Chapter 9 DNA recognition by eukaryotic transcription factors

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1 Chapter 9 DNA recognition by eukaryotic transcription factors

2 TRANSCRIPTION 101

3 Eukaryotic RNA polymerases RNA polymerase RNA polymerase I RNA polymerase II RNA polymerase III RNA polymerase IV Function rrna mrna, snrna, mirna trna sirna (plants) snrna (small nuclear RNA): small RNA found inside the nucleus functioning in RNA splicing and telomere maintenance mirna (microrna): single-stranded RNA with nucleotides functioning in regulating gene expression sirna (small interfering RNA): double-stranded RNA with nucleotides functioning in RNA intereference

4 Transcription is activated by protein-protein interactions

5 Eukaryotic pre-initiation complex

6 TATA-BOX BINDING PROTEIN (TBP)

7 The three-dimensional structures of TBP-TATA box complexes are known

8 A β sheet in TBP forms the DNA-binding site Saddle-shaped molecule : C-terminal 180 residues form two structurally similar motifs (88 residues), anti-parallel β sheet of 5 strands unlike prokaryotic DNA-binding proteins

9 TBP binds in the minor groove and induces large structural changes in DNA 110

The interaction are between TBP and the TATA box is mainly hydrophobic Interaction area: hydrophobic Side chains from the central β strands Phosphate sugar backbone Minor groove

10 The interaction are between TBP and the TATA box is mainly hydrophobic Interaction area: hydrophobic Side chains from the central β strands Phosphate sugar backbone Minor groove DNA sequence-specific contacts No G-C pair allowed DNA sequence-specific hydrogen bonds: At the center of the minor groove Minor groove recognition Easier bendability of A:T pairs

11 Nitrogenous bases Pyrimidines Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA) Purines Adenine (A) Guanine (G)

12 TFIIA and TFIIB bind to both TBP and DNA

13 Eukaryotic helix-turn-helix motif HOMEODOMAIN PROTEINS

14 Homeodomain proteins are involved in the development of many eukaryotic organism

15 Monomers of homeodomain proteins bind to DNA through a helix-turn-helix motif

16 Helix-turn-helix motif of homeodomain is similar to prokaryotic counterparts with deviations Monomer binds DNA Dimer binds DNA

Helix-turn-helix motif of homeodomain is similar to prokaryotic counterparts with deviations - Monomeric homeodomain proteins bind specifically

17 Helix-turn-helix motif of homeodomain is similar to prokaryotic counterparts with deviations - Monomeric homeodomain proteins bind specifically to DNA fragments containing the sequence 5 -A-T-T-A-3 with a K d ~1 nm. - Nonspecifically to different sequences with about 100 times lower affinity

18 Overall arrangement of the homeodomains bound to DNA is virtually identical (seq. identity is only 20%)

19 In vivo specificity of homeodomain transcription factors depends on interactions with other proteins

20 Another eukaryotic helix-turn-helix motif POU DOMAIN

21 POU Domain POU: Pit-1, Oct-1&2, Unc-86 Pituitary-specific Pit-1 Octamer transcription factor proteins Oct-1 and Oct-2 (octamer sequence is ATGCAAAT) neural Unc-86 transcription factor from Caenorhabditis elegans [Ryan and Rosenfeld, Genes Dev. (1997)]

22 POU regions bind to DNA by two tandemly oriented helix-turn-helix motifs POU s POU H

23 Sequence-specific contacts between DNA and the POU region

24 Flexibility of POU domain [Ryan and Rosenfeld, Genes Dev. (1997)]

25 Tumorigenesis and DNA recognition P53

26 [Toledo and Wahl, Nat. Rev. Cancer (2007)]

His (in the hydrophobic core in a dimer); destabilizes dimer - Gly in the turn

27 The monomeric p53 polypeptide chain is divided in 3 domains - The oligomerization domain forms tetramers: some mutations detected in tumor are in this domain - Leu330 His (in the hydrophobic core in a dimer); destabilizes dimer - Gly in the turn between the β-strand and the α-helices; any mutation will cause energetically unfavorable folding

28 Understanding tumorigenic mutations (p53) L330H [Joerger and Fersht, Oncogene (2007)]

29 Structure of the DNA-binding domain of p53 (anti-parallel β barrel: 9 β strands)

- Protruding loops (L1,3) to both minor and major grooves -

conformation (2 Cys from L3 & Cys/His from L2) - There are

helix major groove (conserved DNA sequence) Out of 21 bp, 10

30 - Protruding loops (L1,3) to both minor and major grooves - Two loops and one α helix bind to DNA - Zn stabilizes a loop conformation (2 Cys from L3 & Cys/His from L2) - There are also non-specific interactions between p53 and DNA - R280 in helix major groove (conserved DNA sequence) Out of 21 bp, 10 bp are involved in the sequence-specific binding Yunje POSTECH

31 Tumorigenic mutations occur mainly in three regions involved in DNA binding

GCD3033:Cell Biology. Transcription

GCD3033:Cell Biology. Transcription Transcription Transcription: DNA to RNA A) production of complementary strand of DNA B) RNA types C) transcription start/stop signals D) Initiation of eukaryotic gene expression E) transcription factors