Virus Genomes and Its Replication PART 1

8/3/2019 Virus Genomes and Its Replication PART 1

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rus enomerus enomeVirusReplicationVirusReplication

MukundS.VatsMukundS.Vats



•

orDNA

ora

DNA

virus?



• ………………….

• Ri onuc ease RNAase

• Deoxyribonuclease (DNAase)



• Fourt es:1. dsDNA,

2. ssDNA,3. dsRNA

4. ssRNA.• TwoTypes

1. Circular

2. Linear



•

• May vary between 1.7 kb to over 1000 kb

• T e argest virus genomes, suc as t at o t e

mimivirus, are larger than the smallestgenomes o ce u ar organisms, suc as some

mycoplasmas



• Encodes the virus proteins

• Some cases untranslated RNAs• The virus genome carries additional information, such

Signals for the control of gene expression.

Signals for down regulations of expressed proteins.Signals for viral protein processing.

• Generally by nucleotide sequences,

•

, ,within structure intramolecular base pairing i.e.secondary and tertiary structures have been observed

.



• InsinglestrandedNucleicAcids.

WHY?

• ssDNA complementarysequencesmaybasepairthrough

G–CandA–Thydrogenbonding;

• ssRNA weakerG–Ubondsmay

forminadditiontoG–CandA–U

basepairing.

• ntramo ecu ar asepa r ng

resultsinregionsof secondary

structurewithstemloops andbul es.

• InsomessRNAs intramolecularbasepairingresultsinstructures

knownaspseudoknots



n capp ng agg ng……..n capp ng agg ng……..



•

base paired and folded near their 3 ends to.

•These structures contain sequences that

.



• The genomes of many viruses contain.

• These sequences include promoters, origins of replication and other elements that areinvolved in the control of events in virusreplication.

• Many linear virus genomes have repeat

sequences at the ends (termini), Known asTerminal Re eats

• If the repeats are in the same orientation theyare known as direct terminal repeats (DTRs),

• whereas if they are in the opposite orientation

(ITRs).

• Multiple repeated copies of a gene present insome virus DNAs Known as tandem repeats



(makingof newReplicaof virus(makingof newReplicaof virus



WhatisdifferencebetweenVirusreplication&

genomereplication?



1. Attachmentof aviriontoacell

2. Entryandestablishmentintothecell3. Transcriptionof virusgenesintomessengerRNA

molecules(mRNAs)

4. Translationof virusmRNAsintovirusproteins

.

6. Assemblyof proteinsandgenomesintovirions

. .



• Via Cell receptors and / or co

receptors

• usually glycoprotein

– acting as receptors for

chemokines and growth factors; –

adhesion

• Addition to cell receptor

Conformational Change in virusreceptor attachment to Co

.



Evidencethatacellsurfacemoleculeisavirus

receptor

Soluble derivatives of the molecule block virus

.

The normal ligand for the molecule blocks virus

bindin infectivit .

Introduction of the gene encoding the molecule

into virusresistant cells, and ex ression of that

gene, makes those cells susceptible to infection.





• ,

attractionsandvander Waalforces.

virionsandreceptors

• Itisawea on etween.w y

• Toreducechancesof dualinfection.

• ereceptorcon gurat onmayc angeeas y.



.• After bindin to rece tors viruses must cross the

plasma membrane.They may either fuse to cell surface or

ey may cross e mem rane roug en ocy os sinto the cytoplasm.

• This process is used by cells for a variety of functions, including nutrient uptake and defenseagainst pathogens.

may it e in epen ent o t ese two• Clathrin mediated endocytosis (e.g. adenoviruses)

• Caveolinmediated endocytosis (e.g. simian virus 40)



Changeinconformationmaybe

becauseof:

BindingOf Receptor

ChangeinPH

• Carried to lysosomes where the pH may be further

across the membrane

•

important for those enveloped viruses that need to

carr out acidtri ered fusion of the envelo e with

the vesicle membrane.

• Lipid bilayers do not fuse spontaneously and each

enveloped virus has a specialized glycoprotein

responsible for membrane fusion.



NakedVirusesNakedViruses



EnvelopedVirusesEnvelopedViruses



• Most of DNA viruses the destination of nucleus is reached using one of the

transport systems of the cell, such as the microtubules.

• os v ruses o eu aryo es rep ca e n e cy op asm a or y o emencode all the enzymes for replication of their genomes and they have norequirement for the enzymes from nucleus.

• Retroviruses are RNA viruses, replicate their genomes in the nucleus.

• en t ey wa t n t e cytop asm unt m tos s eg ns.

• During mitosis the nuclear envelope is temporarily broken down and the virus DNA(with associated proteins) is able to enter the nuclear compartment.

• These viruses therefore can replicate only in cells that are dividing.• However DNA (with associated proteins) of a group of retroviruses, however, can

be transported into an intact nucleus. This group (the lentiviruses, which includesHIV) can therefore replicate in nondividing but active cells.

dsDNAdsDNA

ssDNAssDNA

dsDNA

dsRNA

ssRNA ()



• Generaly DNA viruses replicate in the

nucleus (Except few ds DNA viruses).

