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M111220200v1
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Papers In Press, published online ahead of print February 27, 2002
J. Biol. Chem, 10.1074/jbc.M111220200
Submitted on November 26, 2001
Revised on February 19, 2002
Accepted on February 26, 2002

Bacteriophage phi6 RNA-dependent RNA polymerase: Molecular details of initiating nucleic acid synthesis without primer

Minni R. L. Laurila, Eugene V. Makeyev, and Dennis H. Bamford

Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki FIN-00014

Corresponding Author: dennis.bamford{at}helsinki.fi

Like most RNA polymerases, the polymerase of dsRNA bacteriophage phi6 (phi6pol) is capable of primer-independent initiation. Based on the recently solved phi6pol initiation complex structure, a four amino acid long loop (aa 630-633) has been suggested to stabilize the first two incoming NTPs through stacking interactions with tyrosine Y630. A similar loop is also present in the hepatitis C virus polymerase, another enzyme capable of de novo initiation. Here, we use a series of phi6pol mutants to address the role of this element. As predicted, mutants at the Y630 position are inefficient in initiation de novo. Unexpectedly, when the loop is disordered by changing Y630K631W632 to GSG, phi6pol becomes a primer-dependent enzyme, either extending complementary oligonucleotide or, when the template 3' terminus can adopt a hairpin-like conformation, utilizing a "copy-back" initiation mechanism. In contrast to the wild-type phi6pol, the GSG mutant does not require high GTP concentration for its optimal activity. These findings suggest a general model for the initiation of de novo RNA synthesis.


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