Section R – Bacteriophages and eukaryotic viruses

1. Section R – Bacteriophages and eukaryotic viruses

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(毒粒，病毒体): Virus outside of a living cell, exists as a particle

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)

4. Contents R1 Introduction to viruses Viruses, Virus genomes, Replication strategies, Virus virulence R2 Bacteriophages General properties, Lytic and lysogenic infection, Bacteriophage M13, Bacteriophage lambda(λ), Transposable phages R3 DNA viruses DNA genomes: replication and transcription, Small DNA viruses, Large DNA viruses, Herpes simplex virus-1 R4 RNA viruses RNA genomes: general features, Viral reverse transcription, Retroviruses, Oncogenic retroviruses, Retroviral genome structure and expression, Retroviral mutation rates

5. Adenovirus（腺病毒） Human immunodeficiency virus(HIV) T-even bacteriophage（T型噬菌体） R1 Introduction to viruses — Viruses • A virusis a sub-microscopic infectious agent that is unable to grow or reproduce outside a host cell.

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

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.

8. R1 Introduction to viruses — Replication strategies • Viral replication strategies depend largely on the type and size of genome. E.g. • Small DNA viruses may make more use of cellular replication machinery than large DNA viruses, which often encode their own polymerases. • RNA virus require virus-encoded RNA-dependent polymerases for their replication. • Some RNA viruses use an RNA-dependent DNA polymerase( reverse transcriptase) to replicate via a DNA intermediate.

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.

10. The virulence mechanisms of viruses fall into six main categories • Accidental damage to cellular metabolism • Damage to the cell membrane during transmission between cells. • Disease signs important for transmission between hosts • Evasion of the host’s immune system • Accidental induction of deleterious immune responses directed at viral antigens • Transformation of cells and tumor formation

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.

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.

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.

15. R2 Bacteriophages — Bacteriophage lambda(λ) • Probably the best-studied lysogenic phage is bactriophageλ. • 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 cell’s genome.

18. R2 Bacteriophages — Transposable phages • Some phage, for example bacteriophage Mu, routinely integrate into the host cell and replicative transposition.

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 cell’s 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.

20. R3 DNA viruses — Small DNA viruses • One example of a small DNA virus family is the papovaviridae(乳头多瘤空泡病毒科). • Papovaciruses, such as SV40 and polyoma(多瘤) 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.

22. R3 DNA viruses — Large DNA viruses • Example of large DNA viruses include the family Herpesviridae(疱疹病毒科). • Herpesviruses infect a range of vertebrates(脊椎动物), causing a variety of important diseases.

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 (α), early(β) and late(γ) genes are expressed in a defined temporal sequence. • These genes express a cascade(串联) of trans-activating factors which regulate viral transcription and activation. • This virus has the ability to undergo latent infection(潜伏性感染).

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.

25. R4 RNA viruses — Viral reverse transcription • The use of virus-derived reverse transcriptases (RTs,逆转录酶) has revolutionized molecular biology. 3D model of HIV reverse transcriptase

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 cell’s genome. • Retroviruses share many properties with eukaryotic retrotransposons(反转录转座子) such as the yeast Ty elements.

28. Phylogeny of Retroviruses

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.

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 5’LTR and this promoter is responsible foe all retroviral human immunodeficiency virus (HIV).

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 (109-1010 new virions per day in the case of HIV), enable it to adapt to selective pressure.

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.

33. 3． Which three of the following statements about bacteriophage λ are true? A the bacteriophage λ has a double stranded DNA genome. B λ 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 λ genome into the host cell genome. D termination of the N and Cro genes is rho-independent. E λ repressor acts to repress lysogeny. F host cell stress tends to switch on the lytic cycle. 4． Which one of the following statements about DNA viruses is false? A there is often sequence similarity between the promoters of DNA viruses and those of the host cell. B the SV40 genome has overlapping reading frames. C SV40 large T -antigen regulates both viral and host cell transcription and replication. D the ability of DNA viruses to regulate host cell replication may cause tumors in host cells. E SV40 proteins VP1, VP2 and VP3 are important for the tumorigenic properties of the virus.

34. 5． Which one of the following statements about herpes viruses is true? A herpes viruses are not associated with tumorigenesis. B genes are only found on one strand of the herpes virus genome. C HSV-1 encodes its own DNA polymerase. D HSV-1 has a single origin of replication. E latent infection by herpes viruses requires chromosomal integration of the viral genome. F all of the herpes viral genes are required for viral replication. 6． Which one of the following statements about retroviruses is false? A RNA-dependent polymerases are not as accurate as DNA-dependent polymerases. B like retroviruses yeast Ty transposons encode a reverse transcriptase enzyme. C retroviruses have a single stranded RNA genome. D the Rev protein of HIV regulates viral transcription.

35. THANK YOU !