Microbio Chapter 13: viruses, Viroids, and Prions

lytic/virulent phages

exit the host at the end of the infection cycle by lysing the cell - this is a more productive infection because these viral infections result in the formation of new viral particles - a well-studied lytic phage is T4

what happens when a viral genome enters a host cell?

the virus hijack's the cell's replication machinery, inducing the cell to produce more viral particles.

SOS repair system

this system activates a protease that destroys the repressor protein.

Generalized infection cycle of animal viruses

5 step process: 1) attachment 2) genome entry 3) synthesis 4) assembly 5) release

the infection cycle of T4

5 step process: (~30 minutes) 1) attachment 2) genome entry 3) synthesis

tumor suppressor genes

genes that inhibit cell growth - along with proto-onceogenes, tumor suppressor genes are used to control cell growth. expression of proto-oncogenes and tumor suppressor genes is coordinated to regulate growth and cell division.

proto-oncogenes

genes that stimulate cell growth. - along with tumor suppressor genes, proto-onceogenes are used to control cell growth. expression of proto-oncogenes and tumor suppressor genes is coordinated to regulate growth and cell division.

virus

genetic information - either DNA or RNA - contained within a protective protein coat. - incapable of metabolism, replication, or motility - outside of the host cell, viruses are inert. Inside a cell the virus directs the cell's activities. - infectious agents, but NOT organisms - obligate intracellular parasites - too small to be seen with a light microscope; can only be seen with an electron microscope

transduction

- a process where phages transfer DNA from one bacterial cell (the donor) to another (the recipient) - a process by which bacterial DNA is transferred from one bacterium to another by a phage.

benign tumors

- do not metastasize (spread) or invade nearby normal tissue

Defective phage

- phage particles that do not carry a complete set of phage genes. They contain both bacterial and phage genes. - Defective phage particles are released as host cells lyse. - defective phages are produced during specialized transduction.

uncoating

At the second step of the generalized infection cycle of animal viruses, genome entry, nucleic acid separates from its protein coat before replication occurs. - uncoating may occur simultaneously with entry of the virion into the cell, or after the final intracellular destination for viral replication has been reached. - Most DNA viruses multiply in the nucleus. They enter the nucleus through nuclear pores using viral proteins that have nuclear localization signals

most enteric viruses are non-enveloped. Why would this be so?

Naked viruses are more resistant to various chemicals which the enteric viruses are likely to encounter as they are transmitted by the fecal -oral route.

Generalized infection cycle of animal viruses: Step 3 - Replication of the Genome

The replication strategy of viruses can be divided into 3 general categories: 1) those used by DNA viruses 2) those used by RNA viruses 3) those used by reverse transcribing viruses - the type of genome has a significant influence on the viral replication strategy

virion/viral particle

a complete virus in its inert non-replicating form - a virion must bind to specific receptors, therefore a particular virus may be able to infect only a single or a limited number of cell types and tissues (tropism). - similarly, most viruses can infect only a single species (the viral host range). This explains the resistance some animals have to certain disease.

T4

a double-stranded DNA phage. - during its infection cycle, the phage hijacks a bacterial cell, directing that cell to synthesize new phage particles.

arboviruses (arthropod borne)

a group of viruses named because they are spread by arthropods such as mosquitoes, ticks, and sandflies.

host cell consequences of lysogeny

a lysogen is morphologically identical to an uninfected cell, but there are consequences which include: - immunity to superinfection - lysogens are protected against infection by the same phage because the repressor also binds to the operator on incoming phage DNA - lysogenic conversion

receptor-mediated endocytosis

a mechanism by which cells bring certain extracellular material into the cell

cell culture or tissue culture for cultivating animal viruses

cell/tissue culture is commonly used method to cultivate most animal viruses. - animal cells are grown in a liquid medium contained in special screw-capped flasks and are used as host cells for the virus culture. - animal cells provided with the proper nutrients can divide repeatedly. they grow much slower than bacteria, dividing no faster than once every 24 hours. - animal cell types that make up solid tissues typically grow as a monolayer (a single sheet of cells adhering to the bottom of the flask). - white blood cells grow as single cells in suspension. - not all animal viruses can be grown this way. some grow in living animals.

plaques in plaque assays

circular zones of clearing in the bacterial lawn. Each plaque represents a plaque-forming unit (PEU) initiated by a single phage particles infecting a cell.

retrovirus (e.g., HIV)

have a (+) strand RNA genome, and carry reverse transcriptase within the virion. After entering the host cell, the reverse transcriptase uses the RNA genome as a template to make one strand of DNA. The complement to that DNA strand is then synthesized to make double-stranded DNA, which integrates into the host cell chromosome. Once integrated, the viral DNA may remain in ta latent state (similar to what occurs with a lambda phage), or it may be transcribed into RNA that is translated to synthesize viral proteins needed for production of new virions. Either way, the integration is permanent, so the viral DNA copy cannot be eliminated from the cell.

