Chapter 13. Regulation of gene expression References: 1.Stryer: “Biochemistry”, 5 th Ed. 2.Hames & Hooper: “Instant Notes in Biochemistry”, 2 nd Ed.

1. Basic principles of gene control What is gene expression?  It is a process by which a gene's information is converted into the structures and functions of a cell. For a protein encoding gene, it is a process of the transcription of a gene into mRNA, and the latter is translated into protein.

How to control gene expression?  In prokaryotic cells, gene expression is regulated primarily at the level of transcription by metabolites;  In eukaryotes it is controlled by much more complex mechanisms, including the action of protein factors, hormones, etc.

Control of gene expression in prokaryotes  R Structural gene Substrate Product Enzyme mRNA DNA R

Control of gene expression in eukaryotes

2. Regulation of Prokaryotic gene expression– the operon theory  Operons are groups of genes that function to produce proteins needed by the cell.  There are two types of genes in operons A.Structural genes code for proteins needed for the normal operation of the cell. B.Regulator genes code for proteins that regulate other genes.

P lac : promoter; O lac : operator; lac Z:  -galactosidase; lacY: permease; Lac A: transacetylase; lac I: structural gene for lac repressor; P lacI : promoter for lac I. Lactose Operon

Regulation of the lac operon in E. coli. Repressor mRNA Repressor The repressor binds to the operator region and prevents RNA polymerase from transcribing the structural genes

In the presence of lactose mRNA

In the presence of glucose & lactose Low level of transcription

In the absence of glucose and presence of lactose active CAP: catabolite activator protein

Tryptophan Operon The trp operon encodes the genes for the synthesis of tryptophan

Regulation of the trp operon in E. coli.  Binding of Trp to the trp repressor increases the activity of the repressor, and therefore Trp is known as a co- repressor.  Expression of the trp operon is also regulated by attenuation. The attenuator region contains tandem Trp codons, which play a role to attenuate the transcription of the following genes.

Regulation of trp operon by attenuation

1) The regulation of eukaryotic gene expression differs from that of prokaryotes in: A) Eukaryotic RNA polymerases cannot transcribe DNA on their own—a multisubunit transcriptional apparatus must assemble first at the TATA box of the gene. 3. Regulation of eukaryotic gene expression.

B) Activators and repressors of eukaryotic gene expression act by altering the rate of formation of the transcriptional complex, while those of prokaryotes act by binding to the promoter or operator. C) Eukaryotic genes are controlled by multiple proteins rather than by just one or two.

2) Zinc fingers regulate eukaryotic gene expression by binding to DNA strands Zinc finger Linker Zinc finger

 For example, TFIIIA is a transcriptional factor for transcription of the 5S genes by RNA polymerase III. It contains nine Zinc fingers. The Zinc fingers bind to DNA in the major groove to form the initiation complex. C H C H HC H C Zn DNA

 Steroid hormones (e.g. cortisol, testosterone, progesterone) play their roles by forming hormone-receptor complexes, which then bind to specific sites on DNA, and induce or repress the transcription of the particular gene. 3) Regulation of eukaryotic gene expression by hormones

Steroid hormone DNA mRNA proteineffects receptor

 They are eukaryotic transcriptional regulators, which form dimers to bind DNA strands around the major groove.  Leucine zipper proteins mediate the effect of cAMP on transcription by binding to the cAMP response element (CRE). 4) Leucine zipper proteins:

CRE structure is a palindromic 8-bp DNA sequence: 5’-TGACGTCA-3’ 3’-ACTGCAGT-5’ 5’-TGACGTCA-3’ 3’-ACTGCAGT-5’ CRE binding protein

DNA binding of leucine zipper protein Leucine zipper protein DNA helix

For example, cAMP response element binding protein (CREB) has the leucine zipper region: cAMP protein kinase A (PKA) phosphorylation of CREB dimerization of CREB binding of CREB to DNA activation of transcription of the gene.

Signaling through cAMP & PKA to CREB P P Phosphorylation DissociationNuclear translocation Target gene activation Cytoplasm Nucleus    AC cAMP C C C C CBP P PKA CREB

Dimerization of a zipper protein increases its efficacy as a transcriptional activator.  CREB is a target for the Ca 2+ - calmodulin-activated CaM kinase II, protein kinase C, and other kinase, which suggests that it integrates many signals for DNA transcription.

CREB as a target for other signal pathways