Chapter 10: Viral Genomics, Diversity, and Ecology

Pox viruses:

All replication occurs in cytoplasm (rather than the nucleus)

Name three positive strand RNA viruses:

Bacteriophage MS2, Poliovirus, and Coronavirus

___________ bacteriophages dominate; believed to benefit bacterial cells by:

DNA transferring antibiotic resistance or metabolic genes through transduction and lysogen may be first line of defense against some pathogens (e.g., mucosal surfaces)

Ribonuclease activity degrades RNA strand of RNA:

DNA hybrid

Host cells then began to replicate DNA and converted their genomes from RNA to DNA. Why?

DNA more stable than RNA

Adenoviruses:

DNA replication occurs on both DNA template strands (rather than one strand getting replicated)

The Baltimore scheme: RNA viruses RNA polymerases need a

DNA template

Herpesvirus-

DNA viruses that are enveloped; cause many different infections (cold sores, genital herpes, HPV (can cause cervical cancer), mono, Burkett's lymphoma)

_______________ virion forms by budding.

Enveloped

would have been end of "RNA World" _________________ pressure eliminated cells, leaving protein shell to protect genome, and forced dependence on hosts for replication functions.

Evolutionary

Phages make up about ______ percent total microbial biomass

Five

Coronaviruses

translation can happen right away, it causes SARS (sudden acute respiratory syndrome) and is enveloped larger virus that replicates in cytoplasm cause respiratory infections, including SARS, in humans and other animals amorphous shape, enveloped with glycoprotein spikes on surfaces- makes it look like a crown (Figure 10.19a)

Only part of genome encoding ____________ is translated.

RNA replicase

class V: ss(-) RNA viruses

RNA replicase makes (+) strand used as mRNA and template for more (-) strand genomes; transcription of minus strand

Viruses as part of the "RNA world" may have played a role in transition from

RNA to DNA

RNA replicase:

RNA-dependent RNA polymerase- RNA viruses have their own RNA polymerase to copy their RNA based on relationship of genome to mRNA

Reoviruses

Respiratory, Enteric, Orphan virus (REO) cause respiratory infections, intestinal infections, or infect plants

Name two negative strand RNA viruses:

Rhabdovirus and influenza virus

Coronavirus causes

SARS

Viroid structure:

forms hairpin-shaped ds molecule with closed ends (Figure 10.31), providing stability outside host cell; It is single stranded so it can fold back on itself (because of complimentary base pairing) which gives it its circular shape and makes it look double stranded but it is actually single stranded

Nonpathogenic prions Some ___________ have "prions" that do not cause disease and instead

fungi adapt to environmental conditions (e.g., altered nutrient utilization, antibiotic resistance, biofilm formation, nitrogen metabolism)

After attachment, host cytoplasmic membrane

fuses with viral envelope, releasing nucleocapsid into cell

Few groups of viruses have trees assembled from sequences of shared/common

genes/proteins example: nucleocytoplasmic large DNA viruses (NCLDV): Mimivirus and relatives

includes 7 classes: class IV: ss(+) RNA viruses

genome is mRNA; used directly as mRNA

Most symptoms are ____________-related

growth (will stop or stunt growth)

Most viral genes from nature have no existing

homologs, so much of their genomes will be new to biology.

Reovirus replication Replication occurs exclusively in

host cytoplasm within the nucleocapsid

Pox virus are _____________ in size- _________ ______ is the vaccine

huge small pox

Bacteriophage MS2

icosahedral infects E. coli by attaching to pilus (Figure 10.17a) possesses a small genome encoding four proteins including one subunit of RNA replicase required for viral RNA replication possesses overlapping genes translated directly upon entry because (+)RNA is equivalent to mRNA

example: rotavirus (causes diarrhea in 6-24-month olds, it is deadly) You don't see it when you are older because

if you already got it you have developed antibodies against it

Amyloid diseases

include Alzheimer's, Huntington's, Parkinson's, type 2 diabetes

Hepadnaviruses

include hepatitis B (Figure 10.25a) DNA viruses that you reverse transcriptase, have ss part and ds parts unusual tiny, partially double-stranded genomes overlapping genes- part of all of the gene is embedded in another genes, don't have two distinct genes

