Overview of virus life cycle

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1 Overview of virus life cycle Credit: Internet resources cell recognition and internalization release from cells progeny virus assembly membrane breaching nucleus capsid disassembly and genome release replication and translation

2 Replication scheme Class IIa +DNA ±DNA Class I Class IIb -DNA Class VI +RNA Class IV Baltimore classification -RNA Class V mrna ±RNA Class III

3 Replication overview Similar to host DNA leading and lagging strand synthesis, primer required (RNA), DNA polymerase and other host factors required lnicole3.blogspot.com

4 Replication overview Involvement of several enzymes 1) DNA unwinding protein 2) RNA polymerase 3) DNA polymerase III 4) DNA polymerase I (+ exonuclease activity) 5) DNA ligase 1 mistake/ bp replications

5 Replication of animal DNA viruses Enzymes mostly of host origin, some viruses carry their own enzymes Host machinery (enzymes etc) for generating DNA are in the nucleus (and mitochondria). Viruses utilizing host enzymes need to enter the nucleus. Viruses with own enzymes can replicate in the cytosol.

6 Nuclear DNA viruses Cytoplasmic DNA viruses I. Parvoviruses I. Poxvirus II. III. IV. Polyomaviruses Adenoviruses Herpesviruses V. Hepnadviruses May carry some enzymes

7 Example of class I: Polyomaviruses

8 Example of class I: Polyomaviruses Small, icosahedral, ~ 40 nm in diameter Contains circular duplex DNA Replicates in the nucleus DNA associates with host cell histones Utilizes host cell machinery mostly, except some viral proteins Viral proteins required for replication (enzymes, regulatory proteins etc) are expressed first (early genes) Host RNA polymerase II recognizes promoter, mrna produced Post-transcriptional RNA processing carried out by host enzymes Alternative processing of primary transcript produces small and large T antigens (Tag)

9 Example of class I: Polyomaviruses

10 Example of class I: Polyomaviruses Replication starts in the late phase of infection Similar to host DNA replication process Host enzymes are used Host DNA polymerase recognizes SV40 origin of replication in the presence of large T antigen Host histones bind to newly synthesized viral DNA

11 Example of class I: Adenovirus Large non-enveloped icosahedral virus (~ 70 nm diameter) Linear, ds DNA, associated with virally coded basic proteins (not host cell histones)

12 Example of class I: Adenovirus Early gene expression (proteins required for replication) carried out with host RNA pol and RNA modification enzymes Encodes its own DNA polymerase for replication Requires host proteins also DNA replicated by a strand displacement mechanism No Okazaki fragments, continuous synthesis Protein TP acts as primer (attached to 5 end)

13 Example of class I: Adenovirus

14 Example of class I: Herpesvirus Enveloped icosahedral virus, ~ 200 nm in diameter Linear, double stranded DNA

15 Example of class I: Herpesvirus Utilizes host RNA polymerase and host RNA modification enzymes A viral protein VP16 (tegument) enters the nucleus and binds to viral genome. This is part of the transcription factor complex recognized by host RNA polymerase.

16 Example of class I: Herpesvirus Early proteins encoded - DNA polymerase, DNA binding proteins, thymidine kinase, ribonucleotide reductase Comparatively more viral proteins utilized (drug targets) Precise mechanism of replication not known Newly synthesized DNA exists as concatamers, cleaved to appropriate size during packaging

17 Example of class I: Poxvirus Large enveloped virus, diameter ~ 200 nm Contains a double stranded DNA genome (192 kbp) Contains ~ 250 genes

18 Example of class I: Poxvirus Packages its own DNA dependent RNA polymerase Naked poxvirus DNA is not infectious at all Methylation, capping, polyadenylation of mrna carried out by virally encoded and packaged enzymes One of the immediate early mrnas codes for an uncoating protein Replication occurs in the cytoplasm, in viral factories Replication of DNA occurs by strand displacement and concatemer resolution Five major viral proteins are used, along with some cellular proteins

