section r – bacteriophages and eukaryotic viruses

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Section R Bacteriophages and eukaryotic viruses Slide 2 For example--- Human diseases caused by virus: AIDS,polio, influenza,cold sores, measles,and a few types of cancer, Plant disease by virus: tobacco mosaic virus(TMV) Virion( ): Virus outside of a living cell, exists as a particle Slide 3 General features Different shapes,sizes,and constructions. Comprising coat proteins and nucleotides. Obligatory intracellular parasites. Containing a small amount of genetic material( single/double-stranded RNA or DNA) Slide 4 R1 Introduction to viruses Viruses, Virus genomes, Replication strategies, Virus virulenceVirusesVirus genomesReplication strategiesVirus virulence R2 Bacteriophages General properties, Lytic and lysogenic infection, Bacteriophage M13, Bacteriophage lambda(), Transposable phagesGeneral propertiesLytic and lysogenic infection Bacteriophage M13Bacteriophage lambda()Transposable phages R3 DNA viruses DNA genomes: replication and transcription, Small DNA viruses, Large DNA viruses, Herpes simplex virus-1DNA genomes: replication and transcriptionSmall DNA virusesLarge DNA virusesHerpes simplex virus-1 R4 RNA viruses RNA genomes: general features, Viral reverse transcription, Retroviruses, Oncogenic retroviruses, Retroviral genome structure and expression, Retroviral mutation ratesRNA genomes: general featuresViral reverse transcription RetrovirusesOncogenic retrovirusesRetroviral genome structure and expressionRetroviral mutation ratesContents Slide 5 R1 Introduction to viruses Viruses A virus is a sub-microscopic infectious agent that is unable to grow or reproduce outside a host cell. Adenovirus T-even bacteriophage T Human immunodeficiency virus(HIV) Slide 6 Fig. 1. (a) Icosahedral virion (b) Complex bacteriophage with icosahedral head, and tail (c) Helical virion (d) Enveloped icosahedral virion (e) a rhabdovirus s typical bulletshaped, helical, enveloped icosahedral Slide 7 R1 Introduction to viruses Virus genomes Viruses can have genomes consisting of either RNA or DNA, which may be double- strand or single-strand, and, for single- stranded genomes, positive, negative or ambi-sense( defined relative to the mRNA sequence). The genomes vary in size from around 1 kb to nearly 300 kb, and replicate using combinations of viral and cellular enzyme. Slide 8 R1 Introduction to viruses Replication strategies Viral replication strategies depend largely on the type and size of genome. E.g. 1.Small DNA viruses may make more use of cellular replication machinery than large DNA viruses, which often encode their own polymerases. 2.RNA virus require virus-encoded RNA-dependent polymerases for their replication. 3.Some RNA viruses use an RNA-dependent DNA polymerase( reverse transcriptase) to replicate via a DNA intermediate. Slide 9 R1 Introduction to viruses Virus virulence Many viruses do not cause any cause any disease, and often the mechanisms of ciral virulence are accidental to the viral life cycle, although some may enhance transmission. Slide 10 The virulence mechanisms of viruses fall into six main categories a.Accidental damage to cellular metabolism b.Damage to the cell membrane during transmission between cells. c.Disease signs important for transmission between hosts d.Evasion of the hosts immune system e.Accidental induction of deleterious immune responses directed at viral antigens f.Transformation of cells and tumor formation Slide 11 R2 Bacteriophages General properties Bacteriophages infect bacteria. In 1915, British bacteriologist Frederick Twort, superintendent of the Brown Institution of London, discovered a small agent that infected and killed bacteria. Slide 12 R2 Bacteriophages Lytic and lysogenic infection In lytic infection, virions are released from the cell by lysis. However, in lysogenic viruses integrate their genomes into that of the host cell, and may be stably inherited through several generations before returning to lytic infection. Slide 13 R2 Bacteriophages Bacteriophage M13 Bacteriophage M13 has a small single- stranded DNA genomes, replicates via a double-stranded DNA replicative form, and can infect cells without causing lysis. Modified M13 phage has been used extensively as a cloning vector. Slide 14 Slide 15 R2 Bacteriophages Bacteriophage lambda() Probably the best-studied lysogenic phage is bactriophage. Temporally regulated expression of various groups of genes enables the virus to either undergo rapid lytic infections, or, if environmental conditiona are adverse, undergo lysogeny as a prophage integrated into the host cells genome. Slide 16 Slide 17 Slide 18 R2 Bacteriophages Transposable phages Some phage, for example bacteriophage Mu, routinely integrate into the host cell and replicative transposition. Slide 19 R3 DNA viruses DNA genomes: replication and transcription DNA virus genomes can be double-stranded. Almost all eukaryotic DNA viruses replicate in the host cells nucleus and make