Retroviruses: ____________ to form new retrovirus virions

induction

Viroids:

infectious RNA molecules that lack a protein component small, circular, ssRNA molecules (Figure 9.25) smallest known pathogens (246-399 bp) cause a number of important plant diseases, needs to be a cut in the plant for it to get in and cause disease, the plant will wilt and get smaller (Figure 10.30) do not infect animals or microorganisms

Pandoravirus:

infects some marine amoebae larger than some bacteria

An accumulation of prion proteins causes

insoluble amyloid or plaques that destroy the brain. You will get holes in the grey matter of your brain which gives you the symptoms of the prion diseases.

dsDNA with long terminal repeats forms; repeats assist in

integration into genome

In nonpermissive hosts,

integration into host DNA occurs (via integrate; provirus stage), resulting in transformation

Retroviruses:

integration of viral genes into the host genome reverse transcriptase

Bacteriophages can also enhance

pathogenicity (e.g., CTXɸ and Vibrio cholera; CTXɸ are pathogenic because phage genome encodes cholera toxin)

Retroviral DNA becomes _____________ part of host chromosome.

permanent

More class II viruses have _________ hosts instead of animals.

plant

The human virome also usually includes __________ viruses (from food); believed to cause ________________

plant inflammation (because they are proteins and proteins are antigens- and you can have an allergic reaction to the virus)

class VII more common in __________ than animals

plants

The influenza virus has RNA replicase (to make _______ ___________) and RNA endonuclease (to _________________________________________________________)

plus strands cut up the RNA pieces that get copied into smaller pieces

Polio virus causes

polio

All but one ssDNA virus are

positive-strand viruses

Viral tRNA serves as

primer

No known _____________ ss(-)RNA viruses that infect _______________ cells

prokaryotic

Hosts for viruses of each Baltimore class Only certain Baltimore classes infect certain phylogenies. (Figure 10.3a) Class I (dsDNA) are primary

prokaryotic viruses (bacteria phages)

The RNA to DNA transition How did DNA viruses arise?

protection from ribonucleases (enzymes that breakdown RNA, wouldn't break down DNA) Reverse transcriptase may have been key.

Hepadnaviral reverse transcriptase also functions as

protein primer for DNA synthesis.

Viral phylogeny Universal phylogenetic tree constructed from combination of

protein sequences and structural feature

______________ analysis used instead

proteome

Cell lyses and releases virions. has been genetically engineered to make _________________ __________ since it elicits a strong immune response without serious health effects (e.g., influenza, rabies, herpes simplex type 1, hepatitis B)

recombinant vaccines- using a weaker nonpathogenic virus to carry the genes for the antigens for the pathogens so your body makes the antibody for it, so when your body is exposed it already has the antibody to kill the pathogen

the plus strand of Reovirus

replicates to form dsRNA for the new virions

The plus strand of mRNA undergoes

replication and is used as mRNA- it is translated into viral proteins

Retroviruses (RNA viruses; Class VI) and hepadnavir uses (DNA viruses; Class VII) both use ___________ ________________ for replication.

reverse transcriptase

Retrovirus-

reverse transcriptase, ex. HIV

Lack of _______________ presents placement on tree of life using rRNAl.

ribosomes.- are not on the tree of life because they do not have ribosomes and therefore don't have ribosomal rRNA

Replication occurs by

rolling circle mechanisms

Bacteriophages and archaeal viruses in

seawater

Reoviruses genome:

segmented genome (dsRNA) binds to receptor, enters and transported into lysosomes, uncoating nucleocapsid, activates RNA replicase in cytoplasm

The gag encodes

several small viral structural proteins

The gag encodes

several small viral structural proteins; ex. capsid proteins and protease

Viroids are known to yield small interfering RNAs (siRNAs) during replication, may ______________ plant genes

silence/suppress

class III: double-stranded RNA

similar replication as class V; ex. rotavirus; transcription of minus strand

Viroids may mimic or interfere with plant

small regulatory RNA

The Baltimore scheme: RNA viruses class VI (Retroviruses):

ss(+) RNA viruses replicate through DNA intermediate Reverse transcription copies RNA into DNA, catalyzed by reverse transcriptase. example: human immunodeficiency virus (HIV) Reverse transcription makes dsDNA intermediate then transcription of minus strand occurs