19 Hepnadviruses Class I/VII Enveloped, icosahedral viruses containing a partially double stranded, circular, but not covalently closed DNA genome Examples - Hepatitis B virus Replicates through an RNA intermediate Packages its own DNA polymerase, which has reverse transcriptase activity

20 Hepnadviruses Class I/VII DNA repair cccdna RNA pol II transcription Reverse transcription cap pgrna pa RC-DNA Schematic of replication cycle

21 Example of class IIa: x174 Parental genome Parental RF Rolling circle replication and formation of concatemers

22 Example of class IIb: Parvoviruses Small, non-enveloped, icosahedral, nm in diameter Autonomous parvoviruses (MVM) use host cell enzymes for replication, package -ve stranded DNA Defective parvoviruses (AAV) need helper virus co-infection, Package -ve and +ve stranded DNA (in different virions) Contains palindromic terminal sequences which can serve as primers Replication proceeds by single strand displacement, no lagging strand synthesis.

23 Replication strategy

24 Replication scheme Class IIa +DNA ±DNA Class I Class IIb -DNA Class VI +RNA Class IV Baltimore classification -RNA Class V mrna ±RNA Class III

25 Properties of RNA viruses Genome usually smaller than that of DNA viruses Probably because of the higher rate of error accumulation in RNA genomes RNA dependent RNA polymerase necessary (no DNA stage) Relatively few proteins

26 Properties of RNA viruses Strategy to make multiple proteins - a) Producing multiple monocistronic RNAs b) Producing a primary transcript that is processed by host splicing machinery c) Producing a large polypeptide which is cleaved into individual proteins d) Allowing ribosomes to bind internally to viral RNA

27 Example of Class IV Poliovirus Plus stranded RNA virus, functions as mrna Infectious genome Replication proceeds in presence of DNA synthesis inhibitors, so no DNA intermediate Requires a RNA dependent RNA polymerase (translated initially)

28 Example of Class IV Poliovirus Roy, J Gen Virol, 2008

29 Example of Class IV Poliovirus ~ 10 times more +ve strand RNA produced +ve strand RNAs packaged into virions and removed as template quickly, -ve strand RNAs remain available as templates continuously IRES VPg start codon for translation Genomic (+) RNA Polyprotein (includes polymerase) AAAAA stop codon for translation Genome corresponds to mrna, polyadenylated, no methylated cap Contains internal ribosome binding site (IRES) Polyprotein produced, which is cleaved to generate RNA polymerase

30 Example of Class IV Poliovirus VPg serves as primer for replication May be cleaved off and recycled by a host protein TBP2 unlinkase A lot of VPg and polymerase per cell! Needs to replicate in vesicles VPg IRES start codon for translation Genomic (+) RNA Polyprotein (includes polymerase) AAAAA stop codon for translation 5 VPg VP4 structural proteins non-structural proteins VP2 VP3 VP1 2A 2B 2C 3A 3B 3C 3D 3 3C

31 + + Replication scheme of poliovirus RNA SS RI SS RI SS polymerase + + RF RF

32

33 Poliovirus RNA dependent RNA polymerase Hobson et al, EMBO J, 2001

34 Poliovirus RNA dependent RNA polymerase RNA polymerase activity is highly cooperative Interaction via interface I necessary for binding RNA Interaction via interface II necessary for catalysis Hobson et al, EMBO J, 2001

35 Replication scheme of Qbeta RNA ~ 10 times more +ve strand RNA produced +ve strand RNAs packaged into virions and removed as template quickly, -ve strand RNAs remain available as templates continuously RNA dependent RNA polymerase consists of four host encoded and one virus encoded polypeptide Very specific for Qbeta RNA

36 Complete Qbeta polymerase Polypeptide function Source MW (KD) Binding to + strand Initiation Initiation Ribosomal Protein S1 Elongation factor Tu Elongation factor Ts Chain elongation Qbeta encoded 65 Minus strand synthesis Ribosome associated (hexameric protein) 72

