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Accessory factors summary

Accessory factors summary. DNA polymerase can’t replicate a genome. Solution ATP? No single stranded template Helicase + The ss template is unstable SSB (RPA (euks)) - No primer Primase (+) No 3’-->5’ polymerase Replication fork

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Accessory factors summary

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  1. Accessory factors summary • DNA polymerase can’t replicate a genome. • Solution ATP? • No single stranded template Helicase + • The ss template is unstable SSB (RPA (euks)) - • No primer Primase (+) • No 3’-->5’ polymerase Replication fork • Too slow and distributive SSB and sliding clamp - • Sliding clamp can’t get on Clamp loader (/RFC) + Lagging strand contains RNA Pol I 5’-->3’ exo, RNAseH - Lagging strand is nicked DNA ligase + Helicase introduces + supercoils Topoisomerase II + and products tangled 2. DNA replication is fast and processive

  2. DNA polymerase holoenzyme

  3. Maturation of Okazaki fragments

  4. Relaxed/disentangled Topoisomerases control chromosome topology Catenanes/knots Topos • Major therapeutic target - chemotherapeutics/antibacterials • Type II topos transport one DNA through another

  5. Starting and stopping summary DNA replication is controlled at the initiation step. DNA replication starts at specific sites in E. coli and yeast. In E. coli, DnaA recognizes OriC and promotes loading of the DnaB helicase by DnaC (helicase loader) DnaA and DnaC reactions are coupled to ATP hydrolysis. Bacterial chromosomes are circular, and termination occurs opposite OriC. In E. coli, the helicase inhibitor protein, tus, binds 7 ter DNA sites to trap the replisome at the end. Eukaryotic chromosomes are linear, and the chromosome ends cannot be replicated by the replisome. Telomerase extends the leading strand at the end. Telomerase is a ribonucleoprotein (RNP) with RNA (template) and reverse-transcriptase subunits.

  6. Isolating DNA sequences that mediate initiation

  7. Different origin sequences in different organisms E. Coli (bacteria) OriC Yeast ARS (Autonomously Replicating Sequences) Metazoans ????

  8. Initiation in prokaryotes and eukaryotes Bacteria Eukaryotes ORC + other proteins load MCM hexameric helicases MCM (helicase) + RPA (ssbp) Primase + DNA pol  PCNA:pol  MCM (helicase) + RPA (ssbp) PCNA:pol  (clamp loader) Primase + DNA pol  PCNA:pol DNA ligase

  9. Initiation mechanism in bacteria -- 1

  10. Crystal structure of DnaA:ATP revealed mechanism of origin assembly 1. 2. 1. DnaA monomer (a) forms a polar filament (b). 2. DNA binding sites occur on the outside of the filament (model).

  11. Crystal structure of DnaA:ATP revealed mechanism of origin assembly 1. 2. 1. The arrangement of DNA binding sites introduces positive supercoils by wrapping DNA on the outside. Compensating negative supercoils melt the replication bubble at the end. 2. Clamp deposition recruits Had, which promotes ATP hydrolysis and progressive disassembly of the DnaA filament (hypothesis).

  12. Initiation mechanism in bacteria -- 1

  13. Initiation mechanism in bacteria -- 2

  14. Initiation proteins in E. coli (bacteria)

  15. 10 ter sites opposite oriC coordinate the end game Origin Counterclockwise fork Clockwise fork Tus protein binds Ter sites and inhibits the DnaB helicase only from one direction!!! Clockwise fork trap Counterclockwise fork trap The ter/tus system is not essential in E. coli.

  16. Unwinding ter from the “nonpermissive” direction springs a “molecular mousetrap” DNA Half life (s) Kd (nM) 130 (2 min) 1.6 <7 (FAST/permissive) 53 6900 (115 min, SLOW/ 0.4 nonpermissive) terB C6 C6 C6 Releasing C6 springs the trap Mulcair et al. (2006) Cell125, 1309-1319.

  17. Unwinding ter from the “nonpermissive” direction springs a “molecular mousetrap” DNA Half life (s) Kd (nM) 130 (2 min) 1.6 <7 (FAST/permissive) 53 6900 (115 min, SLOW/ 0.4 nonpermissive) terB C6 C6 DnaB 5’ 3’ C6 Releasing C6 springs the trap Mulcair et al. (2006) Cell125, 1309-1319.

  18. Unwinding ter from the “nonpermissive” direction springs a “molecular mousetrap” Releasing C6 springs the trap Mulcair et al. (2006) Cell125, 1309-1319.

  19. Unwinding ter from the nonpermissive direction springs a “molecular mousetrap” Releasing C6 springs the trap Mulcair et al. (2006) Cell125, 1309-1319.

  20. Topoisomerase II unlinks the replicated chromosomes Topoisomerase II - Cuts DNA and passes one duplex through the other. Class II topoisomerases include: Topo IV and DNA gyrase

  21. Summary: What problems do these proteins solve? Tyr OH attacks PO4 and forms a covalent intermediate Structural changes in the protein open the gap by 20 Å!

  22. Summary: What problems do these proteins solve? … other model systems include bacteriophage T4 and yeast

  23. The ends of (linear) eukaryotic chromosomes cannot be replicated by the replisome. Not enough nucleotides for primase to start last lagging strand fragment Chromosome ends shorten every generation!

  24. Telomere shortening signals trouble! Telomere binding proteins (TBPs) 1. Telomere shortening releases telomere binding proteins (TBPs) 2. Further shortening affects expression of telomere-shortening sensitive genes 3. Further shortening leads to DNA damage and mutations.

  25. Telomerase replicates the ends (telomeres) Telomerase is a ribonucleoprotein (RNP). The enzyme contains RNA and proteins. The RNA templates DNA synthesis. The proteins include the telomerase reverse transcriptase TERT. Telomere ssDNA Telomerase extends the leading strand! Synthesis is in the 5’-->3’ direction.

  26. Telomerase cycles at the telomeres TERT protein TER RNA template Telomere ssDNA

  27. Telomerase extends a chromosome 3’ overhang

  28. Conserved structures in TER and TERT 148-209 nucleotides Core secondary structures shared in ciliate and vertebrate telomerase RNAs (TERs). (Sequences highly variable.) 1000s of nucleotides 1300 nucleotides TERT protein sequences conserved

  29. Starting and stopping summary DNA replication is controlled at the initiation step. DNA replication starts at specific sites in E. coli and yeast. In E. coli, DnaA recognizes OriC and promotes loading of the DnaB helicase by DnaC (helicase loader) DnaA and DnaC reactions are coupled to ATP hydrolysis. Bacterial chromosomes are circular, and termination occurs opposite OriC. In E. coli, the helicase inhibitor protein, Tus, binds 10 ter DNA sites to trap the replisome at the end. Eukaryotic chromosomes are linear, and the chromosome ends cannot be replicated by the replisome. Telomerase extends the leading strand at the end. Telomerase is a ribonucleoprotein (RNP) with RNA (template) and reverse-transcriptase subunits.

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