cancerous or malignant tumors

have the potential to metastasize (spread)

superinfection

infection by the same type of phage

productive infection

viral infection in which more viral particles are produced

latent infection

viral infection in which the viral genome is present but not active, so new viral particles are not being produced

lytic infection

viral infection of a host cell with a subsequent production of more viral particles and lysis of the cell - productive infection

Generalized infection cycle of animal viruses: Step 2 - Genome Entry

- The mechanism an animal virus uses to enter its host cell depends in part on whether the virion is enveloped or non-enveloped. - In all cases the entire virion is taken into the cell. This differs from phages, where only nucleic acid enters the bacterial cell and the capsid stays outside. 1) Enveloped viruses enter the host cell by one of tow mechanisms: fusion with the host membrane or endocytosis. After a virion is taken into the cell, the viral envelope is taken into the cell, the viral envelope fuses with the membrane of the endosome, releasing the nucleocapsid into the cytoplasm 1a) With fusion, the lipid envelope of the virion fuses with the cytoplasmic membrane of the cell after the virion attaches to the host cell receptor. As a result of fusion, the nucleocapsid is released directly into the cell's cytoplasm. 1b) Viruses that enter via endocytosis take advantage of receptor-mediated endocytosis. The viral particles bind to the receptors that normally trigger and facilitate the process, causing the cell to take them up (e.g., influenza viruses use their HA envelope glycoproteins to bind to the host cell membrane, facilitating endocytosis and entry into that cell. 2) Non-enveloped viruses (have no lipid envelope) cannot fuse to host membranes to enter cells. Therefore, the virions enter only via endocytosis. Once in the endosome, the nucleocapsid is released into the cytoplasm - in all viruses, the nucleic acid separates from its protein coat before the start of replication. This is called uncoating.

the infection cycle of T4: step 2 - genome entry

- a bacteriophage injects its genome into the cell. the T4 degrades a small part of the bacterial cell wall using an enzyme, T4 lysozyme, located in the tip of its tail. The tail contracts so that the phage particle appears to sit/squat on the surface of the cell. - the squatting action signals the injection of the phage DNA through the host's cell wall and membrane, and into the cell. - the capsid remains on the outside of the cell - the separation of the nucleic acid from its protein coat before replication is a feature of all viruses.

Key characteristics used by the ICTV to classify viruses

1) genome structure: types of nucleic acid and strandedness 2) hosts they infect: bacteria, archaea, animals, plants 3) viral shape 4) disease symptoms 5) etc.

quantitating animal viruses: quantal assay

- a method to estimate a viral titer. - several dilutions of the virus preparation are administered to a number of animals, cells, or chick embryos, depending on the host specificity of the virus. The titer of the virus (the endpoint) is the dilution at which 50% of the inoculated hosts are infected or killed. This can be reported as either the ID50 (infective dose_. or the LD50 (lethal dose)

extrusion

- a process where M13 particles are assembled. - the virus uses extrusion to exit the cell - in this process, the phage coat protein molecules are inserted into the host cell's cytoplasmic membrane. At the same time, other phage-encoded proteins form pores that span the cytoplasmic and outer membrane. Then as the phage DNA is secreted through the pores, the coat protein molecules cover the single-stranded DNA to form the nucleocapsids.

oncogene

- a proto-oncogene that has been changed in such a way that it promotes uncontrolled growth.

replicase

- a virally encoded RNA polymerase used in the replication of RNA viruses in the generalized infection cycle of animal viruses. - The replicase is a RNA-dependent RNA polymerase. This means that it uses an RNA template to synthesize a new strand of RNA (The RNA polymerase used in transcription is an enzyme that synthesizes a strand of RNA from a DNA template and is therefore a DNA-dependent RNA polymerase). - replicases lack proofreading ability, therefore they make more mistakes than DNA polymerases. This leads to mutations during replication, which leads to antigenic variation and allows some RNA viruses to adapt to selective pressures (e.g., influenza viruses exhibit a type of antigenic variation called antigenic drift. because of this a person whose immune response protects them against the influenza virus one year may not be protected against the variant that circulates the next year.)

naming viruses

- all virus names in the suffix -viridae and are italicized. - the names follow no consistent pattern - viruses are referred to only by their species name or by an informal name, neither of which is capitalized - informal terms are often used to refer to groups of animal viruses that are not taxonomically related but share critical characteristics such as the primary route of transmission (e.g., viruses transmitted via the fecal-oral route are referred to as enteric viruses, if transmitted through the respiratory route it is called a respiratory virus)

inclusion body

- an effect of viral replication in cell cultures - type of cytopathic effect - Certain viruses cause an infected cell to form a distinct region called an inclusion body. The position of an inclusion body in a cell depends on the type of virus.

animal viruses vs. bacteriophages

- animal viruses and bacteriophages share similar features in their infection cycle. - many animal viruses are enveloped and phages are not. - Differences exist in the entry and exit - the genome of animal viruses are diverse, influencing viral replication strategies.

