1. Chapter 16 Gene Regulation in Prokaryotes
Molecular Biology Course
Chapter 16
Gene Regulation
in Prokaryotes

2. outline * Principles of Transcriptional Regulation
There are four major parts in this chapter:
* Principles of Transcriptional Regulation
* Regulation of Transcription Initiation
* Examples of Gene Regulation at Steps after Transcription Initiation
* The Case of Phageλ:Layers of Regulation

3. Principles of Transcriptional Regulation
CHAPTER 16 Gene Regulation in Prokaryotes
Part One
Principles of Transcriptional
Regulation

4. Gene Expression is Controlled by Regulation Proteins: Activators and Repressors
1.Activators, or Positive regulators, increase transcription of the regulated gene;
Repressors, or negative regulators, decrease or eliminate that transcription.
2. Many Promoters Are Regulated by Activation that Help RNA Polymerase Bind DNA and by Repressors that Block that Binding.

5. a. Absence of Regulatory Proteins (operator) b. To Repress Expression
Fig 16-1
a. Absence of
Regulatory Proteins
(operator)
b. To Repress
Expression
c. To Activate
Expression

6. 3.Some Activators Work by Allostery and Regulate Steps after RNA Polymerase Binding:
In some cases, RNA Polymerase binds efficiently unaided and forms a stable closed complex, which does not spontaneously undergo transition to the open complex.
Activator that stimulate this kind of promoter wrk by triggering a conformational change in either RNA Polymerase or DNA.
That is, they interact with the stable closed complex and induce a conformational change that causes transition to the open complex.

7. This mechanism is an example of allostery.
Fig 16-2

8. Action at a Distance and DNA Looping.
Some proteins interact with each other even when bound to sites well separated on the DNA
Fig 16-3

9. DNA-bending protein can facilitate interaction between DNA-binding proteins at a distance
Fig 16-4
In this example, we also call the DNA-binding protein “architectural” proteins.

10. Cooperative Binding and Allostery have Many Roles in Gene Regulation
Cooperative binding: the activator interacts simultaneously with DNA and polymerase and so recruits the enzyme to the promoter.
Two roles: IN RESPONSE TO SMALL CHANGES SENSITIVELY and SERVE TO INTEGRATE SIGNALS
Allostery is not only a mechanism of gene activation , it is also often the way that regulators are controlled by their specific signals.

11. Antitermination and Beyond: Not All of Gene Regulation Targets Transcription Initiation
The bulk of gene regulation takes place at the initiation of transcription in both eukaryotes and bacteria.
But regulation is certainly not restricted to that step in either class of organism. In this chapter we will see examples, in bacteria, of gene regulation that involve transcriptional elongation, RNA processing, and translation of the mRNA into protein.

12. Regulation of Transcription Initiation: Examples From Bacteria
CHAPTER 16 Gene Regulation in Prokaryotes
Part Two
Regulation of Transcription Initiation: Examples From Bacteria

13. EXAMPLE ONE------LAC OPERON
The lactose (Lac) Operon (乳糖操纵子)
Fig 16-5

14. Lactose operon: a regulatory gene and 3 stuctural genes, and 2 control elements
Structural Genes
Cis-acting elements
DNA
lacI
lacZ
lacY
lacA
PlacI
Olac
Plac
m-RNA
Protein
β -Galactosidase
Transacetylase
Permease
The LAC operon

15. lacZ
codes for β-galactosidase (半乳糖苷酶) for lactose hydrolysis
lacY
encodes a cell membrane protein called lactose permease (半乳糖苷渗透酶) to transport Lactose across the cell wall
lacA
encodes a thiogalactoside transacetylase (硫代半乳糖苷转乙酰酶)to get rid of the toxic thiogalacosides
The LAC operon

16. An Activator and a Repressor Together Control the lac Genes
The activator is called CAP( Catabolite Activator Protein ) .CAP can bind DNA and activate the lac genes only in the absence of glucose.
The lac repressor can bind DNA and repress transcrition only in the absence of lactose.
Both CAP and lac repressor are DNA-binding proteins and each binds to a specific site n DNA at or near the lac promoter.

