Structural elements of the 3'-terminal coat protein binding site in alfalfa mosaic virus RNAs.

The 3'-terminal of the three genomic RNAs of alfalfa mosaic virus (AIMV) and ilarviruses contain a number of AUGC-motifs separated by hairpin structures. Binding of coat protein (CP) to such elements in the RNAs is required to initiate infection of these viruses. Determinants for CP binding in the 3'-terminal 39 nucleotides (nt) of AIMV RNA 3 were analyzed by band-shift assays. From the 5'- to 3'-end this 39 nt sequence contains AUGC-motif 3, stem-loop structure 2 (STLP2), AUGC-motif 2, stem-loop structure 1 (STLP1) and AUGC-motif 1. A mutational analysis showed that all three AUGC-motifs were involved in CP binding. Mutation of the A- and U-residues of motifs 1 or 3 had no effect on CP binding but similar mutations in motif 2 abolished CP binding. A mutational analysis of the stem of STLP1 and STLP2 confirmed the importance of these hairpins for CP binding. Randomization of the sequence of the stems and loops of STLP1 and STLP2 had no effect on CP binding as long as the secondary structure was maintained. This indicates that the two hairpins are not involved in sequence-specific interactions with CP. They may function in a secondary structure-specific interaction with CP and/or in the assembly of the AUGC-motifs in a configuration required for CP binding.

[1]  E C Koper-Zwarthoff,et al.  Nucleotide sequence of the putative recognition site for coat protein in the RNAs of alfalfa mosaic virus and tobacco streak virus. , 1980, Nucleic acids research.

[2]  J. Bol,et al.  Role of alfalfa mosaic virus coat protein in regulation of the balance between viral plus and minus strand RNA synthesis. , 1991, Virology.

[3]  I. Tinoco,et al.  Structural Elements in RNA , 1991, Progress in Nucleic Acid Research and Molecular Biology.

[4]  C. D'arcy,et al.  The nucleotide sequence of apple mosaic virus coat protein gene has no similarity with other Bromoviridae coat protein genes. , 1994, The Journal of general virology.

[5]  Removal of the N-terminal part of alfalfa mosaic virus coat protein interferes with the specific binding to RNA 1 and genome activation. , 1983, Virology.

[6]  K. Nagai.  RNA-protein interactions , 1992 .

[7]  D. Gonsalves,et al.  Activation of Prunus necrotic ringspot virus and rose mosaic virus by RNA 4 components of some Ilarviruses. , 1977, Virology.

[8]  L. Vloten-Doting.  Coat protein is required for infectivity of tobacco streak virus: biological equivalence of the coat proteins of tobacco streak and alfalfa mosaic viruses. , 1975 .

[9]  C. Gorman,et al.  Growth of adeno-associated satellitte virus under conditions of arginine deprivation. , 1975, Virology.

[10]  O. Uhlenbeck,et al.  Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. , 1987, Nucleic acids research.

[11]  K. Liem,et al.  Nucleotide sequence and structural determinants of specific binding of coat protein or coat protein peptides to the 3' untranslated region of alfalfa mosaic virus RNA 4 , 1994, Journal of virology.

[12]  J. Bol,et al.  Deletion analysis of cis- and trans-acting elements involved in replication of alfalfa mosaic virus RNA 3 in vivo. , 1991, Virology.

[13]  E. Jaspars,et al.  Protein binding sites in nucleation complexes of alfalfa mosaic virus RNA 4. , 1982, Biochemistry.

[14]  D. Draper,et al.  Protein-RNA recognition. , 1995, Annual review of biochemistry.

[15]  E. Jaspars,et al.  Coat protein binds to the 3'-terminal part of RNA 4 of alfalfa mosaic virus. , 1978, Biochemistry.

[16]  J. Bol,et al.  Altered balance of the synthesis of plus- and minus-strand RNAs induced by RNAs 1 and 2 of alfalfa mosaic virus in the absence of RNA 3. , 1983, Virology.

[17]  C. Reusken,et al.  The 3'-untranslated region of alfalfa mosaic virus RNA 3 contains at least two independent binding sites for viral coat protein. , 1994, Nucleic acids research.

[18]  F. Young.  Biochemistry , 1955, The Indian Medical Gazette.

[19]  J. Kaper.  Arrangement and identification of simple isometric viruses according to their dominating stabilizing interactions. , 1973, Virology.

[20]  J. Bol,et al.  Early and late functions of alfalfa mosaic virus coat protein can be mutated separately. , 1994, Virology.

[21]  J. Bol,et al.  Molecular weight of the coat protein of alfalfa mosaic virus. , 1971, Biochemistry.

[22]  L. van Vloten-Doting,et al.  Evidence that alfalfa mosaic virus infection starts with three RNA-protein complexes. , 1981, Virology.

[23]  P. Walstra,et al.  Nucleotide sequence of the 3'-noncoding region of alfalfa mosaic virus RNA 4 and its homology with the genomic RNAs. , 1979, Nucleic acids research.

[24]  V. Pallás,et al.  Nucleotide sequence of apple mosaic ilarvirus RNA 4. , 1994, The Journal of general virology.

[25]  V. Georgiev.  Virology , 1955, Nature.

[26]  D. Gonsalves,et al.  Nucleic acid components of citrus variegation virus and their activation by coat protein. , 1975, Virology.

[27]  S. Scott,et al.  The complete nucleotide sequence of prune dwarf ilarvirus RNA 3: implications for coat protein activation of genome replication in ilarviruses. , 1994, Virology.

[28]  D. A. Roth,et al.  Computer-aided nucleic acid secondary structure modeling incorporating enzymatic digestion data , 1984, Nucleic Acids Res..

[29]  S. Scott,et al.  The complete nucleotide sequence of RNA 3 of citrus leaf rugose and citrus variegation ilarviruses. , 1995, The Journal of general virology.

[30]  C. Burd,et al.  Conserved structures and diversity of functions of RNA-binding proteins. , 1994, Science.

[31]  J. Bol,et al.  Complete nucleotide sequence of tobacco streak virus RNA 3. , 1984, Nucleic acids research.

[32]  S. Scott,et al.  The complete nucleotide sequence of the RNA 3 of lilac ring mottle ilarvirus. , 1995, The Journal of general virology.

[33]  Specificity of RNA and coat protein interaction in alfalfa mosaic virus and related viruses. , 1985, Virology.

[34]  C. Reusken,et al.  Ability of tobacco streak virus coat protein to substitute for late functions of alfalfa mosaic virus coat protein , 1995, Journal of virology.

[35]  R. Quadt,et al.  Analysis of the protein composition of alfalfa mosaic virus RNA-dependent RNA polymerase. , 1991, Virology.