Hemagglutinin

stimulates immune system; anti-hemagglutinin antibodies prevent infection (immunization)- it is a protein that is on the surface of the influenza virus, if you make antibodies against it it will bind to the hemagglutinin which causes red blood cells to agglutinate

generates hybrid virions that express a unique set of _________ ___________ unrecognized by immune system

surface proteins

reverse transcription:

synthesize DNA from RNA template (Figure 10.23) plus retroviral ssRNA to make dsDNA

late proteins

synthesized later structural and assembly proteins made in large amounts

Viral protein synthesis early proteins

synthesized soon after infection usually enzymes made in small amounts nucleic acid polymerases (copy DNA or RNA), proteins that shut down host transcription and translation of the host

class VII: ds DNA

that replicates through RNA intermediate transcription of minus strand needs to occurs to get plus sense mRNA example: hepatitis B also uses reverse transcriptase

The reason the host DNA polymerase is used to replicated the viruses ssDNA is because

the dsDNA will go into the host chromosome and enters the provirus stage and is replicated with the normal DNA

if the influenza virus undergoes antigenic shift,

the new viruses aren't the same strain as the ones for the antibodies we make from vaccination- leads to major outbreaks

All retroviruses have the ______ genes (these are made from the dsDNA that was integrated into the host chromosome)

three

In nucleus, viral DNA uncoated, and ________ classes of mRNA are produced.

three

HIV infections take

time, it will give out some viruses along the way, but it does not take out much of the t cell membrane at all but over time it takes out enough of the cytoplasmic membrane that it causes the cell to die

proteome

total complement of protein

Genes may be expressed or remain latent indefinitely. If induced, retroviral DNA is RNA can be

transcribed packaged into virions or translated.

The env is processed into

two distinct envelope proteins- spikes that stick out of it.

virion surface proteins interact with host cell surface proteins; how we _________ viruses (H1, N1)

type

RNA genomes

typically smaller than DNA viruses RNA viruses also tend to mutate more than DNA viruses

Double-stranded DNA animal viruses that have

unusual replication strategies

Viral genome size:

vary ~1000-fold from smallest to largest

RNA viruses must replicate in _________ or ____________________

virion encode RNA replicase

Once you get the herpesvirus

you can never get rid of it

Some DNA animal viruses can induce

cancer

An important group causes clinical forms of

cancer (e.g., Epstein-Barr virus and Burkitt's lymphoma).

Influenza virus

causes flu or influenza enveloped, pleomorphic (non-uniform), budding virus with segmented genome (separate pieces of the RNA); negative strand RNA animal virus

Rhabdovirus

causes rabies; bullet shape

DNA viruses then infected ancestors of

cellular domains (ex. archaea)

10.12 The Bacterial and Archaeal Virosphere Viruses found everywhere ____________ _______ is present

cellular life (because they have to have host)

smallest:

circovirus: 1.75-kilobase single strand

Adenoviruses: Initial replication yields

complete ds viral genome and ss(-)DNA molecule

Gene expression and protein processing are

complex

Reoviruses and RNA replication RNA replication is

conservative

Virus incorporates into the host cell and loses

contact inhibition, plies onto itself

ss(-)DNA

cyclizes and a complementary ss(+)DNA strand synthesized

Pox virus: All replication occurs in _____________.

cytoplasm

Assembly occurs in of retroviruses _______________; visions released by ________________

cytoplasm budding

Animal viruses include ______________-causing viruses

disease (hepatitis, SARS, influenza, rhinoviruses, coronaviruses, adenoviruses, herpesviruses)- they may be just there or transient or you may be infected with then

