Genetics and replication Flashcards
Principles of viral genetics:
2 Major principles:
A universal function of the viral genome: encode for specific proteins
All viral genomes must be copied to produce mRNA that can be read by the host ribosomes
The Baltimore system integrates these 2 principles:
There are 7 major types of viral genomes within this system
All viruses with RNA genomes must either…
encode an RNA-dependent RNA polymerase (to synthesize mRNA) or reverse transcriptase (RNA-DNA)
Rule:
Viral genomes must make mRNA that can be read by host ribosomes
What info is encoded in a viral genome:
Gene products and regulatory signals required for:
Replication
Efficient expression of the genome
Assembly and packaging of the genome
Regulation and timing of the replication cycle
Modulation of host responses
Spread to other cells and hosts
What information is encoded in a viral genome?
Information not contained in viral genomes
Genes encoding a complete protein synthesis machinery (e.g. ribosomal RNA and translational proteins)
Genes encoding proteins of energy metabolism
Terminology:
mRNA: positive (+) strand because it can be translated ( RNA is ready!)
Negative (-) strand cannot be translated and must first be copied to make the + strand
Ambisense RNA contains both (+) and (-) sequences
A strand of DNA is considered as a (+) strand
DNA VS RNA Genomes:
DNA genomes The host genetic system is based on DNA Many DNA viruses emulate host Use host polymerases to replicate genome Evolved mechanisms
RNA genomes
Cells have no RNA-dependent RNA polymerase (RdRp)
RNA virus genomes encode RdRp
RdRp produce RNA genomes and mRNA from RNA templates
The seven classes of viral genome:
dsDNA Gapped dsDNA ssDNA dsRNA ss(+)RNA ss(-)RNA ss(+)RNA with DNA intermediate
What is dsDNA transcribed by?
dsDNA is transcribed by either host DNA polymerase( generally smaller viruses because of limited space) eg. Polyoma and papilloma
What do other larger DNA genomes encode?
Other larger DNA genomes encode their own DNA polymerase- genome is larger- herpesvirus
Gapped dsDNA ( 7th) Hepadnavirus ( hepatitis B).
Gapped dsDNA ( 7th) Hepadnavirus ( hepatitis B). Partially dbl strand.This genome cannot be transcribed- fill the gap – has an attached RNA – RT – RNA- DNA
Parvovirus linear ssDNA:
small genome genome first made double stranded by cellular enzymes – dbl stranded and transcribed into mRNA
dsRNA (Reoviridae) + and - strand:
Ds RNA( Reovirirdae) + and – strand ds RNA cant be translated directly into MRNA therefore have package their own RdRp.
Structure and complexity of viral genomes:
Linear Circular Segmented Gapped DNA ( 7th Baltimore class) Single-stranded (+) strand Single-stranded (-) strand Single stranded, ambisense ( ambisense RNA contains both (+) and (–) sequences) Double-stranded DNA with short RNA segment
Sources of diversity in viral genomes: Mutations
Mutations: A change in the genotype of an organism not resulting from recombination. In short it is a substitution of one nucleotide for another.
There are different types of mutations
Sources of diversity in viral genomes: Effect of a mutation
Effect of a mutation: may lead to a change in the structure of the protein coded for by a nucleotide sequence or modify gene regulation.
Types of mutations:
- Normal
- Substitution[Silent mutation, Missense mutation, Nonsense mutation]
- Insertion [Frameshift mutation]
- Deletion
- Inversion
- Wild - type mRNA
- Wild - type polypeptide
Types of mutations:
. a. Single nucleotide polymorphism aka point mutation
- when a single nucleotide in a genome differs between members of a species
b. Indels (insertions, deletions) Frameshift mutations - involves single nts or small blocks of nts
Single-nucleotide polymorphism
Transition:
- a mutation changing a purine to another purine, or a pyrimidine to
another pyrimidine
- A ↔ G C ↔T(U)
Transversion:
A mutation changing a purine to a pyrimidine or a pyrimidine to a purine
- A ↔ C A ↔ T(U)
G ↔ C G ↔ T(U
INDELS:
Changes the reading frame of the genetic code- misreading of all downstream nucleotides
Effects of Mutations:
- Synonymous or silent mutation
- does not give rise to an amino acid substitution –
point mutation in 3rd nt of codon often silent – encodes same AA
5’ AUG UUU ACA AAA CUG UAA 3’
met- phe- thr- lys- leu- COOH
5’ AUG UUU ACC AAA CUG UAA 3’
met- phe- thr- lys- leu- COOH
- Non-synonymous or missense mutation
- gives rise to an amino acid substitution - may be lethal because non-functional gene product may be produced
5’ AUG UUU ACA AAA UAA 3’
met- phe- thr- lys- COOH
5’ AUG UUU AUA AAA UAA 3’
met- phe- Ile- lys- COOH
- Neutral mutation (neutral not always = silent)
- does not affect the fitness in the environment under consideration - Nonsense mutation
- point mutation that results in a premature stop codon
5’ AUG UUU AUA AAA CUC UAA 3’
met- phe- Ile- lys- leu- COOH
5’ AUG UUU AUA UAA CUC UAA 3’
met- phe – Ile - COOH
Interaction between viruses:
Genetic recombination between viruses
Recombination
Reassortment
Reassortment: A consequence of segmented genomes
- a type of recombination which occurs in viruses that have segmented genomes, whether ssRNA or dsRNA
- single cell infected with 2 segmented (related) viruses
- exchange of segments
- production of various stable reassortants
{Influenza, Rotavirus}
Recombination:
Formation of new covalently linked combinations of genetic material from 2 different parental genomes or between different sites of the same genome
What does recombination occur with?
Recombination occurs with both DNA and RNA viruses, with participation of the host or viral replication machinery
Two methods of recombination:
Strand breakage and re-ligation (– less common)
Recombination by ‘copy-choice’
Reactivation:
Non-infectious parents infectious progeny
Reactivation is the generation of infectious (recombinant) progeny from non-infectious parental virus genomes.
Reactivation (example):
Example: the rescue of defective, long-dormant HIV proviruses during the long clinical course of acquired immune deficiency syndrome (AIDS) may result in increased antigenic diversity and contribute to the pathogenesis of the disease
Reversion:
A mutant organism sometimes regains its WT characteristics (process of regaining the original phenotype)
– occurs by means of an additional mutation in the mutant which restores function
Phenotypic expression of a mutation in a gene may be reversed by
- a back mutation in the substituted nucleotide
- a suppressor mutation occurring elsewhere in the same gene or even in a different gene → negates the biological effect of the original mutation
Quasispecies:
- Certain viruses e.g. HIV exists as quasispecies
- A complex mixture of rapidly evolving and competing molecular variants of RNA virus genomes that occurs in most populations of RNA viruses
- The population of virus consists of a fleeting majority type that dominates the dynamic equilibrium
What is the purpose of viral replication?
The purpose of viral replication is to generate new viral genomes and proteins in order to continue their infectious cycle and spread to a new host
The replication strategy of viruses is dependent on the coding capacity of the genome:
- Small viruses e.g. parvovirus - heavy reliance on host cell
- Large virus e.g. poxviruses – encode most of the information required for replication. Only needs the cells for its machinery e.g. ribosomes
Where do most genomes replicate?
Most RNA viruses replicate in the cytoplasm
(except Influenza and HIV)
Most DNA viruses replicate in the nucleus
(except Poxvirus)
Overview of viral replication:
Viruses attach to the host cell, enter, release the genome (uncoating), replicate the genome, express whatever structural or non-structural proteins are required, self assemble and then exit
Virus attachment:
Virus particles bind to host cell receptors to initiate entry
Viruses may use more than one receptor – i.e. infect different types of cell
Viruses may use a receptor and a co-receptor
Note: The first cell surface molecule essential for viral attachment is called its RECEPTOR
Virus attachment (Example):
Example: HIV binds to the CD4 cell receptor and then requires an additional co-receptor such as CXCR4 for entry
What does the cell receptor determine?
The cell receptor may determine the tropism of viruses (i.e. the type of cell its able to replicate in) and the host range
What does the binding of virions to cell receptors activate?
