1. Control of Gene Expression in Prokaryotes
Benjamin A. Pierce
GENETICS
A Conceptual Approach
FIFTH EDITION
CHAPTER 16
Control of Gene Expression in Prokaryotes
© 2014 W. H. Freeman and Company 1

2. The expression of genes in bacteria is often regulated through operons, groups of genes that are transcribed as a unit. Shown here is Escherichia coli, a common bacterium found in the intestinal tracts of mammals.

3. 16.1 The Regulation of Gene Expression is Critical for All Organisms
Genes and Regulatory Elements
Levels of Gene Regulation
DNA-Binding Proteins

4. Genes and Regulatory Elements
Structural genes: encoding proteins
Regulatory genes: encoding products that interact with other sequences and affect the transcription and translation of these sequences
Regulatory elements: DNA sequences that are not transcribed but play a role in regulating other nucleotide sequences

5. Genes and Regulatory Elements
Constitutive expression: continuously expressed under normal cellular conditions
Positive control: stimulate gene expression
Negative control: inhibit gene expression

6. Levels of Gene Regulation
Figure 16.1 Gene expression can be controlled at multiple levels.

7. DNA-Binding Proteins
Domains: ~ amino acids, responsible for binding to DNA, forming hydrogen bonds with DNA
Motif: within the binding domain, a simple structure that fits into the major groove of the DNA
Distinctive types of DNA-binding proteins based on the motif

8. Figure DNA-binding proteins can be grouped into several types on the basis of their structures, or motifs.

10. Concept Check 1
How do amino acids in DNA-binding proteins interact with DNA?
By forming covalent bonds with DNA base
By forming hydrogen bonds with DNA base
By forming covalent bonds with sugars

11. Concept Check 1
How do amino acids in DNA-binding proteins interact with DNA?
By forming covalent bonds with DNA base
By forming hydrogen bonds with DNA base
By forming covalent bonds with sugars

12. 16.2 Operons Control Transcription in Bacterial Cells
Operon Structure
Negative and Positive Control: Inducible and Repressible Operons
The lac Operon of E. coli
lac Mutations
Positive Control and Catabolite Repression
The trp Operon of E. coli

13. Operon Structure
Operon: promoter + additional sequences that control transcription (operator) + structure genes
Regulator gene: DNA sequence encoding products that affect the operon function, but are not part of the operon

14. Figure An operon is a single transcriptional unit that includes a series of structural genes, a promoter, and an operator.

15. Concept Check 2
What is the difference between a structural gene and a regulator gene?
Structural genes are transcribed into mRNA, but regulator genes are not.
Structural genes have complex structures; regulator genes have simple structure.
Structural genes encode proteins that function in the structure of the cell; regulator genes carry out metabolic reactions.
Structural genes encode proteins; regulator genes control the transcription of structural genes.

16. Concept Check 2
What is the difference between a structural gene and a regulator gene?
Structural genes are transcribed into mRNA, but regulator genes are not.
Structural genes have complex structures; regulator genes have simple structure.
Structural genes encode proteins that function in the structure of the cell; regulator genes carry out metabolic reactions.
Structural genes encode proteins; regulator genes control the transcription of structural genes.

17. Negative and Positive Control: Inducible and Repressible Operons
Inducible operons: Transcription is usually off and needs to be turned on.
Repressible operons: Transcription is normally on and needs to be turned off.

18. Negative and Positive Control: Inducible and Repressible Operons
Negative inducible operons: The control at the operator site is negative. Molecule binding is to the operator, inhibiting transcription. Such operons are usually off and need to be turned on, so the transcription is inducible.
Inducer: small molecule that turns on the transcription.

19. Figure 16.4 Some operons are inducible.

20. Negative and Positive Control: Inducible and Repressible Operons
Negative repressible operons: The control at the operator site is negative. But such transcription is usually on and needs to be turned off, so the transcription is repressible.
Corepressor: a small molecule that binds to the repressor and makes it capable of binding to the operator to turn off transcription.

21. Figure 16.5 Some operons are repressible.

22. Negative and Positive Control: Inducible and Repressible Operons
Positive inducible operon
Positive repressible operon

23. Figure A summary of the characteristics of positive and negative control in inducible and repressible operons.

24. Concept Check 3
In a negative repressible operon, the regulator protein is synthesized as
an active activator
an inactive activator
an active repressor
an inactive repressor

25. Concept Check 3
In a negative repressible operon, the regulator protein is synthesized as
an active activator
an inactive activator
an active repressor
an inactive repressor

26. A negative inducible operon Lactose metabolism
The lac Operon of E. coli
A negative inducible operon
Lactose metabolism
Regulation of the lac operon
Inducer: allolactose
lacI: repressor encoding gene
lacP: operon promoter
lacO: operon operator

27. The lac Operon of E. coli Structural genes
lacZ: encoding β-galactosidases
lacY: encoding permease
lacA: encoding transacetylase
The repression of the lac operon never completely shuts down transcription.

28. Figure Lactose, a major carbohydrate found in milk, consists of two six-carbon sugars linked together

29. Figure 16.8 The lac operon regulates lactose metabolism.

30. Figure In the lac operon, the operator overlaps the promoter and the 5′ end of the first structural gene.

31. In the presence of allolactose, the lac repressor .
Concept Check 4
In the presence of allolactose, the lac repressor
binds to the operator
binds to the promoter
cannot bind to the operator
binds to the regulator gene

32. In the presence of allolactose, the lac repressor .
Concept Check 4
In the presence of allolactose, the lac repressor
binds to the operator
binds to the promoter
cannot bind to the operator
binds to the regulator gene

33. lac Mutations
Partial diploid: full bacterial chromosome + an extra piece of DNA on F plasmid
Structural gene mutations: affect the structure of the enzymes, but not the regulations of their synthesis
lacZ+lacY−/lacZ−lacY+ produce fully functional β-galactosidase and permease.

