23 and 25 October, 2006

Chapter 16

Regulation in Prokaryotes

Overview• Transcriptional initiation is the most common point to regulate gene expression.• Any of the events of initiation, including polymerase binding and open complex

formation may be regulated either positively or negatively.• Regulation is accomplished by sequence-specific DNA binding proteins.• Binding may be promoter proximal or at a distance.• DNA footprinting and mobility shift assays are used to investigate the binding of

regulatory proteins.• In the E. coli lac operon, there are both repressors and activators, each of which is

allosterically regulated.• Many regulatory systems control a large number of genes and operons, like the

catabolite repression and heat shock regulons.• NtrC is regulated by covalent modification, binds at a distance, and hydrolyzes ATP

to pronmote open complex formation.• MerR activates transcription by twisting the promoter.• Riboswitches regulate transcription or translation without protein mediators.• Phage lambda uses alternative regulatory systems to control lytic or lysogenic growth.• Repressor and Cro compete to determine lytic or lysogenic growth, in response to the

stability of the CII protein.• Downstream regulation in lambda involves antitermination.

Activators and repressors may

regulate binding of polymerase.

Some activators regulate open complex formation.

Cooperative Binding and Transcriptional Regulation at a Distance

The lac operon

lac operon regulation

Control Regions and lac Operator Half-sites

RNA polymerase can

form open complexes even in the presence

of the LacI protein.

RNA polymerase interacts with promoter and CAP

Helix-turn-helix Interactions with DNA

CAP bends DNA

Activator Bypass

Lac repressor binds as a tetramer

Genetic experiments with partial diploids elucidated the ideas behind regulation of gene expression.

Regulation by Alternative -Factors

Regulation of GlnA by -54 and NtrC.

NtrC Acts at a Distance

MerR Regulation

AraC Regulation

Arabinose relaxes loops, and the loops reform in the absence of competitor.

Regulation of the trp operon

Tryptophan Interaction with Trp Repressor

Attenuation

Ribosomal proteins

regulate their own

translation.

Riboswitches regulate gene

expression without

regulatory proteins.

Phage lambda

Lambda Genome

Lambda Control Region

Lambda Repressor and Binding Sites

Cooperative Binding

Cooperative and Non-Cooperative Binding

Lambda Regulation

Negative Autoregulation

DNA Looping Between two lac operators

CII Control of the Lytic / Lysogenic Decision

N and Q Antiterminators

int Regulation

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