA): modifies lactose and lactose analogs, may prevent toxic buildup in bacterial cytoplasm
32
What does the lac operon look like in the absence and presence of lactose?
Absence:
- LacI repressor binds to operator region downstream of promoter
- Inhibits RNA polymerase binding to promoter
Presence:
- LacY permease brings lactose into the cytoplasm
- LacZ converts lactose to allolactose
- Allolactose binds to LacI repressor to inactivate it
- RNA holoenzyme transcribes the lac operon
- LacZ cleaves glucose into galactose
33
What is basal transcription?
Low rate of transcription when "transcription is turned off" to create enough molecules to induce gene expression should environments be favourable
34
What is catabolite repression and the favoured reactant?
Mechanism of global control that controls use of carbon sources if more than one is present. Glucose is preferred over any other sugar and acts as an inhibitor for the synthesis of catabolic enzymes for other carbon sugars.
35
What is diauxic growth?
Two log phases separated by a short lag phase, due to growth via preferred glucose, then growth via second carbon metabolite.
36
What are the phases of diauxic growth in the presence of glucose and lactose?
1. Log 1: lac operon is repressed, glucose is consumed
2. Lag: glucose is exhausted, expression of lac operon begins
3. Log 2: Catabolism of lactose
37
How does the phosphoenol pyruvate phosphotransferase system work?
1. Phosphoenol pyruvate is dephosphorylated by pyruvate kinase
2. Phosporyl group from pyruvate kinase is passed from cytoplasmic protein to protein until it reaches the glucose transporter.
3. Glucose enters cell through glucose transporter and gets phosphorylated to glucose 6 phosphate, driving concentration gradient for uptake of glucose into the cell.
38
What is cAMP's role in the lac operon?
cAMP binds to catabolite activator protein (CAP/CRP) to form an inducer. Inducer binds to CAP binding site on the lac operon, recruiting RNA polymerase (positive control)
39
How does cAMP respond to absence and presence of ?
Absence: high [cAMP] binds to CAP to form CAP-cAMP inducer, inducer binds to CAP site, induces binding of RNA polymerase, transcription proceeds.
Presence: low [cAMP] does not bind to CAP, CAP is inactive and cannot bind activator binding site, RNA polymerase is not recruited, transcription is very low or turned off.
40
What are the conditions for the dual control mechanism of the lac operon?
Positive requirements: glucose must be absent for CAP-cAMP to form and bind to CAP site
Negative requirements: LacI must be absent from operator (which needs allolcatose), lactose must be present
41
What are the parts of the tryptophan operon and its regulator?
Contains genes trpE - trpA needed for synthesis of amino acid tryptophan (polycistronic mRNA) regulated by aporepressor TrpR located upstream of trp operon.
42
What is an aporepressor?
Repressor that is constitutively expressed but inactive.
43
How does the tryptophan operon respond to low levels of tryptophan?
trp operon is transcribed due to inactive TrpR and makes tryptophan
44
How does the tryptophan operon respond to high levels of tryptophan?
Free tryptophan in cytoplasm binds to aporepressor TrpR, triggering conformation into active repressor which binds operator blocking access of promoter to RNA polymerase.
45
What is attenuation?
Form of prokaryotic transcriptional control exerted after transcription initiation, but before completion of transcription.
46
What does the leader sequence fold into?
Secondary structure 1: allows continued synthesis of mRNA
Secondary structure 2: causes premature termination
47
What does the folding of the leader sequence depend on?
Folding of mRNA depends on events at the ribosome or on the activity of regulatory proteins, depending on the organism
48
What is the attenuation regulation of the trp operon?
Formation of hairpin structures (1:2, 2:3, 3:4) based on tRNA^Trp available that determines whether RNA polymerase finishes transcribing the operon or stops early
49
What is the purpose of the 1:2 hairpin structure?
RNA polymerase transcribes region 1 and 2 to form the 1:2 structure that slows down transcription to give the ribosome time to bind to mRNA and begin translating the leader peptide, bumping RNA polymerase off the pause site to continue transcribing the gene.
