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Chapter 16 Gene Regulation in Prokaryotes. Outline Part 1 Principles of Transcriptional Reg ulation Part 2 Regulation of Transcription Initiation Part.

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Presentation on theme: "Chapter 16 Gene Regulation in Prokaryotes. Outline Part 1 Principles of Transcriptional Reg ulation Part 2 Regulation of Transcription Initiation Part."— Presentation transcript:

1 Chapter 16 Gene Regulation in Prokaryotes

2 Outline Part 1 Principles of Transcriptional Reg ulation Part 2 Regulation of Transcription Initiation Part 3 Examples of Gene Regulation after Transc ription Initiation

3 Part 1 Principles of Tr anscriptional Regulati on

4 1-1 Gene Expression is Controlled by Regulatory Proteins Genes are very often controlled by extracellular singals.The singals are communicatedto genes by regula teory proteins : Postive regulators or activators Increase the transcription Negative regulators or repressors Decrease or eliminates the transcr iption

5 1-2 Many promoters are regulated by a ctivators that hel p RNAP bind DNA an d by repressors th at block the bindi ng

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

7 1-3 Targeting transition to the open complex: Some Activators Work by Allo stery and Regulate Steps after RNA Po lymerase Binding Fig 16-2

8 1-4 Action at a Distance and DNA Looping. Some proteins interact with each other even when bound to sites well separated on the DNA

9 Fig 16-4 DNA-binding protein can fac ilitate interaction between DNA-bind ing proteins at a distance

10 1-5 Cooperative Binding and Alloster y have Many Roles in Gene Regulatio n Group of regulators often bind DNA coop eratively: (1) produce sensitive switch es to rapidly turn on a gene expression, (2) integrate signals (some genes are a ctivated when multiple signals are pres ent) Cooperative binding: the activator interacts simultaneously with DNA and polymerase and so recruits the enzyme to the promoter

11 Part 2: Regulati on of Transcript ion Initiation : Examples from Bacteria

12 2-1 Example from bacteria:Lac operon The lactose (Lac) Operon (乳糖操纵子)

13 Lactose operon: a regulatory gene and 3 stuctural genes, and 2 control elements lacI Regulatory gene lacZ lacY lacA DNA m-RNA β -Galactosidase Permease Transacetylase Protein Structural Genes Cis-acting elements P lacI P lac O lac

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

15 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.

16 Fig 16-6

17 2-2 CAP and lac repressor have opposing effects on RNA polymerase binding to the lac promoter 1.Lac operator 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

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

19 Fig 16-9  CTD: C-terminal domain of the  subunit of RNAP 2-3 CAP has separate activatin g and DNA-binding surfaces

20 2-4: CAP and lac repre ssor bind DNA using a common structural moti f

21 Cap use the strucure called helix-tu rn-helix The helix-turn-helix

22 lac repressor alse use the sa me mechanism Fig Hydrogen B onds betw een l repr essor and the major groove of the operat or

23 Cap and Lac repressor are differences i n detail Lac repressor binds as a tetramer not a dimer Lac repressor,other regions of protein,outside t he helix-turn-helix domain interact with the DNA. In many cases,binding of the protein does not alt er the stricture of the DNA

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

25 2-5: The activity of La c repressor and CAP ar e controlled allosteri cally by their signals

26 i p o z y a Very low level of lac mRNA Absence of lactose Active i p o z y a  -Galactosidase Permease Transacetylase Presence of lactose Inactiv e 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. Response to lactose

27 Response to glucose

28 A regulator (CAP) works together with dif ferent repressor at different genes, this i s an example of Combinatorial Control. In fact, CAP acts at more than 100 genes in E.coli, working with an array of partner s. 2-6: Combinatorial Control ( 组 合调控 ): CAP controls other genes as well

29 σFACTORS EXAMPLE TWO---- ALTERNATIVE σFACTORS 2-7 Alternative s factor direct RNA polymerase to alternative site of promoters

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

31 Promoter recognition Different σ factors bind to th e RNA recognize the promoter sequence,for example σ 70. σ 32

32 Third example: NtrC and MerR and allosteric activation Third example: NtrC and MerR and allosteric activation 5/10/2005

33 2-8 NtrC and Mert: Transcriptional Activators t hat Work by Allostery Rather than by Recruitmen t 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, M erR induces a conformational change in the ina ctive RNA polymerase-promoter complex, and thi s change can trigger open complex formation

34 NtrC Has ATPase Activity and Works from DNA Sites Far from the Gene NtrC has separate activating and DNA-binding domains, and binds DNA when the nitrogen levels are low. The phosphorlated by a kinase. NtrC change the structure and display the activator domain Fig activation by NtrC

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

36 2-9: MerR activat es transcription by twisting prom oter DNA

37 MerR bound to the single DNA-bind ing site, in the presence of merc ury MerR activates the MerT gene. And the Mert twists the DNA.

38 Fig Structure of a merT-like promoter

39 2-10 Some repressors hold RNA polymerase at the promoter rather than excluding it

40 Repressors work in different way s By binding to a site overlapping the promoter, it blocks RNA polymerase binding. (lac repres sor) The protein holds the promoter in a conformat ion incompatible with tanscription initiation. (the MerR case) Blocking the transition from the closed to op en complex. Repressors bind to sites beside a promoter, interact with polymerase bound at t hat promoter and inhibit initiation. (E.coli Gal repressor)

41 Fourth example: araBAD operon

42 2-11 AraC and control of the araBAD operon by antiactivation The promoter of araBAD oper on form E.coli is activated in the presence of arabinos e and the absence of glucos e and directs expression of gene encoding enzyme requir ed for required for arabino se metabolism.

