MIC2011 Week 4

Minus strand RNA virus cont.

INfluenza virus problems - RNA dependent RNA polymerase - have segmented genomes & lack in proof reading & unable to correct errors made during replication - so mutations would arise frequently

5) Virion release cont..

Influenza Release

Bacteriophage: Lambda: A temperate Bacteriophage cont......

cIII protein= synthesised @ same time as cII as long as it levels remain high enough cII will be protected But if not protected Cro protein will increase & this protein is a repressor & an activator because it inhibits transcription of cIII & cI genes, decreasing amount cII & lambda repressor If Q protein activate transcription genes required for lytic cycle. How does induction reverse lysogeny? induction occurs in response to environmental factors (ultra violet light) damages DNA. This damage alters activity the host cell's RecA protein (recombination & DNA repair)

Viroids

Viroids= infectitous agents only have RNA cause potato spindle tuber disease, exocortis disease of citrus trees - cause diseaseRNA molecule thought to elicit RNA silencing - destruction of host gene, failure to express requires host gene leasds to disease host plant

Chapter 6

Virus & other Acellular infectious Agents

1) Attachment (adsorption) cont..

Virus evolved that they use host receptors that are alwats present on the cell surface of the host cell & are important for normal host cell function - mutation that change them significatly are not tolerated & ensures virus can infect the host - 2 or more host cell involve in attachment HIV ( bind to 2 different protein on human cells) distribution of host cell to which animal virus atttach also varies @ cellular level - eukaryotic cell membrance have microdomains often called lipid rafts thought to be involved in virion entrance & assembly distribution @ tissue level plays role in determining tropism of virus & outcome of infection (poliovirus inect guy & anterior horn cells whereas measles present in most tissue & disease disseminated throughout the body) Plant viruses notable exception to attachment b/c nothing to bind to rather thye just damage the host cell (plant eating insects carry virions from one plant to another)

3) Synthesis stage cont...

different for RNA virus (b/c lack enzymes needed to replicate RNA or to synthesise mRNA from an RNA genome - so RNA must carry nucleocapsid the enzymes needed to complete the synthesis or they synthesised during infection process Synthesis - tightly regulated - some synthesis early in infection (early protein & usually take over the host cell) other later (late proteins & include capsid & other proteins involved in self-assemble & release)

Bacteriophage T4: A virulent

eg T4 Bacteriophage - only capable only of the lytic cycle T4 attachment begins 1) when tail fibre contacts either the lipopolysaccharide or certain proteins in outer memb of its E. coli host (> tail makes contact, baseplate settles down on surface) 2) baseplate is firmly seated it will change shape & tail sheath recognises so that it shortens from a cylinder 24 rings long to only 12 rings 3) when sheath becomes shorter & wider the central tube, pushed through bacterial cell wall 4) base plate has gp5 protein which has lysozyme activity Lysozyme= breaks bonds linking sugars of peptido together (aids in penetration of tube through peptido layer) 5) linear DNA extruded from head

Enumeration of viruses

to count animal virus indirect method = hemagglutination assay b/c animal virus bind to rbc and when they join they form network that settles out of suspension - hemagglutination titer is the highest dilution of the virus preparation that still causes hemagglutination another inidrect assay based on their infectivity Plaque assay= several dilution of a sample containing virus particles are plated w/ appropriate host cells, when multiplicity of infection is low each plaque in a layer of host is assumed to have rised from multiplication sooo a count of plaques can be used to calculate the plaque forming units (PFU) but no of PFY does not = total no of virions b/c no all of them are infective (alive)

Viruses & Cancer cont..

virus cause cancer= oncovirus (human dsDNA) - encode proteins that bind to & thereby inactivate host (tumor suppressor proteins= regulate cell cycling or monitor or repair DNA damage) 2 tumor suppresser protein 1) Rb= multiple function in nucleus are normal to cell cycling (when this is inactive cell undergo uncontrolled reproduction & are hyperproliferative) 2) p53= guardian of genome b/c initiates either cell cycle arrest or programmed cell death in response to DNA damage (but when inactivated genetic damage persists) - hyperproliferation & lack programmed cell death are beneficial to virus for cell it is catastrophic SOme oncogenic viruses are retrovirus (related to HIV)

