Replication_PaperBash1 - Manel Camps

Question 1

Duplex melting_E coli protein

Answer 1

Dna A

Question 2

Duplex melting_plasmid protein

Answer 2

RepC (SD)

Rep (ThetaC, D, Rolling-c)

Question 3

Primer synthesis_E coli protein

Answer 3

DnaG

Question 4

Primer synthesis_plasmid protein

Answer 4

RepB (SD)

Rep (theta C); only for leading strand and unique

Question 5

Helicase (also helps with duplex melting)_E coli protein

Answer 5

DnaB

Question 6

Helicase (also helps with duplex melting)_plasmid protein

Answer 6

RepA (SD)

Question 7

Slow down primer extension_E-Coli protein

Answer 7

Topo III

Question 8

Slow down primer extension_plasmid protein

Answer 8

TopB (theta D)

Question 9

Duplex melting mechanism (Theta A)

Answer 9

Recruitment of DnaA following iteron binding (Reps+DnaA))

Question 10

Duplex melting mechanism (Theta B)

Answer 10

Transcription and R-loop formation
+ extension (Host RNA Polymerase,
Pol I, RNAseH)

Question 11

Duplex melting mechanism (SD)

Answer 11

Direct melting + helicase unwinding (RepC+RepA)

Question 12

Duplex melting mechanism (RC)

Answer 12

Direct melting by binding to specific bind sequence with bending of the DNA (Rep)

Question 13

Primer Synthesis (Theta A,C)

Answer 13

DnaA recruits the replisome, which stimulates DnaG activity (DnaG)

Question 14

Primer Synthesis (Theta B,D)

Answer 14

PriA recruits the replisome, which stimulates DnaG activity (DnaG)

Question 15

Primer Synthesis (Strand Displacement)

Answer 15

Hairpin recruits the primase (RepB + Pol III)

Question 16

Primer Synthesis (Rolling Circle)

Answer 16

By RNA polymerase after single-stand intermediate is released (Host RNAP)

Question 17

Which types of plasmids do not couple leading-strand and lagging-strand replication? Differences

Answer 17

Strand displacement and rolling circle.

Strand displacement = lagging and leading-strand replication are simultaneous
Rolling circle replication = lagging and leading-strand replication are sequential

Question 18

Why has life gone through the trouble of inventing replication machineries multiple times?

Answer 18

Patrick Forterre’s hypothesis is that there has been an “arms race” between viral and host genomes since the beginning of life and that enzymes of viral origin have displaced ancestral DNA metabolic enzymes multiple times, explaining why these enzymes appear in life in multiple (sometimes structurally unrelated versions) and why they don’t follow the phylogenetic relationships genomic sequence as a whole. Clearest example: replication machinery of archaea related to that of eukaryotes, but replication mode and chromatin structure more similar between prokaryotes and archaea. Archaea appear to have lost PolAlpha initial synthesis for elongation of lagging-strand.