17. The LAC operon
Fig 16-6

18. CAP and lac repressor have opposing effects on RNA polymerase binding to the lac promoter
1.Lac operator the site bound by lac repressor
This 21 bp sequence is twofold summetric and is recognized by two subunits of lac repressor, one binding to each half-site.
Fig 16-7

19. lac operator overlaps promoter, and so repressor bound to the operator physically prevents RNA polymerase from binding to the promoter.
Fig 16-8

20. 2. CAP
CAP binds as a dimer to a site similar in length to the lac operator, but different in sequence and location.
CAP has separate activating and DNA-binding surfaces.
Fig 16-9
At the promoter,where there is no UP-element, a CTD binds to CAP and adjacent DNA instead.

21. CAP and lac repressor bind DNA using a common structural motif
1.The Same
A. The protein binds as a homodimer to a site that is an inverted repeat or near repeat.
B.Both CAP and lac repressor bind DNA using a helix-turn-helix motif.

22. One of the two аhelices in helix-turn-helix domain is the recognition helix that can fits into the major groove of the DNA.
Fig 16-11

23. The second helix of the helix-turn-helix domain sits across the major groove an makes contact with the DNA backbone , ensuring proper presentation of the recognition helix, and at the same time adding binding energy to the overall protein-DNA interaction.

24. DNA binding by a helix-turn-helix motif
Fig Hydrogen Bonds between l repressor and the major groove of the operator
The LAC operon

25. 2. The Difference
Lac repressor binds as a tetramer, with each operator is contacted by a repressor dimer.
Fig 16-13

26. In some cases, other regions of the protein, outside the helix-turn-helix domain, also interact with the DNA.
In many cases, binding of the protein does not alter the structure of the DNA .In some cases, however, various distortions are seen in the protein-DNA complex.

27. The activity of Lac repressor and CAP are controlled allosterically by their signals
Binding of the corresponding signals alter the structure of these two regulatory proteins

28. Very low level of lac mRNA
Response to lactose i p o z y a
Very low level of lac mRNA
Absence of lactose
Active
Lack of inducer: the lac repressor block all but a very low level of trans-cription of lacZYA .
Lactose is present, the low basal level of permease allows its uptake, andβ-galactosidase catalyzes the conversion of some lactose to allolactose.
Allolactose acts as an inducer, binding to the lac repressor and inactivate it.
Presence of lactose i p o z y a
Inactive
Permease
b-Galactosidase
Transacetylase

29. Response to glucose
The LAC operon

30. Combinatorial Control: CAP controls other genes as well
The lac genes provide an example of signal integration: their expression is controlled by two signals, each of which is communicated to the genes via a single regulator—the lac repressor and CAP, respectively.

31. A regulator (CAP) works together with different repressor at different genes, this is an example of Combinatorial Control. In fact, CAP acts at more than 100 genes in E.coli, working with an array of partners.

32. Combinatorial control is a characteristic feature of gene regulation
Combinatorial control is a characteristic feature of gene regulation. More complex organisms—higher eukaryotes in particular---tend to have more signal integration.

33. EXAMPLE TWO---- ALTERNATIVE σFACTORS
Alternative s factor direct RNA polymerase to alternative site of promoters

34. Recall from Chapter 12 that it is the σsubunit of RNA polymerase that recognizes the promoter suquences.

35. Promoter recognition Different σfactors binding to the same RNA Pol
Confer each of them a new promoter specificity

36. Many bacteria produce alternative sets of σfactors to meet the regulation requirements of transcription under normal and extreme growth condition.

37. Heat shock--- 32
When E.coliis subject to heat shock, the amount of this new σfactor increases in the cell, it displaces σ70 from a proportion of RNA polymerases ,and directs those enzymes to transcribe genes whose products protect the cell from the effects of heat shock. The level of 32 is increased by two mechanisms: first, its translation is stimulated---that is,its mRNA is translated with greater efficiency after heat shock than it was before; and second, the protein is transiently stabilized.

38. Bacteriophages Many bacteriophages synthesize
their own σfactors to endow the
host RNA polymerase with a
different promoter specificity and
hence to selectively express their
own phage genes .

39. Fig 16-14
B. subtilis SPO1 phage expresses a cascade of σfactors which allow a defined sequence of expression of different phage genes .

40. Normal bacterial holoenzyme
Express early genes
Encode σ28
Express middle genes (gene 34 and 33 )
Encodeσfactor for transcription of late genes

41. EXAMPLE THREE---NtrC and MerR
NtrC and Mert: Transcriptional Activators that Work by Allostery Rather than by Recruitment
NtrC controls expression of genes involved in nitrogen metabolism, such as the glnA gene. At the glnA gene, Ntrc induces a conformational change in the RNA Polymerase, triggering tansition to the open complex.
MerR controls a gene called merT. Like NtrC, MerR induces a conformational change in the inactive RNA polymerase-promoter complex, and this change can trigger open complex formation.