Icosahedral Capsids

- a regular polyhedron w/ 20 equilateral triangular faces & 12 vertices - most efficient way to enclose a pace (constructed fomr ring/knob shape [capsomeres], each made up of 5 - 6 protomeres) - petamers (5 ptomers & usually @ vertices of icosahedron), hexamers (have 6& form edges & triangular faces) - RNA virus have pentamers & hexamers constructed w/ one subunit - other have penta & hexa composed of differnt proteins - but some only have penta

4) Assembly

- alot of late proteins involved in assembly of mature virions - some are nucleocapsid some are not but still participate in this & still late protein aid in release of virion - proteins & other factors synthesized by the host may be involved in assembling mature virions Assembly process can be quite complex w/ multiple subassembly lines functioning independently & converging later on Bacteriophages assembled in host cytoplasm - some assembled in nucleus - have virus factories which are ;arge paracrystalline clusters of either complete nucleocapsids or procapsids

Viruses & Cancer

- cancer is most serious (tumor growth of tissue (from neoplasia= unregulated abnormal new cell growth & reproduction) Tumor cells - aberrant shapes & altered plasma membrane other form Anaplasia - tumor is benign is cells remain in place to form a compact mass - cells form malignant or cancerous tumors actively spread throughout body (process of mestasis) like leukemia (undifferentiated & malignant white blood cells that circulate throughout body. Carinogenesis= mutation of multiple genes, oncogenesis involved in this - some oncogenesis are introduced by viruses other come from normal genes (proto-oncogenes= required for normal growth) - but proto can mutate into onco (mutation)

Prions

- cause a variety of neurodegenerative diseases in humans inclue scrapie in sheep, bovine sporangiform& human disease KURU, fatal familial insomnia, Creutzfeldt-Jakob disease (CJD)& Gerstann Strassler Scheinker (GSS) all result in progressive degeneration of brain & eventual death

Bacteriophages X174 & fd

- circular ssDNA genome is injected into cell (capsif outside) - ssDNA genome has same base sequence as viral mRNA (plus strand DNA) - for transcription or genome replication to occurphage must be converted to ds DNA (replicative form RF) - RF directs synthesis of more RF copies & + strand DNA both by rolling-circle replication Assembly of X174 - virion begin w/ formation of procapsid - scaffolding proteins that interact w/ capsid causing them to change & for procapsid - procapsid generated ssDNA genome inserted - assembly then host is lysed which block peptido synthesis E.coli phage fd able to be released from host w/o lysis through secretory process - extrusion phage coat insert host cell then coat assemble as DNA is secreted although host is not lysed it grows & divides @ a slightly reduced rate

What is the general structural properties?

- complete virus (virion) Virion - range from 10 - 400nm (smallest are little larger than ribosomes) - most viruses need to be viewed w/ electron microscope - simple viruses have (nucleocapsid= composed of nucleic acid [DNA or RNA] & prtein coat [capsid]) - the capsid protects viral genome & aids in transfer b/w host cells

Viral Multiplication

- different in virion structure & hv important implications for the mechanism a virus uses to ultiply within its host call - general pattern of viral life cycle is discerned b/c virus need a host cell to multiply Viral multiplication 1) Attachment/Adsorption 2) Entry of nucleocapsid/ viral nucleic acid into host 3) Uncoating of genome b/f life cycle continues 4) synthesis begins (viral genes are transcribed & translated) 5) virus to take control of host cell forcing it to manufacture viral genomes & viral proteins 6) Mature virions escape host

3) Synthesis stage

- differs b/c genome of a virus dictates the events that occur dsDNA virus synthesis is a typical flow of info i cells )genetic info stored in DNA & replicated by enzymes [DNAP polymerase] recorded mRNA [transcription] & decoded during protein synthesis [translation] - due to this they depend solely on their host cells biosynthetic machinery to replicate genomes

