BSC 219

Prokaryotic gene expression

10/25/12

 

16.2 Many Aspects of Gene Regulation Are Similar in Bacterial and Eukaryotes

Genes and Regulatory Elements

Structural genes: encoding proteins

 

Regulatory genes: encoding products that interact with other sequences and affect the transcription and translation of these sequences

 

Regulatory elements: DNA sequences that are not transcribed but play a role in regulating other nucleotide sequences

Genes and Regulatory Elements

Constitutive expression: continuously expressed under normal cellular conditions

 

Positive control: stimulate gene expression

 

Negative control: inhibit gene expression

Level of Gene Regulation

Many levels at which gene expression may be regulated

DNA access

Transcription

RNA modification and stability

Translation

Post-translational modification

 

 

DNA-Binding Proteins

Domains: 60 ~ 90 amino acids, responsible for binding to DNA, forming hydrogen bonds with DNA

 

Distinctive types of DNA-binding proteins based on the motif

 

Motif: within the binding domain, a simple structure that fits into the major groove of the DNA

            Helix turn helix-bacterial, binds major groove

            Zinc fingers-eukaryotic, binds major groove

            Leucine zippers-eukaryotic, binds adjacent major grooves

 

 

 

 

 

 

16.3 Operons Control Transcription in Bacterial Cells

Operon: promoter + additional sequences that control transcription (operator) + structure genes

 

Regulator gene: DNA sequence encoding products that affect the operon function, but are not part of the operon

Negative and Positive Control; Inducible and Repressible Operons

Inducible operons: Transcription is usually off and needs to be turned on.

 

Repressible operons: Transcription is normally on and needs to be turned off.

Negative and Positive Control; Inducible and Repressible Operons

Negative inducible operons: The control at the operator site is negative. Molecule binding is to the operator, inhibiting transcription. Such operons are usually off and need to be turned on, so the transcription is inducible.

 

Inducer: small molecule that turns on the transcription

 

 

Negative and Positive Control; Inducible and Repressible Operons

Negative repressible operons: The control at the operator site is negative. But such transcription is usually on and needs to be turned off, so the transcription is repressible.

 

Corepressor: a small molecule that binds to the repressor and makes it capable of binding to the operator to turn off transcription

 

Negative and Positive Control; Inducible and Repressible Operons

Positive inducible operon

 

Positive repressible operon

 

 

The lac Operon of E. coli

A negative inducible operon

 

Inducer: allolactose

 

lacI: repressor encoding gene

 

lacP: operon promoter

 

lacO: operon operator

The lac Operon of E. coli

Structural genes

 

lacZ: encoding β-galactosidases

lacY: encoding permease

lacA: encoding transacetylase

 

The repression of the lac operon never completely shuts down transcription.

 

 

 

Positive control and catabolite repression

Catabolite repression: using glucose when available, and repressing the metabolite of other sugars

 

This is a positive control mechanism: The positive effect is activated by catabolite activator protein (CAP). cAMP is binded to CAP, together CAPcAMP complex binds to a site slightly upstream from the lac gene promoter.

Positive control and catabolite repression

cAMP – adenosine-3′,5-cyclic monophosphate

The concentration of cAMP is inversely proportional to the level of available glucose.

 

The trp Operon of E. coli

A negative repressible operon

 

Five structural genes

 

trpE, trpD, trpC, trpB, and trpA – five enzymes together convert chorismate to typtophane.

 

16.4 Some Operons Regulate Transcription Through Attenuation, the Premature Termination of Transcription

Attenuation: affects the continuation of transcription, not its initiation. This action terminates the transcription before it reaches the structural genes.

Attenuation in the trp Operon of E. coli

Four regions of the long 5 UTR (leader) region of trpE mRNA

 

When tryptophan is high, region 1 binds to region 2, which leads to the binding of region 3 and region 4, terminating transcription prematurely.

            Makes a structure that resembles rho independent loop

 

 

Attenuation in the trp Operon of E. coli

Four regions of the long 5 UTR (leader) region of trpE mRNA

 

When tryptophan is low, region 2 binds to region 3, which prevents the binding of region 3 and region 4, and transcription continues.

 

           

 

16.5 Antisense RNA Molecules Can Affect the Translation of mRNA

Antisense RNA:

 

Complementary to targeted partial sequence of mRNA

16.6 Riboswitches Function as Regulatory Elements in mRNAs

Riboswitch: the regulatory sequence of mRNA molecules where molecules can bind and affect gene expression by influencing the formation of secondary structure in the mRNA