Generalized infection cycle of animal viruses: Step 1 - Attachment

- animal viruses have attachment proteins (spikes) on their surfaces. The receptors to which these proteins bind are usually glycoproteins on the host cell cytoplasmic membrane, and often more than one receptor is required for effective attachment (e.g., HIV must bind to 2 different molecules before it can enter the cell.

viral architecture

- at a minimum a virion consists of nucleic acid surrounded by a protein coat (capsid)

2 major categories of animal virus infections: persistent infections

- can continue with or without symptoms for years, or even for the life span of the host; remain for years sometimes without any symptoms - 2 general types of persistent infections have been identified: 1) chronic infections - characterized by the continuous low-level production of viral particles - in some cases, the infected cell survives and slowly releases viral particles. In other cases, the infected cell lyses, but only a small proportion of cells is infected. The result is that a low number of viral particles are continuously released. * there is a continuous release of viral particles with no disease symptoms. - a person can still transmit the virus to others even in the absence of symptoms. - ex. some people infect with hepatitis B develop a chronic infection. they become carriers of the virus and can pass it others through blood and body fluids. 2) latent infections - the viral genome remains silent within a host cell, but can reactivate to cause a productive - some viruses do nor integrate into the host cell chromosome, but replicate independently of the host genome, similar to a plasmid - the silent viral genome is called a provirus. a provirus cannot be eliminated from the body, which means the disease can recur even after an extended period without symptoms (e.g., shingles, cold sores causes by herpes simplex type 1 (HSV-1)) - what reactivates the virus is not clear, but certain physiological or immunological changes in the host are often involved. - these two categories may overlap in an actual infection with different cells experiencing different types of infection

2 major categories of animal virus infections: acute infections

- characterized by the sudden onset of symptoms of a relatively short duration - results in a burst of virions being released from infected host cells. Although the virus-infected cells often die, the host may survive. This is because the immune system of the animal host may gradually eliminate the virus over a period of days to months. - ex. influenza, mumps, and poliomyelitis - symptoms of the disease result from localized or widespread tissue damage following cell death as well as damage caused by the immune response itself.

antigenic drift

- occurs as mutations accumulate in genes encoding key viral surface proteins that are recognized by the immune system. - occurs because replicases lack proofreading ability when used in the process of Replication of RNA Viruses in the Generalized infection cycle of animal viruses.

obtaining and maintaining cell cultures

- one way to obtain animal cells for culture is to remove tissue from an animal and then process it to get individual cells. These cells can then be grown in a flask with a liquid nutrient medium. Cells acquired in this way form primary cultures. - problem with this approach: normal cells can divide only a limited number of times, so new primary cultures must be regularly made - to avoid the problem: tumor cells are often used in cell culture so that these cells divide indefinitely in vitro, resulting in an established cell line (i.e., HeLa cell line)

prions

- composed only of protein and has no nucleic acid - have been linked to a number of slow fatal human diseases (e.g., Creutzfeldt-Jakob disease and kuru) - linked to some animal diseases (e.g., mad cow disease or bovine spongiform encephalopathy in cattle), chronic wasting disease in deer and elk) - prion proteins accumulate in neural tissue. For unknown reasons, neurons die and brain functions deteriorate as the tissues develop characteristic holes. - characteristic sponge-like appearance of the brain tissues gave rise to transmissible spongiform encephalopathies, which refers to all prion diseases - the mechanisms by which they accumulate in tissue and cause disease is by a normal neuronal protein that is identical in amino acid sequence to a prion protein. The infectious protein is a misfolded version of the normal protein, but the altered shape has severe consequences. - consequences of the misfolded protein: makes the infectious protein resistant to degradation by the host cell proteases that normally destroy older proteins as new ones are synthesized, molecules become insoluble causing them to aggregate in cells - infectious prion proteins are referred to as PrP^SC. normal prion proteins are referred to as PrP^C. - the integration of the infectious prion protein and the normal prion protein is that the infectious one changes the folding of the normal molecules converting them to infectious ones - a prion disease is transmitted only to members of the same species. But the barrier to prion transmission between species also depends on the strain of prion - prions are usually resistant to heat and chemical treatments, making them difficult, if not impossible to eliminate from the environment.