50
When are 2:3 and 3:4 structures formed?
HIGH levels of tRNA^Trp: ribosome translates through trp codons and sits on stop codon, forming 3:4 and preventing 2:3 and creating a terminator helix
LOW levels of tRNA^Trp: ribosome stalls at trp codons, allows 2:3 and prevents 3:4
51
What are the steps of the attenuation regulation of the Trp operon?
1. RNA Polymerase starts transcribing the leader sequence of the trp operon (region 1,2,3,4)
2. Ribosome binds to mRNA and beings translating leader peptide as soon as it is transcribed
3a. Low Trp means low tRNA^Trp, forcing the ribosome to stall at two Trp codons in the leader peptide at region 1. This allows 2:3 pairing, preventing formation of 3:4 terminator hairpin, so RNA pol keeps transcribing the operon to create enzymes made for Trp synthesis
3b. High Trp means high tRNA^Trp, allowing the ribosome to translate through the Trp codons past region 1 and 2. This prevents formation of 2:3 antiterminator hairpin, allowing 3:4 terminator hairpin to form so RNA pol falls off the operon and transcription ends early.
52
What are environmental fluctuations?
Changes in temp, pH, oxygen, nutrient availability, number of cells present (quorum sensing)
53
What are the steps of a two-component regulatory system?
1. sensor kinase is a histidine kinase that autophosphorylates a histidine residue when detecting a signal, using ATP.
2. Phosphate from histidine is transferred to the response regulator, activating its function as a repressor or activator
3. Response regulator is dephosphorylated by phosphatase to terminate the response.
54
What are porins?
Protein channels that allow metabolites to cross the outer membrane. (e.g. OmpF, OmpC porins)
55
What controls OmpF and OmpC?
Low osmotic pressure in cell = larger sized OmpF porins
High osmotic pressure; synthesis of smaller sized OmpC porins
56
What is the OmpR-EnvZ Two component system?
1. Changes in osmotic pressure are detected by EnvZ histidine kinase.
2. When the shift occurs, EnvZ is autophosphorylated, translating phosphate group to response regulator OmpR.
3a. OmpR-P activates transcription of ompF at high osmotic pressure to create larger pores to allow larger molecules in and balance osmotic gradient
3b. OmpR-P represses transcription of ompF at low osmotic pressure and activates transcription of ompC to create smaller pores to prevent excessive water entry
57
How is ompC and ompF expression regulated?
EnvZ acts as a kinase to OmpR, forming OmpR-P in high osmolarity
EnvZ acts as a phosphatase to OmpR-P forming OmpR in low osmolarity
58
What are the two components of the Ntr system?
Nitrogen regulator I: response regulator
Nitrogen regulator II: sensor kinase/phosphatase
59
What is the PII protein?
Signal transducing protein that regulates transcription factors, enzymes and membrane transport proteins in nitrogen metabolism. Activity is based on covalent modifications.
60
What are the modifications that control the activity of the PII protein?
Uridtlylation (adding UMP)
Adenylylation (adding AMP)
61
What is the process and result of the uridylylation of PII?
1.Gln D senses that Glutamine concentration is low when glutamine is not bound to it
2. GlnD transduces signal by adding a UMP onto PII
3. PII-UMP activates glutamine synthetase by removing its AMP group
4. PII-UMP activates kinase activity of NRII by allowing it to phosphorylate itself.
5. Activated NRII activates NRI by phosphorylating it into NRI-P
6. NRI-P can bind to activator site of Nitrogen assimilation genes and recruit RNA polymerase for transcription
62
How is PII deurylylated?
1. Once glutamine levels are sufficient, glutamine binds to GlnD
2.Binding triggers GlnD to remove UMP from PII
3. PII then ads an AMP to glutamine synthetase to inactivate it.
4. Unmodified PII stimulates phosphatase activity of kinase NRII, dephosphorylating NRI-P
5. NRI does not bind to the activator binding site of nitrogen assimilation genes and thus prevents transcription.
63
What are 5uses of phosphorus?
