Question

Explain and give at least one example of each of the following major themes (or strategies) in the control of RNA virus gene expression: linkage between replication and control of expression, multifunctional gene products, overlapping genes, use of secondary structure to control gene expression, leaky termination, use of host proteins for viral functions, mimicking host cap structure, subgenomic mRNA, regulatory protein.

Answer 1

mimicking host cap structure- picornavirus and calicivirus

certain viruses mimick host RNA cap structure and terminates their transcription.

subgenomic mRNA-Nidovirales

in this process, transcription begins from 3' end or jumping of chromosome occur. it helps in regulation of transcription.

leaky termination- TMV or any other plant RNA virus

UAG codon of TMV helps in termination of genes transcription and translation in RNA viruses.

linkage between replication and control of expression- TMV

this occurs through RNA interference in which RNA products balance replication and transcription of certain genes

multifunctional gene products- Tat protein of human immunodeficiency virus type I

tat protein of HIV-1 is involved in many regulatory functions of the virus genome

overlapping genes- plants viruses such as potyvirus

plant viruses and many microviruses contain highly conserved overlapping genes which are involved in regulation of transcription

use of secondary structure to control gene expression- flavivirus, picornavirus, several retroviruses (RNA-RNA Kiss loop structures)

in such type of secondary structures RNA pol fails to produce RNA strand further thus, the transcription terminates.

use of host proteins for viral functions- HIV (retrovirus)

this is seen in many viruses not only in HIV. virus uses host factors or genes to control their gene expression. viruses usually uptake hosts machinery

regulatory protein- tat protein in HIV-1

this multifunctional protein is involved in gene regulation as well as other functions for HIV-1.