Transcriptional Termination

• The intrinsic terminator sequence is an inverted repeat of GC-rich sequence followed by 4 or more adenines. The transcribed RNA forms stem-loop structure at inverted repeats via internal base pairing
• The formation of this stem-loop structure (Fig. 11.1) disrupts hydrogen bonding between RNA uracils and DNA adenines at site of transcription (weak because only 2 H-bonds between A and U as compared to 3 between G and C)
• As a result, RNA is released from the DNA template

 What is an inverted repeat? A sequence of several bases in double-stranded DNA that is repeated in an inverted fashion

 Example:

• 5'.....GCCGCCAG........CTGGCGGC....3'
• 3'.....CGGCGGTC........GACCGCCG....5' (template strand)

 Consequently there are internal sequences in the transcribed RNA that are complementary and can therefore base pair to form a stem-loop structure (Fig. 11.1).
 

 Rho-dependent Termination Signals

• Some termination sequences lack the series of adenines which are transcribed in to URACILS on the RNA. The RNA in such situations needs assistance from a specific protein (termedRho) which is necessary for termination.
• Rho binds at the 5'end of the RNA and scans down the RNA until it catches up with an RNA polymerase  which is paused at a stem-loop structure.
• In Rho dependent termination, the Rho protein forces the RNA to separate from the DNA template.

Eukaryotic Transcriptional Termination

• RNA polymerase I terminates when it comes to a polymerase-specific DNA binding protein attached at the termination site.
• RNA polymerase III terminates at a series of U residues but does not require an upstream stem-loop be present in the mRNA.
• RNA polymerase II transcripts are essentially terminated by the cleavage near the polyadenylation site followed by the addition of the poly(A) tail (Fig. 11.12).  The cleaved 3' transcriptional product is rapidly degraded as are un-polyadenylated transcripts.

Attenuation

• Attenuation provides a secondary mechanism for controlling expression of the  prokaryotic trp operon (Fig. 11.2).
• Attenuation requires simultaneous transcription and translation (Fig. 11.3) and therefore only occurs in prokaryotes.
• In the presence of trp-charged tRNA leader sequence is closely translated behind RNA polymerase (Fig. 11.3, left figure).
• When trp-charged tRNA is low the ribosome pauses before end of leader and allows alternative stem-loop to form that prevents termination (Fig. 11.3, right figure).

Antitermination

• Binding of antitermination proteins, such as the N protein of lambda, between the promoter and the terminator allows a protein complex to form with nus proteins and prevent termination.
• Antiterminators work at Rho-dependent and Rho-independent terminators.
• In eukaryotic cells transcribing he HIV genome the Tat protein functions as an antiterminator (Fig. 11.6) by binding at the TAR site near the 5' end of the transcript.  Without Tat, only short RNAs from the 5' end of the genome are transcribed.

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