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Complete nucleotide sequence and genetic organization of grapevine fanleaf nepovirus RNA1

R. Margis^1,

¹ Institut de Biologie Moléculaire des Plantes du CNRS et Université Louis Pasteur, Laboratoire de Virologie, 12 rue du Général Zimmer, 67084 Strasbourg Cedex
and² Station de Recherches Vigne et Vin, Laboratoire de Pathologie Végétale I.N.R.A., 28 rue de Herrlisheim, 68021 Colmar, France

The nucleotide sequence of the genomic RNAI, 7342 nucleotides (nt) of grapevine fanleaf virus strain F13 (GFLV-F13) has been determined from cDNA clones. The complete sequence contained only one long open reading frame (ORF) of 6852 nucleotides extending from nucleotide 243 to 7101. The putative polyprotein encoded by this ORF is 2284 amino acids in length with an M_r of 253K. The location of genome-linked protein and comparison of the primary structure of the 253K polyprotein to that of other closely related viral proteins of the picornavirus-like family allows the proposal of a scheme for the genetic organization of GFLV-F13 RNA1. The primary structure of the polyprotein includes a putative RNA-dependent RNA polymerase of 92K and a cysteine protease of 25K. This protease shares not only major structural homologies, particularly in the substrate-binding pocket, with the trypsin-like serine proteases of other picorna-like viruses, but also their specificity in terms of cleavage. The large region of M_r 133K upstream of the VPg was found to contain at least two domains, one of which could be easily aligned with the NTP-binding sequence pattern and another which may have the characteristics of a protease cofactor. Thus, the 253K protein possesses the same general genetic organization as the corresponding protein of other picorna-like viruses.

Permanent address: Escola Tecnica Federal de Quimica do Rio de Janeiro, 121 Rua Senador Furtado, 20270 Rio de Janeiro, Brasil.

Received 7 May 1991; accepted 17 June 1991.

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