42. Fig 16-15 activation by NtrC
NtrC Has ATPase Activity and Works from DNA Sites Far from the Gene
NtrC has separate activating and DNA-binding domains, and binds DNA only when the nitrogen levels are low.
Fig activation by NtrC

43. The major process: Low nitrogen levels
Trigger polymerase to initiate transcription
NtrB phosphorylates NtrC
ATP hydrolysis and conformation change in polymerase
NtrC’s DNA-binding domain revealed
NtrC binds four sites located some 150 base pairs upstream of the promoter
NtrC interacts with 54

44. MerR activates transcription by twisting promoter DNA
MerR controls a gene called merT, which encodes an enzyme that makes cells resistant to the toxic effects of mercury
In the presence of mercury, MerR binds to a sequence between –10 and –35 regions of the merT promoter and activates merT expression.

45. The merT promoter is unusual
The merT promoter is unusual. The distance between the -10 and -35 elements is 19bp instead of the 15 to 17 bp typically found in an eddicient 70 promoter. So, these two elements recognized by  are neither optimally seperated nor aligned.
Fig a

46. The binding of MerR locks the promoter in the unpropitious conformation in the absence of Hg2+ .
Fig b

47. When Hg2+ is present, MerR binds Hg2+ and undergo conformational change, which twists the promoter to restore it to the structure close to a strong 70 promoter
Just like this :
Fig c

48. In this new configuration , RNA polymerase can efficiently initiate transcription.

49. Some repressors hold RNA polymerase at the promoter rather than excluding it
Repressors work in different ways :
By binding to a site overlapping the promoter, it blocks RNA polymerase binding. (lac repressor)
The protein holds the promoter in a conformation incompatible with tanscription initiation.(the MerR case)
Blocking the transition from the closed to open complex. Repressors bind to sites beside a promoter, interact with polymerase bound at that promoter and inhibit initiation. (E.coli Gal repressor)

50. EXAMPLE FOUR----araBAD OPERON
AraC and control of the araBAD operon by antiactivation
The promoter of the araBAD operon from E. coli is activated in the presence of arabinose (阿拉伯糖) and the absence of glucose and directs expression of genes encoding enzymes required for arabinose metabolism.

51. Different from the Lac operon, two activators AraC and CAP work together to activate the araBAD operon expression
Fig 16-18

52. The magnitude of induction of the araBAD promoter by arabinose is very large , and for this reason the promoter is often used in expression vectors.
Expression vectors are DNA constructs in which efficient synthesis of any protein can be ensured by fusing a gene to a strong promoter .

53. Transcription Initiation
CHAPTER 16 Gene Regulation in Prokaryotes
Part Three
Examples of
Gene Regulation
at Steps After
Transcription Initiation

54. Amino acid biosynthetic operons are controlled by premature transcription termination
the tryptophan operon:
Fig 16-19

55. The trp operon encodes five structural genes required for tryptophan synthesis.
These genes are regulated to efficiently express only when tryptophan is limiting.
There are two layers of regulation involved: (1) transcription repression by the Trp repressor (initiation); (2) attenuation

56. ---the first layer of regulation
The Trp repressor
---the first layer of regulation
When tryptophan is present, it binds the Trp repressor and induces a conformational change in that protein, enabling it to bind the trp operator and prevent transcription.
When the tryptophan concentration is low, the Trp repressor is free of its corepressor and vacates its operator , allowing the synthesis of trp mRNA to commence from the adjacent promoter.
The ligand that controls the activity of the trp repressor acts not as an inducer but as a corepressor.

57. ---the second layer of regulation
Attenuation
---the second layer of regulation
The key to understanding attenuation came from examining the suquence of the 5’ end of trp operon mRNA.
161 nucleotides of RNA are made from tryptophan promoter before RNA polymerase encounters the first codon of trpE.
Near the end of this leader sequence ,and before trpE , is a transcription terminator, composed of a characteristic hairpin loop in the RNA.

58. The hairpin loop is followed by 8 uridine residues
The hairpin loop is followed by 8 uridine residues. At this so-called attenuator , transcription usually stops,yielding a leader RNA 139 nucleotides long.
Fig 16-20

59. Thre features of the leader sequence:
There is a second hairpin (besides the terminator hairpin) that can form between regions 1 and 2 of the leader sequence.
region 2 also is complementary to region 3; thus , yet another hairpin consisting of regions 2 and 3 can form and when it does prevent the terminator hairpin (3,4) from forming.
The leader RNA contains an open-reading frame encoding a short leader peptide of 14 amino acids, and this open-reading frame is preceded by a strong ribosome binding site.

