Viruses are parasites Viral genomes small -- contain few genes compared with living cells – HIV genome has 9749 nucleotides - Human cells have ~3.2 x 10.

Slides:



Advertisements
Similar presentations
Section 2: Viruses Preview Bellringer Key Ideas Is a Virus Alive?
Advertisements

HIV and its lifecycle Sources: Wikipedia, HIV is a retrovirus (enveloped viruses possessing an RNA genome,
17P2-1 Chapter 17: Outline DNA Mutation Chromosomes and Variations Chromatin SupercoilingGenome Structure RNA (We are here.) Transfer, Ribosomal, Messenger.
Viruses Higher Human Biology. Lesson Aims To describe the structure of a virus To examine the process of viral replication.
Chapter 23.  Agents that cause disease  Many microorganisms: bacteria, fungi, protozoa  Bacteria are prokaryotes, but only a few are pathogens; most.
Viruses.  What is a virus? Defined by their inability to replicate/multiply without utilizing a host cells reproductive mechanisms. Only contain ONE.
Assembly and exit of virions from cells LECTURE 14: Viro100: Virology 3 Credit hours NUST Centre of Virology & Immunology Waqas Nasir Chaudhry.
Introduction to Virus Structure
 Viruses are not alive  A virus in an obligate intracellular parasite  Requires host cell to reproduce  Can be seen at magnifications provided by.
An Overview of Protein Synthesis. Genes A sequence of nucleotides in DNA that performs a specific function such as coding for a particular protein.
The Genetics of Viruses and Bacteria
Bacteria and Viruses.
The Structure and Function of DNA CHAPTER 10 Transcription (DNA  RNA) RNA Polymerase Processing of Eukaryotic RNA Translation (mRNA  Protein) The Three.
Lesson Overview 20.1 Viruses.
Viruses Chapter 19. A Borrowed Life Virus: an infections particle incapable of replicating outside of a cell, which consists of an RNA or DNA genome enclosed.
Chapter 19~Viruses.
Microbial Models I: Genetics of Viruses and Bacteria 7 November, 2005 Text Chapter 18.
Viral disease Learning objective: To be able to describe the structural features of a virus.
Chapter 11 Lecture Outline
Essential knowledge 3.C.3:
Viruses Gene Regulation results in differential Gene Expression, leading to cell Specialization.
BTY328: Virology Dr William Stafford Viral characteristics and isolation-Lecture 1&2 Origin and diversity of viruses?-Tutorial Viral.
 Chapter 18~ Microbial Models: The Genetics of Viruses and Bacteria.
Chapter 3 - Genomes Use chapter as reference.. Chapter 4 - Virus Structure.
VIRUSES Organisms that bridge between living and non-living things.
The Viruses January 14 th, Virus Basics Viruses are nucleic acid and protein structures Very small; typically between nm No cellular structures.
Chapter 19 Viruses. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings I. Discovery Tobacco mosaic disease - stunts growth.
Viruses. Relative sizes  Viruses are one of the smallest biological structures known  Between 20 and 50 nanometers in size.  The average animal cell.
Genetics of Viruses.
Microbiology Ch 17.1: Viruses 17.2: Monera. Virus: A non- cellular particle made up of genetic material and protein that can invade cells.
Viruses. Characteristics of Viruses  Non cellular structures – do not have membranes or any cell organelles.  Consist of an outer protein coat (capsid)
Viruses.
A CELLULAR FORMS (Viruses & Bacteriophages) A cellular forms, most range in size from 5 to 300 nanometers (nm) * in diameter, although some Paramyxoviruses.
Lesson Overview Lesson Overview Studying the Human Genome Lesson Overview 20.1 Viruses.
Microbial Models I: Genetics of Viruses and Bacteria 8 November, 2004 Text Chapter 18.
Viruses and bacteria are the simplest biological systems - microbial models where scientists find life’s fundamental molecular mechanisms in their most.
Chapter What is a virus? A virus is nucleic acid wrapped in a protein coat Can be DNA or RNA Viruses are considering nonliving because they can’t.
Structure, Function, and Reproduction
Fig µm Chapter 19 - Viruses. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings Overview: A Borrowed Life Viruses.
The Structure and Function of DNA Chapter 10. I. DNA: Structure and Replication A. DNA and RNA Structure DNA=deoxyribonucleic acid RNA=ribonucleic acid.
Viruses A “borrowed life”. Characteristics of Life All living things exhibit the following four characteristics: 1.Carry out metabolic activities to meet.
Lesson Overview Lesson Overview Studying the Human Genome Lesson Overview 20.1 Viruses.
1 Zoology 145 course General Animal Biology For Premedical Student H Zoology Department Lecture 3 : Viruses.
Protein Synthesis Chapter 9 p Protein Synthesis Gene- segment of DNA that codes for a protein. Gene Expression/ Protein Synthesis is the process.
Two Cycles and A Bit of Review Remember that viruses are not able to reproduce on their own. They rely on a ‘host cell’ for reproduction In the Lytic Cycle.
Virology Prof. Dr. Kareem Thamir Al-Kaabi. Objectives of the lecture The main objective of the present lecture is to understand the important chemical.
Viruses Lecture 16 Fall Viruses What is a virus? Are viruses alive? Read Discovery of Viruses pgs and Fig
The Genetics of Viruses & Bacteria Chapter 18. Overview Viruses and bacteria –are the simplest biological systems –provided evidence that genes are made.
Chapter 19~Viruses.
An Introduction to the Viruses Non-Living Etiologies
Good teaching is more a giving of right questions than a giving of right answers. – Josef Albers Viruses Chapter 19.
Introduction to Virology.
Viruses Page 328.
Virus Basics - part I Viruses are genetic parasites that are smaller than living cells. They are much more complex than molecules, but clearly not alive,
Viruses.
Chapter 19~Viruses.
Viruses Chapter 19 Page 478.
Objectives To understand the general principles involved in RNA replication discussed in Chapter 6 pages To use the following + stranded RNA viruses.
Introduction to Virus Structure and Diversity
MBI 140 panel (semester 1; H)
General Animal Biology
Chapter 19 Viruses VIRUS Entry and uncoating DNA Capsid Transcription
Essential knowledge 3. C. 3: youtube. com/watch
Packaged Genes – “Ready for Delivery”
Viruses.
Fig Chapter 19: VIRUS Figure 19.1 Are the tiny viruses infecting this E. coli cell alive? 0.5 µm.
Gene Regulation results in differential Gene Expression, leading to cell Specialization Viruses
Good teaching is more a giving of right questions than a giving of right answers. – Josef Albers Viruses Chapter 19.
Viruses Page 328.
Viruses Page 328.
Presentation transcript:

