1 Structural Virology Lecture 9 Pavel Plevka 2 Bacteriophages © 2012 John Wiley & Sons Ltd. www.wiley.com/college/carter 3 Bacteriophages 4 Phages of gram posiHve and gram negaHve bacteria 5 Phage entry 6 Viral aLachment to host cell pilus 7 Viral aLachment to host cell flagellum 8 DegradaHon of host cell envelope components during virus entry 9 Phage penetraHon into host cytoplasm 10 Genome ejecHon through host cell envelope Myoviridae Siphoviridae Podoviridae 11 Viral contracHle tail ejecHon system 12 Viral long flexible tail ejecHon system 13 Viral short tail ejecHon system 14 Viral penetraHon into host cytoplasm via pilus retracHon Phage M13 15 Fusion of virus membrane with host outer membrane Cystoviridae CorHcoviridae 16 Phage-bacteria interacHons 17 SuperinfecHon exclusion 18 ModulaHon of host host virulence by virus 19 DegradaHon of host chromosome by phage T4 – cyHdine modificaHon 20 Phage host transcripHon shutoff 21 InhibiHon of host DNA replicaHon by virus 22 Toxin-anHtoxin systems as anHviral defense 23 RestricHon-modificaHon system evasion by virus 24 DNA end degradaHon evasion by virus 25 CRISPR-cas clustered Regularly Interspaced Short Palindromic Repeats / CRISP-associated proteins 26 Phage genome packaging 27 Tail assembly 28 Phage exit 29 Phage extrusion 30 Holin/endolysin/spanin cell lysis by phage 31 Phage budding Plasmaviridae © 2012 John Wiley & Sons Ltd. www.wiley.com/college/carter 32 Bacteriophage MS2 © 2012 John Wiley & Sons Ltd. www.wiley.com/college/carter 33 MS2 life-cycle 34 Leviviridae gene expression regulaHon The gene for the most abundant protein, the coat protein, can be immediately translated. The translaHon start of the replicase gene is normally hidden within RNA secondary structure, but can be transiently opened as ribosomes pass through the coat protein gene. Replicase translaHon is also shut down once large amounts of coat protein have been made; coat protein dimers bind and stabilize the RNA "operator hairpin", blocking the replicase start. The start of the maturaHon protein gene is accessible in RNA being replicated but hidden within RNA secondary structure in the completed MS2 RNA; this ensures translaHon of only a very few copies of maturaHon protein per RNA. The lysis protein gene can only be iniHated by ribosomes that have completed translaHon of the coat protein gene and "slip back" to the start of the lysis protein gene, at about a 5% frequency. © 2012 John Wiley & Sons Ltd. www.wiley.com/college/carter 35 36 Leviviridae replicaHon 37 38 phiX174 39 phiX174 genome ssDNA(+) genome of 4.4 to 6.1kb 40 phiX174 rolling circle genome replicaHon 41 Non-enveloped, rod of filaments of 7nm in diameter and 700 to 2000nm in length. Helical capsid with adsorpHon proteins on one end. Innoviridae – M13 42 Viral penetraHon into host cytoplasm via pilus retracHon Phage M13 © 2012 John Wiley & Sons Ltd. www.wiley.com/college/carter 43 Innoviridae – gene product III © 2012 John Wiley & Sons Ltd. www.wiley.com/college/carter 44 M13 genome (rolling circle replicaHon) 45 46 Myoviridae – T4 47 48 T4 – genome 49 Podoviridae – phage T7 © 2012 John Wiley & Sons Ltd. www.wiley.com/college/carter 50 Siphoviridae – theta replicaHon © 2012 John Wiley & Sons Ltd. www.wiley.com/college/carter 51 Siphoviridae – rolling circle replicaHon © 2012 John Wiley & Sons Ltd. www.wiley.com/college/carter 52 Learning outcomes •  discuss the replicaHon cycle and control of gene expression in ssRNA coliphages •  outline the infecHon process of dsRNA phages •  review the biology of the filamentous and icosahedral ssDNA phages •  describe the structure and replicaHon cycle of dsDNA phages 53 CRISPR-cas genome ediHng 54 Virus origins © 2012 John Wiley & Sons Ltd. www.wiley.com/college/carter 55 56 PotenHal virus precursors 57 Gene transfer agents 58 Polymerase error rates 59 Quasispecies 60 RecombinaHon 61 Copy-choice recombinaHon 62 Genome fragment re-assortment 63 LTR retrotransposons © 2012 John Wiley & Sons Ltd. www.wiley.com/college/carter 64 • Progressive hypothesis • Regressive hypothesis • Virus-first hypothesis • Nucleocytoplasmic large DNA viruses as precursors of nuclei in eukaryotes © 2012 John Wiley & Sons Ltd. www.wiley.com/college/carter 65 Learning outcomes •  evaluate theories on the origins of viruses •  explain how virus evoluHon occurs through mutaHon, recombinaHon and re-assortment •  assess the value of virus genome sequencing in studies of virus origins and evoluHon •  assess the threats posed to man and animals by rapid virus evoluHon •  discuss the co-evoluHon of viruses and their hosts