viroids

- consist solely of a small single-stranded RNA molecule that forms a closed ring. - are about 1/10 the size of the smallest infectious viral RNA genome known - infect only plants, where they cause serious disease (e.g., potato spindler tuber, chrysanthemum stunt, etc.) - enter plants through wound sites rather than binding to specific receptors

the infection cycle of T4: step 4 - assembly (maturation)

- during this step the copies of the phage genome and the various structural components of the phage are assembled to produce new phage particles - once the phage head is formed, DNA is packed into it; the tail is then attached, followed by the addition of the tail spikes. - some of the above components self-assemble; the proteins joint together spontaneously to form a specific structure. - in other steps, certain phage proteins serve as scaffolds on which various protein components associate. the scaffolds themselves do not become part of the final structure.

Size of a virus

- extremely small (100 to 1,000-fold smaller than the cells they infect - smallest virus is about 10nm in diameter and contains very little nucleic acid (~10 genes) - the largest known virus is 800nm

common temperate phage: lambda

- has a linear chromosome, but the two ends have complementary single-stranded overhangs that join together inside the host cell to form a circular molecule. - Lambda can either direct a lytic infection or lysogenic infection.

the infection cycle of T4: step 5 - release

- late in the infection cycle of T4, lysozyme is produced. Lysozyme is an enzyme that digests the host cell wall from within, causing the cell to lyse, thereby releasing phage particles. - in the case of the T4 phage, the burst size is ~200 - the released phage particles then infect any susceptible cells in the environment, and the process of phage replication is repeated.

Generalized infection cycle of animal viruses: Step 3 - Replication of the Genome - Replication of DNA Viruses

- most DNA viruses replication in the nucleus of the host cell and use host cell components (i.e., ribosomes and enzymes) for DNA synthesis and gene expression. - these viruses often encode their own DNA polymerase, which allows them to replicate even if the host cell is not actively duplicating its own chromosome - replication of double-stranded DNA viruses follows the central dogma of molecular biology. Double-stranded DNA viruses have 2 complementary strands (+ and - strand). The (+/-) genomes can be transcribed to produce mRNA (+RNA). The mRNA is then translated to make proteins. The double-stranded DNA genome serves as a template for DNA replication. - For replication of single-stranded DNA viruses, a complement to the single-stranded DNA molecule must be synthesized to generate a double-stranded (+/-) DNA molecule. Once this happens, the genes can be expressed to produce the encoded proteins. The newly synthesized DNA strand/the strand that is complementary to the single-stranded DNA genome acts as a template for producing more single-stranded DNA genome copies.

Generalized infection cycle of animal viruses: Step 3 - Replication of the Genome - Replication of RNA Viruses

- most RNA viruses are single-stranded and replicate in the cytoplasm - their replication requires a replicase. - the replication strategy for RNA viruses depends on the type of viral genome. (1) Some single-stranded RNA viruses have a (+) RNA strand genome, which also serves as mRNA. (2) Others have a (-) RNA strand genome, which means the genome is the complement to the mRNA. (3) Double stranded RNA viruses have a genome that consists of both a (+) RNA strand and a (-) RNA strand. (1) For RNA viruses that have a single strand (+) RNA genome, the genome functions as mRNA. The viral RNA can immediately bind to the host cell ribosomes and be translated to make proteins. One of the proteins encoded is a viral replicase, and once this is made it can be used to synthesize more copies of the viral genome. --> First the single strand (+) RNA genome makes multiple complementary (-) RNA strands using the (+) as a template. These (-) RNA strands then act as templates to produce more (+) RNA strands. The newly synthesized (+) RNA strands can either be translated to make more viral proteins or be packaged as genomes into new virions being formed. (2) Replication of a single-stranded (-) RNA virus is complicated because a (-) RNA cannot be translated directly. It is first copied into a (+) RNA strand by a replicase carried into the host cell by a virus. Once the (+) RNA strand has been produced, it can be translated to make viral proteins, and can also be used as the template for synthesizing new (-) RNA strands. Once of the proteins made during translation is replicase, and as the new viral particles are assembled, a molecules of the replicase is packaged alone with a (-) RNA molecule into the capsid. (3) Double-stranded RNA viruses must carry their own replicase because the host cell machinery is unable to translate double-stranded RNA. The replicase immediately uses the (-) RNA strand of the double-stranded RNA molecule as a template to make (+) strand DNA. This molecule is then translated to make more replicase, and the infection cycle can continue.