use of host cellular replication and transcription as well as translation. Large dsDNA viruses often have more complex life cycles, including temporal control of transcription, translation and replication of both the virus and the cell. Viruses with small DNA genome may be more dependent on the host cell for replication. Slide 20 R3 DNA viruses Small DNA viruses One example of a small DNA virus family is the papovaviridae( ). Papovaciruses, such as SV40 and polyoma( ) rely on overlapping genes and splicing to encode six genes in a small, 5kb double- stranded genome. These viruses can transactivate cellular replicative processes which mediate not only viral but cellar replication; hence they can cause tumors in their hosts. Slide 21 Slide 22 R3 DNA viruses Large DNA viruses Example of large DNA viruses include the family Herpesviridae( ). Herpesviruses infect a range of vertebrates( ), causing a variety of important diseases. Slide 23 R3 DNA viruses Herpes simplex virus-1 Herpes simplex cirus-1(hsv-1) has over 70 open reading frames (ORFs) and a genome of around 150 kb. After infection of a permissive cell, three classes of genes, the immediate-early (), early() and late() genes are expressed in a defined temporal sequence. These genes express a cascade( ) of trans-activating factors which regulate viral transcription and activation. This virus has the ability to undergo latent infection( ). Slide 24 R4 RNA viruses RNA genomes: general features Viral RNA genomes may be single- or double- stranded, positive or negative sense, and have a wide variety of mechanisms of replication. All however, rely on virus-encode RNA- dependent polymerases, the inaccuracy of which in terms of making complementary RNA is much higher than of DNA-dependent polymerases. This significantly affects the evolution of RNA viruses by increasing their ability to adapt, but limits their size. Slide 25 R4 RNA viruses Viral reverse transcription The use of virus-derived reverse transcriptases (RTs, ) has revolutionized molecular biology. 3D model of HIV reverse transcriptase Slide 26 R4 RNA viruses Retroviruses Reteoviruses have diploid, positive sense RNA genomes, and replicate via a dsDNA intermediate. This intermediate, called the provirus, is inserted into the host cells genome. Retroviruses share many properties with eukaryotic retrotransposons( ) such as the yeast Ty elements. Slide 27 Slide 28 Phylogeny of Retroviruses Slide 29 R4 RNA viruses Oncogenic retroviruses Insertion of the retrocirus into the host genome may cause either de-regulation of host cell genes or, occasionally, may cause recombination with host cell genes (and the acquisition of those genes into the viral genome). This may give rise to cancer if the retrovirus alters the expression or activity of a critical cellar regulatory gene called an oncogene. Slide 30 R4 RNA viruses Retroviral genome structure and expression Retroviral have a basic structure of gag, pol and env genes flanked by 5- and 3- long terminal repeats (LTRs). The retroviral promoter is found in the U3 region of the 5LTR and this promoter is responsible foe all retroviral human immunodeficiency virus (HIV). Slide 31 R4 RNA viruses Retroviral mutation rates The RTs of some retroviruses can have a high error rate of up to one mutation per 10000 nt. Defective genomes may be complementation and recombination. This, combined with the rapid turnover of virus (10 9 -10 10 new virions per day in the case of HIV), enable it to adapt to selective pressure. Slide 32 Multiple choice questions 1. Which one of the following statements about viruses is false? A viruses can only replicate in a host cell. B some viral envelopes contain host cell proteins. C viral genomes may be double stranded or single stranded DNA or RNA. D replication-defective viruses may be replicated through complementation. E all viruses are dependent on the host cell replication and transcription machinery. F some viruses use disease symptoms to aid their transmission between hosts. 2 Which one of the following statements about M13 bacteriophage is true? A bacterophage M13 has a double stranded DNA genome. B the M13 phage particle enters the E. coli host cell following binding to the sex pili. C multiple copies of the M13 replicative form (RF) are produced by normal double stranded DNA replication using RNA priming. D M13 phage particles are released by cell lysis. F there is a highly variable amount of DNA in different M13 phage particles. Slide 33 3 Which three of the following statements about bacteriophage are true? A the bacteriophage has a double stranded DNA genome. B phage particles bind to receptors on the E. coli outer membrane and inject the viral DNA into the cell. C the lytic life cycle requires integration of the bacteriophage genome into the host cell genome. D termination of the N and Cro genes is rho-independent. E repressor acts to repress lysogeny. F host cell stress tends to switch on the lytic

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