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 positive and gram negative bacteria 5 Phage entry 6 Viral attachment to host cell pilus 7 Viral attachment to host cell flagellum 8 Degradation of host cell envelope components during virus entry 9 Phage penetration into host cytoplasm 10 Genome ejection through host cell envelope Myoviridae Siphoviridae Podoviridae 11 Viral contractile tail ejection system 12 Viral long flexible tail ejection system 13 Viral short tail ejection system 14 Viral penetration into host cytoplasm via pilus retraction Phage M13 15 Fusion of virus membrane with host outer membrane Cystoviridae Corticoviridae 16 Phage-bacteria interactions 17 Superinfection exclusion 18 Modulation of host host virulence by virus 19 Degradation of host chromosome by phage T4 – cytidine modification 20 Phage host transcription shutoff 21 Inhibition of host DNA replication by virus 22 Toxin-antitoxin systems as antiviral defense 23 Restriction-modification system evasion by virus 24 DNA end degradation 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 regulation The gene for the most abundant protein, the coat protein, can be immediately translated. The translation 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 translation 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 maturation protein gene is accessible in RNA being replicated but hidden within RNA secondary structure in the completed MS2 RNA; this ensures translation of only a very few copies of maturation protein per RNA. The lysis protein gene can only be initiated by ribosomes that have completed translation 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 replication 37 38 phiX174 39 phiX174 genome ssDNA(+) genome of 4.4 to 6.1kb 40 phiX174 rolling circle genome replication 41 Non-enveloped, rod of filaments of 7nm in diameter and 700 to 2000nm in length. Helical capsid with adsorption proteins on one end. Innoviridae – M13 42 Viral penetration into host cytoplasm via pilus retraction 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 replication) 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 replication © 2012 John Wiley & Sons Ltd. www.wiley.com/college/carter 51 Siphoviridae – rolling circle replication © 2012 John Wiley & Sons Ltd. www.wiley.com/college/carter 52 Learning outcomes • discuss the replication cycle and control of gene expression in ssRNA coliphages • outline the infection process of dsRNA phages • review the biology of the filamentous and icosahedral ssDNA phages • describe the structure and replication cycle of dsDNA phages 53 CRISPR-cas genome editing 54 Virus origins © 2012 John Wiley & Sons Ltd. www.wiley.com/college/carter 55 56 Potential virus precursors 57 Gene transfer agents 58 Polymerase error rates 59 Quasispecies 60 Recombination 61 Copy-choice recombination 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 evolution occurs through mutation, recombination and re-assortment • assess the value of virus genome sequencing in studies of virus origins and evolution • assess the threats posed to man and animals by rapid virus evolution • discuss the co-evolution of viruses and their hosts