Lesson 4. Molecular Virology

Size: px

Start display at page:

Download "Lesson 4. Molecular Virology"

Willis Dwain Wood
5 years ago
Views:

1 Lesson 4 Molecular Virology

2 1. Introduction 1.1. Virus Definition Genetic elements made of living matter molecules, that are capable of growth and multiplication only in living cells DIFFERENCE WITH RESPECT TO OTHER GENETIC ELEMENTS: They can exist in an extracellular phase that allows their spread The extracellular form of the virus (i.e. virion) is metabolically inactive

3 Introduction 1.2. The viral genome ssdna dsdna ssrna dsrna Genome variation (Phase) Circular or Linear / A single molecule or Segmented Size: 3-200kb (Phage G, 670 kb) Gene compaction (overlapping genes )

4 Introduction 1.3. Virus Classification 1. Depending on the host Prokaryotic viruses: Bacterial viruses = bacteriophages or phages; Archaeal viruses Eukaryotic viruses: protozoan-, fungi-, plant-, animal-viruses 2. Formal taxonomy: Taxonomic ranks (taxons): order, family, subfamily, genus and species. FAMILY: unique virion morphology, genome structure (replication strategies). e.g. Ortomixoviridae, Hepadnaviridae, Poxviridae 3. Baltimore classification: Type of genome and its method of replicaton Group I: dsdna (except Group VII) Group II: ssdna Group III: dsrna Group IV: ssrna, positive-sense Group V: ssrna, negative -sense Group VI: Positive-sense ssrna viruses that replicate through a DNA intermediate Group VII: dsdna viruses that replicate through a ssrna intermediate

5 Introduction 1.4. The replication cycle of viruses 1. Attachment (adsorption) 2. Penetration (injection) Latency? 3. Synthesis of nucleic acids and proteins 4. Assembly and packaging 5. Release (lysis)

6 Introduction 1.5. Attachment or Adsorption Interaction between proteins on the outside of the virus and cell receptors Receptors: proteins, carbohydrates, glycoproteins, lipids, lipoproteins or complexes Carry out normal functions in the cell. e.g., Lambda-MalT Related viruses may not share receptors The presence of receptors determine which cells are susceptible: Species Strain (phage typing) Cell type Tissue Examples: M13 / E. coli F + Influenza virus/ Mucous membrane, red blood cells (Sialic acid) Measles / Any human cell, except red blood cells (CD46)

7 2. Prokaryotic Viruses ssrna + dsrna ssdna MS2 ØX174 M13 dsdna*** T7 T4 Mu Lambda

8 Prokaryotic Viruses 2.1. RNA phages MS2 Coliphage Expression (Transcriptional regulation is not possible) Temporal programme based on accessibility to AUG codons (RNA structure): The more accessible AUG is that of C (translated along the infection cycle) Access to the AUG of P is limited. Translation of C grants access to the AUG of P Protein C binds to AUG of P and inhibits its translation The AUG of A is accessible only in nascent RNA+ molecules The AUG of L is partially accessible only when ribosomes reach the stop of C

9 Prokaryotic Viruses 2.2. ssdna Phages (Group II) ssdna +: replication must precede transcription Filamentous: M13 Icosahedral: ØX174

10 Prokaryotic Viruses 2.3. dsdna Phages (Group I) T-uneven phages: T7 T-even phages: T4 Mu phage

11 Prokaryotic Viruses T7 Phage dsdna Viruses Strategies to maximize genetic economy Gene overlap Internal translational reinitiation Internal frame-shifts Genome: Linear 40kb Direct terminal repeat of 160 bp Replication Bidirectional One origin (closer to left end) TEMPORAL EXPRESSION PROFILE: Injection of the genome / Order of genes Left end.: Early genes RM system inhibitor T7 RNA polymerase Inh. Cell. RNA pol Inh. Cell Expr First to penetrate Use the host RNA polymerase Middle region: Intermediate genes Use T7 RNA polymerase Right end: Late genes Use T7 RNA polymerase

12 Prokaryotic Viruses dsdna Viruses T4 Phage Lytic Linear genome (169 kb) Complex capsid Head Neck (with collar) Tail (tube + sheath) End plate Tail fibers

13 Prokaryotic Viruses dsdna Viruses: T4 TEMPORAL EXPRESSION PROFILE Sequential modification of the host RNA polymerase specificity: 1. Early genes: RNApol-σ Intermediate genes: Modification of RNApolα subunit + phage proteins binding 3. Late genes: RNApol-σ Phage Replication Terminal repeats (3-6 Kb) Linear Genome: Ends? - Form concatamers through recombination - Sequence-independent Endonuclease - Regularly spaced cuts (> gene dotation) - Repeated ends - Permuted end sequences

14 Prokaryotic Viruses The Mu Bacteriophage dsdna Viruses Temperate Linear genome Replication through transposition Integration is necessary both for lysis and lysogeny C Protein (repressor) Lysogeny Inhibits Transposase Non-replicative Transposition Lytic cycle Replicative Transposition No repression

15 Prokaryotic Viruses dsdna Viruses: Mu Packaging bp Mu=37 kb 1-2 kb

17 3.1. Positive-strand RNA Picornaviridae Family Polioviruses Rhinoviruses Hepatitis A virus (HAV)