Segments of the RNA genome from two genetically _______ strains of virus infecting the same cell are ____________

distinct reasserted

Partial genomic DNA strand is completed to form

dsDNA

DNA polymerase to make ________ from _________

dsDNA ssDNA

_________ __________________ among best studied of all viruses Include _____ and ___________

dsDNA bacteriophages T4 and lambda

RNA viruses seem to be older than DNA viruses, with _________ being oldest of all

dsRNA

The microbial arms race

dynamic relationship between bacteriophages and hosts Bacteria produce restriction endonucleases; bacteriophage T4 substitutes 5-hydroxymethylcytosine for cytosine in genome so it wont get chopped up by the bacteria's restriction endonuclease Some E. coli evolved altered restriction enzymes that degrade T4 DNA. T4 phages modify DNA by glycosylation instead. (adding glucose) Some E. coli evolved altered restriction enzymes that recognize and degrade glycosylated T4 DNA. Some T4 inhibit these modified restriction enzymes. Some E. coli evolved uninhibited endonucleases- new endonuclease have evolved

human endogenous retrovirus (HERV)

elements in chromosomes; connections proposed between some HERVs and autoimmune and other disorders; when the retrovirus leaves remnants in the host chromosome called human endogenous retrovirus and it is possible that they are linked to autoimmune diseases (like chromes disease, rheumatoid arthritis, lupus, etc.)

delayed early mRNA:

encodes DNA replication proteins

immediate early mRNA:

encodes regulatory proteins

late mRNA:

encodes structural proteins

envelope added during budding through nuclear membrane Release occurs via

endoplasmic reticulum

Viroid function:

enters plant through wound (e.g., insect, mechanical damage) move between cells through plasmodesmata (thin cytoplasmic strands; connections between the plant cells) completely dependent on plant RNA polymerases for replication; it can replicate in both the chloroplast and nucleus Catalytic self-cleaving activity releases individual viroids after replication; once it is replicated it break up into individual viroids. It can move up and down the plant vascular system to infect the whole plant.

virome:

entire population of viruses present in and on human body; unique to every individual (Figure 10.29) unique to an individual and relatively stable over time

Visions contain virus-encoded ____________ necessary to synthesize mRNA and the new RNA genomes.

enzymes

Large intestine contains roughly _________ prokaryotic cells versus viruses

equal (~109 of each per gram of feces)

Class IV (ss(+)RNA) are primary

eukaryotic viruses

Reovirus replication _____________ synthesized using ____________ as template

(+) mRNA ss(-)RNA

Reovirus replication Viral proteins aggregate, trapping RNA replicase. Nucleocapsids take up genomic _______ fragments and RNA replicase forms _________. coat proteins added in host _______________ ________________ and mature revival virions released by budding or lysis

(+)RNA dsRNA endoplasmic reticulum

Synthesis of mRNA occurs only off ____ strand as template. Synthesis of genomic dsRNA occurs only off ____ strand.

(-) (+)

Genomic RNA used as template to produce

(-) strands from which mRNA is produced and translated. Virions assembled in Golgi complex. released from cell surface

class I: Double-stranded DNA:

(which means you have both the plus and minus strand of DNA); transcription of minus strand will get you the plus strand of mRNA that is needed; ex. T4

Bacteriophage MS2: RNA replicase makes (___)RNA, and more (___)RNA is made with (___) template

- + -

The microbial arms race dynamic relationship between bacteriophages and hosts: three other methods defense:

1. alterations in viral receptor sites: modification of receptor or protection with a shield such as a capsule (to prevent the phage from adhering to the host) 2. Viruses can mutate or degrade capsule. 3. Some temperate bacteriophages hijack host's toxin-antitoxin system (which causes the bacteria to make a toxin that kills itself)

Estimated ______ viruses on Earth

1031

about ______ prokaryotes per ml of seawater about _______ viruses per ml of seawater

106 107

Genome is linear dsDNA encoding ~_____ genes. after attachment and entry, nucleocapsids freed in cytoplasm

250

Five to ________ percent of seawater bacteria killed daily by phage (Figure 10.26)

50

antigenic drift

A minor change you do not see the pandemics

Proteomics suggests viruses originated from ancient cells containing segmented ______ genomes that existed _________ last universal common ancestor (LUCA) of modern cells. (Figure 10.4a)

RNA before

The human virome is dominated by __________ viruses such as:

DNA anelloviruses (nonenveloped, do not cause disease), circoviruses (likely from poultry and pigs), adenoviruses, polyomaviruses, papillomaviruses (nonenveloped dsDNA)

Bacteria in your intestines are host for bacteriophages (most effect ________ like Lambda, PI, etc.); these phages (especially lysogenic phages) can help the pathogens make a _______ and become more __________ (ex. vibrio collera- blocks the absorption of sodium= server diarrhea)

