As RNA polymerase moves along the DNA template, it unwinds the duplex at the front of the bubble (the unwinding point), and the DNA  automatically reforms the double helix at the back (the rewinding point).  The length of thetranscription bubble is 12 to 14 bp, but the length of the RNA–DNA hybrid within the bubble is only 8 to 9 bp. As the enzyme moves along the template, the DNA duplex reforms, and the RNA is displaced as a free polynucleotide chain The last 14 ribonucleotides in the growing RNA are complexed with the DNA and/or the enzyme at any given moment.

TLS Online TPP Program

#Id: 2335

#Unit 3. Fundamental Processes

A ribosome-associated protein called RelA receives the “alarm” and produces the “alarmone” ppGpp, which destabilizes open promoter complexes whose lifetimes are normally short, thus inhibiting Transcription.

TLS Online TPP Program

#Id: 2336

#Unit 3. Fundamental Processes

The protein DskA  also plays an important role. It binds to RNA polymerase and reduces the lifetimes of the rrn open promoters to a level at which they are responsive to changes in iNTP and ppGpp concentrations. 

TLS Online TPP Program

#Id: 2337

#Unit 3. Fundamental Processes

DskA is required for the regulation of rrn  transcription by these two small molecules. Indeed, rrn  transcription is insensitive to iNTP and ppGpp in mutants lacking DskA.

TLS Online TPP Program

#Id: 2338

#Unit 3. Fundamental Processes

In E. coli, rRNA synthesis from the seven rRNA operons responds to cellular growth rate and to changes in the availability of crucial nutrients, particularly amino acids. The regulation coordinated with amino acid concentrations is known as the stringent response.

TLS Online TPP Program

#Id: 2339

#Unit 3. Fundamental Processes

Amino acid starvation leads to the binding of uncharged tRNAs to the ribosomal A site; this triggers a sequence of events that begins with the binding of an enzyme called stringent factor (RelA protein) to the ribosome. 

TLS Online TPP Program

#Id: 2340

#Unit 3. Fundamental Processes

When bound to the ribosome, stringent factor catalyzes formation of the unusual nucleotide guanosine tetraphosphate (ppGpp); it adds pyrophosphate to the 3 position of GTP, in the reaction.