Stress Response Flashcards
sigma S
- global regulator of the general stress response
- also called rpoS
- S stands for stationary because sigma S is found in high levels in stationary phase cells of E. Coli
- triggered by starvation that comes after stationary phase
Specific stressers modulated by sigma S
- temperature (heat, cold)
- oxidative stress
sigma factor’s role in transcription
- recognize the promotor and help RNA polymerase bind to the DNA.
regulation by sigma S
- genes recognized by the sigma S version of RNA polymerase have slightly different promotor regions that are only recognized by sigma S and thus will only be transcribed when sigma S is present.
regulation of sigma S
- regulated at the transcriptional and translational level.
- only transcribed until the bacterium senses stress.
- three promotors for rpoS
- each promotor controlled separately
Transcriptional regulators of RpoS
- cAMP levels and CAP - glucose starvation
- pppGpp - stringent response of starvation
- NADH/NAD+ ratio - starvation
- Quorum sensing
- Acetate and weak acids - fermentation produces, acid stress
Three promotors of RpoS
- one directly preceding the gene
- one found within the upstream gene
- one upstream of the preceding gene.
Translational regulators of RpoS
- default for sigma S translation is off
- very little made because ribosome binding site buried in secondary structure
- small regulatory RNAs bind through RNA-RNA interactions that allow for translation
- Temperature - Heat and Cold - dura
- Oxidative Stress - OxyS - down regulates
Stem loop and spacer of DsrA and OxyS
- will melt out certain regions
- DsrA turned on by heat stress
- Oxy S under peroxide stress will stabilize
E. Coli sigma S regulation
- 481 directly regulated by sigma S
- 100 more moderated by sigma S
- 10% of genome
Starvation
- accumulate two molecules
- cAMP - in response to glucose depletions
- (p)ppGpp - in response to amino acid depletions
- act independently but synergistically to help cell overcome starvation
- cell uses ribosome to measure the pool of charged tRNAs
ppGpp
- when a cell runs out of charged, amino acids, the ribosome will contain uncharged tRNAs
- when a ribosome unloads an uncharged tRNA into A site, a ribosomal protein RelA, will catalyze the transfer of a diphosphate from ATP to the 3’ OH of GTP, forming pppGpp.
- quickly converted to ppGpp.
cAMP
- when glucose is present, the level of cAMP is low
- when glucose levels decline, adenylate cyclase is activated
- cAMP binds to CAP and regulates ~100 members of the carbon starvation regulon.
adenylate cyclase
- catalyzes the conversation of ATP to cAMP and pyrophosphate
carbon starvation regulon
- alternative carbon and energy utilization pathways
- encode carbohydrate transport and catabolic operon like those for lactose, arabinose, and maltose.
targets of ppGpp
- binds directly to the beta subunit of RNA polymerase changing specific of promotors it recognizes.
- makes sure cell will stop making ribosomes, will start making amino acids, turn on alternative carbon utilization pathways, and turn on general stress program.
affected due to change in specificity
- rRNA genes are down regulated
- Amino acid biosynthesis genes are up regulated
- CAP synthesis is up regulated
- RpoS is up regulated
Heat shock and protein folding
- the structures the various proteins in the cell are determined by their primary sequence, and the correct structure is thermodynamically defined by the lowest energy level achievable.
- within a narrowly defined temperature range. if taken out of that range, it will not behave properly.
- the proper folding of a protein is critical for its function
- make sure they don’t aggregate
if protein is too cold
it will lose flexibility
if protein is too hot
- it will denature
- if denatured too badly, it will aggregate with other proteins through hydrophobic interactions.