DNA toxin virulent

Viral replication occurs through a ______ ____________________

RNA intermediate

Prion proteins and the prion infection cycle

Host cell contains gene (Prnp) that encodes native form of prion protein (PrPC; prion protein cellular) that is found in neurons/brains of healthy animals. (Figure 10.33a) PrPSc (prion protein scrapie) is pathogenic form with different conformation. Prion proteins are similar but not identical in amino acid sequence. Host range is linked to sequence. PrPSc promotes conversion of PrPC into pathogenic form. Accumulation and aggregation form insoluble amyloids. destroys brain and other nervous tissue

fungi only infected by classes

III and IV

Prions

Infectious proteins whose extracellular form contains no nucleic acid- they are only a protein known to cause disease in animals (transmissible spongiform encephalopathies)

Example: MAVS

MAVS (prion proteins) aggregation in humans triggers interferon production in response to viruses. Interferon will prevent the other cells around it from getting infected with the virus (but since the original cell was infected MAVS will kill it but the other cells will not because of interferon).

Are prion proteins always infectious?

No, you have normal prion proteins (ex. in your brain) but infectious prion proteins cause the normal proteins to change their shape and therefore their function

largest:

Pandoravirus: 2.5-megabase pairs

vaccinia

Put the gene for the pathogenic virus in them to make the antigen and your body makes the antibody against it

______ viruses precede _______ viruses, lead to three domains of cellular life.

RNA DNA

Pox viruses Historically and medically important:

Smallpox was first to be studied and have a vaccine developed (by Jenner) noticed that the milk maids exposed to small pox did not get it, he took the scabs the milk maids would get and inject them into to people are a gene Gave protection against small pox and cow pox among largest animal viruses known also includes cowpox and vaccinia virus (used as smallpox vaccine and lab model)

What are the three genes all retroviruses have?

The gag, pol, and env genes

What diseases do prions cause in animals?

Transmissible spongiform encephalopathies: scrapie (sheep/shaping their heads on the post), bovine spongiform encephalopathy/mad cow, chronic wasting disease (elk and deer), kuru (in cannibals), and Creutzfeldt-Jakob disease (seen in people)

Example: URE3

URE3 normally represses nitrogen-metabolism genes; URE3 prion allows nitrogen sources to be metabolized

Sub viral agents:

Viroids and prions

When did viruses appear?

Viruses may have arisen after cells. remnants of cells that replicate with the help of a live cell

The pol is translated into

a large polyprotein (associated with the capsid?- idk about that; ex. reverse transcriptase and integrase).

The Baltimore scheme:

a way to classify DNA viruses based on relationship of genome to mRNA, includes seven classes (Figure 10.2) The classes describe all variations of DNA or RNA (dsDNA, ssDNA, dsRNA, ssRNA, and plus or minus of each) and know what they need to do in order to get the plus strand of mRNA (which is what is needed)

Are amyloid diseases the same as prion diseases?

amyloid diseases may or may not be prion diseases.

Proteomics support

an early appearance of viruses

Most class I and class V viruses have ______________ hosts instead of plants.

animal

dsRNA (Class III) virus infect

animals, plants, fungi, few bacteria

Influenza virus Segmented genome results in

antigenic shift

Viroid disease Plants may be ________________ or show _______ to ___________ symptoms.

asymptomatic mild lethal

cytomegalovirus often

asymptomatic but can cause pneumonia, retinitis, gastrointestinal diseases

Most abundant viruses in the human virome are

bacteriophages

Why is minus ssDNA unique?

because DNA is replication without a lagging strand (Figure 9.12)

triggers major outbreaks because immunity to new forms absent from population the flu vaccine is the:

best guess of which strains will be in the environment

Neuraminidase

breaks down sialic acid component of host cytoplasmic membrane, functions in virus assembly. Allows the influenza virus to spread, on the surface of the influenza virus.

