1 Assist. Prof. Betül AKCESMEGeneral Microbiology BIO306 Assist. Prof. Betül AKCESME

2 VIRUSES CONTINUE…..

3 Production of Viral Nucleic Acid and ProteinOnce a host has been infected, new copies of the viral genome must be made and virus-specific proteins synthesized in order for the virus to replicate Generation of messenger RNA (mRNA) occurs first Viral genome serves as template for viral mRNA In some RNA viruses, viral RNA itself is the mRNA In some cases essential transcriptional enzymes are contained in the virion

4 https://www.youtube.com/watch?v=Ofd_lgEymto

5 The Baltimore classification scheme is based on the relationship of the viral genome to its mRNA and recognizes seven classes of viruses.

6 RNA viruses mRNA () mRNA ()dsDNA () virus Class I Class VII ssDNA () virus Class II dsRNA () virus Class III ssRNA () virus Class IV ssRNA () virus Class V ssRNA () retrovirus Class VI Synthesis of other strand Used directly as mRNA Reverse transcription Transcription of minus strand Transcription of minus strand dsDNA intermediate Transcription of minus strand Transcription of minus strand dsDNA intermediate mRNA () mRNA () Genome replication: Class I, Class II, Class VII, DNA viruses Genome replication: Class III, Class IV, Class V, Class VI, RNA viruses classical semiconservative classical semiconservative, discard () strand transcription followed by reverse transcription make ssRNA () and transcribe from this to give ssRNA () partner make ssRNA () and transcribe from this to give ssRNA () genome make ssRNA () and transcribe from this to give ssRNA () genome make ssRNA () genome by transcription of () strand of dsDNA Figure 9.11 Formation of mRNA and new genomes in (a) DNA viruses and (b) RNA viruses.

7 Production of Viral Nucleic Acid and ProteinNomenclature used to describe mRNA is used to describe the configuration of the genome of a single-stranded DNA or RNA virus (mRNA is said to be in plus (+) configuration; its complement is in minus () configuration) Positive-strand RNA virus: single-stranded RNA genome with same orientation as its mRNA Negative-strand RNA virus: single-stranded RNA genome with orientation complementary to its mRNA

8 Cellular RNA polymerases do not normally catalyze the formation of RNA from an RNA template, but instead require a DNA template. RNA viruses, whether positive, negative, or double-stranded, require a specific RNA-dependent RNA polymerase.

9 Production of Viral Nucleic Acid and ProteinRetroviruses: animal viruses responsible for causing certain types of cancers and acquired immunodeficiency syndrome (AIDS) Retroviruses have ssRNA in their virions but replicate through a dsDNA intermediate (class VI). incoming RNA of retroviruses is the plus strand, it is not used as mRNA, class VII viruses are those that have double-stranded DNA in their virions but replicate through an RNA intermediate. Both Require reverse transcriptase

10 Production of Viral Nucleic Acid and ProteinViral Proteins Production follows synthesis of viral mRNA Early proteins synthesized soon after infection necessary for replication of virus nucleic acid typically act catalytically synthesized in smaller amounts

11 Production of Viral Nucleic Acid and ProteinProduction of Viral Proteins Late proteins Synthesized later Include proteins of virus coat(capsid) Typically structural components Synthesized in larger amounts

12 Overview of Bacterial VirusesBacteriophages are very diverse Best-studied bacteriophages infect enteric bacteria Examples of hosts: E. coli, Salmonella enterica Most phages contain dsDNA genomes Most are naked, but some possess lipid envelopes They are structurally complex, containing heads, tails, and other components

13 virulent and temperateVirulent (or lytic)mode: viruses lyse or kill their hosts after infection (phage T4 ) Temperate (or lysogenic) mode: viruses replicate their genomes in step with the host genome and without killing their hosts.

14 Time course of events in phage T4 infectionTime course of events in phage T4 infection. Following injection of DNA, early and middle mRNA is produced that codes for nucleases, DNA polymerase, new phage-specific sigma factors, and other proteins needed for DNA replication. Late mRNA codes for structural proteins of the phage virion and for T4 lysozyme, which is needed to lyse the cell and release new phage particles.

