Viruses and Prions (Chapter 13) Lecture Materials for Amy Warenda Czura, Ph.D. Suffolk County Community College Eastern Campus

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1 Viruses and Prions (Chapter 13) Lecture Materials for Amy Warenda Czura, Ph.D. Suffolk County Community College Eastern Campus Primary Source for figures and content: Tortora, G.J. Microbiology An Introduction 8th, 9th, 10th ed. San Francisco: Pearson Benjamin Cummings, 2004, 2007, Amy Warenda Czura, Ph.D. 1 SCCC BIO244 Chapter 13 Lecture Slides

2 Virus: Latin for poison -discovered as contagious fluid -obligate intracellular pathogen -contains few enzymes of its own -must get most enzymes and all biomolecule building blocks and energy from host cell Characteristics of a virus: 1. contains a single type of nucleic acid: either DNA or RNA but not both 2. has a protein coat (capsid) surrounding the nucleic acid, some also have a lipid envelope around the capsid 3. multiply inside living cells by using the synthesizing machinery of the host cell 4. cause the synthesis of specialized viral structures that can transfer the viral nucleic acid to other cells 5. have a specific host range Amy Warenda Czura, Ph.D. 2 SCCC BIO244 Chapter 13 Lecture Slides

3 Host range = the spectrum of host cells types the virus can infect -viruses are usually specific to a single species (or even strain) of host -a virus has molecules on its surface that specifically adhere to some molecule on the host cell surface, each virus is specialized to attach to and infect one type of cell -in multicellular hosts viruses usually infect only certain specific cell types in that species e.g. HIV: human T helper cells -host range is determined by the virus requirements for attachment and entry into the cell and the availability of of host factors necessary for viral replication Amy Warenda Czura, Ph.D. 3 SCCC BIO244 Chapter 13 Lecture Slides

4 Viral Size -must be smaller than the cells they infect: 20-1,000nm in length -smaller than bacteria (E. coli 1000 x 3000nm) -too small to be seen by light microscopy Amy Warenda Czura, Ph.D. 4 SCCC BIO244 Chapter 13 Lecture Slides

5 Viral Structure Virion = infectious viral particle: completely assembled with a protein coat surrounding the nucleic acid 1. Nucleic Acid: - either RNA or DNA, but not both - single or double stranded - linear or circular - if RNA, it can be plus/sense strand (has codons) or minus/antisense (need to make complement sense strand for translation) -2,000 to 250,000 nucleotides (E. coli 4 million, human 3 billion) 2. Capsid = protein coat -composed of subunits called capsomeres Amy Warenda Czura, Ph.D. 5 SCCC BIO244 Chapter 13 Lecture Slides

6 -some capsids have protein-carbohydrate pointed projections called pentons -if pentons are present they are used for attachment to the host cell 3. Envelope (not all viruses) -some viruses have an envelope around the capsid consisting of lipids, proteins and carbohydrates (cell membrane like) -with envelope = enveloped virus -if a virus does not have an envelope it is called a non-enveloped virus -the envelope may be coded for by the virus or taken from the host cell plasma membrane -some envelopes have carbohydrate-protein complexes called spikes which are used for attachment to the host cell Amy Warenda Czura, Ph.D. 6 SCCC BIO244 Chapter 13 Lecture Slides

7 interesting note: -Coronavirus (cold) and influenza virus (flu) have high mutation rate in spike genes -by changing the spikes, they can evade the host immune system -you get infected by colds and the flu over and over since each one with slightly different spikes looks completely new to your immune system Amy Warenda Czura, Ph.D. 7 SCCC BIO244 Chapter 13 Lecture Slides

8 Morphology The capsid architecture can be distinct and sometimes identifies a particular virus 1. Helical -cylindrical capsid -made up of a helical structure of capsomeres with the nucleic acid wound up inside e.g. Rabies virus, Ebola virus t045/t045376a.jpg Amy Warenda Czura, Ph.D. 8 SCCC BIO244 Chapter 13 Lecture Slides

9 2. Polyhedral -most are icosahedrons: 20 equilateral triangle faces & 12 corners -may have pentons e.g. Adenovirus, Polio virus Poliovirus Amy Warenda Czura, Ph.D. 9 SCCC BIO244 Chapter 13 Lecture Slides

10 3. Enveloped Viruses -appear spherical due to the lipid envelope, but contain a shaped capsid: Enveloped helical e.g. influenza virus Enveloped polyhedral e.g. Herpes Simplex Virus -may have spikes Influenza virus luenza_site/influenza_virus.jpg Herpes simplex virus Amy Warenda Czura, Ph.D. 10 SCCC BIO244 Chapter 13 Lecture Slides

