Prokaryotic transcription regulation

Question 1

RNA polymerase

Answer 1

Works in 5’ to 3’ direction
Does not require primer to start synthesis
Core enzyme becomes holoenzyme when sigma binds

Question 2

Promoter recognition

Answer 2

Site upstream of ORF
Core enzyme alone cannot recognise
Sigma factor binding increases affinity for the promoter

Question 3

Diffusion search

Answer 3

Holoenzyme scans DNA for the promoter

Sigma binds promoter and the closed complex forms

Question 4

Promoter consensus sequence

Answer 4

-35 and -10 regions flank promoter
Positions polymerase in correct orientation
Sigma domain 2 binds -10 region
Domain 3 recognises two bases of extended -10 region
Domain 4 recognises -35 element

Question 5

Heat shock sigma factors

Answer 5

sigma70 is housekeeping sigma factor

In elevated temperatures sigma32 levels increase and compete with sigma70.

Leads to expression of 17 heat shock proteins

Question 6

Extreme heat shock factors

Answer 6

Anti-sigma factor RseA normally sequesters sigmaE

In extreme temperatures, RseA is cleaved and sigmaE released

Question 7

SPO1 phage gene expression

Answer 7

bacterial sigma factor gp43 transcribes phage early genes

alternative phage sigma gp28 produced and replaces gp43

Middle genes transcribed including gp33 and gp34

gp33/34 replace gp28 and late genes are transcribed

Question 8

Rho independent terminators

Answer 8

Form GC rich hairpin loop followed by U-run in transcribed message

GC strong pairing within RNA and weak pairing of DNA with U-rich region causes elongation complex to collapse

Question 9

Rho-dependent terminators

Answer 9

Rho (hexameric ATPase) binds Rho utilisation site (RUT)
Ring closes around RNA
ATP hydrolysis drives pulling of RNA through ring away from polymerase

Question 10

Antitermination in Lambda phage

Answer 10

RNA pol transcribes immediate early genes N and cro before terminating

pN antiterminator binds polymerase and allows transcription of delayed early genes (passes terminator)

Question 11

nut sites

Answer 11

N utilisation

pN recognises and binds to nut, enabling polymerase to pass terminators

Question 12

Nus proteins

Answer 12

N utilisation substance proteins
loosely associated with RNA pol
involved in termination (stabilises hairpin) in absence of pN
co-opted by pN and bind to RNA polymerase at nut site to prevent termination

Question 13

SigmaB

Answer 13

Controls around 200 genes in B. subtilis

Response against stresses such as ethanol and osmotic stress