Regulation of sigma factors

Question 1

Why do alternative sigmas need to be regulated, but primary sigmas don’t?

Answer 1

Alternative sigmas are only active under certain circumstances, but the genes transcribed by primary sigmas need to be transcribed all the time

Question 2

What are 3 typical mechanisms to regulate the activity of sigma factors?

Answer 2

1. Competition for free RNAP cores with other sigmas
2. Controlling their abundance (a more abundant sigma is more likely to run into a free core)
3. Activity

Question 3

How do you control the activity of an alternative sigma factor?

Answer 3

Control its ability to associate with an RNAP core

Question 4

What are two ways to control the ability of sigma factors to associate with the RNAP core?

Answer 4

Cleavage of inactive pro-sigmas, and anti-sigmas

Question 5

What are pro-sigmas?

Answer 5

Sigma factors that are translated as longer polypeptides, then are cleaved into an active form in response to certain signals

Question 6

What is an advantage to using post-translational modifications to regulate sigma activity?

Answer 6

It’s much faster to activate them then having to go and transcribe and translate them

Question 7

What is the downside to using post-translational modifications to regulate sigma activity?

Answer 7

If you don’t end up needing the proteins, then you just spent a bunch of energy making them when you could’ve used it somewhere else

Question 8

What are anti-sigmas?

Answer 8

Proteins that bind to sigmas when they aren’t needed

Question 9

How do anti-sigmas work?

Answer 9

They block protein binding domains on sigma so that it can’t interact with the RNAP core

Question 10

What will cause an anti-sigma to release the sigma that its inhibiting?

Answer 10

An extracellular signal that will alter the activity of the anti-sigma

Question 11

How does the anti-sigma RseA regulate the activity of a Group 4 sigma 70 in E coli when the cell is NOT under stress?

Answer 11

RseA is a membrane protein, and sequesters sigma at the membrane. Has a very high affinity for the sigma, so if any RseA is present, it will be binding to sigma

Question 12

How does the anti-sigma RseA regulate the activity of a Group 4 sigma 70 in E coli when the cell IS under stress?

Answer 12

Membrane damage causes DegS protease to become active, which activates a protease cascade until ClpXP degrades RseA. Then sigma is released and it associates with the core to transcribe genes required to respond to the stress

Question 13

How does the anti-sigma RseA regulate the activity of a Group 4 sigma 70 in E coli when the cell stress has been resolved, and sigma needs to shut off?

Answer 13

More RseA will be translated and inserted into the membrane. Then it will resequester the sigma and transcription of the stress genes shuts off

Question 14

How does the anti-sigma RsrA regulate the activity of sigmaR in Streptomyces coelicolor when the cell is NOT under oxidative stress?

Answer 14

RsrA will be binding to a zinc ion, and will be in a conformation that has no disulfide bonds. It binds to sigmaR in this conformation and prevents it from interacting with the RNAP core

Question 15

How does the anti-sigma RsrA regulate the activity of sigmaR in Streptomyces coelicolor when the cell IS under oxidative stress?

Answer 15

The oxidative environment allows disulfide bonds to form in RsrA. It changes conformation and loses the zinc ion, which then causes it to let go of sigmaR. SigmaR then binds to RNAP core and initiates transcription of genes to remove oxidative stress

Question 16

How does the anti-sigma RsrA regulate the activity of sigmaR in Streptomyces coelicolor when the oxidative stress has been resolved, and sigma needs to shut off?

Answer 16

The genes in the sigmaR regulon remove the oxidative stress, which causes RsrA to lose the disulfides. It reassociates with the zinc ion, then with sigmaR to shut it off

Question 17

How does the anti-sigma FlgM regulate the activity of sigmaFliA when the basal body of the flagella is NOT complete?

Answer 17

FlgM accumulates in the cytoplasm and binds to sigmaFliA. It can’t interact with RNAP core, so the genes required for the construction of the flagella filament don’t get expressed

Question 18

How does the anti-sigma FlgM regulate the activity of sigmaFliA when the basal body of the flagella IS complete?

Answer 18

Basal body secretion system becomes active and exports FlgM out of the cytoplasm. It lets go of sigmaFliA, which goes and interacts with the RNAP core. Then it transcribes the filament and motor proteins

Question 19

How does the partner switching mechanism of sigma regulation work?

Answer 19

These systems use an antagonist (anti-anti-sigma) that has a higher affinity for the anti-sigma than the anti-sigma has for the sigma. The anti-sigma will always be bound to one of them, but never both, so it switches partners

Question 20

How does the antagonist PhyR and the anti-sigma NepR regulate the activity of sigmaEcfG1 in Methylobacterium extorquens when the cell is NOT under stress?

Answer 20

PhyR is unphosphorylated and inactive. NepR is binding to sigma and preventing it from binding to the RNAP core and initating transcription of stress genes

Question 21

How does the antagonist PhyR and the anti-sigma NepR regulate the activity of sigmaEcfG1 in Methylobacterium extorquens when the cell IS under stress?

Answer 21

PhyR gets phosphorylated, and it will bind to NepR. NepR then changes conformation, releases sigma, and binds to PhyR instead. Then sigma binds to the RNAP core and transcribes stress genes

Question 22

How does the antagonist PhyR and the anti-sigma NepR regulate the activity of sigmaEcfG1 in Methylobacterium extorquens when the stress has been resolved, and sigma needs to shut off?

Answer 22

A phosphatase will cut the phosphate off PhyR. It will let go of NepR and then NepR will bind to sigma again and sequester it