Binding of virions to cell receptors may activate signalling pathways and facilitate viral entry or stimulate cellular responses that enhance pathogenesis
Entry into the cell:
Is an energy-dependent process that occurs shortly after attachment: 2 mechanisms
Two mechanisms of the entry into the cell:
Receptor mediated endocytosis into intracellular vacuoles via coated pits at the cell membrane
After endocytosis, vacuole fuses with lysosome
Inner environment becomes more acidic, and degradative enzymes accumulate
Fusion – only enveloped viruses. Either at the cell surface, or after internalization
Entry into the cell:
- Membranes of enveloped viruses fuse with each other, membrane fusion takes place during other cellular processes such a cell division and exocytosis.
- Membrane fusion is mediated by binding of receptors eg with HIV hairpin movement of the heptad repeats that place the two membranes in close proximity with each other.
- Virus and cell membrane brought together- the precise mechanisms by which the bilipid layers fuse together is not completely understood but the fusion protein – makes an opening called a fusion pore allowing exchange of material across the membrane. – specific process to ensure viral material goes to the correct compartment of the cell.
Uncoating
- Exposing the viral genome via partial or complete removal of the capsid
- May be triggered by acidification of endosome e.g. influenza
- Some virus genomes are released through a pore which forms by interaction of the capsid proteins with the endosomal membrane – penetration and uncoating are coupled e.g. polio
- Some capsids are involved with trafficking the genome toward the nucleus e.g. herpesviruses
Central dogma of molecular biology:
The central dogma of molecular biology describes the two-step process, transcription and translation, by which the information in genes flows into proteins: DNA → RNA → protein. Transcription is the synthesis of an RNA copy of a segment of DNA
What does the genomes of RNA viruses encode?
The genomes of all RNA viruses encode RNA dep RNA polymerase, except HIV to start the synthesis of new genomes and mRNA.
Group 1:
- dsDNA E.g. herpesviruses, adenovirus
- Most replicate in the nucleus (exception: poxvirus)
- Produce factors which act on host cellular machinery, and control further transcription, regulating the phases of replication (i.e. early – non-structural proteins, late – structural proteins)
Group 2:
- ssDNA e.g. Parvovirus
- Highly reliant on host cell machinery because they possess small genomes
- Replicate in the nucleus
- ds DNA intermediate – forms a template to make progeny ss DNA nucleic acids
Group 3:
*ds RNA with segmented genomes e.g. Reovirus
*Each segment is transcribed separately to produce monocistronic mRNAs
*Each segment is transcribed post cleavage of the polyprotein into small functional proteins
*Partial uncoating – transcription mediated by core associated RdRp
*
Group 4:
*+ve sense ssRNA
2 subgroups –
*Polycistronic mRNA (i.e. polyproteins) e.g. poliovirus
*More complex with two rounds of transcription e.g. rubella
*Regulate expression in terms of ratios of the different proteins and stage of replication cycle in which they’re produced
*Successful class, with multiple members and various hosts
Group 5:
- –ve sense ss RNA
- Two subgroups – segmented (e.g. influenza) and non-segmented (e.g. rabies)
- The genomes is first transcribed by vRdRp to produce monocistronic mRNAs
- This is the template for genome replication
Group 6:
*+ve sense ss RNA with a DNA intermediate
E.g. HIV
*The RNA genome is a template for reverse transcription to dsDNA
*Integrates into the host cell genome
Group 7:
*ds DNA with RNA intermediate
E.g. Hepatitis B virus
*Complex poorly understood replication
*Contain overlapping reading frames – compact genome
Assembly:
- Collection of all the components necessary for the formation of a mature virion
- Viral components may accumulate within compartments in the cell – seen as inclusion bodies
Interactions during encapsidation:
- Between nucleic acid core, capsid, other cargo
* Depends on physical size, electrostatics, sequence-specific interactions
Lipid rafts:
- Membrane microdomains, usually at the cell membrane
- Enriched with glycolipids, tightly packed cholesterol, proteins
- Limited lateral diffusion of lipids in the membrane
Maturation:
Maturation is when the virus becomes infectious
- Involves structural changes of the viral particle
- Frequently requires cleavage of larger proteins into smaller ones – usually requires proteases
- Some viruses mature within the cell. Some mature after release from the cell.
Release - Lytic:
- Infected cell breaks open and releases the virus
* Usually non-enveloped viruses
Release - Budding:
- Virus buds through cell membrane or an intracellular vesicle to acquire envelope
- May (e.g. paramyxoviruses) or may not (e.g. hepadnaviruses) be damaging to the cell