Single Stranded DNA viruses

- double stranded but important once have single stranded DNA - life cycle similar to dsDNA but one major exception ( additional step must occur in synthesis b/c ssDNA needs to be converted to dsDNA)

Bacteriophage 6

- enveloped Life cycle - envelope spike to facilitate adsorption - retractin of pilus brings phage into contact w/ outer memb of Gram (-) host - fusion of 2 memb delivers nucleocapsid into periplasmic space - digests peptido allowing nucleocapsid to enter cell wall - enters through endocytosis - once inside viral RNA polymerase act as transcriptase (catalyzing synthesis of viral mRNA from each dsRNA segment while they are still inside capsid. - virus rna polymerase become replicase (synthesising + strand RNA from each segment) & serve as template for - strand regenerating dsRNA genome

1) Attachment (adsorption)

- exception of plant viruses must associate w/ a potential host cell long enough to gain entry into cell - attachment to host is accomplished by specific interaction b/w molecules on the surface of the virion (ligands) & receptor - bacteriophages use cell wall others use teichoic acids flagella or pili Binding animal causes conformational change that facilitate interaction w/ 2ndary receptors entry into host & uncoating - variation in receptors for attachment partly responsible for host preferences Bacteriophages= infect a particular species - receptor specificity accounts for the observation that animal viruses specific animals

Tobacco Mosaic Virus (TMV)

- filamentous w/ coat proteins arranged in helical pattern & enter thru abrasion or wound on plant - entry genome is translated & 2 proteins produced 1 smaller (125kd) other larger - larger protein (185kd) produced by read through of stop codon - 185 kd RNA dependent RNA polymerase & function transcriptase & replicase ( synthesise - strand using +strand genome as template) - not sure if ds RF is created in vivo but RF observed in vitro - after coat protein they assmble into complete TMV - protomers come together to form disks composed of two layers of protomers arranged in helical spirl - coating proteins begin @ 3' end - RNA easily fit as a spira b/c helical capsid grow and rod lengthens the RNA passes through channnel in its center & forms a loop @ growing end

Minus strand RNA virus

- found in many families, filoviridae & ebola, paramyxoviridae (measles & mumps), orthomyxoviridae (influenza) - most are enveloped that infect plants & animals - from spherical to filamentous, rod shaped, bullet shaped & leomorphic - non segmented linear genomes grouped into order Mononegavirales - remaining - strand RNA viruses have segmented genomes that range from 2 to 8 segments - cant function as mRNA therefore they got to bring RNA polymerase into host - first template then switch to genome replication Neuraminidase (NA) thought to hyrrohydrolyse the mucus that covers epithelium allows hemagglutinin (HA) to interact w/ receptors on the surface of epithelial cells & virion enters by receptor mediated endocytosis - HA envelope undergoes change when endosomal pH decreases, hydrophobic ends of HA spring outward & extend toward endosomal memb - virions exit by budding acquiring their envelope NA facilitates release of the progeny virions by cleaving the sialic acid groups from glycoporteins on host cell

Retrovirus

- genomes do not function as mRNA - convert ssRNA into dsDNA using reverse transcriptase - AID - Severse transcriptases (RTs) use an RNA template and a short primer complementary to the 3' end of the RNA to direct the synthesis of the first strand cDNA, which can be used directly as a template for the Polymerase Chain Reaction (PCR). This combination of reverse transcription and PCR (RT-PCR) allows the detection of low abundance RNAs in a sample, and production of the corresponding cDNA, thereby facilitating the cloning of low copy genes. Alternatively, the first-strand cDNA can be made double-stranded using DNA Polymerase I and DNA Ligase. These reaction products can be used for direct cloning without amplification. In this case, RNase H activity, from either the RT or supplied exogenously, is require

Plus-Strand RNA viruses

- have genome that can act as mRNA & be translated upon entry into host cell - first products is an RNA dependent RNA polymerase which catalyzes synthesis of (-) strand used to make > + strands - cause polio, SARS & hepatitis A