• The structural proteins of some of these

viruses have sequences that allow them

to attach to microtubules.

system to take their nucleocapsid, fromthe periphery of the cytoplasm to a

location close to the nucleus.

• Viruses must either shed some of their

load to form slimmer structures or un

coat at a nuclear pore.• Depending on the virus, the process can

take place

at the cell surface, the capsid remaining

on the exterior surface of the cell;

within the cytoplasm; at a nuclear pore;

within the nucleus.



3. Transcri tion of virus enes into mRNAs



•1958FrancisCrickProposedCentralDogma,whichismodifiedin1970



• viruses transcribe theirgenes by similarprocesses, some of them

transcription machinery.

• Hence, the expression of vira gene is a socontrolled by varioussequences in the DNA:

Enhancers binding sites for transcription factors,

which affect the rate of transcription

Promoter T A T A A/T A A/T A/G



• Viruses that replicate in thenucleus generally use a cellenzyme, while viruses thatreplicate in the cytoplasmencode their own.

• An RNA virus in cytoplasmneeds an RNAdependent

transcribe.

• Each virus in Classes III, IV

enzyme, in spite of the factthat the cells of plants and

encode ssRNAdependentRNA polymerases.



• All the viruses that carry out transcription in

,virion. (except the (+) RNA viruses)

transcription they must translate copies of the.

• Among the synthesized mRNA most

‘ ’ ’tail at the 3’ end.



• Splicing of mRNA

• Some primary transcripts of viruses that replicate in the nucleus

are processe in t e same way to pro uce t e virus mRNAs• The HIV1 genome has a number of splice donor sites and

acceptor sites; splicing of the primary transcript results in more



4.Translation

of

virus

mRNAs

into

virus

roteins

• Eukaryotic mRNA is

monocystronic.

• methylated nucleotide cap at

the 5 end and a poly(A)sequence at the 3 end play key

roles in the initiation of

translation

Cap binding site foreukaryotic initiation factors

(eIFs),

Pol A tail ol A tail

binding protein binds to itwhich further bound at the

ends of the RNA and are

able to interact and

stimulates translation.



• There are a number of virus

mRNAs t at ave two or

more ORFs• In many bicistronic mRNAs

t e s over ap; n ot ersthere is an ORF within an

ORFRotavirusNSP5

• rames ng occurs w enthe ribosome moving alongthe RNA encounters a

sequence) followed by asecondary structure, usuallya pseudoknot

HIV1Gagand

GagPol



• Once rotein s nthesized ma under o one or

more modifications, including• Glycosylation – in RER Addition of

oligosaccharide groups to the polypeptide chain,

• Acylation – Addition of an acyl group (R–CO–) toa molecule – facilitates attachment to plasmamembrane.

• osp ory a on nvo ves e rans er o aphosphate group from a nucleotide by protein – .



Bacterial Translation & Eukar otic Translation

• Bacterial translation differs from eukaryotic translation in a number of

features.

– Translation may start before transcription is complete. The lack of a nucleusallows transcription and translation to be coupled.

– The ribosomes are smaller (the ribosomal subunits have sedimentation

coefficients of 30S and 50S).

– The 30S ribosomal subunit binds directly to a translation initiation region on.

sequence at the ribosome binding site (RBS) on mRNA and the antiSD

sequence at the 3 end of 16S rRNA in the 30S subunit.

– The methionine of the initiator methion l tRNA is enerall form lated.

– A much smaller number of initiation factors areinvolved.

– All ORFs within an mRNA are translated and several may be translated

concurrently.

– A few phages have overlapping genes, which may be translated by reading

through a stop codon or by ribosomal frameshifting



• Virus molecules synthesized in the

infected cell must also beranspor e .

• Virus mRNAs are transported fromthe nucleus to the cytoplasm, andvirus proteins may be transportedto various locations, including thenucleus

• Proteinsynthesisbeginsonafree

ribosome butwhenthesi nal

sequencehasbeensynthesizedit

directsthepolypeptide–ribosome

complextotheendoplasmic

reticulum where roteins nthesis

continues.• Manyproteinshaveasequenceof

aminoacids(postcode)that

.



• Many of the proteins synthesized in the rough endoplasmic reticulum aretransported via vesicles to the Golgi complex

• From here the glycoproteins may be transported to other membranes,such as the plasma membrane or the nuclear envelope.

• Progeny virions may bud from these membranes

•transported back to nucleus.

• These proteins have a nuclear localization signal which drive them tonucleus.

• RNAs are also transported within the cell

• mRNAs synthesized in the nucleus must be exported through nuclearpores to the cytoplasm. The RNAs are taken to their destinations by

roteins.• The Rev protein of HIV1 has both a nuclear localization signal and a

nuclear export signal.

• The nuclear localization signal ensures that Rev is transported into the, .

ensures that Rev and its RNA cargo are transported from the nucleus tothe cytoplasm via a nuclear pore.

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Virus Genomes and Its Replication PART 1