1. Nucleic acids DNA and RNA
2. Membrane synthesis
3. Energy generation
4. Cell signalling
5. Buffer for pH homeostasis
64
What are the two components of the Pho system?
PhoR: dimeric histidine kinase/phosphatase
PhoB: response regulator that when phosphorylated, binds to Pho boxes within promoter regions upstream of genes.
65
What are the parts of the PhoR dimer from the membrane down?
1. TM: transmembrane domain
2. Charged region
3. PAS: senses activity of transporter
4. Catalytic and ATP binding domain (kinase/phosphatase)
5. DHp: dimerization and histidine phosphorylation domain.
66
What is the function of PstSCAB proteins?
1. Periplasmic PstS protein binds and presents Pi to transmembrane components PstC and PstA
2. ATP binding across the PstB dimer interface undergoes hydrolysis triggering conformational change of the gate from outward to inward facing, allowing Pi access into the cytoplasm.
3. ADP is released from PstB and ATP rebinds and the cycle starts again.
67
What is the function of PhoU?
Peripheral membrane protein that modulates Pi through the PstSCAB complex, preventing too much Pi import
68
How is PhoR activity controlled by PstSCAB and PhoU?
High environmental and cytoplasmic levels: favours PhoR in phosphatase conformation, to dephosphorylate PhoB
Low environmental cytoplasmic levels: favours PhoR in autokinase formation, to phosphorylate PhoB
69
What are the operons within the Pho regulon?
phoA: encodes scavenger of Pi
phnCDEFGHIJKLMNOP: encode phosphonate transport system to use phosphonate instead of Pi
phoE: encodes porin for Pi uptake
ytfK: stress response
70
What is streptomyces relation to the Pho regulon?
Genus of gram-positive Bacteria produce antibiotics in an energy intensive process to kill other bacteria in competition for Phosphate. When there are high levels of phosphate, the process is halted.
71
What are the steps of Streptomyces creating antibiotics?
1. Low Pi: PstSCAB is not transporting much phosphate, PhoU inhibition on PhoR is relieved, and PhoR autophosphorylates to kinase
2. PhoR switches to a kinase and phosphorylates PhoP
3. PhoP binds to Pho boxes on genes encoding activators for antibiotic synthesis, phosphate uptake proteins, and REPRESSES genes glnA and amtB
4. Activators increase antibiotic production, uptake proteins increase phosphorus metabolism, GlnA and AmtB are not produces to limit nitrogen metabolism.
72
What is Quorum sensing?
Regulatory mechanism that asses population density (esp in gram-negative bacteria) to ensure sufficient cell numbers before starting processes that require a certain cell density to work.
73
What is quorum sensing quantified by?
Specific signal molecules produces by bacterial cells of the same species (autoinducer) that diffuses across the cell envelope.
74
What are the classes of autoinducers?
1. Specific to bacteria: e.g. acyl gonoserine lactones (AHL)
2. Interspecies communication: e.g. cyclic furan Al-2 of gram negative bacteria
3. Small peptides: gram positive bacteria and archaea
75
How do Auto-inducers trigger gene transcription?
Directly bind transcriptional regulator (activator/repressor) or activating a two component system
76
What is the auto-inducer process of staphylococcus aureus?
1. agr operon transcribes AgrD (pre-AIP)
2. AgrD (Pre-AIP) is processed into Autoinducing peptide AIP by ArgB as it is sent out of the cell. This differentiates extracellular AIP from intracellular AIP
3. AIP (autoinducer) triggers two-component AtgC (sensor)/ArgA (regulator) system which activates expression of virulence genes.
77
what is the autoinducing pathway of the Shiga-toxin?
1. Increase in E. coli population within intestine elevates Autoinducer -3 (AI-3)
2. AI-3 and host stress hormones (epi/norepi) triggers sensor kinase
3. Activated sensor kinase causes cascade that activates lytic cycle of the phage, producing enterotoxins such as Shiga-toxin.
78
What is the autoinducing pathway of bioluminescent aliivibrio fischerii?
