Introduction to RNA Virus Biosynthesis:
Many families of animal viruses have RNA as their genetic material. These RNA genomes can be single stranded (+ sense, – sense, antisense) or double stranded. Each class of genome has a different replication and gene expression strategy, and there is considerable variation within each class. The cytoplasm of infected cells is where the majority fully multiply. Exceptions are orthomyxoviruses and retroviruses. They generally have high mutation rates due to high error rates of RNA dependent RNA polymerases, which have no proofreading function. In the case of viruses with segmented genomes, there can be “reassortment” of the segments in cells infected by more than one strain/variant of virus.
Negative (-) Strand Non segmented RNA Viruses:
Example: Paramyxoviruses, Rhabdoviruses, Filoviruses
After entrance, virion-packaged transcriptase mediates the transcription of the (-) strand. Proteins are made; (+) strand RNAs are created. The freshly formed virions are packed with full-length (-) strand RNAs. The cytoplasm of infected cells is where transcription and translation occur exclusively.
The genomes of negative stranded RNA viruses cannot function as mRNA. Therefore, these viruses must bring at least one RNA dependent RNA polymerase into host cell during entry. Initially the viral genome serves as template for mRNA synthesis. Later virus switches from mRNA synthesis to genome synthesis, as the RNA dependent RNA polymerase synthesize distinct plus stranded RNA for replication. During this phase of life cycle, plus stranded RNA molecule synthesized from minus strand genome serves as template for manufacture of new negative stranded RNA.
Biosynthesis in negative stranded segmented RNA virus:
Example: Influenza virus:
After adherence on respiratory epithelium with Neuraminidase and Hemagglutinin on sialic acid receptor, virion enters by receptor mediated endocytosis. This encloses virus in an endosome. When the endosomal pH drops, hemagglutinin experiences a significant conformational shift. Hemagglutinin’s hydrophobic ends protrude outward and reach the endosomal membrane. After they contact the membrane, fusion occurs and nucleocapsids are released into cytoplasm. Once genome and its associated RNA dependent RNA polymerase enter the host cell, genome serves as template for mRNA synthesis. Later virus switches from mRNA synthesis to genome replication. During this phase of life cycle, plus stranded mRNA synthesized from minus strand genome segments serve as template for new negative stranded RNA genome. The virus exit cell by budding and thus acquire envelope.
mRNAs are synthesized from each segment. Viral proteins are synthesized. (+) strand RNA’s are synthesized and serve as templates for (-) strand genomic RNA’s
Biosynthesis in Positive (+) Strand RNA Viruses Coding for One Genome-Sized mRNA:
Example Poliovirus
The virus attaches to the human PV receptor. The nucleocapsid enters cell and once inside host cell, plus stranded RNA genome is released into cytoplasm. It acts as mRNA and is translated by host ribosome. The virus tricks the host into translating its capless RNA using a 5′ region on the RNA called internal ribosome binding site (IRES). Translation yields a large protein called polyprotein. Protease activity in the polyprotein causes it to split into three smaller pieces. All of the proteins needed for capsid development and the virus’s RNA-dependent RNA polymerase are produced by further cuts in these proteins. This polymerase generates negative stranded RNA molecules that serve as template for plus stranded RNA synthesis. Some of these are translated but eventually most will be used as new genomes and incorporated into capsids. Mature particles are released from cell by host lysis.
Positive (+) Strand RNA Viruses Coding for SubgenomicRNA:
Example: Togaviruses
Some plus stranded RNA containing viruses after synthesizing RNA dependent RNA polymerase from genomic plus stranded RNA, use polymerase in later life to synthesize mRNA that are smaller than genomic RNA. These subgenomic mRNA molecules are translated to yield their encoded proteins. The genomic RNA binds to ribosomes but only a portion of the 5’-end is translated into non-structural proteins. (-) strand RNA is synthesized. There are various size classes of (+) RNAs. Translation results in a polyprotein that is broken down to create structural proteins. Another is full length and acts as the genomic RNA for newly formed virions.
Biosynthesis in Single Strand RNA Viruses with Two Identical Strands:
Example: Retrovirus
The virus attaches to host cell surface proteins, CD4 via its gp120 viral envelope proteins and enters via receptor mediated endocytosis. Inside the infected cell, core protein dissociates from RNA and RNA is copied into a single strand of DNA by reverse transcriptase. The RNA is next degraded by reverse transcriptase and DNA strand is duplicated to form a double stranded DNA copy of the original RNA genome. Once double stranded DNA is formed, a complex of dsDNA, integrase and other factors move into nucleus. Then proviral DNA is integrated into host DNA by integrase enzyme. Once integrated, the provirus forces cell to synthesize viral mRNA. Both full length mRNA and shorter mRNA formed by alternative splicing are translated into 10 proteins needed to form HIV virion. All mRNA yield polyproteins that are cleaved to give rise to needed proteins. Also, some early proteins synthesized are involved in regulating cell processes so that HIV genes are preferentially expressed. Eventually viral proteins and the complete HIV-1 RNA genome are assembled into new nucleocapsid that bud from infected host cell.
References:
- ScienceDirect. (n.d.). Reverse transcriptase. In Topics in Neuroscience. Elsevier. https://www.sciencedirect.com/topics/neuroscience/reverse-transcriptase
- ScienceDirect. (n.d.). Poliovirus. In Topics in Neuroscience. Elsevier. https://www.sciencedirect.com/topics/neuroscience/poliovirus
- ScienceDirect. (n.d.). Polyprotein. In Topics in Medicine and Dentistry. Elsevier. https://www.sciencedirect.com/topics/medicine-and-dentistry/polyprotein