Regulation of Gene Expression

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

2. 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

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

4. 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)

5. cAMP receptor protein (CRP)

6. Activation of lac operon by CAP

7. 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

8. Ara operon

9. Regulation of Ara operon

10. Regulation of Ara operon

11. Regulation of Ara operon

12. 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

13. 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

14. The trp operon

15. The trp operon

16. Trp receptor

17. 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]

18. Transcriptional attenuation in the trp operon

19. Transcriptional attenuation in the trp operon

20. 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

21. 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

22. SOS response in E. coli

23. 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

24. 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

25. 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

26. Salmonellatyphimurium

27. Regulation of flagellin genes in Salmonella: Phase variation

28. Regulation of flagellin genes in Salmonella: Phase variation

29. 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

30. Gene Regulation in Eukaryotes • Mechanisms resemble those in prokaryotes

31. 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”

32. 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

33. 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

34. Regulation of Gene Expression • End of part two