virus genomes and its replication part 1
TRANSCRIPT
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 1/35
rus enomerus enomeVirusReplicationVirusReplication
MukundS.VatsMukundS.Vats
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 2/35
•
orDNA
ora
DNA
virus?
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 3/35
• ………………….
• Ri onuc ease RNAase
• Deoxyribonuclease (DNAase)
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 4/35
• Fourt es:1. dsDNA,
2. ssDNA,3. dsRNA
4. ssRNA.• TwoTypes
1. Circular
2. Linear
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 5/35
•
• 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
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 6/35
• 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
.
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 7/35
• 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
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 8/35
n capp ng agg ng……..n capp ng agg ng……..
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 9/35
•
base paired and folded near their 3 ends to.
•These structures contain sequences that
.
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 10/35
• 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
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 11/35
(makingof newReplicaof virus(makingof newReplicaof virus
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 12/35
WhatisdifferencebetweenVirusreplication&
genomereplication?
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 13/35
1. Attachmentof aviriontoacell
2. Entryandestablishmentintothecell3. Transcriptionof virusgenesintomessengerRNA
molecules(mRNAs)
4. Translationof virusmRNAsintovirusproteins
.
6. Assemblyof proteinsandgenomesintovirions
. .
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 14/35
• 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
.
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 15/35
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.
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 16/35
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 17/35
• ,
attractionsandvander Waalforces.
virionsandreceptors
• Itisawea on etween.w y
• Toreducechancesof dualinfection.
• ereceptorcon gurat onmayc angeeas y.
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 18/35
.• 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)
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 19/35
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.
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 20/35
NakedVirusesNakedViruses
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 21/35
EnvelopedVirusesEnvelopedViruses
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 22/35
• 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 ()
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 23/35
• 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.
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 24/35
3. Transcri tion of virus enes into mRNAs
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 25/35
•1958FrancisCrickProposedCentralDogma,whichismodifiedin1970
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 26/35
• 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
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 27/35
• 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.
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 28/35
• 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.
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 29/35
• 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
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 30/35
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.
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 31/35
• 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
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 32/35
• 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 – .
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 33/35
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
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 34/35
• 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
.
8/3/2019 Virus Genomes and Its Replication PART 1
http://slidepdf.com/reader/full/virus-genomes-and-its-replication-part-1 35/35
• 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.