the infection cycle of T4: step 1 - attachment

- phage particles collide with their host cells by chance. - upon contact with the host cell, a phage attaches to a receptor on the host cell surface of to an appendage (i.e., pilus) - for the T4, the receptor is on the bacterial cell wall - the receptors normally perform important functions for the cell. Phages exploit the molecules for their own use. - cells that lack the receptor used by a particular phage are resistant to infection by that specific phage

operator

- regulatory region that controls the expression of the genes that direct a lytic infection. - helps to provide immunity to superinfection - the repressor binds to the operator on an incoming phage DNA to prevent a lysogen from infection from the same phage

Generalized Transduction

- results from a packaging error during phage assembly - some phages degrade the bacterial chromosome into many fragments during lytic infection. Any of these short bacterial DNA fragments can be mistakenly packaged into the phage head during assembly. Phage heads the contain only bacterial genes instead of phage genes cannot direct a phage replication cycle. If the phage head contains only bacterial genes they are called transducing particles rather than phage particles - after the release of the transducing particle from the phage-infected host, the transducing particle binds to another bacterial cell and injects its DNA. That bacterial DNA may then integrate into the recipient cell by homologous recombination. - any gene of the donor cell can be transferred this way

specialized transduction

- results from an excision mistake made by a temperate phage during its transition from lysogenic to a lytic cycle. - following phage induction, the phage DNA is usually excised precisely from the bacterial chromosome. However on rare occasions, a short piece of bacterial DNA on each side of the phage DNA is taken, and a piece of phage DNA remains in the bacterial chromosome. The excised DNA (containing both bacterial and phage genes) replicates and then becomes incorporated into phage heads during assembly. These phage particles do not carry the complete set of phage genes, so they are DEFECTIVE. Defective phage particles are released as host cells lyse. - When a defective phage injects it s DNA into another bacterial cell, both phage and bacterial DNA enter. The bacterial genes may then integrate into the recipient's genome via homologous recombination - in this process only bacterial genes adjacent to the integrated phage DNA can be transferred

Generalized infection cycle of animal viruses: Step 3 - Replication of the Genome - Reverse-Transcribing Viruses

- reverse-transcribing viruses encode the enzyme reverse transcriptase, which synthesizes DNA from an RNA template.

plaque assays

- routinely used method to determine the concentration of phage particles in samples such as sewage, sea water, and soil. Used to quantitate phage particles. - a melter, cooled soft agar medium is inoculated with both a bacterial host and the phage-containing specimen. That mixture is then poured over the surface of a nutrient agar plate, creating a top layer over a base plate. The bacteria present in the top layer multiple rapidly, producing a dense lawn (turbid layer) of bacterial growth. - Phage particles in the specimen infect susceptible bacteria and lyse the,. The lysed bacteria release progeny phage that diffuse through the soft agar layer to neighboring bacteria, which they then infect. Lysis of these cells leads to the formation of plaques. - different dilutions of the phage suspension are used when doing a plaque assay. This is to ensure that one plate will have a statistically valid number of plaques to be accurately counted. The number is used to determine the titer.

filamentous phages

- single-stranded DNA phages that look like long fibers. - cause productive infections, but the process does not kill the host cell - infected calls, grow more slowly than uninfected cells - extruded from the host cell without killing the cell

transmitters of plant viruses

- soil contamination, growers, contaminated seeds, tubers, or pollen, grafting of healthy plant to health seedlings on the hands of workers who have been in contact with the virus from infected plants, insects

Reassortment

- some RNA viruses have segmented genomes. this means that the genome consists of more than one piece of RNA. - If two different strains of such a virus infect the same host cell, the new viral particles that are synthesized in that cell can have a mix of segments from each of the two original virus strains. This outcome is called reassortment. - Ex. a virus strain that has RNA segments designated "a" through "e" and a different strain that has segments "A" through "E." All new viral particles produced must have a total of 5 segments, but these can originate from either of the parent strains. New viruses can have different combinations of capitalized and lowercase letters (e.g., influenza virus)

proto-oncogene to oncogene

- spontaneous and induced mutations can lead to conversion of a host's normal proto-oncogene into an oncogene, leading to tumor formation. - Sometimes the change is associated with viral infection. Viruses that insert their genome into the host cell's chromosome may cause changes at the insertion site that convert a proto-oncogene into an oncogene. - DNA damage resulting from long-term inflammation associated with chronic infections can also cause the conversion. - certain viruses carry an oncogene, so the infection interferes with the host cell's own growth control mechanisms.

temperate phages

- temperate phages have the options of either directing a lytic infection (productive infection) or incorporating their DNA into the host cell genome (lysogenic infection) - which cycle occurs is random, but the metabolic state of the host cell has an influence (e.g., if a bacterial cell is growing slowly because of nutrient limitation, then a lysogenic infection is more likely to occur)

nucleocapsid

- the capsid with nucleic acid encloses the nucleocapsid.