Viruses are parasites Viral genomes small -- contain few genes compared with living cells – HIV genome has 9749 nucleotides - Human cells have ~3.2 x 10 9 base pairs (~30,000 genes) Viruses must hijack host cells. They can only reproduce if they force the host cell to make viral copies. New viruses leave host cell and infect similar cells. Some viruses cause diseases in their hosts.

Clicker question Viruses can infect 1) Humans 2) Animals 3) Plants 4) Bacteria 5) Bi 1 students 6) All of the above

Raison d’etre of a virus Deliver nucleic acid (single or double stranded; RNA or DNA) to host cell. Take over host’s biosynthetic machinery for replication, transcription, and translation of viral genes. Assembly progeny viruses in infected cell. Release progeny to infect other cells. Avoid host immune system.

Clicker question Are you currently symptomatic of a rhinovirus infection? 1)Yes 2)No 3)Decline to reveal 4)Huh?

Baker et al., 1999 Adding the third dimension to virus life cycles: 3D reconstructions of icosahedral viruses from cryoelectron microscopy. Microbiol. Mol. Biol. Rev. 63: Many viruses are icosahedral We will look at two icosahedral viruses: rhinovirus (causes common cold) and poliovirus. Both are much smaller than HIV (diameters ~300 Å or 30 nm for rhino- and polioviruses compared with ~1000 Å for HIV) and both are non- enveloped (no lipid bilayer) viruses.

Icosahedral viruses Foxtrot by Bill Amend Human rhinovirus (HRV) and poliovirus are both picorna viruses (pico = small; rna refers to RNA). Lots of people are interested in picorna viruses.

Poliovirus Inserts RNA Directly into Target Cell Poliovirus RNA is then translated in the cytoplasm of the host cell Principals of Virology. Flint et al. Fig. 5.13

Clicker question Poliovirus and rhinovirus are retroviruses. 1) True 2) False

Clicker question Poliovirus and rhinovirus are retroviruses. 1) True 2) False -- Picornaviruses are plus strand RNA viruses, so their genomic RNA can serve directly as messenger RNA to translate viral proteins. One such viral protein is an RNA-dependent RNA polymerase, which makes a negative strand copy of the viral RNA that then serves as a template to make more viral RNA for packaging into new viruses.

Viral nucleic acid must be protected Viruses have protein shells to enclose their nucleic acid. Can’t make a single protein that is big enough to enclose and protect nucleic acid. Protein shells of viruses built up from many copies of one or more polypeptide chains, often resulting in rod-like or spherical shapes.

