Chapter 8 DNA Recognition in Prokaryotes by Helix-Turn-Helix Motifs

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1 Chapter 8 DNA Recognition in Prokaryotes by Helix-Turn-Helix Motifs 1. Helix-turn-helix proteins 2. Zinc finger proteins 3. Leucine zipper proteins 4. Beta-scaffold factors 5. Others

2 λ-repressor AND CRO

3 A molecular mechanism for genetic switch Bacteriophage λ: A temperate bacteriophage infecting E. coli Phage Phage DNA The phage injects its DNA. Bacterial chromosome Phage DNA circularizes. Daughter cell with prophage Occasionally, a prophage exits the bacterial chromosome, initiating a lytic cycle. Cell divisions produce population of bacteria infected with the prophage. The cell lyses, releasing phages. Lytic cycle Lytic cycle is induced or Lysogenic cycle is entered Lysogenic cycle Prophage The bacterium reproduces, copying the prophage and transmitting it to daughter cells. New phage DNA and proteins are synthesized and assembled into phages. Phage DNA integrates into the bacterial chromosome, becoming a prophage.

4 A molecular mechanism for genetic switch

5 Repressor and Cro proteins operate a prokaryotic genetic switch region ci: clear I Cro: Control of Repressor s Operator Lytic phase Turning off synthesis of Cro or activator for its own synthesis Turning off synthesis of repressor

6 Repressor and Cro proteins operate a prokaryotic genetic switch region Palindrome: the same forward as it is backward Examples: RACECAR, OTTO EcoRI DNA: read base pairs Examples: Restriction enzyme recognition sequences

7 Repressor and Cro proteins operate a prokaryotic genetic switch region Palindromic sequences: 8 bp per a monomer Sequence information shows a pseudo 2-fold symmetry

8 The x-ray structure of the complete lambda Cro protein is known

9 Dimeric structure of N-terminal domain of lambda repressor

10 Structure of C-terminal domain of lambda repressor K192 S149 Residues for self-cleavage Residues mediating dimerization [Bell et al., Cell (2000)]

11 Lambda repressor C-terminal domain forms tetramers in the crystal [Bell et al., Cell (2000)]

12

13 (Lysogenic promoter) (Lytic promoter)

14 Both lambda Cro and repressor proteins have a specific DNA-binding motif

15 Model building predicts Cro-DNA interactions 34 Å apart between two α3 helices in a dimer 10 bp apart DNA recognition helix (α3) / stabilizing helix (α2)

16 Genetic studies agree with the structural model Altered DNA binding specificity by redesigning recognition helix (by Mark Ptashne's group at Harvard) Recognition helix swap between repressor and Cro changes in the binding affinity Changes in a single amino acid of repressor between 434 and P22 phage engineered 434 repressor binds to P22 operator, not to 434 operator

17

18 PROKARYOTIC DNA BINDING PROTEINS

19 The structures of DNA-binding domain are very similar (434 Cro vs 434 repressor: 48% sequence identity) (434 Cro vs lambda repressor: 26% sequence identity) 434 Cro lambda repressor 434 repressor Monomer in solution Dimer complexed with DNA

20 The proteins impose precise distortions on the B-DNA in the complexes DNA helix axis bent toward a repressor Normal B-DNA Distorted DNA complexed with 434 Cro & repressor

21 Sequence specific protein-dna interactions recognize operator regions Recognition helix A major groove H-bonding / hydrophobic interaction (Q28 & Q29 form H-bonds to A1-C2) / (methyl-group on T)

22 Protein-DNA backbone interactions determine DNA conformation

23 Main features of the interactions between DNA and the helix-turn-helix motif in DNA binding protein

24 DNA binding is regulated by allosteric control Binding of the small molecules (i.e., allosteric effectors) to the sites quite different from the functional binding sites of repressor or activator causes the conformational changes

25 w/o Trp, repressor is inactive turn on operon for the synthesis of Trp w Trp, repressor is active turn off operon Major groove binding of α5 via water-mediated interactions Structural changes by the binding of Trp into a pocket Inactive (28-29 Å between two α5 helices) active (34 Å) Binding of Trp to the cavity alters the orientation of α5 helices

26 LAC REPRESSOR

27 Lac repressor (LacI : 360 residues negative regulator) In the absence of lactose, Lac repressor binds to an OR site [RNAP can t bind to the site, hence operon is off] In the presence of inducer (lactose or IPTG), repressor-effector complex no longer binds to the OR site [Operon is on] Four domains in monomer (HTH - hinge helix - core domains -tetramerization domain)

28 E. coli lac operon: review

29 Inducer of Lac repressor Lactose (galactose-(β1->4)-glucose) Allolactose (galactose-(β1->6)-glucose) IPTG (isopropyl β-d-1-thiogalactopyranoside) A molecular mimic of allolactose

30 Tetrameric Lac repressor binds to both the major and the minor grooves inducing a sharp bend in the DNA Each dimer binds to the separated palindromic DNA sequence

31 Tetrameric Lac repressor binds to both the major and the minor grooves inducing a sharp bend in the DNA - Major (HTH) & minor (hinge helix) groove binding (seq. specific) - HTH binding as were seen in Cro and repressor in a phage - Hinge helix: Leu opens up the minor groove and DNA is bent away from the protein

32 CATABOLITE GENE ACTIVATING PROTEIN

33 CAP-induced DNA bending could activate transcription 40 O kink 40 O kink

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