Amino-terminal sequence analysis of alphavirus polypeptides

Area of Science:

• Virology
• Molecular Biology
• Genetics

Background:

• The single late 26S mRNA of Semliki Forest virus (SFV) encodes multiple viral structural and nonstructural proteins.
• Understanding the gene order and protein relationships is crucial for deciphering viral replication mechanisms.

Purpose of the Study:

• To determine the precise gene order of proteins encoded by the 26S mRNA of Semliki Forest virus (SFV).
• To identify the location of the nonstructural 6K protein gene within the viral genome.
• To compare gene organization with related alphaviruses like Sindbis virus.

Main Methods:

• Partial NH2-terminal amino acid sequencing of SFV polypeptides E3, 6K, and p62 (precursor to E3 and E2).
• Sequencing of the Sindbis virus homolog of 6K, the 4.2K protein.
• Comparison of determined amino acid sequences with deduced sequences from viral 26S mRNA.

Main Results:

• Identical NH2-terminal amino acid sequences were found for p62 and E3 of SFV.
• The genes for SFV 6K and Sindbis virus 4.2K proteins are located between the genes for E2 and E1.
• The gene order on the 26S mRNA of alphaviruses was established as 5'-C-E3-E2-6K-E1-3'.

Conclusions:

• The gene order 5'-C-E3-E2-6K-E1-3' is conserved in alphaviruses.
• This finding clarifies the genomic organization and protein synthesis pathway.
• The study provides insights into mechanisms of viral glycoprotein insertion into the endoplasmic reticulum membrane.