Virus Taxonomy & Phylogeny

- < satisfactory in comparison than that of cellular microorganisms - presence or absence of envelope, symmtery of capsid & dimension of virion & capsid Order names - (order names) -virales - (family names)-viridae - (subfamily names)-virinae - (genus name)-virus On top of the other strands they also have plus strand (+ strand RNA) - other ssRNA viruses have genomes that are complementary to mRNA they produce & those are said to be minus strand (- strand RNA) Retrovirus & reverse transcribing DNA share a common evolutionary history

RNA viruses: Unity Amidst diversity

- host cell have dsDNA & lack enzyme needed to generaate mRNA - ds, + strand & - strand RNA virus complete life cycle w/ RNA depended RNA polymerase uses RNA template to make new RNA molecule - when enzyme used to replicate viral RNA genome (replicase) - used to synthesise mRNA have transcriptase activity - have genomes composed > than 1 distinct RNA molecule - rna segemnt encode > than 1 protein - unsegmented genomes code for several proteins yet their genomes only have a single RNA polymerase recognition site which the host polymerase initiates transcritption How RNA virus ensure production of protein? - dsRNA viruses produce polycistronic mRNA's that when translated give rise to two or more proteins - + strand & - strand virus able to generate mRNA's (subgenomic mRNA) shorter than genomic RNA

Polio virus

- human enterovirus C causative agent of poliomyelitis - recognised in 1789 - targets w/ children w/ paralysis - nonenveloped virus enter host by ingestion - attaches to human PV (poliovirus), nucleocapsid enter & + strand RNA released into cytoplas, while virion is @ cell periphery - virus's RNA no have the 5' cap found on eukaryotic mRNA important for ribosome binding Poliovirus tricks its host into translating its capless RNA using 5' region on the RNA (internal riboeom entry site IRES) - translatie into yields polyprotein into 3 smaller proteins

Double stranded RNA viruses

- less abundant but share commmon multiplication strategy

Herpesvirus

- members of the order Hepesvirales, cause cold sored & genital herpes & varicella zoster virus (chicken pox & shingles), cytomegaloviruses & Epstein Barr virus ( causes infectious mononucleosis & implicated in some human cancers - some what pleomorphic & enveloped ( hv spikes that are regularly dispersed over the surface & contain a layer of tegument) - linear & encode 70 - 200 - cause both productive infections ( virus multiplies, host cell metabolism is inhibited & host DNA degraded) & latent infections (virions cant be detected, but virus can be reactivated in neurons leading to productive infection) Productive infection= caused by HSV-1 (herpes simplex virus type 1) - begin w/ receptor mediated attachment followed by fusion of viral envelope w/ host cell memb - association w/ proteoglycans of epithelial cell surfae & viral glycoproteins followed by interaction w/ cellular receptors tegument is released in cytoplasm & transported to host cell microtubule

Double stranded DNA virus

- most bacteriophages hv dsDNA genomes as do several insect viruses & a no of important vertebrate viruses include hepreviruses & poxvirus

5) Virion release

- nonenveloped lse thei host cells @ the end of intracellular phase (activity of viral proteins) Lysis of E.coli involve T4 (lysozyme that attacks peptido in host cell wall & other is holin which creates holes in E.coli plasma memb enabling T4 to move from cytoplasm to peptido) Another release is budding usually in enveloped (enveloped + release= concurrent process) - host cell may survive & continue releasing virions 1) virus encoded protein incorporated into membrane 2) nucloecapsid simultaneosly release & envelope released & envelope form by memb budding sometime a matric protein attach to plasma memb aiding budding ER & golgi help form envelopes Vaccinia elicit formation of long actin tails that propel nucleocapsid through plasma memb directly into an adjacent cell ( virus avoids detection by host immune system)

2) Entry into host

- nucleocapsid enter cytoplasm - bacteriophages inject nucleic acid into cytoplasm of their host leaving the capsid outside & attached to the ell - inside they shed their capsid preteinds (uncoating) other remain encapsidates b/c penetration & uncoatnf often coupled Animal virus= detailed mechanisms of penetration are unclear (3 different modes of entry: 1) fusion of viral envelope w/ host cell, 2) entry by endocytosis & injection of viral nucleic acid into cytoplasm of host cell leaving capsid outside)

