MIMM 211 Lecture 2 - 2024 PDF

Register for Slido We will be doing some interactive polling questions! Live polls using Slido: https://www.mcgill.ca/polling/ or sign in via Webex Enter # 8885731 1...

Register for Slido We will be doing some interactive polling questions! Live polls using Slido: https://www.mcgill.ca/polling/ or sign in via Webex Enter # 8885731 1  Please download and install the Slido app on all computers you use Check-in: How are you? ⓘ Start presenting to display the poll results on this slide. 2  Lecture 2 Virus Structure, Genomes and Classification MIMM 211 – Introductory Microbiology Monday November 4th, 2024 Dr. Jasmin Chahal 3 Structure of Viruses 4  Virus Structure Virion: a complete, fully developed, infectious viral particle Capsid: Protein coat surrounding nucleic acid (“capsa” in Latin meaning “box”). Composed of protein subunits called capsomeres Nucleocapsid (core): Nucleic acid + capsid Envelope: Consists of combination of lipids and proteins (host-derived) - May posses viral glycoproteins (spikes) - Recognize and bind receptor of host cell Most bacterial and plant viruses are naked/nonenveloped Most animal viruses are enveloped From 1st Lecture 5 © 2021, 2018, 2015 Pearson Education, Inc.  Viral genome Functions of the capsid inside capsid Empty capsid Protection of the genome: Packaging of the nucleic acid genome Receptors on cytoplasmic host membrane Viral genome Delivery of the genome (nonenveloped Direct penetration viruses): Capsid binds host cell receptors (b) Endocytosis Direct penetration: - Genome alone enters the cell Endocytosis: - The host cell endocytoses the entire virus - Uncoating of capsid, releasing genome 6 © 2021, 2018, 2015 Pearson Education, Inc. General morphology/symmetry of capsids Helical viruses—hollow, cylindrical capsid Icosahedral viruses—many-sided Complex viruses—complicated structures 7  Helical Capsid Viruses Spiral or Rod-shaped Length determined by length of nucleic acid Width determined by size and packaging of capsomeres Helical capsids can only package ssRNA because of the rigidity of double-stranded nucleic acids e.g., tobacco mosaic virus or Ebola 8 © 2021, 2018, 2015 Pearson Education, Inc. Icosahedral Capsid Viruses Vertex Spherical and rigid Posses a closed shell enclosing the nucleic Triangular face Edge acid inside Used to package single-or dsRNA or DNA Pentamer Identical triangular faces, edges, vertices; 5, 3, or 2 identical segments Proteins of the icosahedral capsid can be assembled as pentamers and/or hexamers Building larger icosahedral capsids Most efficient arrangement of subunits - requires fewest capsomeres Proteins that constitute the icosahedral capsid can assemble either as pentamers or hexamers Most animal viruses have icosahedral capsids Larger icosahedral capsids can be constructed e.g., adenovirus, poliovirus, human from pentamers and hexamers papillomavirus Models of icosahedral capsids containing 12 pentamers (purple) with an increasing number of hexamers (light blue). 9 Pentamer Hexamer  Complex viruses The capsid symmetry is neither Bacteriophages icosahedral or helical Particularly bacterial viruses, bacteriophages, are complex viruses - Capsid is polyhedral and then the tail sheath is helical Poxviruses – overall shape is described as brick-shaped - Doesn’t contain clearly identifiable capsids but do have several coats around the nucleic acid Poxvirus 11 © 2021, 2018, 2015 Pearson Education, Inc.  Enveloped virions Acquired from host cell during viral replication or release (budding) Envelope proteins and glycoproteins often play role in host recognition Envelope provides some protection to the virus from the immune system - Enveloped viruses are more fragile than naked viruses - Lipid bilayer of the envelope is sensitive to changes in the environment (pH, temperature) - Easily disrupted by physical and chemical agents and can dry out easily 12 © 2021, 2018, 2015 Pearson Education, Inc.  Delivery of genome from enveloped virions First step is attachment of the virus to the host cell membrane (via receptors) Endocytosis: Engulfing of the virus by the host cell (ex. Herpesviruses) Membrane fusion: Viral envelope and host membrane fuse, releasing capsid into the cell’s cytoplasm (ex. Measles) Uncoating of capsid takes place to release genome Will come up again in a later lecture 13 © 2021, 2018, 2015 Pearson Education, Inc.  