cytopathic effect

- the distinct morphological alterations in infected cells caused by a virus propagated in cell culture. - since cytopathic effects are often characteristic of a particular virus, they are useful to scientists studying and identifying viruses

Generalized infection cycle of animal viruses: Step 3 - Synthesis of Viral Proteins

- the production of viral particles in an infected cell requires two distinct but interrelated events: 1) expression of viral genes to produce structural and catalytic proteins, such as capsid proteins and any enzymes required for replication 2) synthesis of multiple copies of the viral genome The viral proteins are sometimes synthesized as a polyprotein that is subsequently cleaved by viral proteases into individual proteins. The viral proteases that cleave the polyproteins can be useful targets for antiviral medications (e.g., medications used to treat HIV infection inhibit the HIV protease)

capsid

- the protein coat that protects the nucleic acid in virions from enzymes and toxic chemicals in the environment. - also carries any enzymes required by the virus for infection of host cells - simple chemical structure composed of: identical protein subunits (capsomeres), arranged in a precise manner

enveloped viruses

- these virions obtain a lipid bilayer that sits outside the capsid, from the host cell - enveloped viruses also have a matrix protein which sits between the nucleocapsid and the envelope - enveloped viruses are more susceptible to disinfectants because these chemicals damage the envelope, making the virus non-infectious

Generalized infection cycle of animal viruses: Step 4 - Assembly and Maturation

- this step involves bringing together newly formed viral nucleic acid with capsid proteins and packaging them to form the nucleocapsid. - the assembly process is similar in all viruses - the process is a spontaneous self-assembly that occurs when an appropriate amount of viral nucleic acid and capsid proteins have accumulated in the host cell. - The site of assembly and maturation differs according to the virus. Non-enveloped viruses mature fully in the host cell cytoplasm. In the case enveloped viruses, some maturation steps occur as the virion leaves the host cell. The virus deposits protein into the host cytoplasmic membrane and the assembled nucleocapsid then binds to these regions of the membrane before exiting the host cell. Some DNA viruses (e.g., herpesviruses) assemble their nucleocapsids in the nucleus of the host cell. - The site of virion assembly and the type of virus affect the way in which viral particles are released from the host cell.

M13

- type of filamentous phage - initiates infection by attaching to a protein on the F pilus of E.coli - single-stranded DNA genome that enters the cytoplasm of the bacterial cell, where a host cell DNA polymerase synthesizes the complementary strand. This double-stranded DNA is called a replicative form (RF). One strand of the replicative form is used as a template to make mRNA as well as multiple copies of the phage's single-stranded genome. - M13 particles are assembled in a process called extrusion

Classifying viruses based on nucleic acid

- viruses contain only a single type of nucleic acid - either RNA of DNA - never both - the genome may be linear, circular, either double-stranded, or single stranded

bacteriophages/phages

- viruses that infect bacteria - easy to cultivate in the lab - serve as whole vehicle for horizontal gene transfer in bacteria - kill bacteria, thus reducing the bacterial population in nature. Through this application the FDA has used bacteriophages to prevent the growth of food-contaminating pathogens on various food products.

lysogenic infection

- when a temperate phage chooses to incorporate their DNA into the host cell genome instead of doing a lytic infection (productive infection) - the phage DNA exists within in the cell without causing damage. - in this state, the integrated phage DNA/prophage, is replicated along with the host cell chromosome. - when the cell divides, the prophage is passed onto the cell's progeny. - later the prophage can begin the process that leads to a productive/lytic infection

differences in plant virus compared to phages and animal viruses

- when plant viruses infect a cell they do not attach to specific receptors. Instead they enter through wound sites in the cell wall, which is otherwise tough and rigid. infection in the plant can then spread from cell to cell through channels (the plasmodesmata) that interconnect cells..

the infection cycle of T4: step 3 - synthesis of phage proteins and genome

- within minutes after the T4 DNA is injected into the host cell, some of the genes on that viral genome are transcribed and translated by the infected cell - phage-encoded proteins are made in a specific time sequence to control the course of infection. Early on, the phage directs the bacterial cell to synthesize proteins (early proteins) needed to initiate phage replication (e.g., a nuclease that degrades the cell's DNA is made). - after early proteins are made, the phage genome is synthesized. - toward the end of the infection cycle, the phage directs the bacterial cell to synthesize late proteins. - late proteins - structural proteins that make up the phage, including those that make up the capsid and the tail

recognizable signs of viral infection of plants

- yellowing of foliage with irregular lines appearing on the leaves and fruits. - individual cells or specialized organs of the plant may die, and tumors may appear. - usually, infected plants ate stunted in their growth, although in some cases growth is stimulated leading to deformed structures - plants do not recover from viral infections because they are not capable of developing specific immunity to rid themselves of invading viruses. in severely infected plants, virions accumulate in enormous quantities