What are Viral envelopes & Enzymes

- nucleocapsids of many viruses, some plant ciruses are surrounded by an outer memb layer ( envelope) - animal virus envelope arise from plasma or nuclear memb of host cells - envelope proteins code for by viral genes & project from envelope as spikes (peplomers), the spikes involved in virion attachment to host cell surface & can also identify virus b/c they are different - enveloped viruses have virions with a vriable shape (pleomorphic) Bullet shape rabies= firmly attach to nucleocapsid & endow the virion w/ constant shape Influenza= have 2 spikes, some consist (neuramnidase- function release of mature virions from host cell), other (hemagglutinin- bind virions to rbc & cause cells to clump together) - envelope are glycoproteins - some virus have enzyme within capsid and these enzymes aid in nucleic acid replication

What is the general structural properties? cont..

- protein encode by viral genomes (protomers) - capsid sel assembles but some virus use noncapsid protesin as scaffoliding upon which the capsid assemble ADV= viral genome used w/ max efficiency - block of proteins are amino acid encoded by 3 nucleotides Various morhological types are resulted from the comnbination of a particular type of capsid symmetry w/ the presence or absence of an envelope Viruses w/ virions have an envelope (enveloped viruses), lacking envelope (naked viruses)

Rotavirus

- responsible for deaths of 600,000 children worldwide each year, cause severe diarrhea causes dehydration & death - viewed by electron microscopy, rotavirus vvirions have a characteristi wheel like appearance & nonenveloped & composed of 11 segemtnof dsRNA surronded by 3 layer of proteins - RNA segnets code for 6 structural & 6 nonstructural proteins - very stable in environment infective for several days - transmitted by ingestion of fecal material that is present in H2O or food or contaminated surfaces - when enter loses outermst protein layer & in cytoplasm genome is transcribed (transcriptase) -mRNA passes through channel in double layered particle (DLP) & released in cytopasm of host - mrna translated newly formed protein cluster together forming an inclusion (virplasm)

Infection on Eukaryotic cells

- result in cell death (cytocidal infection) can occur by lysis to host- can cause microscopic or macroscopic degenerative changes or abnormalities that are distinct from lysis (cytopathic effects)

Helical Capsids

- shaped like a hollow tube w/ protein walls Tobacco mosaic virus is a well- studied (example of helical capsid) - TV protomers into helical arrangement produces a rigid tube - capsid encloses an RNA genome, wound in a spiral & lies within a groove by the protein subunits Influenza virus= enclosed in thin, flexible helical capsids that are folded within an envelope - size of helical capsid influenced by both protomeres & nucleic acid enclosed within capsid - diameter of the capsid is a function of the size, shape & interaction of the protomeres - helical capsid do not extend beyond the end of the ciral genome

Satelites

- similiar to vioirds consist of DNA or RNA - differ from viroids they may encode one or more gene & need helper virus to replicate & infect host cell - no homology b/w genome - divided in 3 parts (satelite viruses, RNA & DNA) - satelite virus encode own capsid proteins, but sateline RNA & DNA do not

Viruses

- virology studies viruses ( unique group of infctious agens whose distinctiveness resides in their simple, acellular organization & pattern of multiplication - can exist extracelluarly ( inactive b/c possess few enzymes & cant reporduce outside living cells) or intracellularly - can infect all cell types - affect bacteria (bacteriphages), few archaeal viruses detected

Nuceocytoplasmic Large DNA viruses (NCLD)

- viruses of eukaryotic cells - events occur in cytoplasm of their hosts - have icosahedral capsid that encloses lipid memb - @center of virion is large dsDNA genome - Poxviridae (small pox), iridoviridae ( infect fish), mimiviridae (protozoa) [family of NCLD] - large genomes enable em to encode many proteins for DNA replication involved in recombination, RNA polymerase & chaperone proteins - self sufficient & rely on hosts <

