Regulation of Gene Expression

Regulation of Gene Expression Part 2: Gene Regulation in Prokaryotes and Eukaryotes

Gene Regulation in Prokaryotes • The lac operon is also subject to positive regulation • What happens if both glucose and lactose are present? • Involves catabolite repressor • Represses genes for catabolism of other sugars if glucose is present • Mediated by cAMP and CAP • CAP: catabolite gene activator protein • also CRP: cAMP receptor protein

Effects of glucose and lactose levels on the expression of the lac operon

Gene Regulation in Prokaryotes • The lac operon is also subject to positive regulation (cont): • Mechanism: • [increase] cAMP and [decreased] glucose: allows CAP binding to DNA • Stimulates transcription of lac operon • Lactose-metabolizing enzymes produced • [increased] glucose depresses [cAMP] • Restricts expression of lac • Supresses use of secondary sugars • Regulon: coordinates regulated operons (CAP and cAMP)

cAMP receptor protein (CRP)

Activation of lac operon by CAP

Gene Regulation in Prokaryotes • The ara operon is (+) and (-) regulated by a single protein • E. coli arabinose operon • One protein exerts both + and – regulation • Binding a signal molecule alters conformation from repressor form • Repressor binds one DNA regulatory site • Activator, without signal molecules, binds to another DNA sequence

Ara operon

Regulation of Ara operon

Gene Regulation in Prokaryotes • The ara operon is (+) and (-) regulated by a single protein • Ara C : regulates its own synthesis • Represses transcription of its gene • Called Autoregulation • Effects of some regulatory DNA sequences can be exerted from a distance via DNA looping

Gene Regulation in Prokaryotes • Transcription Attenuation: regulates genes for a.a. biosynthesis • Genes for amino acid synthesizing enzymes are clustered in operons • Operons expressed when [a.a.] are inadequate • Trp operon of E. coli: • 5 genes for conversion of chorismate to tryptophan • mRNA from trp operon has 3 min half-life • When [trp] increases, trp binds to trp repressor • Causes conformational change in repressor protein that permits binding to the operator • Trp operator overlaps promoter, binding repressor blocks RNA polymerase • A ‘self-regulation’ mechanism

The trp operon

Trp receptor

Gene Regulation in Prokaryotes • Transcription Attenuation: regulates genes for a.a. biosynthesis (cont) • Transcription attenuation is a second trp regulating mechnism • Uses translation termination site • “leader” blocks transcription • Halts transcription before operon; halts RNA –polymerase • Couples transcription to translation via leader peptide • Attenuation of transcripts increases as [trp] increases due to sensitivity of leader peptide to [trp]

Transcriptional attenuation in the trp operon

Gene Regulation in Prokaryotes • Transcription Attenuation: regulates genes for a.a. biosynthesis (cont): • Each a.a. biosynthetic operon uses a similar strategy • Induction of SOS response requires destruction of repressor

Gene Regulation in Prokaryotes • Induction of SOS response requires destruction of repressor • SOS response is induced if chromosome is damaged • An example of coordinated regulation of unlinked genes • Multiple unlinked genes repressed by Lex A protein • All genes induced simultaneously when DNA is damaged • Triggers lysis of repressor • Mediated by Rec A protein • Rec A only binds to single stranded DNA

SOS response in E. coli

Gene Regulation in Prokaryotes • Regulated Developmental Switch: bacteriophage • Objective is assembly of new viruses without cell destruction • Choices are lysis or lysogeny • Lysis: results in destruction of infected cell • Lysogenic cycle • Virus may inhabit host cell for generations • Viral DNA inserts into host, replicates passively • Phage in this state: Prophage • Some trigger induction • Virus enters lytic phase

Gene Regulation in Prokaryotes • Regulated Developmental Switch: bacteriophage lamda (cont): • Bacteriophage lambda has a complex regulatory circuit • Oversees ‘choice’ between pathways • Involves many lambda proteins • Two (N and Q) act as anti-terminators • Modify host RNA polymerase to by-pass termination sites • Other proteins serve as promoters or activators

Gene Regulation in Prokaryotes • Some genes are regulated by genetic recombination • Occurs spontaneously in prokaryotes • Called: Phase Variation • Physically moves promoters relative to genes regulated • Mechanism used by some pathogens as defense against host immune system • E.g.:Salmonella

Salmonellatyphimurium

Regulation of flagellin genes in Salmonella: Phase variation

Gene Regulation in Eukaryotes • Mechanisms resemble those in prokaryotes • Positive regulation more common • Involves selective binding of proteins to control sequences • Effect is modulation of rate of transcription initiation

Gene Regulation in Eukaryotes • Mechanisms resemble those in prokaryotes

Gene Regulation in Eukaryotes • Eukaryotic promoter and enhancer elements mediate expression of cell-specific genes • Cells contain factors that recognize promoters and enhancers in the genes they transcribe • Transcription is accompanied by changes in chromosomal structure • Lampbrush chromosomes • Chromosome “puffs”

Gene Regulation in Eukaryotes • Transcription activator proteins required for binding RNA polymerase • Some have general function • Others are specific: • TATA-binding protein at “TATA-box” • Activators required because eukaryotic RNA-polymerase lacks ability to bind promoters

Gene Regulation in Eukaryotes • Complex regulatory problems seen in development of multicellular animals • Genes function temporally and spatially • Must act in succession • Must be highly coordinated • Most genes expressed early in development • Genes must be turned “off”, “on” in cell to facilitate function • Regulation involves expression and location of genes and their products in developing organisms

Regulation of Gene Expression • End of part two

Regulation of Gene Expression