Roles of human parainfluenza virus type 3 bases 13 to 78 in replication and transcription: identification of an additional replication promoter element and evidence for internal transcription initiation

Structure and function of negative-strand RNA virus polymerase complexes

Viruses with negative-strand RNA genomes (NSVs) include many highly pathogenic and economically devastating disease-causing agents of humans, livestock, and plants-highlighted by recent Ebola and measles virus epidemics, and continuously circulating influenza virus. Because of their protein-coding orientation, NSVs face unique challenges for efficient gene expression and genome replication. To overcome these barriers, NSVs deliver a large and multifunctional RNA-dependent RNA polymerase into infected host cells. NSV-encoded polymerases contain all the enzymatic activities required for transcription and replication of their genome-including RNA synthesis and mRNA capping. Here, we review the structures and functions of NSV polymerases with a focus on key domains responsible for viral replication and gene expression. We highlight shared and unique features among polymerases of NSVs from the Mononegavirales, Bunyavirales, and Articulavirales orders.

Initiation and regulation of paramyxovirus transcription and replication

The paramyxovirus family has a genome consisting of a single strand of negative sense RNA. This genome acts as a template for two distinct processes: transcription to generate subgenomic, capped and polyadenylated mRNAs, and genome replication. These viruses only encode one polymerase. Thus, an intriguing question is, how does the viral polymerase initiate and become committed to either transcription or replication? By answering this we can begin to understand how these two processes are regulated. In this review article, we present recent findings from studies on the paramyxovirus, respiratory syncytial virus, which show how its polymerase is able to initiate transcription and replication from a single promoter. We discuss how these findings apply to other paramyxoviruses. Then, we examine how trans-acting proteins and promoter secondary structure might serve to regulate transcription and replication during different phases of the paramyxovirus replication cycle.

Analysis of nucleotides 13-96 of the human parainfluenza virus type 3 antigenomic promoter reveals positive- and negative-acting replication elements

During replication of human parainfluenza virus type 3 (HPIV3), the 96-nucleotide antigenomic promoter (AGP) of HPIV3 directs the synthesis of genomic RNA. Previous work showed that nucleotides 1-12 were critical in promoting replication of an HPIV3 minireplicon, but nucleotides 13-96 were not investigated. In this study, the role of nucleotides 13-96 in AGP function was analyzed by creating and assaying mutations in an HPIV3 minireplicon. A replication promoting element known as promoter element II (nt 79-96) was confirmed in the HPIV3 AGP. Additionally, nucleotides 13-39 were found to constitute an additional positive-acting cis-element. However, detailed analysis of the 13-39 element revealed a complicated control element with both stimulatory and repressing elements. Specifically, nucleotides 21-28 were shown to repress RNA replication, while flanking sequences had a stimulatory effect.

Cis-acting elements in the antigenomic promoter of Nipah virus

Genome synthesis in paramyxoviruses, including Nipah virus (NiV), is controlled by sequence elements that reside in the non-coding nucleotides at the 5'-trailer (3'-antigenomic) end that make up the antigenomic promoter (AGP). Using a chloramphenicol acetyl transferase-based plasmid-driven minigenome system, the terminal 96 nt of NiV AGP were first mutagenized in blocks of three hexamers to enable broad mapping of the minigenome functional regions. This was followed by further dissection of these functional regions to define the cis-acting elements contained therein. Results based on RNA analysis and reporter gene activity identified a bipartite promoter structure similar to that seen in related viruses, but with some distinct differences: in NiV, each of the two discrete replication control elements was bimodal, characterized by a critical conserved region (nt 1-12 and 79-91) and a contiguous non-conserved region (nt 13-36 and 73-78), which appeared less important. The regulatory role of these less critical regions was underscored by the use of a two-step mutation strategy, which revealed the additive detrimental effect of substitutions in this part of the terminal element. The structure and sequence characteristics of the internal control element was also different: it involved four contiguous hexamers, and the region encompassing three of these (nt 79-96, corresponding to hexamers 14, 15 and 16), although analogous in position to the equivalent element in the Sendai virus AGP, was characterized by the distinct 5'-(GNNNUG)(14-15)(GNNNNN)(16) motif.

Further characterization of a paramyxovirus transcription initiation signal: search for required nucleotides upstream and importance of the N phase context

Paramyxovirus genomes contain a linear array of five to ten genes sequentially transcribed by the viral RNA polymerase. mRNA synthesis initiates at a nucleotide signal (gs1) within the genomic promoter located at the genome 3' end. To gain information about the mechanism involved in transcription initiation, a search was carried out for upstream nucleotides required for gs1 and the effects of the gs1 nucleocapsid protein (N) phase context on transcription regulation were determined. For both purposes, tandem promoter mini-genomes carrying a transcription signal ectopically positioned downstream of a replication-only signal were used. The requirement for hygromycin resistance gene expression was used in an attempt to select essential nucleotides within randomized stretches of nucleotides. Nucleotide insertions or deletions were also made on either side of the transcription signal to change its original N phase context in the five remaining possibilities and GFP expression from these modified signals was assessed. Cell cultures resistant to hygromycin treatment were readily obtained following amplification of mini-genomes harbouring randomized sequences. However, selected nucleotides upstream of gs1 could not be identified under conditions where nucleotides within gs1 were selected. In contrast, it was observed that changing the gs1 N phase context progressively decreased transcription by five- to tenfold. These results are discussed in relation to two different mechanisms of transcription initiation.