Parovirus

- viruses of eukaryotic cells (infect animal hoss like crustaceans, dogs, cats & mice & humans) - discover in 1974 & uniform, icosahedral, nonenveloped 26 diameter - ssDNA molecule of 5000bases - simplest DNA virus - genome small that directs synthesis of 3 proteins & some smaller polypeptides (none has enzyme activity= so must use host cell for all biosynthetic processes= viral DNA can only replicate in nucleus during S phase) -ends or parovirus are palindromic sequence that can fold back on themselves - formation of hairpin @ 3' end provides primer needed for replication (DNa polymerase) - DNA polymerase & replication similar to rolling circle replication - rolling hairpin replication b/c DNA polymerase seem to shuttle back & forth as it synthesise genomes B19 virus use molecule found only on the surface of progenitors of RBC - virion enter through endocytosis

2) Entry into host cont...

1) fusion involves envelope glycoproteins that interact with proteins in plams memb of host cell - virion of enveloped and non enter cell by endocytosis & may be engulfed by receptor-mediated endocytosis - resulting vesicles are filled ith virions & fuse w/ endosomes (aid in virion uncoatinf & low pH trigger uncoating process Non-enveloped animal viruses cannot employ the membrane fusion mechanism for release from the endosome (low pH in endosome cause conformational change in cpasi) then altered capsid contacts the vesicle memb & either release the viral nucleic acid into cytoplasm or rupture the memb to release itact nucleocapsid

What are 3 types of capsid symmetry?

1) helical 2) icosahedral 3) complex

Infections of Bacterial & Archaeal Cells: (Lysis & Lysogeny)

Bacteriophages can be either virulent or temperate virulent = only one option (begin multiplying immediate upon entering, followed by release from host by lysis, T4 is this eg) Temperate= 2 options ( upon entry they multiply like virulent & lyse or they remain within host w/o destroying it & Bacteriophage Lambda is eg) - temperate & host is lysogeny = remain within its host (prophage= viral nucleic acid either integrated into bacterial chromosome or free in cytoplasm) - infected bacteria (lysogens) = 2 characteristics (cant reinfect same virus & they reproduce by replication & inherited by progeny cells.) [ can continue for many generations until something cause prophage to initiate synthesis & to assemble new virions (using induction= commonly caused by changed in growth conditions) as a result of induction lysogenic cycle ends & lytic cycle commence (host cell lyses & progeny phage particles are released)

Viral genomes

Cellular genomes- always double tranded DNA Viruses= 4 possible nucleic acid types dsDNA, single stranded DNA, ssRNA(ss-single stranded), dsRNA (all used by animal viruses) - most plant viruses have ssRNA genomes & bacterial hv dsDNA -DNA viruses use dsDNA as genetic material & genomes may be linear or circular & some can switch from one form to another E.coli phage lambda has a linear genome in its capsid, bu it becomes circular once it enters host cell

CRIPR/Cas System: Bacteria & Archaea fight back

Defense mechanism - discovered when analyses of numerous bacterial & archaeal genome led to the identification of sets of repeated sequences separated by short spacers - CRIPR short for clustered, regularly interspaced short palindromic repeats - associated w/ a set of genes encoding proteins (cas proteins) Function 1) adaptation stage= occur when cell is infected by a virus, if it survives it adds portions of genome to CRISPR region (addition made @ end of region closest to CAS genes). CRISPR sequences = growth rings on a tree 2) CRISPR oldes infection located on 3 end & most recent closest to CAS genes - interference stage=occur when cell infected a second time by same virus - CRISPR rranscribed to yield RNA w/ repeats & spacers - Cas proteins make RNA's smaller (crRNA's w/ each consisting 1 repeat & 1 spacer) - Cas-crRna associate w/ either viral DNA or mRNA lead to destruction of molecule= prevent virus multiplication & infection thwarted

CRIPR/Cas System: Bacteria & Archaea fight back cont..

Eukaryotic system - small dsRNA come from large dsRNA which are formed during replication which results in RNA silencing RNA (siRNA) - these siRNA associate w/ complex of proteins that bind to viral mRNA whic are degraded

Bacteriophage T4: A virulent cont....