18 Positive strand RNA Viruses Picornaviridae - pico means small - Naked - Icosahedral - ssrna +

19 Poliovirus Fam. Picornaviridae Positive strand RNA Viruses - Capsid: 4 proteins, (VP1-4) x 60 - Intracellular cycle in the cytoplasm - Genome: 3 terminus poly-a tail (copied during replication) Absence of 5 cap (Vpg protein) Vpg AAAAAA - Polymerase is not present in the virion 7.5 kb - Translation of viral proteins must take place before replication

20 Positive strand RNA Viruses: Poliovirus Degradation of EIF-4B (binding of the ribosome to the methylguanosine cap) Translation of host proteins is blocked Replication Requires priming!!: Vpg - UU Expression 1 ORF (6620 nt) 1 Polyprotein (proteolytic activity) Equal amount of every viral protein (anti-economic regulation)

21 3.2. Negative-strand RNA viruses - Ortomyxovirus - Rhabdovirus - Ebola virus

22 Negative strand RNA Viruses Ortomyxovirus Fam. Ortomyxoviridae Influenza virus mixo = mucus New variants (antigenic shift): Epidemics Nucleocapsid: N Protein Transcriptase complex (endonuclease) Envelope: M Protein Hemagglutinin Neuraminidase Genome: Segmented in 8 RNA fragments

23 Negative strand RNA Viruses: Ortomyxovirus Transcriptase requires 5 priming to initiate transcription: stolen caps Poly-A: Polymerase slippage 5 -G Host s mrna Endonuclease 5 -G Viral RNA 5 -G Primer 5 -G AAAAAAA

24 3.3. dsrna: Reoviridae Family REO: Respiratory Enteric Orphan Rotavirus: Childhood Diarrhea Naked Double-shell Icosahedral capsid (Transcriptase) Segmented Genome (10-12 dsrna) Facilitates unwinding (replication) Antigenic shift

25 3.4. DNA Viruses Pros The virus can utilize the cellular transcription machinery The virus con utilize part or all the replication machinery of the cell Cons Most cells in an organisms are in a non-division stage DNA in eukaryotic cells only replicates during the S-phase ssdna Parvovirus dsdna Papovaviridae (SV40) Papillomaviridae Adenoviridae Herpesviridae Poxviridae

26 ssdna Parvovirus Parvoviridae Genome: 4,5-5 Kb (2 genes) 3 Terminal hairpin Replication primer Depends on the replication machinery of the host cell Infect tumor cells or those infected with other viruses (e.g., Adenovirus)

27 dsdna Viruses Adenovirus Herpesvirus Poxvirus

28 Adenovirus Adenoviridae dsdna Viruses Adeno : Gland Genome TP protein Linear of 36 kb Inverted terminal repeats ( pb) Naked Icosahedral virion - Replication and assembly in the nucleus - DNA is associated with histones

29 dsdna Viruses: Adenovirus Replication - Virus-encoded replication proteins (DNA polymerase) - Primer: ptp-c - Initiates at either end: No Okazaki fragments Asynchronously ssdna strand Cyclization, DBPs

30 dsdna Viruses Herpesvirus Herpesviridae Herpes simplex Varicella-Zoster Epstein-Barr virus Latent in neurons of the sensory ganglia Multilayer Virion Linear Genome of 150 kb Envelope with spikes Amorphous Tegument Icosahedral Nucleocapsid

31 dsdna Viruses: Herpesvirus TRANSCRIPTION α Genes (immediate early) β Genes (delayed early) γ Genes (late) REPLICATION In the nucleus Circularizes Rolling circle replication Concatamers ASSEMBLY In the nucleus Envelope via budding of the nucleus inner membrane Release through the endoplasmic reticulum

32 dsdna Viruses Poxvirus Poxviridae - The largest animal viruses (300nm Ø): Smallpox, Cowpox, Myxomatosis - Replication IN THE CYTOPLASM VIRION Proteins envelope Genome: kb Direct terminal repeat of 10 kb Covalently closed Replication??

33 3.5. Group VI: Retroviridae Rous sarcoma Virus (RSV) Human T-cell leukemia Virus (HTLV) Avian Myeloblastosis Virus (AMV) AIDS Virus (HIV) Envelope Glycoproteins Icosahedral Virion 2 copies of the genome (ssrna +) Genome 2 copies of ssrna + of 7-10 kb Nucleocapsid Retrotranscriptase Integrase trna from the previous host Direct terminal repeats Cap and Poly-A Not translated!!

34 Retrovirus ssrna + Retrotranscription dsdna in cytoplasm Integration in the genome Transcription: ssrna + (genomes, mrna) THE REVERSE TRANSCRIPTASE 4 activities : - RNA-dependent DNA polymerase - DNA-dependent DNA polymerase - RNase H, degrades RNA in DNA-RNA hydrids - Endonuclease

35 Retrovirus Retrovirus cccdna Viral Integrase Host DNA LTR gag pol env LTR ssrna + (mrna, Genomes)

36 Retrovirus Expression (1 RNA = Genome) GENE ORGANIZATION Three regions: Polyprotein gag (capsid proteins + protease) pol ( Retrotranscriptase and Integrase) env ( Envelope glycoproteins)

Chapter 25. 바이러스 (The Viruses)

Chapter 25. 바이러스 (The Viruses) Chapter 25 바이러스 (The Viruses) Generalized Structure of Viruses 2 2 Virus Classification Classification based on numerous characteristics Nucleic acid type Presence or absence of envelope Capsid symmetry