Virus (Latin: slimy toxin, venom) Edward Jenner English, 1798 We say viruses, plural but actually should be viri=infectious agent you could pass through a 0.2um (micrometer) filter Beijerinick 1899I. Virus - An acellular obligate intracellular parasite with a protein capsid and a nucleic acid genome (DNA, RNA, single or double stranded)Other acellular agents which are not viruses (see Box 14.1): prion ,protein folded abnormally (Ex. scrapie, BSE, Creutzfeld-Jacob disease)viroid ,smallest nucleic acid based pathogens,250bases, ssRNA circle (Ex.potato spindle tuber viroid)Evolutionary relationships within virus families Table 14.2Bacteriophage- virus that infects prokaryotic cells (bacteria and archaea)Bacteriophage T4 http://www.pnas.org/content/98/20/11411/F5.large.jpgFigure 5An unrooted phenogram based on a 76-aa concatenated sequence from the T4-related bacteriophage major capsid proteins derived by maximum likelihood Cyanophages S-PM2 and S-PWM3 are representative of what we suggest be called the exoT-even group.A. Size: small, from 20nm(Microviridae, X174) to 400nm(Poxviridea, smallpox) hard to see w/ EM(www.ncbi.nlm.nih.gov) conventional microscope (www.stanford.edu)Genomes:5386 bases single stranded(ss) circle and 186,000 double stranded(ds) linearNote: E.coli 4,000,000 base pairs and 3000nm longB. Host cell specificity: most infect a single species of host cell, often relying on binding to a specific receptor: M13 phage infects E.coli F pilus and so able to infect only one subtype of E.coli , HIV attaches to CD4,CxCR4, intergrin 47 and CCR5 on Tcell surface proteins human only, Rabies virus attaches to nicotinic acetylcholine receptor andother conserved nerve proteins, most warm blooded animals, nerve cellsC. Life Cycle: Virion- complete virus particle (infectious form) nucleic acid inside protein capsid T4 Phage virionTable 14.1 and 14.5 Types of genomesGenome type Pathway for mRNA Exampleds DNA mRNA transcribed directly Poxvirusesss DNA require opposite copy parvoviruses+ssRNA behaves as mRNA poliovirus+ssRNA reverse transcribes to dsDNA mRNA transcribed HIV-ssRNA mRNA made by RNA dependant polymerase Influenzads RNA rotavirusII. Lytic Bacteriophage Infection- leads to death of host cell, and replication of virusExample: T4 phage, ds DNA, 170kilobase pair genome, icosahedral head, tail with tail fibers. Icosahedral (Fig 14.5) T4 mug shot Fig 14.14 Replication Cycle:1. attachment (adsorbsion) to LPS-core polysaccharide (wide host range: E.coli, Salmonella, Shigella, Pasturella)2. penetration –ATPase, expends energystrategy to avoid restriction enzyme digestion of DNA by host: hydroxymethylcytosine-glucose to imitate methylation (restriction methylation systems are a major anti-phage defense of prokaryotes)cut DNA at specific sequences, often palidromes 3. early transcription 30 sec to 7 min, host polymerase and sigma 70, products: unusual T7 specific tRNA, mRNAs for proteins synthesis, DNA polymerase, RNA polymerase, ribosylation complex, sigma 70 modifying protein, T4 gp55 sigma factor, Ndd exonuclease destroys host cell DNA infection irreversibly fatallate transcription, with Nucleic acid of T4 copied (6 min) and protein synthesis using host ribosomes (10 min) different promoters head, tails, fibers, lysozyme4. assembly and packaging of phage genomes as repeats, ligated (20min) maturation5. lysis of host cell to release virus progeny (about 200 for T4)III. Lysogenic Bacteriophage Infection- infection does not always destroy the host cell. temperate phage is old name Example: Lambda phage, ds DNA, 48.5 kilobase pair linear genome, icosahedral head, tail with single fiber. diagramFig. 14.9 Map of lambda circular due to overlapping 12 base COS sitesFig. 14.6 Infection by a temperate phage1. adsorbsion – to maltose porin protein2. penetration3. a. early transcription and protein synthesisDecision Fig. 14.9 operator right with cI. lambda repressor vs. CRO b. delayed early (N antitermination)4.Nucleic acid replication 4. Integration of phage genome (Prophage)Rolling circle Integrase and cI repressor5. Late protein synthesis 5. Replication of virus genetic material with immune hostQ- antiterminator cI repressor Prm promotor = lysogenized host Corynebacterium diphtheriaStreptococcus pyogenesE. coli (Shiga toxin-lamboid phage)Clostrium botulinumStaphylococcus aureus6. Assembly and packaging7. Lysis of hostEpilogue:SOS DNA repair system of host RecA protease accidentally cleaves cI repressor (LexA)http://www.pris m.gatech.edu/~gh19/b1510/8lytic.jpg IV. Animal Viruses (Table 14.3 )Retrovirus(+ssDNA) AIDS, SIV, feline leukemiaPoxvirus(dsDNA) smallpox in humans, vaccinia, myxomavirus in rabbitsHerpesvirus(dsDNA) chickenpox, shigles, herpes cold sores, infectious monoOrthomyxovirus(-ssRNA) influenza human, avian influenza Rhinovirus(+ssRNA) coldAdenovirus(dsDNA) cold, animal adenovirus tumorsCornonavirus(+ssRNA) cold, SARS, stomach fluV. Replication of HIV- transmissionFig. 14.19Identifies targets for anti-viral drugs and vaccines1. HIV attaches to CD42. virus membrane joins cell membrane, virus uncoats3. reverse transciptase (in virion) makes ssDNA and 4. viral RNA degrades5. dsDNA6. dsDNA integrates, may be maintained 7. host RNApolymerase transcribes mRNA8. in cytoplasm translation of capsids, reverse transcriptase9. virus budsVI. Ecological importanceMost abundant life forms in oceans (10 30 )Approximately 15X more than bacteria and archea in oceansReduces by 20-40% the stock of prokaryotes each dayKill the "winners", enhances diversity transfer genetic material, and destroy blooms May unfortunately contribute to carbon cycling and perhaps to global warmingPhilosophical Debate:Alive: replicates Not: no metabolism outside host mutates no cell structureevolves by natural