Spherical viruses Genetic economy -- build shell from many copies of a few kinds of subunit. Specificity -- subunits recognize each other to form interface of non-covalent interactions. Leads to SYMMETRY because of specific repeated bonding patterns of identical building blocks. Problem: protein shell is symmetrical, nucleic acid is not. Usually can’t see nucleic acid in crystal structures of spherical viruses.

How do you make a spherical object from identical units? Answered >2000 years ago by Greek mathematicians: icosahedron and dodecahedron have highest possible symmetry and therefore allow a maximum number of identical objects to form a closed symmetrical shell. EM by Aaron Klug in 1950s and 60s showed that viruses are icosahedral.

Buckminster Fuller Montreal Biosphere by R. Buckminster Fuller

Properties of an icosahedron Made from 20 identical equilateral triangles Put asymmetric object on icosahedron -- it is repeated 60 times by combining symmetry operations of 5-fold, 3-fold and 2-fold symmetry axes. Branden & Tooze, Fig

Clicker question What is the minimum number of protein subunits in the shell of an icosahedral virus? 1)1 2)5 3)20 4)60 5)120 6)None -- the shell of an icosahedral viruses is formed by a lipid membrane

How many protein subunits in an icosahedral virus? Look at number of symmetry related units in an icosahedron. Tiles on surface have 3-fold symmetry -- therefore 3 identical objects required to form one tile. 20 (# of tiles) x 3 (# of objects in a tile) = 60. Icosahedron has 20 3-fold axes, 12 5-fold axes, and 30 2-fold axes. One triangular face (20 total) divided into 3 A.U.’s Three objects related by icosahedral 3-fold placed on face Icosahedron with 60 objects: 1 per A.U. Branden & Tooze, Fig

The simplest icosahedral virus: STNV, a T=1 virus STNV (satellite tobacco necrosis virus) Smallest known virus (diameter = 180 Å). STNV is a satellite virus. It needs helper virus (TNV) in order to replicate. Self-sufficient viruses have more nucleic acid than STNV, so they are larger. RNA inside STNV only encodes viral coat protein. STNV has 60 identical protein subunits: T (triangulation number) = 1 (More about triangulation numbers later)

How to make a larger shell to enclose larger genome of a self-sufficient virus? Not by increasing size of each subunit (viral shell becomes thicker as subunits are enlarged). Instead, increase the number of subunits by having more than one subunit in each asymmetric unit of the icosahedron. Icosahedron has 60 asymmetric units, so number of subunits is a multiple of 60. Subunits can be identical or different, but more genetically economical if identical.

Poliovirus

Proteolysis (protein cleavage) is an important step in the maturation of many viruses Poliovirus RNA is translated into a poly-protein that is cleaved into separate proteins by a viral protease. Proteolysis by HIV protease is critical for HIV maturation. HIV protease is one of the targets of HAART (highly active anti-retroviral therapy).

Sites where antibodies bind to poliovirus Antibodies are proteins that are produced by B lymphocytes (B cells) in response to infection by a pathogen. Antibodies can neutralize the virus so it can’t infect cells. However, if the virus changes by mutation, antibodies usually can’t bind it anymore (rapid mutation of HIV is one of the main reasons antibodies aren’t very effective against HIV). Antibody binding sites on poliovirus represent sites of rapid mutation.

How are antibody binding sites identified? Passage virus in tissue culture cells in presence of neutralizing antibody. Viruses that are neutralized by the antibody can’t infect cells; mutant viruses can infect cells. Sequence RNA of viruses that are produced in the presence of the neutralizing antibody. Changes pinpoint the binding site (epitope) of the antibody. This process (growth of mutant viruses that aren’t affected by antibodies) is an excellent example of natural selection.

1) Viruses mutate rapidly to avoid host immune system 2) Viruses enter cells by binding to host receptors 3) Mutation of host receptors would be deleterious for the host. How to reconcile these three points?

A canyon containing conserved residues encircles 5-fold axes in picornaviruses Host cell receptors bind in the canyon.

The Canyon Hypothesis

Host receptors for some viruses are structurally-similar proteins containing antibody-like domains Loop structures represent protein domains of ~100 residues each. Although the receptor domains are related to antibodies, the receptor proteins are monomers, whereas antibody binding sites are dimers. Antibodies are therefore “fatter” than these viral receptors and are excluded from places where these receptors can fit. Note that these proteins all serve vital functions for the host (e.g., CD4 is a T cell coreceptor), so the host cannot easily evolve to mutate or eliminate the receptor. Rossmann, MG (1994) Viral Recognition and Entry. Protein Sci. 3:

Sequencing and analyses of all known human rhinovirus (HRV) genomes reveal structure and evolution Palmenberg et al., 2009, Science 324: strains HRV-A and HRV-C share a common ancestor HRV-B is a sister group to the -A and -C common ancestor Branch lengths in the tree are proportional to similarity (p-distance). An example of a phylogenetic tree -- see Freeman Chapter 27. Also see B-3 “Reading a Phylogenetic Tree” in your textbook.

