Transcriptional regulation Chapter 18 Opener Transcriptional regulation Chapter 18 Opener Transcriptional regulation

Principles of Transcriptional Regulation Gene expression is controlled by regulatory proteins. Most activators and repressors are act at the level of transcription initiation. Many promoters are regulated by activators that help RNA polymerase bind DNA and by repressors that block that binding.

Principles of Transcriptional Regulation Some activators and repressors works by allostery and regulate steps in transcriptional initiation after RNA polymerase binding. Action at a distance and DNA looping Cooperative binding and allostery have many roles in gene regulation. Antitermination and beyond: Not all of gene regulation targets transcriptional initiation

Regulation of transcription initiation: examples from prokaryotes An activator and a repressor together control the lac genes CAP and Lac repressor have opposing effects on RNA polymerase CAP has separate activating and DNA binding surfaces

Figure 18-1 Activation by recruitment of RNA polymerase by regulatory proteins (activator) (constitutive expression: basal level – RNA pol occasionally bind) Figure 18-1 Activation by recruitment of RNA polymerase (constitutive expression: basal level – RNA pol occasionally bind) 5

Figure 18-2 Some activators and repressors works by allostery and regulate steps in transcriptional initiation after RNA polymerase binding. RNA pol binds but no transcription Figure 18-2 RNA pol binds but no transcription works by allostery 6

Interactions between proteins bound to DNA Figure 18-3 Interactions between proteins bound to DNA Cooperative binding of proteins to adjacent sites Action at a distance and DNA looping Figure 18-3 Cooperative binding of proteins to adjacent sites 7

Figure 18-4 A DNA-bending protein can facilitate (가능하게 하다) interaction between distantly bound DNA binding proteins. Figure 18-4 8

Regulation of transcription initiation : examples from prokaryotes Figure 18-5 Regulation of transcription initiation : examples from prokaryotes Lac operon Catabolite activator protein (CAP: CRP-cAMP receptor) Figure 18-5 Regulation of transcription initiation : examples from prokaryotes Lac operon catabolite activator protein 9

Figure 18-6 Expression of lac gene Figure 18-6 Expression 10

Symmetric half sites of lac operator Figure 18-7 Symmetric half sites of lac operator Figure 18-7 Symmetric half sites 11

Control region of lac operon Figure 18-8 Control region of lac operon Figure 18-8 Control region of lac operon 12

Figure 18-9 Activation of lac promoter by CAP (activating region bind to C-term of RNA pol) Figure 18-9 Activation of lac promoter by CAP 13

Structure of CAP-αCTD(of RNA Pol)-DNA complex Figure 18-10 Structure of CAP-αCTD(of RNA Pol)-DNA complex activating region Figure 18-10 Structure of CAP-αCTD-DNA complex DNA binding region DNA binding region 14

Binding of a protein with a helix-turn-helix motif to DNA Figure 18-11 Binding of a protein with a helix-turn-helix motif to DNA Figure 18-11 Binding of a protein with a helix-turn-helix motif to DNA 15

Lac repressor binds as a tetramer to two operators Figure 18-12 Lac repressor binds as a tetramer to two operators Figure 18-12 Lac repressor binds as a tetramer to two operators. 16

Inducer of lac operon is allolactose. Figure 18-13 Inducer of lac operon is allolactose. Lactose is converted into allolactose that binds to repressor. Figure 18-13 Inducer of Lac operon is allolactose. Substrate for assay, releasing blue color Synthetic inducer 17

CRP: cAMP receptor protein Figure 18-14 Mechanism of allosteric (다른자리입체성) control(제어) of CAP(catabolite activator protein or CRP) Figure 18-14 Mechanism of allosteric control of CAP CRP: cAMP receptor protein CRP: cAMP receptor protein 18

Figure 18-15 Alternative sigma factors (other sigma factor than 70)control the ordered expression of genes in a bacterial virus (in here B. subtilis bacteriophage SPO1) Figure 18-15 Alternative sigma factors control the ordered expression of genes in a bacterial virus (bacteriophage) Other alternative sigma factors in stead of sigma 70 are used under certain circumstances, i.e. heat shock sigma factor 32, etc.) 19

In recruitment, activators bring RNA Pol . Figure 18-16 NtrC and MerR : Transcriptional activators that work by allostery rather than recruitment. In recruitment, activators bring RNA Pol . In contrast in allostery, RNA Pol bind to promoter first as inactive complex but triggered by activator (NtrC and MerR). Allosteric transcriptional activator (NtrC) Figure 18-16 NtrC and MerR : Transcriptional activators that work by allostery rather than recrutiment Allosteric transcriptional activator 20