1. LuxI produces acyl-homoserine lactone (AHL) diffusing into cells located in Squid light organ
2. At low density, AHL binds to LuxR (transcriptional activator)
3. AHL-LuxR complex activates lux operon to produce luciferase enzyme that catalyzes reaction that emits blue green light to help squid camoflauge
79
What is chemotaxis?
Behaviour of cells moving towards attractants and away from toxins through the change in concentration of a chemical over time.
80
What are Methyl-accepting chemotaxis proteins? How many does E. coli have?
MCPs are cytoplasmic sensor kinases that cluster in hexagonal arrays called chemo receptors to DIRECTLY bind to attractants/repellants. E. coli has 5 MCPs
81
What is the pathway of chemotaxis for E. coli?
1. MCP binds repellant/releases attractant
2. conformational change activates cytoplasmic CheW
3. Activated CheW helps activate CheA, allowing autophosphorylation.
4. CheA-P phosphorylates CheY to CheY-P
5. CheY-P leads to CW flagellar rotation (tumbling)
6. MCP binds attractant/releases repellant
7. Conformational change inactivates CheW
8. CheA autophosphorylation is inhibited, preventing activation and phosphorylation of CheY
9. CheZ dephosphorylates remaining CheY, leading to CCW flagellar rotation (running)
82
What is chemotaxis adaptation?
Bacteria reset sensory system after detecting an attractant or repellant, allowing them to respond to new changes in environment
83
How does the varying methylation of MCP allow adaptation to signals?
Fully methylated MCP: do not respond to attractants, but sensitive to repellents
Unmethylated MCP: respond strongly to attractants, but insensitive to repellents
84
What controls the methylation of Methyl-accepting Chemotaxis proteins?
Methylation: CheR Demethylation:CheB-P
85
How does chemotaxis occur in a high level of attractants?
1. Binding attractant to MCP inhibits CheA autophosphorylation via CheW
2.Inhibited CheA cannot phosphorylate CheB into CheB-P
3. Without CheB-P MPC's remain methylated
4. Fully methylated MPCs become insensitive to attractant leading to release
5. Release of attractant allows CheW to reactivate CheA, allowing CheA-P to phosphorylate CheY-P (causes tumbling) AND CheB-P (resets receptor sensitivity)
86
How does chemotaxis occur in the presence of a high level of repllents?
1. Repellent binding to MCP causes a conformational change in the MCP, which activates CheW
2. CheW now stimulates CheA to undergo autophosphorylation, resulting in CheA-P (the phosphorylated form).
3. CheA-P can now phosphorylate CheY to form CheY-P, which triggers tumbling (this makes the bacterium change direction).
4. Additionally, CheA-P phosphorylates CheB, resulting in CheB-P.
5. CheB-P then demethylates the MCPs, reducing their sensitivity to the repellent.
6. This demethylation process reduces the MCP's ability to bind the repellent, which eventually leads to the release of the repellent, allowing the bacterium to reorient its movement.
87
How does bacteria know how to tumble in the presence of repellents?
As repellent concentration gets higher, fully methylated MCPs are better at sending signals for cell tumbling to move into another direction while MCPs are slowly demethylated.
88
What RNA type is involved in RNA-based regulation and how?
sRNA molecules act as regulators by base pairing with other RNA molecuels (mRNA) to modulate translation rate of target mRNA
89
What are two mechanisms in which sRNAs base pair to target mRNA to affect changes to protein expression?
1. Changing secondary structure to block previously accessible ribosome binding site to decrease protein expression level
2. Open previous blocked ribosome binding site to increase protein expression level.
90
What are two mechanisms in which sRNAs base pair to target mRNA to affect mRNA stability post transcription?
1. sRNA interaction decreases mRNA stability, increasing degradation of the transcript, resulting in less protein expression
2. sRNA interaction increases mrNA stability, decreasing degradation of the transcript, resulting in more protein expression
91
What is sRNA MicF?
One of the first sRNAs discovered that inhibits OmpF by complementary base pairing along the 5' end of the ompF gene, including translation initiation region. It is regulated by 4 activators, including OmpR.