11 4. Complex Viruses -unique shape e.g. bacteriophage: capsid & accessory structures e.g. pox virus: no clear capsid, just several protein layers around the nucleic acid Amy Warenda Czura, Ph.D. 11 SCCC BIO244 Chapter 13 Lecture Slides

12 Taxonomy -a viral species is a group of viruses sharing the same genetic information and the same ecological niche (host range) -species names are not used; usually viruses are just given a Genus name (ends in virus ) and a common name Viruses are grouped into families (names end in -viridae ) based on: 1) Nucleic acid type 2) Strategy for replication 3) Morphology Viruses are more commonly identified by their common name learning the family groups has little relevance to disease ID. e.g. Family: Herpesviridae Genus: Simplexvirus Herpes Simplex Virus 2 (HSV2) (Also known as HHV-2: human herpesvirus 2) Amy Warenda Czura, Ph.D. 12 SCCC BIO244 Chapter 13 Lecture Slides

13 Chart of families Table 13.2 Note all the various possibilities: -Single stranded DNA, non-enveloped -Double stranded DNA, non-enveloped -Double stranded DNA, enveloped -Single stranded RNA, plus strand, non-enveloped -Single stranded RNA, plus strand, enveloped -Single stranded RNA, minus strand, enveloped -Single stranded RNA, minus strand, non-enveloped -Multiple strand RNA, minus strand, enveloped -Double strand RNA, non-enveloped -Double strand RNA, enveloped Viruses are more commonly identified by their common name learning the family groups has little relevance to disease ID. Amy Warenda Czura, Ph.D. 13 SCCC BIO244 Chapter 13 Lecture Slides

14 Amy Warenda Czura, Ph.D. 14 SCCC BIO244 Chapter 13 Lecture Slides

15 enveloped nonenveloped enveloped Double strand RNA enveloped Amy Warenda Czura, Ph.D. 15 SCCC BIO244 Chapter 13 Lecture Slides

16 Cultivation of viruses for study: -viruses must be grown in living cells, usually their specific host -viruses cannot be grown in culture media alone (obligate intracellular parasites) Three ways to grow animal viruses in lab: 1. Animal Models -infect live animals with the virus positive aspects: -provides the potential to study the complete infection and disease process caused by the virus in a living animal and the immune response to the infection which allows for study of drug treatments and preventative vaccines negative aspects: -only if the virus will infect an animal: many human viruses only infect humans thus no animal model exists Amy Warenda Czura, Ph.D. 16 SCCC BIO244 Chapter 13 Lecture Slides

17 e.g. There are no exact models for HIV/AIDS: it infects and causes disease only in humans HIV and AIDS can be studied only in existing human patients All drug treatments and vaccines also have to be tested using humans 2. Embryonated Eggs -fertilized egg, usually chicken, with a growing embryo -used as a "container" to grow virus for vaccine production or molecular studies positive aspects: -most viruses will grow abundantly in some part of the egg Amy Warenda Czura, Ph.D. 17 SCCC BIO244 Chapter 13 Lecture Slides

18 negative aspects: -no ability to study infection or disease processes or immune response or drug therapies or vaccines: wrong cells & not a live functioning animal 3. Cell Culture -grow the virus in living cells in a Petri dish -must culture the cells before growing the virus in them A. Primary cell lines : -direct tissue sample grown in culture positive aspects: -use the cell type the virus normally infects: can study normal infection process negative aspects: -primary cells die off quickly: new cells must be harvested from donors -cannot study disease process or immune response: no live animal Amy Warenda Czura, Ph.D. 18 SCCC BIO244 Chapter 13 Lecture Slides

19 B. Continuous cell lines: -immortalized, transformed cancer cells that grow and divide forever no contact inhibition or monolayer, no death positive aspects: -cells can be grown infinitely in lab: can grown large quantities of both cells and virus forever negative aspects: -cancer cells are not normal: infection process being observed may not be normal -cannot study disease process or immune reactions Amy Warenda Czura, Ph.D. 19 SCCC BIO244 Chapter 13 Lecture Slides

20 Viral Identification -viruses are so small they can only be seen by electron microscopy -some are so distinct they can be recognized on sight -others are identified by: -symptoms of the disease -cytopathic effects -serological methods (ELISA, Western blot) -sequencing of DNA or RNA (RFLP/DNA fingerprinting, PCR) Viral Multiplication -replication must occur in a host cell -the viral genome codes for viral structural components and a few viral enzymes needed for processing the viral nucleic acid -everything else is supplied by the host: ribosomes, trna, nucleotides, amino acids, energy, etc. Amy Warenda Czura, Ph.D. 20 SCCC BIO244 Chapter 13 Lecture Slides

