Satellite Tobacco Mosaic Virus
Created by Frances Allen
Satellite Tobacco Mosaic Virus (STMV) is an icosahedral satellite virus that coinfects members of the tobacco plant family with Tobacco Mosaic Virus (TMV). Satellite viruses are a class of viruses that depend on a helper virus, in this case TMV, in order to replicate because they lack the required molecular machinery (Valverde, 99). STMV exacerbates the symptoms of TMV, which damages the leaves of the domesticated tobacco plant Nicotiana tabacum. The study of STMV may help clarify the complex interactions between satellite viruses and their associated helper viruses. Further research regarding the structure, function, and replication of STMV may also provide insight for the development of drugs to inhibit the virus and avoid its deleterious effects on commercial tobacco production.
The molecular weight of Satellite Tobacco Mosaic Virus coat protein (PDB ID: 1A34) is 17513.98 Da, and the isoelectric point of this protein is 10.03, as provided by the Expasy Database (Artimo, 1). The primary structure consists of 159 amino acid residues, and the viral RNA genome contains 1059 bases (Larson, 38). The overall secondary structure of STMV consists of 6% 3/10 helices and 35% beta sheets. The secondary structure of the first 12 amino terminal residues of STMV could not be visualized due to their location within the virus, and residues13-36 form an extended loop structure (Larson, 37). Residues 37-159 form an eight-stranded, antiparallel, Swiss roll beta barrel (Larson, 39). Beta barrels maximize hydrogen bonding along the peptide backbone and are characterized by highly stability (Garret & Grisham, 271). This structural feature directly correlates with the function of this protein: the formation of a stable viral capsid in order to protect the viral genome.
Satellite Tobacco Mosaic Virus exists physiologically as a virion with a diameter of 17nm and icosahedral symmetry. Sixty identical copies of the coat protein form the external viral capsid that surrounds a core of RNA. By assembling a relatively large protein structure from a small repetitive element, this design achieves a high level of genetic economy and efficiency (Garrett & Grisham, 187). As a result, STMV both protects its RNA and saves valuable genomic space for encoding other proteins that are essential for its replication.
The RNA core is composed of 30 double helices connected by single-stranded RNA (Larson, 38). These helices interact directly with the STMV coat proteins and are essential for the structural integrity of the viral particle (Schroeder, 167). A combination of salt bridges between the positively charged Arg-79 residue and negatively charged RNA backbone hold this highly ordered assembly together. A free nucleotide also associates with each capsid monomer via hydrogen bonds with Arg-125 and Arg-131 (Larson, 42). This nucleotide is thought to be part of a single-stranded RNA loop independent of the 30 double helices, but its structure has yet to be solved. Water, likewise, plays a significant role in mediating contacts and establishing bonds in both protein-protein and protein-RNA interactions (Larson, 47). The precise mechanism of virion assembly has yet to be determined, but one hypothesis suggests that the viral RNA core assembles first, then coat protein dimers associate with the RNA, and finally, all of the dimers join together to form the full capsid (Freddolino, 446). The integrity of its structure is therefore critical to the successful assembly of a STMV particle.
Sulfate ions are located exactly on 5-fold axes within the assembled virion and serve as anchors, joining adjacent STMV coat proteins. The Asn-115 and Asn-117 residues from five coat proteins form a cage structure around the sulfate anion with hydrogen bonds to the sulfate oxygen atoms (Larson, 42). These interactions serve to reinforce the attachments between coat- protein monomers. Thus, the interlocking structure of the physiological form imparts the strength and stability necessary for the function of the STMV capsid as a whole.
Satellite Tobacco Mosaic Virus particles deform when exposed to extreme conditions (Kuznetsov, 223). At high pH levels, the virion expands to approximately 18 nm in diameter. When dried, viral particles shrink, lose their mechanical rigidity, and experience deformation. This demonstrates that the RNA and the protein shell are capable of coordinated movement, and that neither structure is rigidly defined or independent of the other (Kuznetsov, 231). The function of STMV is therefore dependent on the complex interactions between proteins, nucleic acid, and the extensive water networks that constitute its structure.
Proteins with similar primary structures often have similar functions because of conservation of amino acid residues within their active sites. A Basic Local Alignment Search Tool (BLAST) protein search compares the amino acid sequence of proteins, and an E-value less than 0.5 indicates high similarity between proteins (Altschul). A BLAST search for the primary structure of STMV, however, yielded no matches. This result was reasonable because STMV differs significantly from other satellite viruses in nucleic acid sequence, lacks serological relatedness, and requires different specific helper viruses for its replication (Valverde, 99). The small size and high mutation rate of this viral protein also predict a high level of divergence in primary structure from a related viral protein.
Proteins with similar tertiary structures frequently have similar functions because tertiary structure directly relates to function. The Dali server searches for similarities in tertiary structure by comparing intramolecular distances via the “sum of pairs method,” and a Z-score greater than 2 indicates a significant degree of similarity (Holm). A search for STMV in the Dali server revealed that the Satellite Pancium Mosaic Virus coat protein (PDB ID: 1STM) has a Z-score of 10.1, indicating that these two proteins have similar tertiary structures.
Satellite Pancium Mosaic Virus (SPMV) is also an icosahedral satellite virus that infects plants. It requires Pancium Mosaic Virus (rather than TMV) for replication within the host grass Stenotaphrum secundatum. The alpha subunit of SPMV coat protein contains 157 residues and has a secondary structure composition comparable to that of STMV – 5% 3/10 helical and 40% beta strand (Ban, 884). This protein contains an 8-stranded Swiss barrel roll that is structurally analogous to the barrel roll in STMV, but it is located in the central portion of the polypeptide (Ban, 882). While the amino acid sequences of STMV and SPMV lack substantial homology, each virus accomplishes the same function using this conserved structural motif. The presence of such a beta barrel in Satellite Tobacco Necrosis Virus, another icosahedral satellite virus, provides additional support for the existence of a beta barrel motif within an ancestral satellite virus that underwent divergent evolution. Unlike STMV, however, SPMV lacks an ionic species at its 5-fold axes, utilizing hydrophobic interactions instead to link coat-protein monomers together (Ban, 888).