Transcription Termination

Question 1

What is the terminator in bacteria?

Answer 1

the terminator is t (a specific site on the transcript)

Question 2

What are the similar features of transcription initiation and termination?

Answer 2

1) Both require H-bond breaking
a. Initiation: DNA melting (the transcription bubble)
b. Termination: RNA-DNA dissociation to release the RNA
2) Both require additional factors associated with the core enzyme
a. Initiation: σ factor
b. Termination: nus complex
 Allows core to terminate at t
3) Both represent control points in bacterial gene expression
a. Initiation: alternate σ factors: differential gene expression
b. Termination: antitermination

Question 3

What are the transcription terminators in E. coli?

Answer 3

• E. coli has 2 terminators (each responsible for about 50% of gene termination)
o Intrinsic terminator
 Termination dependent on structural features of RNA
 No other protein required
o Rho Terminator
 Requires rho factor to terminate
 Rho: hexameric complex

Question 4

What is the intrinsic terminator?

Answer 4

•	Inverted repeats along the intrinsic terminator are complementary based paired (not 100% paired)
o	A loop forms between the inverted repeats
•	GC-rich region in stem
o	Clamping region
•	Stem is followed by poly U region
o	Weak hybrid structure
o	Poly U and DNA are stalled together
o	Eventually dissociates

Question 5

What are the elements of a rho-dependent terminator?

Answer 5

• Rho-factor

- RUT site

Question 6

What is the rho-factor? What are its roles/activity?

Answer 6

o	Terminator protein
o	Functions as a hexamer
o	2 activities
1.	RNA-dependent ATPase activity
2.	Helicase

Question 7

What is the RUT site?

Answer 7

•	Rho-Utilization site 
o	Rut site is on RNA; site on which Rho binds
o	Position can be variable
o	C-rich, G-poor
o	Function: Rho hexamer binding site

Question 8

How does the rho-dependent terminator function?

Answer 8

•	Hot-pursuit model
o	Rho attaches to Rut
o	Follows RNA Pol
o	Once it catches up to RNA Pol, it has its helicase activity
	Unwinds the DNA-RNA hybrid
	Termination occurs

Question 9

What is the nus factor?

Answer 9

• This complex binds the core enzyme as RNA Pol passes nut site
• Nut: N-utilization site

Question 10

What is the control point of transcription termination?

Answer 10

Antitermination

Question 11

What is antitermination?

Answer 11

• Antitermination controls secondary transcription unit downstream of termination
o 2 transcription units are separated by terminator
o The second transcription unit doesn’t have a promoter sequence

Question 12

How does antitermination work?

Answer 12

• In antitermination, RNA Pol continunes after the 1st terminator
o With antiterminator protein = pN
o N associates with nus on core enzyme (as it passes nut)
o They accelerate the core enzyme through terminator
 Poly A/U doesn’t have time to dissociate
 Or rho never catches up to core enzyme (cannot bind core, no helicase activity)