Glycosylated HMC protect T4 DNA from attack by E.coli endo nucleases (restriction enzymes), cleave the viral DNA & destroy it Bacteria has a defense (restiction) Linear dsDNA genome is formed of long DNA molecules (concatemers) DNA packaging within T4 is accomplished by a complex of a protein (packasome) Packasome= set of proteins (terminase complex) creates double stranded during replication - double stranded used for packaging T4 & use energy by ATP hydrolysis to move the viral genome into head and concatemer is cut when the phage head has DNA (which is 3% longer than one set of T4 gene) T4 lyses E.coli when 150 virus particles have accumulated in host cell

Arcaeal Virus

Lags significantly behind - have dsDNA, lone exception have ssDNA - unusual morphology (bottle-shaped, droplet shaped & spindle shaped) - enveloped and archaeal virus genomes can be either linear or cirular Sulfolobus - turreted icosahedral (surrounded lipid bilayer) virus (STIV) - genome enters transcription begins, vira gene redulate host cell genes for replication using host's DNA replication, transcription & translation machinery. - then assembly begins virion releases in formation of pyramid like structure on surface of host cell

Infections of Bacterial & Archaeal Cells: (Lysis & Lysogeny) cont..

Lysogenic conversion - occur when temperate chnges phenotype of its host eg Salmonella infected by epsilon phage, phage changed activities of several enzymes involved in construction of carbs which eliminates epsilon & baterium become immune to infection by another epsilon Infection bacterium by temperate has significant effects on host b/c - lysogeny allow viral nucleic acid to be maintained within dormant host, bacteria become dormant due to nutrient deprivation & do not sythesise nucleic acids or proteins * genome would degrade the host entered dormancy - any more phages in environment that host virologist refer as to high multiplicity, lysogeny enable survival of infected host cells, virulent would destroy available host cells, but prophage will be replicated as the host cell repordces Archaeal can be virulent or temperate but most are temperate

Infections of Bacterial & Archaeal Cells: (Lysis & Lysogeny) cont......

Lystic & lysogenic cycles of temperate phages

Bacteriophage: Lambda: A temperate Bacteriophage cont..

Most genes are clustered according to their function, w/ separate groups involve in head synthesis, tail synthesis, lysogeny, DNA replication & cell lysis ( This is important b/c once genome is circle, a cascade of regulatory events occur that determine if phage pursue lytic cycle or lysogenic) - this regulation is facilitated by clustering & coordinated transcription from same promoters - these events that lead them to choose which process involves the action of several regulatory proteins that function as repressors or activators or both (proteins that regulate transcription, termination & antisense RNA molecules) Protein cII (activator protein)= role in determining if lambda will establish lysogeny or follow lytic pathway - reach high enough levels early on=lysogeny - if does not reach critical level=lytic

Bacteriophage: Lambda: A temperate Bacteriophage

Phage Lambda (Siphoviridae), either lytic or lysogenic upon affecting a host cell if enters lysogenic, the dsDNA is integrated into hosts chromosome, where is resides until conditions for induction occur - viral genome is excised from host cell which initiates lytic cycle How does a temperate phage "decide" which cycle to folow? - bacteriophage lambda infects E.coli has an icosahedral head & noncontractile tail. DNA genome is linear molecule w/ cohesive ends 1) attaches to host & injects genome into cytoplasm (capsid outside) 2) inside linear genome circularised when 2 cohesive ends base pair w/ each other 3) beaks in the strands are sealed by host cell's DNA ligase

Why Capsids known as a complex symmetry?

Pox viruses (animal viruses w/ this complex w/ internal structure w/ an ovoid to brick shaped exterior) - show viron morphology of a vacinia virus (double stranded DNA associate w/ proteind & contained in core w/ central biconcave disk surrounded by memb Large bacteriophages have this - more elaborate than pox virus - T2, T4 & T6 infect E.coli have binal symmetry b/c have head that resembles icosadron & tail that is helical - the head is elongated by on or two rows of hexamers & have DNA - the tail composed of collar joinign to the head a central hollow tube, sheath surrounding the tube & complex baseplate

Viral genomes cont...

