Notes on Genus: Alfamovirus

bacilliform

Type member: Alfalfa mosaic virus

Contents

Members of this Genus
General Description
Morphology
Electron Micrograph
Genome
Genus Genomic Organization
Genome Map
Type Member Genomic Organization
All Known Sequences
Curated Sequences

General Description

The genus Alfamovirus (from the type member alfalfa mosaic virus) is one of 6 genera in the family Bromoviridae. In common with other members of the family, it has a tripartite genome and an encapsidated subgenomic RNA from which the coat protein is expressed. It differs from the other genera in having bacilliform particles of several sizes and three major RNA species. At present it contains only one member, alfalfa mosaic virus, and the description below is based on that virus.

Morphology

Virions bacilliform, or quasi-isometric elongated, not enveloped, c. 18 nm in diameter and of various lengths: 56 nm (B), 43 nm (M), 35 nm (Tb) and c. 20 nm (Ta). Symmetry icosahedral. with particles composed of 240 (B), 186 (M), 150 (Tb) or 132 (Ta) subunits.

Virions composed of about 16 % nucleic acid (in all particle types).

Genome

Tripartite, linear, single-stranded, positive sense RNA, with segments of 3644 (RNA1), 2593 (RNA2) and 2037 (RNA3) nucleotides. RNA4, a subgenomic fragment of RNA3, 881 nucleotides long, is also encapsidated. Each virion contains one molecule of either RNA1 (B), or RNA2 (M), or RNA3 (Tb); Ta contains two molecules of RNA4. The 5'-terminus of each RNA has a methylated nucleotide cap (m7G5'ppp5'Gp...). There is a homologous region of 145 nucleotides at the 3'-termini of all RNAs. The 3' terminus has neither a poly(A) tract nor a tRNA-like structure.

Genus Genomic Organization

There are four open reading frames (ORFs), one each on RNA1 and RNA2 and two on RNA3. ORF4 is expressed from the subgenomic RNA4 (the 3' half of RNA 3).

Type Member Genomic Organization

The four open reading frames result in the following proteins:
  1. Replication protein 1a (RNA1) containing methyltransferase and helicase domains, 126 kDa
  2. Polymerase 2a (RNA2), RNA-dependent RNA polymerase, 90 kDa
  3. Movement protein 3a (5' half of RNA3), 32 kDa, involved in cell-to-cell transport
  4. Coat protein 3b (3' half of RNA3 but expressed from the subgenomic RNA4), 24 kDa