21 Bacteriophages -viruses that infect a specific bacteria -serves as a well studied example of a virus life cycle (easy to grow in lab in bacteria) Two possible types of infections cycle: 1. Lytic cycle -ends with the lysis and death of the host bacterial cell 2. Lysogenic cycle -host cell remains alive, but carries the virus in its genome Amy Warenda Czura, Ph.D. 21 SCCC BIO244 Chapter 13 Lecture Slides

22 The Lytic Cycle 1. Attachment -the phage contacts a bacterium and uses the tail fibers to attach to proteins on the bacterial cell wall (all viruses have an attachment site on their surface which binds to a receptor site on their host cell in this case the attachment site = tail fibers receptor site = specific cell wall proteins) 2. Penetration/Entry -the phage injects its DNA into the bacterium: -the phage tail releases lysozyme to break down the bacterial cell wall -the sheath contracts to drive the tail core through the weakened cell wall and plasma membrane Amy Warenda Czura, Ph.D. 22 SCCC BIO244 Chapter 13 Lecture Slides

23 -the DNA is injected into the bacterium through the tail core 3. Biosynthesis -synthesis of the viral nucleic acid and protein occur: -the virus degrades the host DNA and/or disrupts host protein synthesis -the virus then directs viral nucleic acid replication and transcription and translation of viral genes -this results in a pool of viral genomes and capsid parts Amy Warenda Czura, Ph.D. 23 SCCC BIO244 Chapter 13 Lecture Slides

24 4. Maturation -the bacteriophage DNA and capsid spontaneously assemble into complete virions 5. Release -virions leave the bacteria: -lysozyme encoded by viral genes causes the cell wall to break down -the bacteria lyses releasing the virions Cycle then repeats with new phages (Phage therapy: using bacteriophage to treat bacterial infections - experimental) Amy Warenda Czura, Ph.D. 24 SCCC BIO244 Chapter 13 Lecture Slides

25 The Lysogenic Cycle -the lysogenic phage infects the cell, but remains inactive in a stage called lysogeny 1. the phage attaches to the host cell and injects its DNA 2. the phage genome circularizes -at this point, the phage could begin a normal lytic cycle or it can begin the lysogenic cycle / lysogeny Amy Warenda Czura, Ph.D. 25 SCCC BIO244 Chapter 13 Lecture Slides

26 3. the phage DNA integrates into the bacterial chromosome -the phage DNA is now called a prophage -it synthesizes viral repressor proteins to keep the rest of its genome inactive (suppress virion production) 4. replication of the bacterial chromosome replicates the prophage as well and thus all progeny cells will also be infected with the lysogenic virus 5. occasionally, the prophage will recombine back out of the bacterial chromosome and initiate a lytic cycle Amy Warenda Czura, Ph.D. 26 SCCC BIO244 Chapter 13 Lecture Slides

27 Three Results of Lysogeny: 1. The host cell is immune to reinfection by the same phage (but not different types) 2. Phage conversion: the host cell may exhibit new properties due to the integration of prophage DNA e.g. cholera toxin (diarrhea) of Vibrio cholerae is due to a phage gene 3. Makes specialized transduction possible: -viral genome can move one of the host s genes to a new bacterium when it goes lytic from first cell lysogenic in second cell e.g. gene for galactose metabolism Amy Warenda Czura, Ph.D. 27 SCCC BIO244 Chapter 13 Lecture Slides

28 Multiplication Of Animal Viruses 1. Attachment: virus attachment sites bind host receptor proteins on plasma membrane 1 2. Penetration: A. Non-enveloped viruses are endocytosed into a vesicle B. Enveloped viruses enter by fusion 2A 2B 3. Uncoating: enzymes degrade capsid releasing nucleic acid A. Non-enveloped: viral enzymes for escape from vesicle B. Enveloped: host cytoplasm enzymes 3 4. Biosynthesis A. DNA viruses: DNA replicated in nucleus, protein made in cytoplasm, virion assembly in nucleus B. RNA viruses: RNA and protein made in cytoplasm, virions assemble in cytoplasm C. Retroviruses: reverse transcribe dsrna genome to dsdna, DNA integrated into host genome as provirus, provirus remains latent or is expressed to create virions in the cytoplasm 4A 4C 5A 4B 5. Maturation and Release: capsule and nucleic acid assemble into virion A. Enveloped: buds out of cell taking membrane, cell survives B. Non-enveloped: ruptures out of cell membrane, cell dies. 5B Amy Warenda Czura, Ph.D. 28 SCCC BIO244 Chapter 13 Lecture Slides

29 Multiplication of Animal Viruses 1. Attachment -virus binds to proteins or glycoproteins on the host cell plasma membrane by its attachment sites: -pentons or spikes or capsid proteins: no tail fibers 2. Penetration / Entry -non-enveloped viruses are endocytosed by the host cell into a vesicle (endosome) -enveloped viruses can enter by fusion: the envelope and cell membrane fuse and the capsid is released into the cytoplasm Amy Warenda Czura, Ph.D. 29 SCCC BIO244 Chapter 13 Lecture Slides