Figure 18-17 Allosteric transcriptional activator (MerR): activate transcription by twisting promoter DNA twist Figure 18-17 twist 21

Structure of a MerT like promoter Figure 18-18 Structure of a MerT like promoter Active form Figure 18-18 Structure of a MerT like promoter Active form 22

Some repressors hold RNA polymerase at the promoter rather than excluding. i.e. E. coli Gal repressor and PA2C binding repressor P4 protein (in Ф29 phage of B. subtilis) so strongly bind to RNA pol that polymerase is unable to escape the promoter. Some repressors hold RNA polymerase at the promoter rather than excluding. i.e. E. coli Gal repressor, PA2C binding repressor P4 protein so strongly bind to RNA pol that polymerase is unable to escape the promoter.

Figure 18-19 Control of the araBAD operon and the promoter is also controlled by CAP Arabinose binds to AraC, changing the shape of the activator CAP binding site is just upstream of araI1 and araI2 Figure 18-19 Control of the araBAD operon Arabinose CAP binding site is just upstream of araI1 and araI2 24

Box 18-3-1 Quorom sensing of LuxR Box 18-3-1 Quorom sensing of LuxR 25

The case of bacteriophage lambda : layers of regulation

Growth and Induction of lambda lysogen Figure 18-20 Growth and Induction of lambda lysogen Figure 18-20 The case of bacteriophage lambda : layers of regulation prophage prophage 27

Map of phage λ in the circular form Figure 18-21 Map of phage λ in the circular form Figure 18-21 Map of phage λ in the circular form 28

Promoters in the right and left control regions of phage λ Figure 18-22 Promoters in the right and left control regions of phage λ Cro (Control of repressor and other things) λ repressor gene (cI) Figure 18-22 Promoters in the right and left control regions of phage λ repressor gene Control of repressor and other things 29

Transcription in the λ control regions Figure 18-23 Transcription in the λ control regions Figure 18-23 30

Figure 18-24 λ repressor (monomer) Figure 18-24 λ repressor 31

cI expression: lysogenic cro expression: lytic Figure 18-25 cI expression: lysogenic cro expression: lytic Figure 18-25 32

Figure 18-26 λ repressor dimer Figure 18-26 dimer 33

Figure 18-27 Figure 18-27 34

Figure 18-28 Figure 18-28 35

Genes and promoters involved in the lytic and lysogenic choice Figure 18-30 Genes and promoters involved in the lytic and lysogenic choice cI expression: lysogenic cro expression: lytic Figure 18-30 Also cII and cIII (control decision of between lytic and lysogenic) expression: lysogenic These are transcriptional activator s binding PRE and stimulate cI gene expression. 36

Box 18-5-1 Box 18-5-1 37

Establishment of lysogeny Figure 18-31 Establishment of lysogeny Figure 18-31 Establishment of lysogeny 38

In transcriptional antitermination in a lambda development N gene regulates(express) early gene expression by acting at three terminators: to the left of N, to the right of cro, between P and Q

Figure 18-32 Recognition sites and sites of action of the lambda N and Q transcription antiterminators (positive transcriptional regulation) (In transcriptional anti-termination(no termination) in a lambda development) N binds to the left of N, to the right of cro, between P and Q Initial terminator N on the left of PR Figure 18-32 Region for essential Q protein function Initial terminator . Terminator Region for essential Q protein function (Q recognize QBE): late gene expression 40

How λ Q engage in RNA pol during early elongation Figure 18-33 How λ Q engage in RNA pol during early elongation Figure 18-33 How λ Q engage in RNA pol during early elongation 41

Figure 18-34 DNA site and transcribed RNA structures active in retroregulation of int (integrase) Figure 18-34 DNA site and transcribed RNA structures active in retroregulation of int Not degraded if no N protein degraded if N protein (in lytic) (anti-terminate at terminator) is present. Not degraded if no N protein (lysogeny) (terminate at terminator) 42

Retroregulation (degradation proceeds backwards basically through the gene but not by enzyme) RNA initiated at PI stops at a terminator about 300 nucleotides after end of the int (integrase) gene (this short mRNA stable) RNA initiated at PL is transcribed beyond the terminator. This longer mRNA is degraded by nuclease (when lytic is favored and at low cII activity).

When prophage is induced (meaning virus escapes from bacteria), phage needs to make integrase that is transcribed by PL but this is not degraded. During lysogeny establishment, phage attachment site is between the end of int gene and those sequences encoding the extended stem from which mRNA degradation is begun. Thus the site causing degradation is removed from the end of int gene, and so mRNA made from PL is stable. When prophage is induced (meaning virus escape from bacteria), phage needs to make integrase that is transcribed by PL but this is not degraded.