15 Temperate Bacteriophages, Lambda, and P1Temperate viruses: can undergo a stable genetic relationship within the host But can also kill cells through lytic cycle Lysogeny: state where most virus genes are not expressed and virus genome is replicated in synchrony with host chromosome. (prophage) Lysogen: a bacterium containing a prophage Under certain conditions lysogenic viruses may revert to the lytic pathway and begin to produce virions

16 Temperate virus Lytic pathway Lysogenic pathway Induction Host DNAViral DNA Attachment Cell (host) Injection Lytic pathway Lysogenic pathway Viral DNA replicates Induction Coat proteins synthesized; virus particles assembled Viral DNA is integrated into host DNA Figure 9.16 The consequences of infection by a temperate bacteriophage. Lysogenized cell Prophage Lysis Cell division

17 Bacteriophage lambda Infects E.coli, has been studied in great detail.Linear dsDNA with ssDNA 5`terminus. Both virulent and the temperate pathways are possible. WT lambda does have tail fibers. (no tail in commonly used lab strain).

18 Integration of lambda DNA into the hostIntegration of lambda DNA into the host. Integration always occurs at specific attachment sites (att sites) on both the host DNA and the phage. Some host genes near the attachment site are given: gal operon, galactose utilization; bio operon, biotin synthesis; moa operon, molybdenum cofactor synthesis. A site-specific enzyme (integrase) is required, and specific pairing of the complementary ends results in integration of phage DNA.

19 Figure 9.17 Capsid Tail Figure 9.17 Bacteriophage lambda.

20 Overview of Animal VirusesEntire virion enters the animal cell, unlike in prokaryotes. Eukaryotic cells contain a nucleus, the site of replication for many animal viruses Animal viruses contain all known modes of viral genome replication Many more kinds of enveloped animal viruses than enveloped bacterial viruses exist As animal viruses leave host cell, they can remove part of host cell’s lipid bilayer for their envelope

21

22 Diversity of animal virusesDiversity of animal viruses. The shapes and relative sizes of the major groups of vertebrate viruses. Nonenveloped Enveloped Nonenveloped Enveloped all ssRNA partially dsDNA ssDNA Parvovirus Hepadnavirus Rhabdovirus dsDNA ssRNA Togavirus Papovavirus Picornavirus dsDNA Orthomyxovirus dsDNA Poxvirus Adenovirus dsRNA Bunyavirus Coronavirus Reovirus dsDNA dsDNA 100 nm Diversity of animal viruses. The shapes and relative sizes of the major groups of vertebrate viruses. The hepadnavirus genome has one complete DNA strand and part of the complementary strand. Herpesvirus Paramyxovirus Iridovirus Retrovirus 100 nm Arenavirus DNA viruses RNA viruses

23 Overview of Animal VirusesConsequences of Virus Infection in Animal Cells Persistent infections: release of virions from host cell does not result in cell lysis Infected cell remains alive and continues to produce virus Latent infections: delay between infection by the virus and lytic events Transformation: conversion of normal cell into tumor cell Cell fusion: two or more cells become one cell with many nuclei

24 Persistent infection Latent infectionTumor cell division Transformation Transformation into tumor cell Cell Lysis Virus Death of cell and release of virus Attachment and penetration Persistent infection Virus multiplication May revert to lytic infection Slow release of virus without cell death Cell fusion Figure 9.22 Possible effects that animal viruses may have on cells they infect. Latent infection Virus present but not replicating

25 Retroviruses Retroviruses: RNA viruses that replicate through a DNA intermediate Enveloped viruses Contain a reverse transcriptase (copies information from its RNA genome into DNA), integrase, and protease Virion contains specific tRNA molecules Carcinogenic Chracteristics HIV, AIDS,..