92
What are riboswitches?
RNA molecules that fold into 3D structure that recognizes target molecules and bind. Binding affects gene expression levels through transcriptional or translation control depending on the type of switch,
93
What do riboswitches control?
controls synthesis of enzymes in biosynthetic pathways for vitamins, amino acids, nitrogen bases and peptidoglycan precursors.
94
How does the thiamine operon work using thiamine pyrophosphate?
Low thiamine: region 1 and 2 on mRNA complementary base pair to form a hairpin structure, allowing access to ribosome binding site and promoting translation.
High thiamine: thiamine pyrophosphate binds to region 1 on mRNA, preventing formation of 1:2 hairloop structure, allowing region 2 to form a hairloop with the ribosome binding site, preventing translation.
95
How does the methionine operon work using S-adenosylmethionine in Bacillus subtilis?
When SAM levels are low: leader sequence forms correct hairpin and transcription continues as normal
When SAM levels are high: SAM binds to hairpin altering structure, inducing formation of termination structure, followed by polyU sequence
96
What is the stringent response mechanism?
Regulatory mechanism bacteria use to balance their metabolic state to survive nutrient (AA) deprivation and environmental stresses. This occurs by shutting down macromolecule synthesis.
97
What are the steps of the stringent response?
1. Low AA leads to large pool of uncharged tRNAs which enter the ribosome and cause stalling.
2. RelA is activated at binidng of uncharged tRNA and transfers two phosphates from ATP to GTP to form pppGpp. This is quickly converted to (p)ppGpp or alarmones by phosphatase Gpp
3. High levels of alarmones cause a decrease in rRNA and tRNA synthesis and the downregulation of ribosomal genes to prevent unecessary translation
98
What is the function of SpoT?
When carbon/fatty acids are limited, SpoT synthesizes (p)ppGpp to trigger stringent response. When nutrients are plentiful, Spot hydrolyses (p)ppGpp to reset normal cellular functions and allow growth.
99
How does acyl carrier proteins help regulate SpoT?
ACP bound by short chain fatty acids (low carbon levels) has a high affinity to SpoT, stimulating SpoT's (p)ppGpp synthetase domain and inhibiting its (p)ppGpp hydrolase activity.
ACP bound by long chain fatty acids (high carbon levels) have a low affinity to SpoT, allowing (p)ppGpp hydrolase domain to function and inhibits the synthetase domain.
100
When is the stringent response used in E. coli
When E. coli leaves the nutrient rich intestine and enters an open water system, reduction in utrients trigger synthesis of ppGpp
101
When is the stringent response used in C. crescentus?
When C. crescentus nutrient poor environment results in carbon and ammonia starvation, stringent response turns stalked cells (fixed) are turned to swarmer cells (mobile)
102
When is the stringent response used in Mycobacterium tuberculosis?
1. Mtb faces stress (low nutrients, low oxygen, antibiotic exposure, immune system granulomas)
2. RelA and SpoT produce (p)ppGpp to activate stringent response, putting Mtb in a non growing, dormant persister state to avoid antibiotics.
3. Non growing dormant cells may exit the persister state and resume vegetative growth after being dormant.
103
What controls the switch to the stationary phase in the face of stressors?
Activating stress response genes recognized by RpoS (stationary sigma factor)
104
What is RpoS?
Sigma factor that recognizes the RpoS regulon containing over 400 stress response genes including nutrient limitation, resistance to DNA damage, biofilm formation, and responses to osmotic, oxidative and acid stress.
105
How is RpoS controlled?
transcriptional: rpoS transcription increases in response to ppGpp
Translation: RpoS translation is positively regulated by sRNAs expressed in stress conditions
Post translation: RpoS is susceptible to degradation in non-stressful conditions
106
What is RpoH?
Sigma factor that controls the heat shock regulon, degraded by DnaK in normal conditions. In heat shock conditions, DnaK is busy folding denatured proteins, leaving RpoH alone to complex with RNA polymerase for transcription initiation of heat shock genes.
