Lecture Connections 28 | Regulation of Gene Expression

CHAPTER 28Regulation of Gene Expression – DNA elements that control transcription – Protein factors that control transcription – Lac operon as a model for regulation – Regulation of prot

Lecture Connections

28 | Regulation of Gene Expression

© 2009 W H Freeman and Company

CHAPTER 28

Regulation of Gene Expression

– DNA elements that control transcription

– Protein factors that control transcription

– Lac operon as a model for regulation

– Regulation of protein synthesis by RNA

Key topics:

How to Control Protein’s Activity

in The Cell?

• How much primary RNA transcript to make?

• How to process this RNA into mRNA?

• How rapidly to degrade the mRNA?

• How much protein to make from this mRNA?

• How efficiently to target the protein to its location?

• How to alter the intrinsic activity of this protein?

• How rapidly to degrade the protein?

Processes that Affect Protein’s

Concentration and Activity

DNA Sequences Involved in

Regulation of Gene Expression

• Most bacterial promoters include the conserved –10 and –35 regions that interact with the 

factor of RNA polymerase

• Some promoters also include the upstream

element that interacts with the  subunit of RNA polymerase

Two Main Mechanisms to Regulate Transcription in Bacteria

• Use of different  factors

– These recognize different classes of promoters

– Allows coordinated expression of different sets of genes

• Binding other proteins ( transcription factors ) to

promoters

– These recognize promoters of specific genes

– These may bind small signaling molecules

– These may undergo post-translational modifications

– The protein’s affinity toward DNA is altered by ligand binding

or post-translational modifications

– Allows expression of a specific genes in response to signals

in the environment

Regulation by  Factors

Regulation by Transcription Factors (1)

• Bound repressor inhibits transcription

Regulation by Transcription Factors (3)

• Bound activator facilitates transcription

Bacterial Operon

• Operon includes binding sites for activators

and repressors, the promoter to which the

factor binds, and one or more genes whose

expression is controlled by the operon

• In this example, A, B, and C are transcribed as one polycistronic mRNA that is translated into three proteins

Lactose Metabolism in E coli

• When glucose is aplenty and lactose is

lacking, cells make very low levels of

enzymes for lactose metabolisms

• If cells are fed lactose but not glucose, cells can use it as their energy source given that:– Lactose is effectively entering the cell

– Lactose is hydrolyzed into

monosaccharides

The lac Operon has Three Sites

for Binding the Lac Repressor

Binding of Proteins to DNA Often

Involves Hydrogen Bonding

Helix-Turn-Helix Motif is Common

in DNA-Binding Proteins

• One of the helixes (red) fits into the major

groove of DNA

• Four DNA-binding helix-turn-helix motifs (gray)

in the Lac repressor

Conformational Change in

Repressor Upon Ligand Binding

• Binding of allolactose or other lactose

analogs, such as IPTG induces a

conformational change in repressor

• The ligand-bound repressor dissociates

from DNA

• Genes needed for lactose metabolism are transcribed

Activation of Transcription of the

lac Operon by CRP

• cAMP receptor protein (CRP) is a positive

regulator of the lac operon

• CRP binds to the lac operon in the absence of

glucose

• Binding of CRP stimulates expression of the

lac operon

CRP Homodimer Binds and

Bends DNA

polymerase, stimulating transcription of genes

in the lac operon

Combined Effects of Glucose and

Lactose on the lac Operon

• When lactose is low, repressor is bound:

The trp Operon

Dimeric Trp Repressor Binds to DNA in the Presence of Tryptophan

• Notice that helix-turn-helix motifs interact with DNA via the major groove

Regulation of Transcription in

Eukaryotes

• General transcription factors

– TATA box binding protein (TBP)

– Transcription factors for the assembly of the initiation complex

• Promoter proximal / distal enhancer binding factors

– Homeodomain proteins share similarities with helix-turn-helix

bacterial counterparts nut often involve water bridges between

DNA and protein

– Leucine zippers are made of two amphipathic polypeptides One side of each peptide is hydrophobic, facilitating

dimerization

– Zinc fingers form elongated loops held together by a single

Zn ++ ion

Homeodomain Proteins

• Notice that an -helix interacts with DNA via the major groove

Leucine Zippers

Eukaryotic Promoters and

Regulatory Proteins

Activation of Bacterial Translation

by small RNA Molecules

• The ribosome-binding Shine-Dalgarno

sequence is sequestered into a stem-loop

structure in the mRNA

• In the presence of protein Hfq, small regulatory RNA DsrA binds to the mRNA

• The binding of DsrA opens up the stem-loop

and allows mRNA binding to ribosome

• DsrA RNA promotes translation

Inhibition of Bacterial Translation

by small RNA Molecules

• The ribosome-binding Shine-Dalgarno

sequence is sequestered into a stem-loop

structure in the mRNA

• In the presence of protein Hfq, small

regulatory RNA OxyS binds to the mRNA

• The binding of OxyS blocks the ribosome

binding site in mRNA

• OxyS RNA inhibits translation

Chapter 28: Summary

• Regulation of gene transcription is a common and efficient way to control protein’s activity in the cell

• Regulation of transcription is commonly achieved via binding

of inhibiting and activating proteins to the DNA near the

beginning of the gene

• Transcription factors frequently bind via an  helix that

protrudes into the major groove of dsDNA

• Binding of mRNA to ribosome is modulated by small

regulatory RNA molecules

In this chapter, we learned that: