(34) DNA Viruses/RNA Viruses

lecture 34

all characterized viruses have

DNA genomes; most have circular dsDNA genomes

DNA viruses host are

euyarchaeota and arenarchaeota

most euryarchaeota viruses are

“head and tail” type similar to those that infect enteric bacteria (e.g., T4)

one novel archaeal virus infects a

halophile (grows in saline environments); unusual because it is both enveloped and has a ssDNA genome

a large number of unusually shaped and structural tough archaeal viruses have been discovered in

acidic hot springs that support large communities of crenarchaeota → grown in the lab, all have been DNA viruses

no archaeal RNA viruses have been

isolated to date, but environmental genomics studies suggest they exist

two groups of dsDNA animal viruses have unusual replication strategies

pox viruses and adenoviruses

pox viruses unusual replication

all replication events, including DNA replication, occur in the host cell cytoplasm

adenoviruses unusual replication

DNA replication occurs via leading strand synthesis on both DNA template strands

pox viruses - major historical and medical importance:

• smallpox was the first virus to be studied in detail

• first virus for which a vaccine was developed and only virus to be eradicated from the population by vaccination

pox viruses - among largest

animal viruses known

pox viruses - virions contain

an envelope, a capsid, the dsDNA genome and several viral enzymes including DNAP and RNAP

pox viruses: vaccina virus

linear dsDNA, 190 kbp, encodes 250 genes

pox viruses: vaccina virus - following attachment and entry (via cell surface fusion or endocytosis),

nucleocapsids are released in the cytoplasm

pox viruses: vaccina virus - all replication events occur

in the cytoplasm

pox viruses: vaccina virus - genome unceasing requires

a viral protein that is synthesized after infection

• gene encoding this protein is transcribed by a viral RNAP contained within the virion

pox viruses: vaccina virus - following viral gene expression, genome replication, and assembly,

progeny version are released by host cell lysis

pox viruses: vaccina virus - because it elicits a strong immune response without serious eyelash effects, it has been genetically engineered to encode

proteins from other viruses to generate recombinant vaccines against influenza, rabies, herpes simplex type 1, and hepatitis B

adenoviruses - group of

small, naked, icosahdreal viruses with linear, dsDNA viruses

adenoviruses - heath

minor importance cause mild respiratory infections in humans

adenoviruses - are unique to due to the mechanism by which they

replicate their genomes and have been explored as viral vectors for their gene therapy delivery

adenoviruses - following entry, the nucleocapsid is

released int the host cell nucleus

adenoviruses - early genes are

transcribed by the host RNAP

adenoviruses - genome contains a

terminal protein attached to the 5’ end that is required for replication

adenoviruses - ssDNA cyclizes via

base-pairing of the inverted terminal repeats → looks like ds DNA

adenoviruses - initial replication yields a

complete ds viral genome and a ssDNA molecule

adenoviruses - replicated without

lagging strand synthesis

some animal DNA viruses can

induce caner

polymavirus SV40

naked icosahedral virus that causes tumors in small mammals (e.g., hamsters and rats)

polymavirus SV40 discovered as a

comtanimant of the Salk and Sabin poliovirus vaccines; source was monkey kidney cells used to produce the vaccine

SV40 DNA found in some

human tumors; ongoing debate as to whether it is a contributing factor in human cancers

polymavirus SV40 - structure

circular dsDNA genome, 5.2 kbp

polymavirus SV40 - in a permissive host, the virus uses the host

DNA polymerase for replication (genome too small to encode its own DNAP)

polymavirus SV40 - some genome contains

overlapping genes

polymavirus SV40 - transcription occurs in the

nucleus (host RNAP) → mRNAs are exported to the cytoplasm for translation → proteins are imported into the nucleus for virus assembly

polymavirus SV40 - virions

released after cell lysis

polymavirus SV40 - in nonpermissive host,

lytic events do not occur

polymavirus SV40 - in nonpermissive hosts, the viral genome becomes integrated into

the host genome, resulting in transformation = loss of growth inhibition and malignancy

expression of specific SV40 genes is required to convert the

cell to a transformed state

polymavirus SV40 - the tumor-inducing proteins bind to and

inactivate host cell protein that control the cell cycle, thereby promoting uncontrolled cell division

herpesviruses (herpesviridae family)

large group of dsDNA viruses that causes a variety of diseases

herpesviruses diseases

• herpes simplex virus 1 and 2 (fever blisters, venereal herpes)

• varicella zoster virus (chicken pox, shingles)

• expstein-barr virus (mononucleosis)

herpesviruses - an important group causes clinical forms of cancer

epstein-barr virus causes burrito’s lymphoma = cancer epidemic in children in central Africa and New Guinea

herpesviruses = cytomegalovirus (CMV) is a widespread virus (present in 75% of adults over 40 years);

often asymptomatic but can cause pneumonia, retinitis, gastrointestinal diseases, as well as more serious illness or even death in immunocompromised

herpesviruses establish a

life-long latent infection which can reactivate under stream or when the immune system is compromised

herpesviruses structure

linear dsDNA genome, icosahedral capsid, a layer of tegument of viral enzymes, and a membrane envelope

herpesviruses - attachment via

envelope glycoproteins and cell receptors

herpesviruses enters via

cell surface fusion or endocytosis

herpesviruses - nucleocapsid is transported to

the nucleus, the viral genome enters the nucleus

herpesviruses - genome filled capsids bud through

the inner nuclear membrane obtaining a primary envelope; primary envelope is lost when it uses with the outer nuclear membrane

herpesviruses - double envelope obtained via

Golgi-derived vesicles

herpesviruses - release occurs via

fusion of the outer envelope with the plasma membrane

herpesviruses - in the nucleus, three classes of mRNA are produced by the host RNAP

immediate early, delayed early, late

immediate early mRNA -

encodes regulatory proteins

delayed early mRNA

encodes DNA replication proteins

late mRNA

encodes structural proteins

herpesviruses - transcripts are exported to

the cytoplasm for translation

herpesviruses - viral genome replication occurs via

rolling circle replication in the nucleus

herpesviruses - capsid proteins are imported into the

nucleus for assembly into procapsids

herpesviruses - genomes are cut from

concatemers and packaged into procapsids

herpesviruses - a few tegument proteins are

added to the capsid in the nucleus

herpesviruses - remains dormant in

nucleus and can reactivate (life-long)

human papillomaviruses - family of

double-stranded DNA viruses

human papillomaviruses - of more than

100 different strains, about 30 are transmitted sexually, and several of these cause genital warts and cervical cancer

human papillomaviruses - over 6 million people acquire new

PHV infections annually, leading to almost 10,000 cases of cervical cancer and about 3700 deaths

• in some cases resolves spontaneously, or leads to neoplasia, and some progress to cervical cancer

HPV vaccine are

available

• a widely used one is marketed as Gardasil

phage MS2 virions

3500 nucleotide, (+)ssRNA genome inside a 23-nm icosahedral capsid

phage MS2 virions - infects E. coli by

attaching to pilus (normally used for horizontal gene transfer via conjugation)

phage MS2 virions - small genomes encodes four proteins

maturation protein, coat protein, lysis protein, one subunit of RdRp required for viral RNA replication (other three subunits are encoded on the host genome)

phage MS2 virions - genome comprised of

overlapping genes and is translated directly upon entry [(+)ssRNA is equivalent to mRNA]

phage MS2 virions - translated RdRp makes

(-)ssRNAs → used at templates to make more (+)ssRNAs

phage MS2 virions - some of the nerdy synthesized (+)ssRNAs are used as

mRNAs for virions protein synthesis, some are used as genomes in progeny virions

poliovirus

named icosahedral virus (T = 1 capsid, 30nm) with (+)ssRNA genome

poliovirus - attach occurs via

interactions between the capsid and host cell surface receptors

poliovirus - entry typically occurs via

endocytosis

poliovirus - viral genome released into

the cytoplasm; all steps in virus replication take place in the cytoplasm

poliovirus - (+)ssRNA genome is covalently linked to

VPg protein at the 5’-end and contains a poly(A) tail at the 3’-end

poly(A) tail protects the mRNA from

nucleases, aids in mRNA export to the cytoplasm, and increases the rate of translation intiation

poliovirus - +)ssRNA genome serves as a

mRNA upon entry

poliovirus - viral genome is treated as a single ORF →

translation yield a single long protein (polyprotein) that undergoes self-cleavage (post-translational cleavage) to generate 20 smaller proteins necessary to nucleic acid replication and virus assembly

poliovirus - RdRp produced following

translation and polyprotien cleavage makes (-)ssRNAs which are used to make (+)ssRNAs; VPg protein is uridylated → 3’ OH is used to prime RNA synthesis

poliovirus - following progeny virion assembly,

cell lysis occurs releases new virions

coronavirus

largest known (+)ssRNA viruses

coronavirus structure

helical enveloped capsids; envelope contains glycoproteins thatt give virions a crown (“corona”) appearance

coronavirus - cause

respiratory infections, including SARS (SARS-CoV-1 virus) and COVID-19, in humans and other animals like bats

coronavirus - following attachment via

envelope glycoproteins and entry (via endocytosis), virus replication occurs in the cytoplasm

coronavirus - intially only the region of the

(+)ssRNA genome that encodes the RdRp is translated

coronavirus - genomic RNA is then used as a

template to produce (-)RNA strands form which individual gene-length mRNAs are produced and translated

coronavirus - full length genome RNAS are also made

off the (-) strand templates

coronavirus - progeny virions are assembled in the

golgi complex and are released from the cell surface when Golgi-derived vesicles containing virions fuse with the plasma membrane (exocytosis)

rhabdovirus structures

bullet-shaped, enveloped viruses with helical nucleocapsids that carry several enzymes (including RdRp)

rhabdovirus causes

rabies in animals and transmissible to humans

rhabdovirus (rabies) attach to host cells via

interactions between envelope glycoproteins and cell surface receptors

rhabdovirus (rabies)- entry is via

endocytosis; genome is released into the cytoplasm where virus replication occurs

rhabdovirus (rabies) - (-)ssRNA genome cannot be

directly translated; must first be transpired by viral RdRp in host cytoplasm

rhabdovirus (rabies) - viral RdRp produces two distinct classes of RNAs

• individual gene-length mRNAs

• genome-length (+)RNAs used as template to make (-)ssRNA genomes

rhabdovirus (rabies) - following translation, capsid proteins

coat the progeny (-)ssRNA genomes

rhabdovirus (rabies) - envelope glycoproteins transported to the

plasma membrane via the sectrory pathway; virions acquire envelopes as they bud through the plasma membrane

influenza virus

• envelope, helical nucleocapsid

• segmented genome (separate pieces of (-)ssRNA)

• influenza a virus - 8 segments

influenza virus - viral envelope contains several virally0encoded proteins

hemagglutinin and nueramidase