34. lac Mutations
Regulator gene mutations: lacI− leads to constitutive transcription of three structure genes.
lacI+ is dominant over lacI− and is trans acting. A single copy of lacI+ brings about normal regulation of lac operon.
lacI+lacZ−/lacI−lacZ+ produce fully functional β-galactosidase.

35. Figure The partial diploid lacI + lacZ −/lacI − lacZ + produces β-galactosidase only in the presence of lactose because the lacI gene is trans dominant.

36. Figure The partial diploid lacI s lacZ +/lacI + lacZ + fails to produce β-galactosidase in the presence and absence of lactose because the lacIs gene encodes a superrepressor.

37. lac Mutations Operator mutations: lacOc: C = constitutive
lacOc is dominant over lacO+, which is cis acting.
lacI+lacO+Z−/lacI+lacOclacZ+ produce fully functional β-galactosidase constitutively.

38. Figure 16. 12 Mutations in lacO are constitutive and cis acting
Figure Mutations in lacO are constitutive and cis acting. (a) The partial diploid lacI + lacO + lacZ −/ lacI + lacOc lacZ+ is constitutive, producing β-galactosidase in the presence and absence of lactose. (b) The partial diploid lacI + lacO + lacZ+/lacI + lacOc lacZ− is inducible (produces β-galactosidase only when lactose is present), demonstrating that the lacO gene is cis acting.

39. lac Mutations Promoter mutations lacP−: cis acting
lacI+lacP−lacZ+/lacI+lacP+lacZ− fails to produce functional β-galactosidase.

40. Characteristics of lac operon mutations.

41. Positive Control and Catabolite Repression
Catabolite repression: using glucose when available, and repressing the metabolite of other sugars.
This is a positive control mechanism. The positive effect is activated by catabolite activator protein (CAP). cAMP is binded to CAP, together CAP–cAMP complex binds to a site slightly upstream from the lac gene promoter.

42. Positive Control and Catabolite Repression
cAMP: adenosine-3′, 5′-cyclic monophosphate
The concentration of cAMP is inversely proportional to the level of available glucose.

43. Figure The catabolite activator protein (CAP) binds to the promoter of the lac operon and stimulates transcription. CAP must complex with adenosine-3′, 5′-cyclic monophosphate (cAMP) before binding to the promoter of the lac operon. The binding of cAMP–CAP to the promoter activates transcription by facilitating the binding of RNA polymerase. Levels of cAMP are inversely related to glucose: low glucose stimulates high cAMP; high glucose stimulates low cAMP.

44. Figure The binding of the cAMP–CAP complex to DNA produces a sharp bend in DNA that activates transcription.

45. What is the effect of high levels of glucose on the lac operon?
Concept Check 5
What is the effect of high levels of glucose on the lac operon?
Transcription is stimulated.
Little transcription takes place.
Transcription is not affected.
Transcription may be stimulated or inhibited, depending on the levels of lactose.

46. What is the effect of high levels of glucose on the lac operon?
Concept Check 5
What is the effect of high levels of glucose on the lac operon?
Transcription is stimulated.
Little transcription takes place.
Transcription is not affected.
Transcription may be stimulated or inhibited, depending on the levels of lactose.

47. The trp Operon of E. coli A negative repressible operon
Five structural genes
trpE, trpD, trpC, trpB, and trpA—five enzymes together convert chorismate to typtophane.

48. Figure 16.15 The trp operon controls the biosynthesis of the amino acid tryptophan in E. coli.

49. Concept Check 6
In the trp operon, what happens to the trp repressor in the absence of tryptophan?
It binds to the operator and represses transcription.
It cannot bind to the operator and transcription takes place.
It binds to the regulator gene and represses transcription.
It cannot bind to the regulator gene and transcription takes place.

50. Concept Check 6
In the trp operon, what happens to the trp repressor in the absence of tryptophan?
It binds to the operator and represses transcription.
It cannot bind to the operator and transcription takes place.
It binds to the regulator gene and represses transcription.
It cannot bind to the regulator gene and transcription takes place.

51. 16.3 Some Operons Regulate Transcription Through Attenuation, the Premature Termination of Transcription
Attenuation: affects the continuation of transcription, not its initiation. This action terminates the transcription before it reaches the structural genes.
Attenuator
Antiterminator

52. Attenuation in the trp Operon of E. coli
Four regions of the long 5′ UTR (leader) region of trpE mRNA
When tryptophan is high, region 1 binds to region 2, which leads to the binding of region 3 and region 4, terminating transcription prematurely.

53. Figure Two different secondary structures can be formed by the 5′ UTR of the mRNA transcript of the trp operon.

54. Attenuation in the trp Operon of E. coli
Four regions of the long 5′ UTR (leader) region of trpE mRNA
When tryptophan is low, region 2 binds to region 3, which prevents the binding of region 3 and region 4, and transcription continues.

55. Figure Whether the premature termination of transcription (attenuation) takes place in the trp operon depends on the cellular level of tryptophan.

56. Events in the process of attenuation.

57. 16.4 RNA Molecules Control the Expression of Some Bacterial Genes
Antisense RNA: complementary to targeted partial sequence of mRNA
Riboswitches: molecules influence the formation of secondary structures in mRNA
Ribozymes: mRNA molecules with catalytic activity

58. Figure 16.18 Antisense RNA can regulate translation.

59. Figure 16.19 Riboswitches are RNA sequences in mRNA that affect gene expression.