Sailen Barik

Gene expression of vesicular stomatitis virus genome RNA

It is just over 20 years since the landmark discovery was made by Baltimore et al. (1970) that vesicular stomatitis virus (VSV) packages within the mature virion the vital RNA-dependent RNA polymerase that transcribes the negative sense (anti-message sense) genome RNA into messenger RNAs. This unique observation provided the window of opportunity to study the regulation of VSV gene expression in the test tube and made VSV an early paradigm for RNA viral gene expression, a position that it has maintained ever since. In the past two decades, availability of information pertaining to the mechanism of gene expression of VSV has burgeoned, providing a better understanding of the structure and function of not only the VSV genome and its products but also those of negative-strand RNA viruses in general. The complete nucleotide sequence of the genome is now known (Rose and Schubert, 1987) and hence the sequence of the mRNAs and the deduced amino acid sequences of the viral proteins. All virus-coded proteins have been identified and their possible functions in the viral life cycle assigned. Notwithstanding this progress, the precise mechanisms by which the linear, single-strand RNA genome is transcribed into mRNAs and eventually replicated still remain a challenge to molecular virologists. VSV, a rhabdovirus, is thus a prototype model of all nonsegmented negative-strand RNA viruses, such as rabies, measles, mumps, parainfluenza, respiratory syncytial, and Sendai, to mention a few. While rabies is a rhabdovirus, all the other examples belong to the Paramyxoviridae family. The gene order and overall mechanism of gene expression in these two families of viruses are generally expected to be very similar. Available evidence has in fact demonstrated a commonality in their modes of transcription and replication. However, there are specific differences between VSV and the paramyxoviruses (as there are among the individual members of the Paramyxoviridae family) that warrant

An intronic microRNA silences genes that are functionally antagonistic to its host gene

MicroRNAs (miRNAs) are short noncoding RNAs that down-regulate gene expression by silencing specific target mRNAs. While many miRNAs are transcribed from their own genes, nearly half map within introns of ‘host’ genes, the significance of which remains unclear. We report that transcriptional activation of apoptosis-associated tyrosine kinase (AATK), essential for neuronal differentiation, also generates miR-338 from an AATK gene intron that silences a family of mRNAs whose protein products are negative regulators of neuronal differentiation. We conclude that an intronic miRNA, transcribed together with the host gene mRNA, may serve the interest of its host gene by silencing a cohort of genes that are functionally antagonistic to the host gene itself.

Gene expression of nonsegmented negative strand RNA viruses

Nonsegmented negative strand RNA viruses comprise major human and animal pathogens in nature. This class of viruses is ubiquitous and infects vertebrates, invertebrates, and plants. Our laboratory has been working on the gene expression of two prototype nonsegmented negative strand RNA viruses, vesicular stomatitis virus (a rhabdovirus) and human parainfluenza virus 3 (a paramyxovirus). An RNA-dependent RNA polymerase (L and P protein) is packaged within the virion which faithfully copies the genome RNA in vitro and in vivo; this enzyme complex, in association with the nucleocapsid protein (N), is also involved in the replication process. In this review, we have presented up-to-date information of the structure and function of the RNA polymerases of these two viruses, the mechanisms of transcription and replication, and the role of host proteins in the life-cycle of the viruses. These detailed studies have led us to a better understanding of the roles of viral and cellular proteins in the viral gene expression.

Nucleotide sequence analysis of the L gene of vesicular stomatitis virus (New Jersey serotype): identification of conserved domains in L proteins of nonsegmented negative-strand RNA viruses.

We have determined the nucleotide sequence of the L gene of vesicular stomatitis virus (VSV), New Jersey serotype (Ogden strain) by primer extension dideoxy sequencing of the genomic RNA with reverse transcriptase. This analysis completes the entire genomic sequence of the VSVNJ (Ogden). Comparison of the deduced amino acid sequence of this L protein with those reported for L proteins of Indiana serotype and Hazelhurst strain of New Jersey serotype revealed an extensive sequence similarity among all three proteins. The comparison was further extended to the L proteins of other nonsegmented negative-strand RNA viruses, namely the rabies virus and four members of the paramyxovirus family: measles, Newcastle disease, human parainfluenza 3, and Sendai viruses. Our findings confirmed the existence of conserved as well as unique domains in the L proteins, suggesting an evolutionary relationship among these viruses.