mature virions exported by

budding

Rabies virus rhabdovirus:

bullet-shaped, enveloped, helical nucleocapsid containing several enzymes; it is a ss(—)RNA virus (Figure 10.20a) Don't really need to know below: must first be transcribed by viral replicase in host cytoplasm into two distinct classes (first needs to be replicated because it is the minus strand) series of mRNAs encoding the structural genes of the virus- will be translated into viral enzymes/protein and will go into the capsids of new virions positive-strand RNA that is a copy of the complete viral genome (template for genomic RNA)- it needs to make a positive strand so that the positive strand can be replicated back into the negative strands to make more virions complex assembly process release by budding

Retroviruses:

integration of viral genes into the host genome in the latent stage when they are proviruses enveloped virions that contain two identical copies of the RNA genome (two plus strands) Virion contains several enzymes, including reverse transcriptase, and viral tRNA (to go through translation). Retroviral genome is not used as mRNA; converted to DNA by reverse transcriptase and integrated into genome. You get transcription from being in the genome so you don't use the plus strand RNA to make the mRNA

Adenovirus

is in the adenoids and cause upper respiratory infections

Is the herpesvirus enveloped or not?

it is enveloped

You want to replicate the plus strands because

it will give you the minus strand which is the template for making more of the plus strand

Bacteriophage MS2 controls access of host ribosome to translational start sites on ________ spontaneous assembly, release upon lysis

its RNA

Adenoviruses

just know that they infect your adenoids! major group of small, naked, icosahedral, linear, double-stranded DNA viruses (Figure 10.14a) minor health importance; cause mild respiratory infections in humans Adenoviral terminal protein attaches to 5' end of adenoviral genomic DNA required for genome replication.

Poliovirus

know that polio virus causes polio! Will make the structural proteins, proteases (which will cut up the polyprotein (into structural coat proteins, more proteases, and RNA replicases)- protein after translation), and RNA replicase small icosahedral virus 5'-terminus of RNA covalently bound to VPg protein that facilitates binding to ribosomes, 3'-terminus has poly(A) tail Translation yields a single long, giant protein (polyprotein) that undergoes self-cleavage (post-translational cleavage) to generate ~20 smaller proteins necessary for nucleic acid replication and virus assembly. Replication occurs in cytoplasm. Lysis occurs, releasing new virions

dsDNA viruses:

lambda and T4 are dsDNA phages, Hep B causes serum hepatitis (in the blood)- you get vaccinated for

Herpesviruses

large group of dsDNA viruses that cause diseases, incorporate into the host chromosome (e.g., fever blisters, venereal herpes, chicken pox, shingles (when chicken pox goes from the latent stage to the lytic stage), mononucleosis, cancer)

The Herpesvirus is able to remain ________ for extended periods of time reactivate under ___________ or ___________________________

latent stress or weakened immune system

Hepadnaviruses host cells are __________ cells, they are __________________

liver enveloped

transformation:

loss of growth inhibition and malignancy

eventually, new virions assembled and exit by

lysis or budding (budding is in nonlytic viruses)

Positive-Strand RNA Viruses have the same configuration as ________ and therefore

mRNA can be translated right away

Reovirus is a dsRNA so the minus strand makes

mRNA (it needs to be replicated to the + strand be mRNA before translation) which will make the viral protein

Viruses may have been first forms of life (pre cellular). Why did viruses appear?

mechanism to quickly move genes from one cell to another

Polyomavirus SV40

naked icosahedral virus that causes tumors in small mammals (e.g., hamsters and rats) circular dsDNA (Figure 10.15a) host DNA polymerase used for replication small genome with overlapping genes transcription and virion assembly occur in nucleus virions released after lysis (permissive host)

class II: Single-stranded positive- or plus-strand DNA

needs replicative form: double-stranded DNA intermediate; synthesis of the minus strand

mixing up the RNA strands, this causes a mutation and a _____________ to be produced

new virus

Reovirus structure:

non enveloped nucleocapsid with a double shell of icosahedral symmetry

_______________ enters host nucleus

nucleocapsid

In adenoviruses DNA replicates in the

nucleus

Nucleocapsid goes to _________ for transcription

nucleus

nucleocapsids assembled in

nucleus (translation is in the cytoplasm so it has to go back to the nucleus to be assembled)

Class VI (Retroviruses) infect

only animals

Once you have made more plus strands, you can

package that and the viral proteins (made by translating the original strand when it underwent translation) into the capsid

Parvovirus causes

parvo in puppies