© 2014 Pearson Education, Inc. Chapter 18 Opener Transcriptional regulation

© 2014 Pearson Education, Inc. 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.

© 2014 Pearson Education, Inc. 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

© 2014 Pearson Education, Inc. 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

© 2014 Pearson Education, Inc. Figure 18-1 Activation by recruitment of RNA polymerase by regulatory proteins (activator) (constitutive expression: basal level – RNA pol occasionally bind)

© 2014 Pearson Education, Inc. Figure 18-2 Some activators and repressors works by allostery and regulate steps in transcriptional initiation after RNA polymerase binding. works by allostery RNA pol binds but no transcription

© 2014 Pearson Education, Inc. Figure 18-3 Action at a distance and DNA looping Interactions between proteins bound to DNA Cooperative binding of proteins to adjacent sites

© 2014 Pearson Education, Inc. Figure 18-4 A DNA-bending protein can facilitate ( 가능하게 하다 ) interaction between distantly bound DNA binding proteins.

© 2014 Pearson Education, Inc. Figure 18-5 Regulation of transcription initiation : examples from prokaryotes Lac operon Catabolite activator protein (CAP: CRP-cAMP receptor)

© 2014 Pearson Education, Inc. Figure 18-6 Expression of lac gene

© 2014 Pearson Education, Inc. Figure 18-7 Symmetric half sites of lac operator

© 2014 Pearson Education, Inc. Figure 18-8 Control region of lac operon

© 2014 Pearson Education, Inc. Figure 18-9 Activation of lac promoter by CAP (activating region bind to C-term of RNA pol)

© 2014 Pearson Education, Inc. Figure Structure of CAP- α CTD(of RNA Pol)- DNA complex DNA binding region activating region

© 2014 Pearson Education, Inc. Figure Binding of a protein with a helix-turn-helix motif to DNA

© 2014 Pearson Education, Inc. Figure Lac repressor binds as a tetramer to two operators

© 2014 Pearson Education, Inc. Figure Inducer of lac operon is allolactose. Lactose is converted into allolactose that binds to repressor. Synthetic inducer Substrate for assay, releasing blue color

© 2014 Pearson Education, Inc. Figure Mechanism of allosteric ( 다른자리입체성 ) control( 제어 ) of CAP(catabolite activator protein or CRP) CRP: cAMP receptor protein

© 2014 Pearson Education, Inc. Figure Alternative sigma factors (other sigma factor than 70)control the ordered expression of genes in a bacterial virus (in here B. subtilis bacteriophage SPO1) Other alternative sigma factors in stead of sigma 70 are used under certain circumstances, i.e. heat shock sigma factor 32, etc.)

© 2014 Pearson Education, Inc. Figure 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)

© 2014 Pearson Education, Inc. Figure Allosteric transcriptional activator (MerR): activate transcription by twisting promoter DNA twist

© 2014 Pearson Education, Inc. Figure Structure of a MerT like promoter Active form

© 2014 Pearson Education, Inc. Some repressors hold RNA polymerase at the promoter rather than excluding. i.e. E. coli Gal repressor and P A2C binding repressor P 4 protein (in Ф29 phage of B. subtilis) so strongly bind to RNA pol that polymerase is unable to escape the promoter.

© 2014 Pearson Education, Inc. Figure 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 araI 1 and araI 2

© 2014 Pearson Education, Inc. Box Quorom sensing of LuxR

© 2014 Pearson Education, Inc. The case of bacteriophage lambda : layers of regulation

© 2014 Pearson Education, Inc. Figure Growth and Induction of lambda lysogen prophage

© 2014 Pearson Education, Inc. Figure Map of phage λ in the circular form

© 2014 Pearson Education, Inc. Figure Promoters in the right and left control regions of phage λ λ repressor gene (cI) Cro (Control of repressor and other things)

© 2014 Pearson Education, Inc. Figure Transcription in the λ control regions

© 2014 Pearson Education, Inc. Figure λ repressor (monomer)

© 2014 Pearson Education, Inc. Figure cI expression: lysogenic cro expression: lytic

© 2014 Pearson Education, Inc. Figure λ repressor dimer

© 2014 Pearson Education, Inc. Figure 18-27

© 2014 Pearson Education, Inc. Figure 18-28

© 2014 Pearson Education, Inc. Figure Genes and promoters involved in the lytic and lysogenic choice cI expression: lysogenic cro expression: lytic Also cII and cIII (control decision of between lytic and lysogenic) expression: lysogenic These are transcriptional activator s binding P RE and stimulate cI gene expression.

© 2014 Pearson Education, Inc. Box

© 2014 Pearson Education, Inc. Figure Establishment of lysogeny

© 2014 Pearson Education, Inc. 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

© 2014 Pearson Education, Inc. Figure Recognition sites and sites of action of the lambda N and Q transcription antiterminators (positive transcriptional regulation) (In transcriptional antitermination in a lambda development) Region for essential Q protein function (Q recognize QBE): late gene expression Initial terminator Terminator N binds to the left of N, to the right of cro, between P and Q N on the left of P R

© 2014 Pearson Education, Inc. Figure How λ Q engage in RNA pol during early elongation

© 2014 Pearson Education, Inc. Figure DNA site and transcribed RNA structures active in retroregulation of int (integrase) Not degraded if no N protein