RNA Viruses: Replication & Gene Expression

RNA Viruses: Replication & Gene Expression

• RNA viruses replicate in the cytoplasm of host cells.
• (+)RNA viruses have genomes that function as mRNAs, often capped and polyadenylated.
• (-)RNA viruses carry RdRp within their capsid, essential for initiating replication.
• Host cell ribosomes translate viral genomes upon entry, producing viral proteins.
• The first viral proteins synthesized are those needed for new genome synthesis and RdRp.

Viral Replication Complexes (VRCs)

• Many RNA viruses compartmentalize genome replication and protein transcription within VRCs.
• VRCs are assembled from viral proteins, genomes, and host lipids and proteins.
• VRCs provide protection from host defenses and toll-like receptors.
• The (+) strand genome serves as a template to synthesize (-) strand anti-genomes, which stay bound to the (+) strand.

Class IV (+) RNA Viruses

• Class IV (+) RNA viruses utilize a single genome to express multiple proteins.
• Eukaryotic mRNA normally encodes one protein, while (+)RNA viruses require at least two: a capsomer and an RdRp.
• Immediate translation is critical for creating RdRp, which then synthesizes replicative forms and viral mRNA.
• Class IV viruses encode a polyprotein that is proteolytically cleaved into multiple individual proteins, including capsomers and RdRp.

Poliovirus: 5' Internal Ribosome Entry Site (IRES)

• Poliovirus lacks a 5' cap and uses an IRES to bind ribosomes for translation.
• The IRES allows the ribosome to bind internally, circumventing the need for a 5' cap.
• VPg, a viral protein, is a primer for genome replication.

Translation Initiation: eIF4G

• eIF4G (eukaryotic initiation factor) acts as a docking site for initiation factors and proteins involved in RNA translation.

Cap-Dependent vs. Poliovirus Initiation Complexes

• Cap-dependent translation initiation involves eIF4E binding to the 5' cap and forming a complex with PABP, leading to ribosome binding near the AUG start codon.
• Poliovirus uses ITAF, a host protein, to bind the IRES, replacing eIF4E.
• Poliovirus degrades eIF4E, preventing cap-dependent host mRNA translation.
• The poliovirus IRES is a complex stem-loop structure in the 5' untranslated region (UTR).

Overview of (+)RNA Virus Replication

• Example Viruses: Poliovirus, Hepatitis C virus
• The IRES allows for immediate translation of the genome (1).
• The translated polyprotein is cleaved into individual proteins (2).
• These proteins form virus replication compartments (3).
• Within these compartments, double-stranded replicative forms are used to produce mRNA and new genomes (4).
• These new genomes are used to form new infectious virions (5).

Class V ss(-) RNA Viruses

• Class V ss(-) RNA viruses may have segmented or non-segmented genomes.
• Examples: Orthobunyaviruses, Orthomyxoviridae, Paramyxoviridae
• (-)RNA viruses cannot directly use their genome as mRNA.
• They package RdRp within the virion to initiate transcription.

Mononegavirales: ss(-)RNA viruses with non-segmented genomes

• Example: Measles virus

Class III dsRNA Viruses: Reoviridae

• Example: Rotavirus
• Rotaviruses have a non-enveloped, icosahedral capsid with a triple-layered structure.
• Uncoating exposes a double-layered particle (DLP).
• Rotaviruses have a segmented, linear dsRNA genome with 11 segments encoding 12 proteins.
• Each segment has a 5' cap, but no polyA tail.
• Co-infection with different rotavirus strains can lead to reassortment of genome segments.

Rotavirus Genome Organization & Replication

• The rotavirus genome is segmented, with each segment encoding a specific protein.
• Replication occurs within viroplasms, cytoplasmic structures formed during infection.
• The DLP contains the viral RdRp, VP1/VP3, which transcribes capped (+)RNAs from each segment.
• These (+)RNAs function as mRNAs for protein synthesis and templates for (-)RNA synthesis.
• DLPs are fenestrated, allowing entry of NTPs and exit of newly synthesized mRNA.

Rotavirus mRNA: Translation Initiation

• Rotavirus mRNA has a 5' cap but lacks a polyA tail.
• Viral nonstructural protein NSP3 binds to a conserved sequence near the 3' end of mRNA, substituting for PABP.
• This allows for efficient translation of viral mRNA.

Rotavirus Replication Cycle: Summary

• The DLP catalyzes primary transcription, producing capped mRNA (1).
• Translated proteins form viroplasms, encapsulating mRNA with new DLPs (2).
• Inside new DLPs, (+)RNA templates are copied, forming DLPs with dsRNA genomes (3).
• This process leads to exponential increases in viral mRNA and protein (4).
• After a few hours, the virus switches from transcription and replication to assembly (5).

dsRNA Viruses: Key Points

• Rotaviruses have three-layered capsids surrounding a segmented dsRNA genome.
• The DLP is the transcriptionally active form of rotavirus.
• Many DLP components are enzymes involved in nucleic acid synthesis and structural proteins.
• VP1/VP3, a structural protein, synthesizes the 5' cap and mRNA using dsRNA as a template.
• Rotavirus mRNA lacks a polyA tail, but NSP3 binds to a conserved sequence near the 3' end, replacing PABP.

Explore the intricate processes of RNA virus replication and gene expression. Learn about the roles of (+) and (-) RNA viruses, the significance of viral replication complexes (VRCs), and how these viruses utilize their genomes to express multiple proteins. Test your understanding of the complexities involved in RNA viral biology.