Lecture 2 viral genomes, proteins, lipids dinman

Lecture 2 BSCI437. VIRAL GENOMES,

PROTEINS, AND LIPIDS.

Criteria for viral genomes

• Must use same genetic code as host • Must use same biomolecules as host:

Nucleic Acids. Proteins, carbohydrates and lipids.

• Modifications (polyadenylation of mRNA, capping, splicing) must either depend on viral enzymes or host enzymes

• Continuous pressure to minimize size• Fast replication (especially important

in bacteria where virus must keep up with host)

• Genome packaging. – It takes a capsid of several million Daltons

to package a 10 kb genome. – The larger the genome the larger the

capsid must be and this means more energy and time required for synthesis).

All varieties of genomes

– (+) ssRNA– (-) ssRNA– dsRNA– retrovirus (+ssRNA dsDNA)– ssDNA– dsDNA– Mixed DNA and RNA

Thymidine tautomers

Basepairs with Adenine

Basepairs with Guanine

10-4

104

Tautomerization of pyramidines: the primary chemical basis for mutagenesis.

Tautomerization of pyramidines: Cytosine tautomerization is an order of

magnitude less.

Basepairs with Guanine

Basepairs with Adenine

10-5

105

H

Enamine Enimine

Cytosine tautomers

Properties of viruses relative to genome

type

• Size Range: Range from encoding as little ≈2 kb (Circoviruses), to as large as 800 kb (Mimiviruses)

• Variations (single molecule or segmented)

• NTP Polymerases: Viral or host origin

• Fidelity of replication – From high fidelity (<10-9/nt) to

low fidelity (10-4/nt)

• Recombination• Reassortment

Genome topologies

Includes every possible combination of: • double stranded or single stranded, • linear or circular, • contiguous, segmented, or gapped• polarity: Single stranded (+) strand, (-) strand, or

ambisense

Structure & Composition of Genomes: Generally, any and all possible combinations are

known.

Composition. Can be RNA, DNA, and/or any combination thereof!

•DNA or RNA•DNA with short RNA segments•DNA or RNA with covalently attached protein (e.g. polio)

Cicrcular ds DNA genomes

Linear dsDNA genomes

Linear dsDNA genomes

Gapped circular dsDNA genomes

Circular ssDNA genomes

dsRNA genomes

(+) ssRNA genomes

(+) ssRNA with DNA intermediate

Linear (-) ssRNA genomes

Segmented (-) ssRNA genomes

Ambisense ssRNA genomes

Special properties

• Terminal Redundancy: genomes of many viruses are terminally redundant. Used as tools for replication, expression, integration into host chromosomes, and for protection of ends. Examples include λ, retro-, adeno-, parvo-, pox-, bunya-, and arenaviruses.

Special properties

• Covalent Modifications: Includes modifications to nucleic acids (eg. methylation, pseudouridylation, etc.), and covalent linkage with proteins. Of the latter, proteins covalently linked to the 5' ends of picorna- and adenoviruse RNAs play important roles in cap-independent translation.

Genome condensation

strategies• Hijack host proteins for some

or all replication functions• Overlapping genes • Genes on both strands of

dsDNA in opposite directions• Multiple splicing of the same

transcript to make many different proteins (only need 1 promoter)

• Polyprotein production from one mRNA and subsequent proteolytic cleavage

• Frameshift mechanisms allow downstream out of frame genes to be made at appropriate proportions

Viral adaptation and evolution through

mutation

• Three major phenomena are used:1. Base misincorporations by

polymerases.2. Recombination by breakage

and religation in all DNA viruses or RNA viruses with a DNA intermediate or by Copy-choice with many ssRNA viruses.

3. Reassortment in the case of viruses with multipartite genomes (more than one segment)

Mutation• Viruses are subject to the same type of

mutations as other organisms: – Transitions and transversions – Deletions – Insertions – Nonsense mutations.

• Mutations can be spontaneous or induced. – Inducing agents commonly used to directly

mutate the virus for study.– Mutations can be used to map genes in viruses

just as they are used to map in bacteria. • Mutations are also useful in determining

the function of a protein. – Conditional mutants- a mutant phenotype that is

replication competent under “permissive” but not “restrictive” or “nonpermissive” conditions.

• Mutations are subject to reversion either at the same or a different (pseudorevertant) location in the genome.

• Mutants can also be complemented by other viral strains in a superinfection.

Genome related phenomena

• Reassortment: exchange of genome segments in segmented viruses. e.g. Influenza

• Transduction: Incorporation of host cellular genes into viral genome, e.g. RSV

• Attenuation: virulence lost but virus can still replicate in host.

• Recombination: Exchange of genetic information between two or more virus genomes.

Non-Genome related

phenomena• Interference: inhibition of

replication or infection of one type of virus by another. e.g. HIV-1 prevention of CD4 expression in infected cell; Defective Interfering Particles in plant viruses.

• Phenotypic mixing: exchange of envelopes or coat proteins between different viruses. “Pseudotypes”

Viral ProteinsAs few as 2 and as many as >50 virus-encoded

proteins. Generally divided into “Structural” and “Non-structural”.

• Structural: These compose the capsids/nucleocapsids, and envelope proteins. – Primary function of those involved in

capsid/nucleocapsids is to serve as building blocks for the virion (viral particle).

• Envelope proteins are typically glycoproteins in the form of spikes or projections. – Typically, these serve as receptors for host cell-

surface glycoproteins and are involved in viral attachment and entry into cells (infection).

• Non-structural: proteins with enzymatic, virus replicative, or for interactions with host-cell encoded factors. – Examples from HIV include Pol, Int, RNase H,

Integrase, Nef, Vif, and Tat.

Viral Lipids

• Viral envelopes contain complex mixtures of neutral lipids, phospholipids and glycolipids.

• As a rule, their composition resembles that of the host cell membrane from which the envelope was derived.

Host-encoded molecules

• Viruses can pick up molecules from host cells.

• Lipids. – Make up bulk of viral

envelopes. – Taken from host cellular

membranes.

• RNAs. – tRNAs used for priming. – 5S rRNA and other trans-

acting factors used in translation initiation.