DNA and RNA viruses can be enveloped Take home messages: There is no correlation Examples between of DNA andthe structure RNA of the genome and whether the virus viruses has an envelope or not - Ex: dsDNA viruses: Adenovirus is nonenveloped and Herpesvirus is enveloped DNA RNA viruses viruses 14 © 2018 Pearson Education, Inc.  Virus particles (virions) are metastable Stable: Must protect the genome Unstable: must come apart quickly upon infection, undergo structural changes to release viral genome in infected cell How is metastability achieved? Stable structure: created by symmetrical arrangement of many identical proteins to provide maximal contact Unstable structure: structure is not permanently bonded together and can be taken apart and loosened upon infection 15  Please download and install the Slido app on all computers you use What do nonenveloped and enveloped viruses have in common? ⓘ Start presenting to display the poll results on this slide. 16 Viral Genomes 17  Please download and install the Slido app on all computers you use Correctly label the figure: ⓘ Start presenting to display the poll results on this slide. 18 Proof that Proof thatthe viral the viral nucleic nucleic acid genome acid genome is the geneticiscode the genetic code Virology breakthrough in the 1950’s: 2 classic experiments Virology breakthrough in the 1950s: 2 classic experiments: Hershey-Chase experiment Hershey-Chase with phage experiment T2 T2 with phage - DNA virus that infects bacteria Fraenkel-Conrat’s work with Fraenkel-Conrat’s TMV work with TMV Fraenkel-Conrat’s work with TMV - RNA virus that infects tobacco leaves 19  Based on differential radio-labeling of phage proteins ( S) vs Hershey-Chase experiment in 1952 Phage proteins labeled with 35S Proof Chase that DNA is the genetic material of bacteriophage T2 experiment Viruses grown in radioactive sulfur (35S) had radiolabelled proteins (sulfur is present in proteins but not DNA) DNA is the genetic material of bacteriophage T2 32 Viruses grown in radioactive phosphorus ( P) had radiolabeled DNA (phosphorus differential radio-labeling is present in DNAof phage but proteins (35S) vs DNA (32P) not proteins) ns Phage DNA 35S labeled with 32P Phage proteins labeled with 35S → no Phage proteins labeled with 32P → radioactivity enters the cell → protein is not radioactivity enters the cell → DNA is 32P inherited inherited 20  Fraenkel-Conrat experiment Fraenkel-Conrat Experiment Proof that RNA is the genetic material of TMV. Proof that RNA is the genetic material of TMV Based on the creation of hybrid viruses. Based on the creation of hybrid viruses RNA from TMV A and protein from TMV B → TMV A progeny RNA from TMV B and Infection protein from of aTMV A → tobacco leaf showing TMV B progeny TMV-associated mosaic 21  Overview of Viral genomes (I) Viruses are called DNA viruses or RNA viruses based on their genome. Composition of viral genomes: Double or single-stranded DNA (dsDNA or ssDNA) Double or single-stranded RNA (dsRNA or ssRNA) - Ss viral genome can be positive-sense or negative-sense Shape of viral genomes: Linear Circular Segmented genome of influenza virus Segmented (several parts) Coding capacity of viral genomes: Viral genomes typically contain only a few genes (4 to hundreds) 22  (+) vs. (-) sense RNA and DNA mRNA (ribosome ready) is always the positive (+) strand RNA and DNA complements of (+) strands are negative (-) strands - Negative-sense (−) viral RNA cannot be directly translated But not all (+) RNA is mRNA - They are not all translated as we will see next lecture! 23  Viral genomes (II) Overview of Viral genomes (II) DNA viruses replicate their Eukaryotic DNA viruses genomes in nucleus Eukaryotic DNA viruses (ds) DNA genomes Mostly double-stranded - Different structure than host cell chromosomes DNA Mostly double stranded replication (ds) DNA usually takes placegenomes. in the nucleus o Different - Except structure which poxviruses, than host cell chromosomes. replicate in the cytoplasm DNA replication Eukaryotic RNA viruses usually takes place in the nucleus. Mostly o Except poxviruses, which single-stranded replicate (ss) RNA in the cytoplasm. genomes RNA replication usually takes place in the cytoplasm Eukaryotic RNA exceptions - With some viruses like retroviruses, which require Eukaryotic cell an intra-nuclear step RNA viruses replicate their Mostly single-stranded (ss) RNA genomes. Viral replication will be discussed in more detail genomes in cytoplasm 24 next lecture  RNA viruses