Summary of concepts Genetic economy leads to one or a few capsid subunits, which leads to symmetry. Viruses mutate to escape the host immune system. Mutations are on surface-exposed regions of viral proteins that can be accessed by host antibodies. Binding sites for host receptors must remain constant. These are inaccessible to antibodies.

Extra slides (not included in lecture) More examples of virus structures; additional details about triangulation numbers and quasi-equivalent symmetry

Relative size and shape of RNA-containing viruses Granoff and Webster (1999, Vol. 1, p. 401) ~300 nm

Relative size and shape of DNA-containing viruses Granoff and Webster (1999, Vol. 1, p. 401) ~300 nm

Triangulation numbers For specific values of multiples of 60, can pack subunits with only slightly different environments in a quasi-equivalent way. Multiples of 60 are called “Triangulation numbers”. Values of T are restricted: T = (h 2 + hk + k 2 )f 2, where h,k,f are integers. Specific values of T: 1,3,4,7... Extra slides at end of lecture discuss triangulation numbers, quasi- equivalent symmetry, and other interesting aspects of icosahedral virus symmetry.

Organization of different types of icosahedral viruses 180 identical subunits; 3 different environments Examples: plant viruses such as TBSV, TCV 60 identical subunits; identical environments Example: STNV, a satellite virus that co-infects plants together with TNV Pseudo T= 3 60 copies each of 3 different subunits; 3 different environments Examples: rhinovirus, polio virus T = 1 T = 3 P = 3 Picorna viruses

Considerations about minimum size for a virus Self-sufficient RNA virus must contain genes for an RNA-directed RNA polymerase (an enzyme to copy the viral RNA) and a capsid protein. Minimum size RNA for these viruses is 1.5 x 10 6 Da -- won’t fit in a T=1 shell. T=3 capsids can package 3 x 10 6 Da. But see e.g., TBSV e.g., STNV Diameter = 330 Å Diameter = 180 Å T=3 can package ~4x more RNA than T=1

Quasi-equivalent symmetry (Casper and Klug, 1962) Need to pack subunits in the same (or nearly the same) environment Not a problem for T=1 viruses -- all subunits have exactly the same environment and the same packing interactions If >1 subunit in each icosahedral asymmetric unit, the subunits see different environments depending on where they are in the asymmetric unit For certain multiples of 60, can pack subunits into icosahedron so that they are packed with “quasi-equivalence” T=3 virus. 180 subunits total A subunits around 5-fold B and C alternate around 3-fold -- result is pseudo 6-fold Note 3-fold relating A, B, and C is not exact. Branden & Tooze, Fig. 16.6

Compare T=3 and T=4 T=3; 180 subunits total T=4; 240 subunits total T=3. A,B,C in asymmetric unit. 3 environments: A around 5-fold, C across 2-fold, B and C alternate around 3-fold T=4. A,B,C,D in asymmetric unit. 4 environments: A around 5-fold, D around 3-fold, B,C,D around 2-fold to form pseudo 6-fold. 20 real 3-folds, 60 pseudo 3-folds (formed by A,B,C), so 80 3-folds. Branden & Tooze, Figs. 16.6, 16.7

Canyon in rhinovirus

Direct demonstration of the Canyon Hypothesis: CryoEM reconstructions of receptors bound to poliovirus and rhinovirus show that host cell receptors bind in the “canyons”

Viruses that infect bacteria (bacteriophage or phage) look like syringes Levine, A. “Viruses” p. 34

Why are viruses constructed from similar or identical subunits? Genetic economy: Nucleic acid codes for only ~11% of its weight as a protein (MW of triplet codon ~1000 Da; MW of amino acid ~110 Da). Viruses are 50-90% by weight protein, so must construct virus from limited number of different kinds of subunits. Fidelity: There are errors in DNA, RNA and protein synthesis. Less chance of deleterious error if use smaller protein/gene. Same argument for advantages of oligomeric proteins, e.g., if there is 1 error per 1000 residues, then the number of correct copies is: Single chain (1000 residues)e x 1/1000 = 37% Four chains (250 residues each) e -250 x 1/1000 = 78% Stability and Complexity: The small number of contacts in, e.g., octahedron or tetrahedron insufficient for stability (holes between subunits too big, particle would be leaky). More subunits --> more stability Larger virus particle --> more complex genome

Clicker question Which of these are the most numerous on Earth? A)Bacteria B)Phage ~10 31 phage on earth; 10x more than the next most numerous group, bacteria C)Humans D)Cockroaches E)Bi 1 students