2 types of transduction

1) generalized transduction 2) specialized transduction - these are due to 2 different types of errors in the phage replication process in horizontal gene transfer

phage replication results in two possible outcomes

1) a productive infection - new viral particles are produced 2) latent state - the viral genome remains silent within the cell but is replicated along with the host cell genome - for a productive infection, some types of viruses kill their hosts but others do not

2 major categories of animal virus infections

1) acute 2) persistent - some infections do not fall neatly into one category (e.g., when a person is first infected with HIV, the virus replicates to high levels, causing acute symptoms, including fever, fatigues, swollen lymph nodes, and headache. The immune system soon eliminates most virions, and the symptoms subside. However, the DNA copy of the viral genome integrates in to the host cell chromosome, resulting in a persistent infection with subsequent symptoms associated with AIDS developing after many years. The HIV infections has features of both acute and persistent infections.)

two general types of viruses

1) bacteriophages/phages 2) viruses that infect prokaryotic cells and eukaryotic cells

Virus group - mechanism of transmission - common viruses transmitted

1) enteric group - fecal-oral route - enteroviruses (polio); noroviruses; rotaviruses (diarrhea) 2) respiratory group - respiratory or salivary route - influenza; measles; rhinoviruses (colds) 3) Sexually transmitted group - sexual contact - herpes simplex virus 2 (genital herpes); HIV 4) Zoonotic group - Vector (i.e., arthropods) - West Nile encephalitis; Zika virus disease; dengue fever 5) animal to human directly - rabies; cowpox

reverse transcriptase

an enzyme used in the replication process by reverse-transcribing viruses in the Generalized infection cycle of animal viruses. This enzyme is a RNA-dependent DNA polymerase, which synthesizes DNA from an RNA template.

Generalized infection cycle of animal viruses: Step 5 - Release

The release of the virion depends on whether it is enveloped or non-enveloped. Enveloped: - most enveloped viruses are released by budding. Before budding occurs, virally encoded protein spikes insert into specific regions of the host cell's membrane. Matrix protein accumulates on the inside surface of those same regions. Assembled nucleocapsids are then extruded from the cell at these regions, becoming covered with a layer of matrix protein and lipid envelope in the process. - not all enveloped viruses have cytoplasmic membrane derived envelopes. Some obtain their envelope from the membrane of an organelle such as the golgi apparatus or the rough endoplasmic reticulum. They do this by budding into the organelle. From there, they are transported in vesicles to the outside of the cell. Budding may not destroy the cell because the membranes can be repaired after the viral particles exit. Non-enveloped: - non-enveloped viruses are released when the host cell dies. - Many viruses trigger a normal cellular process called apoptosis/programmed cell death, prior to the release of the viral particles. The immune response of an animal, which is directed toward eliminating the virus can also lead to the same process. The virions released form the dead cells may then invade any healthy cells in the area. - to be maintained in nature, infectious virions must spread to various animal hosts. Viral particles can be shed though feces, urine, genital secretions, blood, or mucus and saliva released from the respiratory tract during coughing and sneezing.

viroid

an infectious agent of plants that consists only of RNA

prion

an infectious protein that causes a neurodegenerative disease

Why understanding the infection cycle of animal viruses is important

Virus replication depends on virally encoded enzymes, which are potential targets of antiviral drugs. By interfering with the activities of the enzymes required for viral replication, antiviral medications can slow the progression of a viral infection, often giving host defense systems enough time to eliminate the virus before symptoms appear.

Virus Shapes

Viruses generally come in 3 different shapes: 1) icosahedral - appear spherical when viewed with the electron microscope, but their surface is actually 20 flat triangles 2) helical - appear cylindrical when viewed under the electron microscopy. their capsomeres are arranged in a helix similar to a spiral staircase. Some helical structures are short and rigid, whereas others are long and filamentous 3) complex - have more complicated structures (i.e., many phages have an icosahedral nucleocapsid, referred to as the head with a long helical component, the tail)

Phage induction

When the SOS repair system is activated, the prophage is excised from the chromosome, thus allowing the prophage to enter the lytic cycle. The phage escapes from the damaged host.

lysogen

a bacterium that carries phage DNA (a prophage) integrated into its genome - infected cell

lysogenic conversion

a change in the phenotype of a lysogen as a consequence of the specific prophage it carries. - if a toxin is encoded exclusively by phage genes, then only bacterial strains that carry the prophage will synthesize the toxin.

lysogenic conversion

a change in the properties of a bacterium, conferred by a prophage.