challenge the dogma of molecular biology Central dogma: Cellular enzymes RNA virus enzymes - DNA replicate into DNA using DNA polymerase DNA Polymerase DNA - DNA transcribe into RNA using RNA polymerase Retroviruses - RNA translated into protein using Reverse transcriptase ribosomes RNA Polymerase (RNA-dependent DNA polymerase) RNA viruses encode or carry enzymes that RNA-dependent can: RNA RNA polymerase - Reverse-transcribe RNA into DNA using (RdRP) reverse transcriptase (RNA → DNA) All RNA viruses (except Ribosome retroviruses) require - Synthesize RNA from an RNA template using RNA-dependent RNA polymerase RdRP for replication (RdRP) (RNA → RNA) Protein 25  Polymerases DNA polymerases Examples Synthesize DNA using - DNA template: DNA-dependent DNA polymerase DNA polymerase ⍺ - RNA template: RNA-dependent DNA polymerase Viral reverse transcriptase RNA polymerases Synthesize RNA using - DNA template: DNA-dependent RNA polymerase RNA polymerase II - RNA template: RNA-dependent RNA polymerase Viral RdRP Polymerases synthesize complementary strands 26 © 2021, 2018, 2015 Pearson Education, Inc.  Genome replication and expression of RNA viruses All RNA viruses, except retroviruses, require an RdRP to replicate their genome and synthesize viral mRNAs RNA virus genomes encode or carry RdRP since mammalian cells do not have it RdRP = RNA-dependent RNA polymerase = RNA transcriptase = RNA replicase 27 © 2021, 2018, 2015 Pearson Education, Inc.  Please download and install the Slido app on all computers you use A virus with RNA-dependent RNA polymerase ⓘ Start presenting to display the poll results on this slide. 28  Viral Classification To name viruses and place them into groups 29 Classification of viruses based on viral attributes Various viral attributes can be used: - Nature of nucleic acid in virion - Symmetry of protein shell (capsid) - Presence or absence of phospholipid membrane (envelope) - Host range RNA or DNA Single-stranded or double-stranded Nucleic acid Non-segmented or segmented Linear or circular Positive-sense or negative-sense Symmetry (icosahedral, helical, complex) Virion Enveloped or not enveloped Structure Number of capsomers or size of virion 30  ICTV classification International Committee on Taxonomy of Viruses Classify and provide nomenclature of viruses Taxonomy based on classical hierarchical system Order names end in – virales (example: Amarillovirales) Family names end in –viridae (example: Flaviviridae) Genus names end in –virus (example: Hepacivirus) Viral species: - Descriptive common names are used - Subspecies are designated by a number or letter - Examples: Herpes simplex virus 1 (HSV-1), Hepatitis C virus (HCV) 31  Baltimore’s system of virus classification In general, viruses of the same genome class (such as double-stranded DNA) show greater evidence of shared ancestry with each other than viruses of different class of genome (such as RNA) Devised by American biologist David Baltimore to classify animal viruses Based on 3 criteria: 1. The nucleic acid composition of the viral genome 2. The way the viral genome is replicated 3. The way the virus makes mRNAs for expression of the viral proteins (i.e. the way the viral genome is expressed) All cells and viruses need to make messenger RNA to produce their fundamental protein components 32  Please download and install the Slido app on all computers you use Which statement(s) is/are FALSE? ⓘ Start presenting to display the poll results on this slide. 33  Summary (I) Viruses have a capsid made of capsomeres - Helical, icosahedral or complex structures - Protection of genome Naked vs. enveloped viruses - Enveloped may possess glycoproteins – imp’t for host recognition Delivery of genome: - Naked viruses: direct penetration or endocytosis - Enveloped viruses: endocytosis or membrane fusion Virions are metastable Viral nucleic acid genome is the genetic code - Can be linear, circular and segmented - Viral genome is either ss- or dsDNA or RNA/ (+) or (-) single-stranded 34  Summary (II) DNA polymerase, RNA dependent RNA polymerase and reverse transcriptase ICTV classification (order-virales; family- viridae; genus-virus; species- descriptive, number or letter) Baltimore classification: based on nucleic acid composition of viral genome I. dsDNA viruses II. (+) ssDNA viruses III. dsRNA viruses We will look at their replication IV. (+) ssRNA viruses next class! V. (-) ssRNA viruses VI. ssRNA-RT VII. dsDNA-RT 35