60. The sequence encoding the leader peptide has a striking feature : two tyrptophan codons in a row.
The fuction of these codons is to stop a ribosome attempting to translate the leader peotide.
Above all , how transcription termination at the trp operon attenuator is controlled by the availability of tryptophan ?

61. Fig 16-21

62. The Importance of Attenuation
Use of both repression and attenuation allows a fine tuning of the level of the intracellular tryptophan.
Attenuation alone can provide robust regulation: other amino acids operons like his and leu have no repressors and rely entirely on attenuation for their regulation.
Provides an example of regulation without the use of a regulatory protein, but using RNA structure instead.
A typical negative feed-back regulation.

63. Ribosomal Protein Are Translational Repressors of their Own Synthesis
The ribosome protein synthesis has challenges:
Each ribosome contains some 50 distinct proteins that must be made at the same rate
The rate of the ribosome protein synthesis is tightly closed to the cell’s growth rate

64. How to overcome the challenges:
Control of ribosome protein genes is simplified by their organization to several operons , each containing genes for up to 11 ribisomal proteins.
Some nonribosomal proteins whose synthesis is also linked to growth rate are contained in these operons, including those for RNAP subunits a, b and b’.
The primary control is at the level of translation, not transcription.

65. How to overcome the challenges:
For each operon,one ribosomal protein binds the messenger near the translation initiation sequence of the first genes in the operon, preventing ribosomes from binding and initiating translation.
Repressing translation of the first gene also prevents expression of some or all of the rest.
The strategy is very sensitive. A few unused molecule of protein L4, for example, will shut down synthesis of that protein and other proteins in this operon.

66. Ribosomal protein operons
The protein that acts as a translational repressor of the other proteins is shaded red.
Fig 16-22

67. The mechanism of one ribosomal protein also functions as a regulator of its own translation: the protein binds to the similar sites on the ribosomal RNA and to the regulated mRNA
Fig 16-23

68. The Case of Phage λ: Layers of Regulation
CHAPTER 16 Gene Regulation in Prokaryotes
Part Four
The Case of Phage λ: Layers of Regulation

69. Bacteriophage λis a virus that infects E. coli
Bacteriophage λis a virus that infects E.coli. Upon infection, the phage can propagate in either of two ways: lytically or lysogenically.
A lysogen is extremely stable under normal circumstances ,but the phage dormant within it---the prophage---can efficiently switch to lytic growth if the cell is exposed to agents that damaged DNA . This switch from lysogenic to lytic growth is called lysogenic induction.

70. Lytic cycle
and
Establishment of lysogeny

71. Alternative Patterns of Genes Expression Control Lytic and Lysogenic Growth

72. Regulatory Proteins and Their Binding Sites
The cI gene encodes λrepressor, a protein of two domains joined by a flexible linker egion. λrepressor can both activate and repress trandcription.
Cro only represses transcription.

73. Repressor and Cro Bind in Different Patterns to Control Lytic and Lysogenic Growth
Repressor bound to OR1and OR2 turns off transcription from PR . And Repressor bound at OR2 contacts RNA polymerase at PRM, activating expression of the cI gene. OR3 lies with PRM; Cro bound there represses transcription of cI.

75. Another Activator, λcII, Controls the Decision between Lytic and Lysogenic Growth upon Infection of a new Host
cII is a transcriptional activator. It binds to a site upstream of a promoter called PRE and stimulates transcription of the cI gene from that promoter.

77. Transcriptional Antitermination in λ Development
The transcripts controlled by λN and Q proteins are initiated perfectly well in the absence of those regulators. But the transcripts terminate a few hundred to a thousand nucleotides downstream of the promoter unless RNA polymerase has been modified by the regulator; λN and Q protein are therefore called antiterminators.

80. Key points of the chapter
Principles of gene regulation. (1) The targeted gene expression events; (2) the mechanisms: by recruitment/exclusion or allostery
Regulation of transcription initiation in bacteria: the lac operon, alternative s factors, NtrC, MerR, Gal rep, araBAD operon
Examples of gene regulation after transcription initiation: the trp operon, riboswitch, regulation of the synthesis of ribosomal proteins