43 Figure control of the araBAD o peron Different from the Lac operon, two a ctivators AraC and CAP work together to activate the araBAD operon expres sion

44 Part three: Examples of gene reg ulation at steps aft er transcription ini tiation

45 3-1 Amino acid biosynthetic operons are c ontrolled by premature transcription term ination Transcription of the trp operon is prema turally stopped if the tryptophan level is not low enough, which results in the production of a leader RNA of 161 nt. Fig 16-19

46 The trp operon encodes five structu ral genes required for tryptophan synthesis.These genes are regulate d to efficiently express only when tryptophan is limiting.There are t wo layers of regulation involved: (1) transcription repression by th e Trp repressor (2) attenuation

47 The Trp repressor When tryptophan is present, it binds the Trp repressor and in duces a conformational change in that protein, enabling it t o bind the trp operator and pr event transcription.When the t ryptophan concentration is low, the Trp repressor is free of i ts corepressor and vacates its operator, allowing the synthe sis of trp mRNA to commence fr om the adjacent promoter

48 Attenuation a regulation at the trans cription termination step & a second mechanism to c onfirm that little trypto phan is available

49 The using of the Repressor and Atten uation Repressor serves as the p rimary switch to regulate the expression of genes i n the trp operon Attenuation serves as the fine switch to determine if the genes need to be e fficiently expressed

50 The hairpin loop is followed by 8 uridine residues. At this so-called attenuator, transcription usually stops,yielding a leader RNA 139 nucleotides long Figure trp operator leader RNA

51 1 Transcription and translation in bacteria are coupled. Therefore, synthesis of the leader peptide immediately follows the transcription of leader RNA. 2 The leader peptide contains two tryptophan codons. If the tryptophan level is very low, the ribosome will pause at these sites. 3 Ribosome pause at these sites alter the secondary structure of the leader RNA, which eliminates the intrinsic terminator structure and allow the successful transcription of the trp operon.

52 Figure transcription at the tr p attenuator

53 3-2 Ribosomal Protein Are Translatio nal Repressors of their Own Synthesi s Control of ribosome protein genes is si mplified by their organization to sever al operons, each containing genes for up to 11 ribisomal proteins. Some nonri bosomal proteins whose synthesis is als o linked to growth rate are contained i n these operons, including those for RN AP subunits a, b and b ’. The primary co ntrol is at the level of translation, n ot transcription

54 Ribosomal protein operons

55 Ribosomal protein are repre ssors of their own translat ion One ribosomal proteins bind s the messenger near the tr anslation initiation sequen ce of one the first genes i n the operon,preventing ri bosomes from binding and in itiating translation.repre ssing translation of the fi rst genes also prevents exp ression of some or all of t he rest.

56 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.

57 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

58 Part four The case of phage λ: layers of regulation

59 lysogeny The alternative propagation pathway –invo lves integration of the phage DNA into the bacterial chromosome where it is passively replicated at each division –just as though i t were a legitimate part of the bacterial gen ome

60 When the cell is exposed to ag ents that damage DNA. This swi tch from Lysogenic to lytic gr owth is called lysogenic induc tion. Lysogenic induction

61 Lytic cycleand Establishment of lysogeny 1. Figure 16-24

62 4-1 Alternative patterns of gene expres sion control lytic and lysogenic growth 1. Figure 16-25

63 Promoters in the right and left cont rol regions of phage λ

64 Transcription in the λcontrol regions i n lytic and lysogenic Arrows indicate which promoters are active at the decisive period during lytic and lysogenic growth, respectively.the arrows also show the direction of transcription from each promoter

65 4-2 Regulatory Proteins and Their Bi nding Sites λrepressor, a protein of two domains joined by a f lexible linker egion. λr epressor can both activat e and repress trandcripti on Cro only represses tra nscription

66 4-3 Repressor and Cro Bind in Different Patterns to Control Lytic and Lysogenic Growth Repressor bound to O R1 and O R2 turns off transcription from P R. And Repressor bound at O R2 contacts RNA polymerase at P RM, activating expression of the cI gene. O R3 lies with P RM ; Cro bound there represses transcription of cI.

67 Relative positions of promoter and o perator sites in O R

68 1. Figure The action of λ repressor and Cro

69 Lysogenic induction requires proteol ytic cleavage Postiive autoregulation: when the level is too low the repressor activates its own repression. Negative autoregulation: when the level is too high the repressor will bind to Or3 and repressing Rrm.

70 Negative autoregulation of repressor require long-distance interations an d a large DNA loop

71 Another Activator, λcII, Controls the Decision between Lytic and Lysogenic Growth upon Infecti on 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.

72 Interaction between the c-terminal d omain of λ repressors 1. Figure 16-33

73 Growth conditions of E.coil control the stabi lity of CII protein and thus/lysogenic choice

74 ► 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.

75 1. Figure 16-36

76 Retoregulation:an interplay of control on R NA synthesis and stability determines int g ene expression

77 Key points of the chapter Principles of gene regulation. (1) The targeted gene expression events; (2) the mechanisms: by recruitment/e xclusion or allostery Regulation of transcription initiat ion in bacteria: the lac operon, alt ernative s factors, NtrC, MerR, Gal rep, araBAD operon Examples of gene regulation after t ranscription initiation: the trp ope ron, riboswitch, regulation of the s ynthesis of ribosomal proteins


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