26 Surface envelope proteinRNA Transmembrane envelope protein Enzymes (reverse transcriptase, integrase, protease) Lipid membrane bilayer Figure 9.23 Retrovirus structure and function. Core shell protein Core protein

27 Retroviruses Retroviruses have a unique genomeTwo identical ssRNA molecules of the plus (+) orientation Contain specific genes gag: encode structural proteins pol: encode reverse transcriptase and integrase env: encode envelope proteins

28 Retroviruses Process of Replication of a RetrovirusEntrance into the cell (at site of specific receptor) Removal of virion envelope at the membrane Reverse transcription of one of the two RNA genomes Integration of retroviral DNA into host genome Transcription of retroviral DNA Assembly and packaging of genomic RNA into the nucloecapsid. Budding of enveloped virions; release from cell

29 Figure 9.24 Replication process of a retrovirus.Retrovirus virion containing ssRNA (two copies) Entrance Uncoating R R ssRNA Reverse transcription LTR dsDNA LTR Travel to nucleus and integration into host DNA Host DNA LTR Provirus LTR Transcription R R Viral mRNA and genomic RNA ssRNA Encapsidation Figure 9.24 Replication process of a retrovirus. ssRNA Nucleocapsid Budding Host cytoplasmic membrane Release Progeny retrovirus virions

30 Subviral Entities Defective Viruses Viroids Prions

31 Defective Viruses Defective viruses: viruses that are parasitic on other viruses Require other virus (helper virus) to provide some function Some rely on intact virus of same type Satellite viruses: defective viruses for which no intact version exists; rely on unrelated viruses as helpers Example: bacteriophage P4, of E coli needs P2 for major capsid proteins. Example: Adeno Associate Virus, Adenovirus

32 Viroids Viroids: infectious RNA molecules that lack a protein coat (capsid) Smallest known pathogens (246–399 bp) Cause a number of important plant diseases(not animals or prokaryotes) Small, circular, ssRNA molecules Do not encode proteins; completely dependent on host-encoded enzymes

33 This apparently makes the viroid sufficiently stable to exist outside the host cell.Because it lacks a capsid, the viroid does not use a receptor to enter the host cell. Enters a plant cell through a wound, as from insect or other mechanical damage. No protein-encoding genes, and therefore the viroid is almost totally dependent on host function for its replication

34 Prions They have distinct extracellular form, which consist entirely of proteins. The prion particle contains neither DNA nor RNA. Known to cause disease in animals. (scrapie in sheep) As prions lack nucleic acid, how is the protein they consist of encoded? The host cell contains a gene, Prnp (standing for “Prion protein”) which encodes the native form of the prion protein, known as PrPC (Prion Protein Cellular), that is primarily found in the neurons of healthy animals, especially in the brain.

35 Prions animal prion diseases are known as transmissible spongiform encephalopathies (TSEs). The pathogenic form of the prion protein,PrPSc (prion protein Scrapie), because the first prion disease to be discovered was scrapie in sheep. PrPSc is identical in amino acid sequence to PrPC from the same species, but has a different conformation.

36 Native prions consist largely of α-helical segments,whereas pathogenic prions have less α -helix and moreβ -sheet regions instead. This causes the prion protein to lose its normal function, to become partially resistant to proteases, and to become insoluble, leading to aggregation within the neural cell

37 The pathogenic prion does not subvert host enzymes or genes as a virus does,it “replicates” by converting native prion proteins that already exist in the host cell into the pathogenic form. Infectious prion disease, PrPSc is transmitted between animals or humans. Sporadic prion disease, random misfolding of a PrPC molecule occurs in a normal, uninfected individual. Inherited prion disease, a mutation in the prion gene yields a prion protein that changes more often into PrPSc

38 Why The Flu Virus Is More Infectious In Cold Winter TemperaturesA new finding may account for why the flu virus is more infectious in cold winter temperatures than during the warmer months. At winter temperatures, the virus's outer covering, or envelope, hardens to a rubbery gel that could shield the virus as it passes from person to person, the researchers have found. At warmer temperatures, however, the protective gel melts to a liquid phase. But this liquid phase apparently isn't tough enough to protect the virus against the elements, and so the virus loses its ability to spread from person to person. ANOTHER LINK