Regulation of Gene Expression

1. 11 Regulation of Gene Expression

2. Chapter 11 Regulation of Gene Expression • Key Concepts • 11.1 Many Prokaryotic Genes Are Regulated in Operons • 11.2 Eukaryotic Genes Are Regulated by Transcription Factors • 11.3 Gene Expression Can Be Regulated via Epigenetic Changes to Chromatin • 11.4 Eukaryotic Gene Expression Can Be Regulated after Transcription

3. Chapter 11 Opening Question How does CREB regulate the expression of many genes?

4. Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons • Gene expression can be precisely regulated at many different points: • Before or during transcription • Before or during translation • After translation

5. Figure 11.1 Potential Points for the Regulation of Gene Expression

6. Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons • Gene expression begins at the promoter. • Regulatory proteins called transcription factors control gene activity: • Repressors prevent transcription (negative regulation) • Activators stimulate transcription (positive regulation)

7. Figure 11.2 Positive and Negative Regulation

8. Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons • Prokaryotes conserve energy and resources by making certain proteins only when they are needed. • They can rapidly change expression levels as environmental conditions change. • Example: lactose catabolism in E. coli

9. Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons • Uptake and metabolism of lactose involves three proteins: • β-galactoside permease—moves lactose into the cell • β-galactosidase—hydrolyses lactose • β-galactoside transacetylase—transfers acetyl groups to β-galactosides; role is unclear • If E. coli is grown with glucose but no lactose, these enzymes are very low (basal level).

10. Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons • If cells are transferred to lactose medium, they begin making all 3 enzymes within 10 minutes.

11. Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons After lactose is added, the mRNA level increases before β-galactosidase begins to rise:

12. Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons • If lactose is removed, the mRNA level goes down. • Response of the bacteria to lactose is at the level of transcription. • Compounds that stimulate transcription of specific genes are called inducers, the genes are inducible genes. • Genes that are expressed most the time at a constant rate are called constitutive genes.

13. Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons • The three genes for lactose enzymes form an operon: they are adjacent on the chromosome, share a promoter, and are transcribed together. • The lac operon is very efficient but activity can be reduced when it is not needed—an example of transcriptional regulation.

14. Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons • The operon includes an operator—a short stretch of DNA near the promoter that controls transcription. • Repressor proteins bind at the operator. • Inducible operons are turned off unless needed. • Repressible operons are turned on unless not needed.

15. Figure 11.3 The lac Operon of E. coli

16. Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons • The lac operon is inducible: the repressor prevents transcription until a β-galactoside predominates. • A repressor protein is normally bound to the operator, blocking transcription. • In the presence of lactose, the repressor detaches and allows RNA polymerase to initiate transcription.

17. Figure 11.4 The lac Operon: An Inducible System (Part 1)

18. Figure 11.4 The lac Operon: An Inducible System (Part 2)

19. Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons • The repressor protein gene is constitutive (one that is always active), so the repressor is always present. • It binds to the operator, but also has an allosteric binding site for the inducer (allolactose). • When the inducer binds, the repressor changes shape and can no longer bind to the operator.

20. Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons • The lac repressor gene (lac i) is upstream of the lac operon. • It is a regulatory gene—it encodes a regulatory protein (transcription factor). • Structural genes encode proteins that are not directly involved in gene regulation.

21. Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons • A repressible operon is switched off when its repressor is bound to its operator. • The repressor only binds in the presence of a corepressor. • The corepressor causes the repressor to change shape and bind to the operator to inhibit transcription.

22. Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons • The trp operon for tryptophan synthesis is repressible. • When tryptophan is present in adequate quantities, the cell can stop making enzymes for its synthesis. • Tryptophan itself functions is the corepressor: it binds to the repressor, causing the repressor to bind to the trp operator to prevent transcription.

23. Figure 11.5 The trp Operon: A Repressible System (Part 1)

24. Figure 11.5 The trp Operon: A Repressible System (Part 2)

25. Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons • Inducible system—a metabolic substrate (inducer) interacts with a regulatory protein (repressor); the repressor cannot bind and transcription proceeds. • Generally controls catabolic pathways. • Repressible system—a metabolic product (co-repressor) binds to a regulatory protein, which then binds to the operator and blockstranscription. • Generally controls anabolic pathways.

26. Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons • Transcription in prokaryotes can also be regulated by activator proteins that bind to DNA sequences at or near the promoter and promote transcription. • Activators can regulate both inducible and repressible systems. • Many genes and operons are controlled by more than one regulatory mechanism.

27. Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons • Two systems for regulating metabolic pathways: • Allosteric regulation of enzyme activity (feedback inhibition) • Regulation of transcription—slower, but results in greater savings of energy and resources

28. Figure 11.6 Systems to Regulate a Metabolic Pathway

29. Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons • Sigma factors can bind to RNA polymerase and direct it to specific promoters. • Global gene regulation: genes that encode proteins with related functions may be at different locations but have the same promoter sequence—thus they can be expressed at the same time. • RNA polymerase is directed to the promoter in each case by a specific sigma factor.

30. Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons • A virus injects its genetic material into a host cell, often turning it into a virus factory:

31. Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons • Viruses are not cells and are dependent on living cells to reproduce. • Viral genomes may be double- or single- stranded DNA or RNA. • Lytic life cycle: the host cell immediately starts producing new viral particles (virions), which are released as the cell breaks open, or lyses

32. Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons • Lysogenic life cycle: viral genome is incorporated into host cell genome and is replicated along with host genome • The virus may survive in this way for many host cell generations. • An environmental signal can cause the host cell to start producing virions, and the viral reproductive cycle enters the lytic phase.

33. Concept 11.1 Many Prokaryotic Genes Are Regulated in Operons • The lytic cycle has two stages: • Early—viral genes adjacent to a promoter that binds host RNA polymerase are transcribed. • Early genes encode proteins that shut down expression of host genes, stimulate viral genome replication, and activate transcription of viral late genes. • Late—viral late genes encode viral capsid proteins and enzymes that lyse the host cell.

34. Figure 11.7 A Gene Regulation Strategy for Viral Reproduction

35. Concept 11.2 Eukaryotic Genes Are Regulated by Transcription Factors • Eukaryotic cells must also regulate expression of their genes. Some are constitutive; others are inducible. • This is especially important in multicellular organisms. • There are significant differences between prokaryotes and eukaryotes, which generally reflect the greater complexity of eukaryotes.

36. Table 11.1

37. Concept 11.2 Eukaryotic Genes Are Regulated by Transcription Factors and DNA Changes • Eukaryotic promoters are DNA regions where RNA polymerase binds and initiates transcription. • A common core sequence is the TATA box (rich in A–T base pairs). • General transcription factors bind to the core promoter, then RNA polymerase II binds and initiates transcription.

38. Figure 11.8 The Initiation of Transcription in Eukaryotes

39. Concept 11.2 Eukaryotic Genes Are Regulated by Transcription Factors • Other promoter sequences are specific to a few genes and are recognized by specific transcription factors.

40. Concept 11.2 Eukaryotic Genes Are Regulated by Transcription Factors • DNA sequences that bind activators are enhancers, those that bind repressors are silencers. • The combination of factors present determines whether transcription is initiated.

41. Concept 11.2 Eukaryotic Genes Are Regulated by Transcription Factors • Transcription factors recognize particular nucleotide sequences. • Example: NFATs (nuclear factors of activated T cells) control genes in the immune system. • NFAT proteins bind to a recognition sequence by hydrogen bonding and hydrophobic interactions. • There is an induced fit between the NFAT and the DNA, and the protein undergoes a conformational change.

42. Figure 11.9 A Transcription Factor Protein Binds to DNA

43. Concept 11.2 Eukaryotic Genes Are Regulated by Transcription Factors • In multicellular organisms, all differentiated cells contain the entire genome; their specific characteristics arise from differential gene expression. • Figuring out how to get undifferentiated cells, such as fibroblasts, to differentiate into specialized cells, such as neurons, may prove to be effective in treating many diseases, such as Alzheimer’s, which involves degeneration of neurons.

44. Figure 11.10 Expression of Specific Transcription Factors Turns Fibroblasts into Neurons (Part 1)

45. Figure 11.10 Expression of Specific Transcription Factors Turns Fibroblasts into Neurons (Part 2)

46. Figure 11.10 Expression of Specific Transcription Factors Turns Fibroblasts into Neurons (Part 3)

47. Concept 11.2 Eukaryotic Genes Are Regulated by Transcription Factors • Coordination of gene expression: • Even if they are far apart, genes can share regulatory sequences that bind the same transcription factors. • Example: plant response to drought—the scattered stress response genes all have a regulatory sequence called the dehydration response element. • The resulting proteins help the plant conserve water and protect against freezing or excess salt.

48. Figure 11.11 Coordinating Gene Expression

49. Concept 11.2 Eukaryotic Genes Are Regulated by Transcription Factors • Human immunodeficiency virus (HIV) has a complex life cycle. • It infects only cells in the immune system that have the surface receptor CD4. • The virion is enclosed in a membrane from the previous host cell, which fuses with the new host cell’s membrane.

50. Figure 11.12 The Reproductive Cycle of HIV