37 Poliovirus replication occurs in large cytoplasmic vesicles Uninfected cell Infected cell Host factors are important Doedens et al, J Virol, 2001

38 Class V RNA viruses Minus stranded RNA virus Non-Infectious genome Requires a RNA dependent RNA polymerase, which is packaged in the virus Initial event after infection is synthesis of plus stranded RNA Examples orthomyxoviruses (influenza), Paramyxoviruses (measles), Rhabdoviruses (rabies)

39 Example of class V - Rhabdovirus polymerase and other proteins Virion RNA polymerase

40 Example of class V - Rhabdovirus Occurs in the cytosol Synthesis of mrnas can occur from partially packaged nucleocapsids mrna modification etc carried out by packaged genome 5 proteins are synthesized - N, P, M, G, L New copies of -ve strand RNA are coated with N

41 Example of class V Influenza virus Contains a fragmented genome - 8 -ve strand RNA wrapped with nucleocapsid mrna synthesis and replication occurs in the nucleus with viral polymerase Unique mechanism for capping the mrnas Nascent strands immediately wrapped with nucleocapsid

42 Synthesis of influenza virus mrnas Cleavage site cap A A Host mrna Viral exonuclease A U Influenza virus nucleocapsid A U Viral polymerase Viral mrna

43 Influenza virus RNA polymerase Three subunits - PB1, PB2, PA PB1 recognizes cellular mrna caps, has exonuclease activity PB2 elongates the cleaved primer PA involved in synthesis of -ve strand RNAs

44 Replication scheme of reoviruses Entire cycle occurs in the cytoplasm Reovirus partially uncoats into cores (infectious)

45 Example of class III - Reovirus Double stranded RNA virus, contains 10 segments of ds RNA Requires a RNA dependent RNA polymerase, which is packaged in the virus First step is to make mrna - produced by viral polymerase and modified by virally encoded proteins in the core mrna extruded through channels at the 5-fold axes of symmetry of the particles Old (input) mrna is conserved inside cores, serve as templates New +ve strand RNA packaged into progeny virions, where the complementary strand is synthesized

46 Replication scheme of reoviruses Core assortment of +ve RNA mrna + - proteins new virion

47 Schematic of bluetongue virus (orbivirus) core VP3 and VP7 form the core surface Roy, J Gen Virol, 2008

48 BTV core VP7 VP3 VP1+VP4 Roy, J Gen Virol, 2008

49 Example of class VI - HIV Plus stranded RNA virus, contains 2 RNA molecules with 5 cap and 3 polya tail Physically linked through hydrogen bonds Not released into the cytosol, cannot function as mrna Non-infectious genome Replication cannot proceed in presence of DNA synthesis inhibitors (actinomycin D)

50 Example of class VI - HIV An RNA dependent DNA polymerase (reverse transcriptase) is used to convert the ssrna genome into dsdna The existence of the enzyme first proposed by Howard Temin Enzyme isolated by Temin and Baltimore Mistake prone enzyme - 1 mistake/20,000 bases, contains Rnase H, Integrase and protease activities, utilizes trna as primer Enzyme and trna packaged into the particles along with genome

51 Example of class VI - HIV

52

53 Example of class VI - HIV Cap R U5 Leader Coding area U3 R PBS PPT A(n) R - terminally redundant region U3, U5 - unique, non-coding region, form 5 and 3 end of provirus genome, contains promoter elements for provirus transcription PBS - primer binding site Leader region - non-coding, present at 5 of viral mrnas PPT - polypurine tract, initiates +ve strand synthesis during reverse transcription

54 Example of class VI - HIV Cap R U5 Leader Coding area U3 R PBS PPT A(n)

55

56 U3 LTR R U5 U3 LTR R U5 Viral dsdna Integrated into host genome by Integrase

57 Expression of HIV mrna Transcription by host RNA polymerase II Utilize splicing and ribosomal frameshifting to make proteins Tat - transcription activator protein Rev - Helps in the export of mrna and genomic RNA to the cytosol

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