The Primary Structure of the Coat Protein of Alfalfa Mosaic Virus Strain VRU. A Hypothesis on the Occurrence of Two Conformations in the Assembly of the Protein Shell

Abstract

The complete primary structure of the coat protein of strain VRU of alfalfa mosaic virus (AMV) is reported. The strain is morphologically different from all other AMV strains as it contains large amounts of unusually long virus particles. This is caused by structural differences in the coat protein chain. The amino acid sequence has mainly been established by the characterization of peptides obtained after cleavage with cyanogen bromide and digestion with trypsin, chymotrypsin, thermolysin or Staphylococcus aureus protease. The major sequencing technique used was the dansyl-Edman procedure. The VRU coat protein consists of 219 amino acid residues corresponding to a molecular weight of 24056. Compared to the coat protein of strain 425 [Van Beynum et al. (1977) Eur. J. Biochem. 72,[63][64][65][66][67][68][69][70][71][72][73][74][75][76][77][78], 15 amino acid substitutions were localized. Most of them have a conservative character and may be explained by single-point mutations. A correction is given for the AMV 425 coat protein: Asn-216 was shown to be Asp-216.The prediction of the secondary structure for the two viral coat proteins was not significantly influenced by the various amino acid substitutions except for the region containing residues 65 -100. This led us to the hypothesis that the AMV coat protein may occur in two different conformations favouring its incorporation into either a pentagonal or hexagonal quasi-equivalent position in the lattice of the protein shell. The substitutions in the above-mentioned region of the VRU coat protein may have caused a strong preference for the hexagonal lattice conformation. The model is supported by preliminary sequence data of the same coat protein region in AMV 15/64, a strain morphologically intermediate between 425 and VRU Alfalfa mosaic virus (AMV) is an interesting virus from both a biological and a structural point of view. This small plant virus belongs to the group of viruses with a tripartite single-stranded RNA genome encapsidated by one single type of coat protein subunits into rods of different but discrete lengths. Like the other heterocapsidic viruses within this group, AMV needs a small amount of coat protein to start an infection cycle (see [l -31 for a review). This remarkable biological activity of the coat protein was already discovered in 1971 [4], but the underlying mechanism is not known as yet.In our group we have established the complete primary structure of the coat protein of AMV strain 425, which consists of 220 amino acids [5]. Knowledge of the primary structure appeared to be of great help in several other lines of investigation concerning this plant virus. It was possible to make a precise comparison between the authentic coat protein and the biosynthetic products synthesized in various cell-free systems programmed with the subgenomic AMV RNA 4 [6-91. The amino acid sequence data greatly facilitated the nucleotide sequence determination of the coat protein cistron in the monocistronic AMV RNA 4 [lo, 1 I]. Furthermore, this knowledge is ...

Complete nucleotide sequence of alfalfa mosaic virus RNA 2

“…In the present paper the complete primary structure of RNA 4 is presented. The nucleotide sequence of the coat protein cistron is in perfect agreement with the amino acid se-Nucleic Acids Research quence of the viral coat protein as deduced in this laboratory (6,7).…”

“…An example of this technique is shown in Figure 2A. The 5'-terminal sequences of all fragments could be aligned either with the known amino acid sequence of the coat protein (6,7) or with the sequences of the extracistronic regions deduced previously (3,4,5). An analysis of about 50 fragments yielded 85% of the sequence of the coat protein cistron.…”

A kirromycin resistant elongation factor EF‐Tu from Escherichia coli contains a threonine instead of an alanine residue in position 375

“…Amino acid analysis of the eluted peptides and their sequence determination by means of the dansylEdman degradation procedure were done as in [27].…”

p‐Hyroxybenzoate Hydroxylase from Pseudomonas fluorescens

“…On the other hand, cleavage proceeded readily in the C-terminal part, resulting in almost the same set of peptides (yields approximately 38 %) as was obtained from peptide CB2aT4. The poor cleavage of peptide CB2a may be explained by its rather hydrophobic character [28].…”