An error-prone viral DNA ligase.
Our recent demonstration that DNA polymerase X (Pol X), the DNA repair polymerase encoded by the African swine fever virus (ASFV), is extremely error prone during single-nucleotide gap filling led us to hypothesize that it might contribute to genetic variability in ASFV. For the infidelity of Pol X to be relevant, however, the DNA ligase working downstream of it would need to be capable of sealing nicks containing 3'-OH mismatches. We therefore examined the nick ligation capabilities of the ASFV-encoded DNA ligase and here report the first complete 3' fidelity analysis, employing catalytic parameters, for any DNA ligase. The catalytic efficiency of nick sealing by both ASFV DNA ligase and bacteriophage T4 DNA ligase was determined in the steady state for substrates containing all 16 possible matched and mismatched base pair combinations at the 3' side of a nick. Our results indicate that ASFV DNA ligase is the lowest-fidelity DNA ligase ever reported, capable of ligating a 3' C:T mismatched nick (where C and T are the templating and nascent nucleotides, respectively) more efficiently than nicks containing Watson-Crick base pairs. Comparison of the mismatch specificity of Pol X with that of ASFV DNA ligase suggests that the latter may have evolved toward low fidelity for the purpose of generating the broadest possible spectrum of sealed mismatches. These findings are discussed in light of the genetic and antigenic variability observed among some ASFV isolates. Two novel assays for determining the concentration of active DNA ligase are also reported.
Lamarche
Brandon J
BJ
Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA.
Showalter
Alexander K
AK
Tsai
Ming-Daw
MD
D020413:3' Untranslated Regions / Q000235:genetics; D000358:African Swine Fever Virus / Q000201:enzymology* / Q000235:genetics; D020137:Base Pair Mismatch / Q000235:genetics; D002021:Buffers; D000072481:DNA Ligase ATP; D011088:DNA Ligases / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D004260:DNA Repair / Q000235:genetics; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004789:Enzyme Activation / Q000235:genetics; D019143:Evolution, Molecular; D014644:Genetic Variation; D007700:Kinetics; D009994:Osmolar Concentration; D011189:Potassium Chloride / Q000737:chemistry; D013379:Substrate Specificity / Q000235:genetics
D020413:3' Untranslated Regions; D002021:Buffers; D004279:DNA, Viral; D011189:Potassium Chloride; C109534:DNA polymerase X; D004259:DNA-Directed DNA Polymerase; D011088:DNA Ligases; D000072481:DNA Ligase ATP