30 3. Uncoating uncoating = separation of the viral nucleic acid from its protein coat -Non-enveloped: viral or host enzymes digest the capsid, viral enzymes allow the genetic material to escape the vesicle -Enveloped: done by host enzymes in the host cytoplasm (proteases) 4. Biosynthesis A. Biosynthesis of DNA viruses -viral DNA is replicated in the host nucleus -viral proteins are made in the cytoplasm -viral proteins migrate to the nucleus to join the DNA and assemble into virions -the virions are then transported through the host endoplasmic reticulum for release Amy Warenda Czura, Ph.D. 30 SCCC BIO244 Chapter 13 Lecture Slides

31 B. Biosynthesis of RNA viruses -both the viral RNA and proteins are synthesized in the cytoplasm -virions assemble in the cytoplasm C. Biosynthesis of Retroviruses -retroviruses have a ds RNA genome and make the enzyme reverse transcriptase -they synthesize a ds DNA copy of their RNA using reverse transcriptase and incorporate the DNA into the host cell genome as a provirus -the provirus can then remain latent in the genome (protected from host immune system), or the genes can be expressed to create virions (e.g. HIV: can remain latent 20+ years before it starts replicating) Amy Warenda Czura, Ph.D. 31 SCCC BIO244 Chapter 13 Lecture Slides

32 5. Maturation and Release -the viral capsid assembles spontaneously around the viral nucleic acid A. if a virus is enveloped, viral envelope proteins will be deposited in the host cell membrane and the virion will bud out of the host cell taking an envelope of membrane with it -the host cell can survive if not too many virions are released at once B. if the virus is not enveloped it usually ruptures out of the membrane causing lysis of the host cell Amy Warenda Czura, Ph.D. 32 SCCC BIO244 Chapter 13 Lecture Slides

33 Latency vs. Active Infection for integrating proviruses: -some viral infections spend long periods as latent infections and activate a replication cycle only on rare occasions e.g. Herpes -many integrating viruses activate a persistent / chronic replication cycle and will continue to produce virions until either the host immune system neutralizes it or until the virus kills the host e.g. HIV Viruses and Cancer -infectious cancer was first observed in chickens and mice (early 1900s) -Chicken leukemia was passed to healthy chickens by cell-free filtrate from sick chickens -Mouse mammary gland tumors were transmitted from mother to offspring in milk Amy Warenda Czura, Ph.D. 33 SCCC BIO244 Chapter 13 Lecture Slides

34 A viral cause of cancer in humans was hard to recognize because: 1. most virions infect cells without inducing cancer (cold, flu, mumps, measles, etc.) 2. cancer often develops long after the viral infection (hard to link cause and effect) 3. most cancers are not contagious (prostate, colon, breast, brain tumor, etc.) Cell Transformation normal cells tumor cells -viruses that integrate into the host genome (retroviruses and some DNA viruses) change the genetic material of the host which has the potential to cause cancer -segments of the DNA where cancer causing alterations occur are called oncogenes -oncogene = some kind of cell regulatory or growth control gene -an oncogenic virus / oncovirus is capable of inducing tumors in animals Amy Warenda Czura, Ph.D. 34 SCCC BIO244 Chapter 13 Lecture Slides

35 -when the virus integrates, an oncogene is expressed resulting in a transformed cell -transformed cells grow uncontrolled: they do not respect contact inhibition and lead to tumor formation -oncogenic viruses are either DNA viruses or retroviruses that integrate into a chromosome. They carry a whole oncogene (some kind of regulatory or growth gene derived from the animal host) or carry just a promoter that turns on an oncogene in the host cell e.g. Human Papilloma Virus Cervical cancer Hepatitis B Virus Liver cancer (Oncolytic viruses: viruses that will naturally infect and lyse tumor cells. Currently being studied as possible cancer treatment) Amy Warenda Czura, Ph.D. 35 SCCC BIO244 Chapter 13 Lecture Slides

36 Prions (Proteinaceous infectious particle) -infectious protein PrP Sc -it is a protein molecule that is misfolded and can cause misfolding of normal proteins -results in spongiform encephalopathies e.g. Mad Cow disease, Sheep scrapie Creutzfeldt-Jacob Disease, Kuru Gerstmann-Straussler-Scheinker Fatal Familial Insomnia -prion protein in the brain converts normal proteins PrP C into prion proteins PrP Sc -prion proteins cause plaques and holes in neural tissue resulting in progressive loss of function and eventual death Amy Warenda Czura, Ph.D. 36 SCCC BIO244 Chapter 13 Lecture Slides