Adaptive responses (regulation of transcription) Flashcards
(17 cards)
environmental stimuli
starvation, anti-microbial, host cell, surface
specific gene expression
understanding the regulatory mechanisms in sensing and responding to host environment –> novel anti bacterial targets and new strategies to prevent systemic disease
promoter
RNA polymerase (alfa and beta) + sigma factor (recognizes promoter sequences to initiate transcription)
transcriptional site (+1)
activator linked to alfa subunit
regulation: sigma factor, action of repressor binding to TSS or activator binds to alfa
Stimulon and regulon
stimulon: genes dependent of stimulus to express
regulon: all genes controlled by a regulator
Sigma factors
specificity factor (promoter sequence) - melts dsDNA to initiate transcription
Exponential phase: sigma 70 - RpoD (common)
Heat shock: sigma H (RpoH) and sigma E (RpoE)
control activity: transcriptional iniation, mRNA stability, control of translation, proteolytic degradation and anti-sigma factors
Adaptive responses - transcriptional regulation
sigma factors
two component regulators (TCR)
post transcriptional regulation
Anti-sigma factors- heat shock system
Controlled by sigma H and sigma E - proteins expressed through their regulation prevent and repair protein damage (re-fold or degrade)
H - dnaJ, dnaK, groEL, groES, rpoD
E- rpoH, rpoE, htrA
The RseABC system (RpoE)
normal T: low transcription of operon by sigma 70
Heat shock activates rpoE (operon: rpoE, rseA,B,C) - sigma E increases transcription
RseA: inner membrane protein and anti-sigma inactivates RpoE by connecting to sigma E- periplasmic (C-) w/ RseB and cytoplasmic (N-) with sigma E (inhibitor)
RseB: periplasmic
RseC: inner membrane anti-anti sigma factor (promotes RpoE activity)
1- DegS (inner membrane protease) senses C- terminus of misfolded proteins in the periplasm and cleaves RseB relieving inhibition of RseP
2- RseP cleaves RseA-RpoE
3- ClpXP (cytoplamic ATP dependent protease) cleaves rest of RseA from sigma E
4- Sigma E is available and increases transcription/expression of operon
RpoH
Activated when there are misfolded proteins in cytoplasm (more expression and stability)
normal: dnaJ and dnaK bind to sigma H (surround it) - degradation by FtsH
heat shock: dnaJ and dnaK bind to misfolded proteins and sigma H binds to RNApol transcribing the heat shock regulon (repair and degradation)
NOTE: RpoE increases expression of RpoH
TCR - transduction
Histidine protein kinase
- input domain senses specific signal
- transmitter gets phosphorylated (conserved histidine and ATP domain - kinase)
Response regulator
- receiver gets phosphorylated at Asp (from P-histidine)
-output domain: sends output signal and binds to specific DNA sequence
TCR- trasmission
depends on ligand dependent conformational changes
kinase activity and dimerisation of Hbox (intermolecular phosphotylation)
also has de-phosphorylation
HPKs
1 for various RR or various to 1 RR
-dephosphorylation of RR (pair isn´t phosphorylated)
-molecular specificity - HPK and RR paired
-spatial localization - diff
- temporal control- express at diff times
RR
usually transcription factors (bind promoters - affect gene expression)
receiver domain is conserved and interacts with P-HPK, catalyse transfer of phosphate, regulates activity of output domain (many inhibit)
output domain is system specific, heterogeneous in sequence and structure, DNA binding, determines promoter specificity
1/2 life of Asp-P affects response
Dephosphorylation: HPK, external phosphotases, autophosphatase
EnvZ /OmpR
EnvZ (HPK) - transmembrane sensor
- periplasm sensor
- cytoplasmic His-dimer
-cytoplasmic ATP binding domain
OmpR (RR)- activator and repressor
- transduces signal from EnvZ and changes transcritpion, regulates OmpC and OmpF, DNA binding with winged HtH - OmpR-P levels
low osmolarity - low OmpR-P and high OmpR –> OmpR-P bind to OmpF activating transcription and OmpC only has one affinity site being repressed (phosphatase dominant)
high osmolarity- high OmpR-P –< OmpF has too many OmpR-P binding that bend the DNA and RNA pol can´t bind (repress) and OmpC is activated and expressed (kinase dominant)
Post transcriptional regulation (3)
-during transcritpion (antitermination/attenuation)
-at initiation of translation (trans encoded regulatory small RNAs and cis-encoded antissense RNA)
-during translation
explain cis and trans
cis encoded antisense RNA - encoded on opposite strand of mRNA, base pair with complementary - specific (opposite direction) - inhibits or activates
trans-encoded regulatory (small RNAs)
- not specific (partial duplex)
- 50-200nt
-no operons, intergenic
-varies with environment
- interacts with transcritptional regulators of many genes
small RNAs regulation
negative regulation:
- blocks ribosome sites -> not translation
- target mRNA for degradation by ribonucleases - no translation
positive regulation:
- exposes RBS structure binding to them - translation
- binds to 5´of mRNA to ensure prossessing and RNase can´t bind
- blocks degradation (bends and protects)
micF
TCR+small RNA
regulates OmpF
signal from micF - smal RNA binds to 5´end of OmpR (RBS) - no translation (no OmpF porin)