RNA virus have dsRNA (most common ssRNA genome= Polio, tobacco mosaic, SARS, rabies, mumps, measles, influenza, human immunodeficiendy & brome mosaic viruses) - RNA virus are segmented genomes (consists of more than 1 piece & enclosed in the same capsid but not always the case) Genome Brome mosaic virus (infect certain grasses is composed of 3 segments distributed aong 3 different virions)

RNA viruses: Unity Amidst diversity cont..

Subgenomic mRNA - synthesis dicated by internal transcription start sites, internal transcription termination sites or both - some - strand (splicing removes introns) & retrovirus ( splicing bring different coding regions together w/ elimination of any intervening coding regions) use alternate plicing to generate different mRNA molecule - numerous RNA virus produce mRNA that are translated to give a single large protein (polyprotein), cleaved by enzymes (proteases) into several smaller protein - other translation= ribosomal frameshifting & readthrough Ribosomal frameshifting= when viral genes overlap but are in different reading frames - can be regulated ibe protein then other is synthesised - occur @ specific sites that hv 2ndary structure (cause ribosome to pause then shift its reading frame) Readthrough - occur when ribosome reach stop codon 1) stop as codon directs 2) ignore stop insert amino acid & continue translation - generates longer protein Ribosomal frameshiftin & readthrough work together

4) Assembly cont...

T4 - assembled separately - baseplate done then tail tube built on & sheath assembled around tube - head constructed w/ scaffolding proteins that are degraded after assembly completed - DNA incorporated in head by packasome (helps to move DNA into head)

Bacteriophage: Lambda: A temperate Bacteriophage cont....

Transcription of Lambda genome catalysed by (DNA dependent RNA polymerase) & cII protein high enough will increase transcription which encodes Integrase. Integrase catalyzes integration of lambda genome into host cell (which is lysogeny) but have a repressor protein to repress transcription of all genes which mantains lysogeic state Integration into host takes place @ attachment site (ATT) Homologous site= present on phage gennome, so phage & bacterial ATT can base-pair w/ each other - this site is located b/w galactose (gal) & biotin (bio) operons = integration Because some cII protein infects early it could ensure lysogeny but this protein can also be degraded by the host enzyme unless it is protected by a viral protein cIII protein

Tobacco Mosaic Virus (TMV) cont..

multiplicatio of plant virus depend on virus ability to spread throughou the plant - virus can move long distance through plant vasculature (travel in phloem) - spread of plant virus is hindered by presence of tough cell walls, so it spreads slowly through holes in adjacent cell wall & join plant cells by narrow bridges - plasmodesmata needed to coat viral RNA causing RNA to assume linear conformation rather than helical conformation found in TMV virions - linear conformation allow it to fit through plasmodesmata - movement protein associate w/ microtubules - several cytological changes can take place in TMV infected cells (micrscopically visible intracellular inclusions that are similar to replication complexes observed in animal cells infect w/ + strand virus - host cell chloroplasts become abnormal & often degenrate while new chloroplast synthesis inhibited

Herpes virus cont

once enter DNA circles & transcribed by host DNA dependent RNA polymerase to form mRNA's which are translated to yield several immediateearly & early proteins - acquisition of the tegument & envelope & exit from host cell interesting processes that require several steps to complete - primary envelope is lost when it fuses w/ outer memb releasing herpesvirus

Bacteriophage T4: A virulent cont..

within 2 mins of injection RNA begins to synthesise T4 mRNA (early mRNA b/c made b/f viral DNA is made) Within 5 mis viral DNA synthesis commences, catalysed by virus encoded DNA (dependent DNA polymerase) expression of T4 genes is temporally ordered & transcripts & protein products of genes named to reflec time of appearance T4 controls this by regulating activity of E.coli RNA polymerase viral stigma helps host cell's RNA polymerase core enzyme bind to viral late promoters & transcribe the late genes (10-12 mins) Early & late genes are clustered separately on the genome, even transcibed in different directions, early genes in the counter-clockwise direction & late genes clockwise Hydroxymethylcytosine (HMC) important component for T4 because it modifies to replace cytosine, & once synthesised it ensures replication in bacteria