The NPH-II helicase displays efficient DNA x RNA helicase activity and a pronounced purine sequence bias.
The superfamily 2 vaccinia viral helicase nucleoside triphosphate phosphohydrolase-II (NPH-II) exhibits robust RNA helicase activity but typically displays little activity on DNA substrates. NPH-II is thus believed to make primary contacts with backbone residues of an RNA substrate. We report an unusual nucleobase bias, previously unreported in any superfamily 1 or 2 helicase, whereby purines are heavily preferred as components of both RNA and DNA tracking strands. The observed sequence bias allows NPH-II to efficiently unwind a DNA x RNA hybrid containing a purine-rich DNA track derived from the 3'-untranslated region of an early vaccinia gene. These results provide insight into potential biological functions of NPH-II and the role of sequence in targeting NPH-II to appropriate substrates. Furthermore, they demonstrate that in addition to backbone contacts, nucleotide bases play an important role in modulating the behavior of NPH-II. They also establish that processive helicase enzymes can display sequence selectivity.
Taylor
Sean David
SD
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA.
Solem
Amanda
A
Kawaoka
Jane
J
Pyle
Anna Marie
AM
D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D005821:Genetic Techniques; D007700:Kinetics; D008969:Molecular Sequence Data; D009696:Nucleic Acids / Q000737:chemistry; D043583:Nucleoside-Triphosphatase / Q000378:metabolism*; D011506:Proteins / Q000737:chemistry; D011687:Purines / Q000737:chemistry*; D011743:Pyrimidines / Q000737:chemistry; D020365:RNA Helicases / Q000378:metabolism*; D013379:Substrate Specificity; D014616:Vaccinia virus / Q000201:enzymology
D009696:Nucleic Acids; D011506:Proteins; D011687:Purines; D011743:Pyrimidines; D004247:DNA; D043583:Nucleoside-Triphosphatase; D020365:RNA Helicases; C030985:purine