Virology- RNA Virus Intro
What are the 3 groups of RNA viruses whose genomes are not mRNAs
- negative strand RNA viruses -closely related ambisense RNA viruses -double stranded RNA viruses
Will RNA viruses ever use DNA at any point in the replication process?
-NO -a molecule of RNA is always the template and a molecule of RNA is the product
What viral families are positive strand RNA viruses?
-Picornaviridea -Flaviviridae -Togaviridae -Hepeviridae -Coronaviridae -Artiriviridae -Toroviridae
RNA viruses replicate their genomes using virally encoded_______________________
-RNA-dependednt-RNA polymerase (RdRp)
Polyprotein
-RdRp and other viral proteins needed for viral RNA synthesis are encoded as polyprotein -the polyprotein is cleaved by virally encoded proteases
Non-coding regions
-all genomes have this -located at the 5' and 3' ends -referred to as untranslated regions (UTRs), noncoding regions (NCRs), nontranslated regions (NTRs) -vary in size -are required and sufficient to direct genome replication
Transcription/ replication complexes usually contain ______________ proteins
-between 2 and 4 proteins
What does the replicase complex consist of?
-consists of the set of proteins required to produce infectious genome -RdRp and other proteins needed for viral synthesis -may contain RNA-helicases (to unwind highly base paired regions of the RNA genome) -ATPases (to supply energy for the polymerization process)
dsRNA viruses
-ex: Family Reoviridae -have segmented genomes, packaging 11-12 segments of dsRNA -Reoviridae: nonenveloped, and particles consist of 2 or 3 concentric icosohedral capsid layers -segments are found in the innermost T=1 icosohedral shell
How are RNA viruses further subdivided into groups?
-further subdivided into groups based on type of RNA that serves the genome
Positive or plus (+) strand RNA viruses
-have genomes that are functional mRNAs -genomes are single stranded molecules of RNA and may be capped and polyadenylated -the infecting genomes has two functions: -it is the mRNA serves as the template for synthesis of additional viral RNAs -it is an mRNA and also serves as the template for synthesis of additional viral RNAs
RNA promoters
-help to direct synthesis of subgenomic mRNAs -provide a means to direct the RdRp to internal sites on the genome
What happens with the naked genomic RNA during transcription and replication?
-it is not infectious, so it cannot be translated and will eventually be degraded if transcription is blocked
Negative sense versus ambisense
-negative strand RNA viruses transcribe all viral mRNAs from the genome strand of the RNA -ambisense use a coding strategy to transcribe some mRNAs from the copy genome
RdRp
-non-structural protein, meaning that it is not found in the assembled virion -it is translated directly from directly from the infecting genome shortly after penetration
Negative and Ambisense RNA Viruses
-purified genomes (or chemically infectious genomes) are NOT infectious -RdRp is packaged within the virion -genomes serve as the templates for transcription and the first synthetic event in the replication cycle is mRNA synthesis -some replicate in the cytoplasm, a few families replicate in the nucleus -viral genomes are often tightly associated with a nucleocapsid (N) protein
Positive Strand RNA Viruses Overview
-purified genomes (or chemically synthesizes genomes) are infectious if introduced into a permissive cell -the genomes serves as an mRNA -the first synthetic event in the replication cycle is protein synthesis -genome replication is cytoplasmic -genomes of positive strand RNA viruses fold into complex structures. these RNA structural elements some have key roles in genome replication, transcription, and translation
Functional Definition of positive strand virus
-purified or chemically synthesized genomes are infectious
Internal Ribosome Entry Sites (IRES)
-serve as assembly platforms for ribosome assembly -
What is the template for synthesis of additional RNA strands?
-the RNA genome
Replicase Complex
-the RdRp and other proteins required for viral genome synthesis
For the 3 groups of RNA viruses whose gemones are not mRNAs, what is the first synthetic event after genome penetration?
-the first synthetic event after genome penetration is TRANSCRIPTION -this is accomplished by viral proteins (including the RdRp_ that enter cell along with the genome
During replication of RNA viruses, what are the 3 (at least) types of RNA that must be synthesized?
-the genome -a copy of the genome (genome copy) -mRNAs
What is a unique feature of the reovirus replication cycle?
-the infecting genome segments are transcribed within the capsid -the mRNA products leave the capsid through the pores at the vertices of the capsid
What do RNA viruses also use RdRp for?
-they also use RdRp to synthesize mRNAs (and some synthesize mRNA caps)
Transcription Complex
-when two processes differ (use different sets of proteins) -used to describe the particular set of proteins required for viral mRNA synthesis
Transcription and replication for negative sense RNA virus genomes
1. negative sense genome is bound by N protein and RdRp is also associated with RNA and N protein 2. Transcription begins, individual mRNAs are capped and polyadenylated 3. mRNAs are translated 4. as sufficient quantities of viral proteins are synthesized, the RdRp switches from transcription to genome replication to generate a complete end copt of the genome, called the copyRNA 5. the copyRNA serves as the template for additional genomes
Basic Replication Scheme for positive strand RNA viruses
1.Ribosomes assemble on the uncoated genome 2. Viral proteins (including the RdRp) are synthesized 3. RdRp synthesizes copyRNA 4. RdRp synthesizes mRNAs and genomes (some RNAs may be initiated at internal promoters) 5. Protein synthesis from mRNAs when sufficient capsid proteins have been synthesized, genomes will be packaged