quantitating animal viruses: plaque assay

a monolayer of cultured tissue cells serves as the host. Clear zones surrounded by the uninfected cells are counted to determine the viral titer. - if a sample contains a high enough concentration of viruses to be seen with an electron microscope, direct counts can be used tp determine the number of viral particles in a suspension - viruses that lyse their host cells can be assayed by counting plauqes

quantitating animal viruses: Hemagglutination

a phenomenon in which certain viruses cause red blood cells to agglutinate (clump). This occurs when individual viral particles attach to surface molecules of multiple red blood cells simultaneously, connective the cells to form an aggregate - visible only at high concentrations of viruses, and can be used to determine only the relative concentration of viral particles. - measured by mixing serial dilutions of the viral suspension with a standard amount of red blood cels. - the highest dilution showing maximum agglutination is the titer of the virus. - ex. orthomyxoviruses is a group of animal virus that can agglutinate red blood cells. Influenza virus is a member of this group.

antigenic shift

a phenomenon where a new subtype of a virus is formed by reassortment between different strains of a RNA virus or even between different RNA viruses

budding

a process whereby the virus acquires its envelope. - budding occurs for most enveloped viruses upon release in the Generalized infection cycle of animal viruses.

zoonotic viruses

a virus that causes zoonoses, which is a disease transmitted from an animal to human

tumor

abnormal growth of tissue resulting from a malfunction in the normally highly regulated process of cell growth. - some tumors are benign

effects of viral replication on cell cultures

many viruses can be detected by their effects on cells in cell cultures. a virus propagated in cell culture often causes distinct morphological alterations in infected cells, called a cytopathic effect. - ex. the host cell may change shape, detach from the surface, or lyse. Infected cells may fuse into a giant multinuclear cell (syncytium), a mechanism of viral spread (e.g., HIV). Certain viruses cause an infected cell to form a distinct region called an inclusion body.

abnormal/uncontrolled cell growth

mutations that either increase the expression of proto-oncogenes or decrease the expression of tumor suppressor genes are the most common cause of abnormal cell growth. - a single change in the DNA sequence of these regulatory genes is probably not enough to cause a tumor; rather multiple changes at different sites are required.

repressor protein

one of the proteins that prevents expression of the gene required for excision. - the repressor protein is essential for maintaining the lysogenic infection state

viruses have specific protein components that allow the virion to attached to specific receptor sites on host cells

protein components: 1) phages have tail fibers 2) animal viruses have spikes that stick out from the lipid bilayer of enveloped viruses or the capsid of non-enveloped viruses

Which is more likely to be a specialized transducing phage - a lytic or temperate phage?

temperate phage

titer

the concentration of infectious phage particles in the original phage suspension in a plaque assay.

prophage

the integrated phage DNA. when a temperate phage incorporates their DNA into the host cell genome during a lysogenic infection the phage is called a prophage.

temperate phage lambda lysogenic infection

the integration process in a lysogenic infection uses a phage encoded enzyme called an integrase that inserts the phage DNA into the host cell chromosome at a specific site. The prophage replicates along with the host chromosome prior to cell division. Although the prophage can remain integrated indefinitely, it can also be excised from the host chromosome by a phage-encoded enzyme. This is the start of a lytic infection. - the phage DNA is excised from the chromosome 1/10,000 divisions of the lysogen. - under abnormal growth conditions, such as when a lysogenic culture is treated with a DNA damaging agent like UV light, the SOS repair system comes into play and destroys the repressor protein thus leading to phage induction.

burst size

the number of phage particles released in step 5, release, of the infection cycle

provirus

the silent viral genome in a latent infection. a provirus cannot be eliminated from the body, which means the disease can recur even after an extended period without symptoms - ex. person can get shingles only if he or she has previously had chickenpox, the VZV genome goes dormant in nerve ganglia. Under certain circumstances, the virus can reactivate. Newly formed VZV particles move down the peripheral nerves and spread locally, causing painful skin lesions - ex. HSV-1 causes an acute infection in mucosal epithelial cells, leading to the typical symptoms of cold sores. From there, the virus can spread to the sensory nerve cells where it remains latent. Later, the latent virus can reactivate to cause another episode of cold sores.

non-enveloped/naked viruses

viruses that do not have an envelope. - nearly all phages are non-enveloped

oncogenic viruses

viruses that lead to cancer formation - most virus-induced tumors are caused by certain DNA viruses. - the majority of tumors are not caused by oncogenic viruses, but by mutations in host genes that regulate cell growth

transducing particles

when a phage head contains only bacterial genes instead of phage genes. -transducing particles cannot direct a phage replication cycle - this can happen during generalized transduction