BIO 504 - Prokaryotic Genome IV - Elongation

NusA

__ competitively binds RNA poly replacing the sigma factor in the holoenzyme

Elongation factor that binds the nascent RNA near the polymerase exit. Facilitates pausing and termination.

nut

__ site is the site in RNA recognized by some proteins of the Nus family

NusE, NusB

___ and ___ are proteins essential for anti-termination aka prevent termination so that operons can be transcribed by inducing more open reading frames

• used by lambda phage via N protein

NusE

__ protein that is an actual component of the 30S subunit of ribosome and its interaction with NusB physically tether first ribosome to RNA polymerase

NusG

__ protein suppresses pausing thus suppresses termination by increasing the rate of transcription

• BUT facilitates termination in presence of factor Rho

Prokaryotic transcription overall

1. Holoenzyme binds to sigma factor

2. sigma factor recruit RNA poly to promoter aka DNA binding

3. Open complex confirmation triggers the start of transcription

4. NusA protein and Rho factor bind and read RNA as it is made and elongated

5. Sigma factor leaves once region of promoter escaped, NusG and NusB binds to recruit first ribosome to physically attach to RNA poly

6. Nus B leaves when ribosome binds

7. Once elongation is ending ribosome falls off and termination complex forms

Rho independent termination

1. 2 inverted GC rich sequences which form a hair pin when transcribed to RNA

2. The hairpin causes RNA poly to pause

3. The U rich sequence following the hairpin sequence has weaker H bonds that end up breaking when in the transcription bubble

4. RN transcript (hairpin) separates from template hence terminating transcription

Rho

transcription termination factor recruited in the transcription complex early on with NusA, always present no matter if it is used or not

RNA-binding ATP-dependent hexameric RNA/DNA helicase

• binds to rut site which recognize specific 3D structure of RNA and pulls on it to destabilize RNA-DNA duplex in transcription bubble

N, Cro

PL and PR are phage promoters recognized by bacterial RNA poly

• PL codes for protein __

• PR codes for protein __

protein N

buildup of ___ following lambda phage infection leads to it interacting with Nus protein on RNA poly complex thus preventing termination by preventing from being recognized termination sites tL and tR from being recognized.

• __ does NOT discriminate between rho dependent and rho independent: rho cannot catch up to RNA poly if it doesn’t stop & if RNA poly does not pause with U rich sequence in transcription bubble, then it doesn’t work.

anti-termination

preventing terminators from doing their jobs

• observed in phages but also in some rRNA such as rRNA of protein S4

non-coding RNA

RNA that does NOT get translated into proteins but can regulate translation in a positive or negative manner by base pairing with different sequences.

• can also control mRNA stability

• typically, small RNA molecules with a lot of different 3D structures, able to bind to ss or ds regions

• can mark mRNA for degradation

translation initiation region

non-coding RNAs can inhibit translation by base pairing anywhere within the ___

allow

ncRNA can also ___ translation by base pairing with the 5‘end of the sequence that originally was blocking translation by being paired with the translation initiation site

Hfq

host factor involved in replication of phage q & is actually an RNA chaperone binding to RNA and ncRNA allowing them to stabilize and find their target

small RNA binding protein that facilitates base pairing of ncRNA with their target

RNaseE

ncRNA can mark mRNA for degradation by binding to Hfq, which brings them and bind to a specific ss region in message, and recruits ribonuclease ___

RNase III

ribonuclease usually associated with larger ncRNA fragments binding to target in big ds regions and cleaves them

polyadenylation

ncRNA can stimulate ___ pf target mRNA by PAP followed by exo degradation

ribonuclease

ncRNA marks their targets for degradation through the use of a ribonuclease

stress

ncRNA usually regulates __ pathways