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CMMB 421 > MT2 > Flashcards

MT2 Flashcards

1
Q

What was the first virus discovered?

A

Tobacco mosaic virus

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2
Q

Phage P1 belongs to which family?

A

Myoviridae

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3
Q

What is the morphology of Geminiviridae?

A

Two icosahedral capsids stuck together. Have ssDNA circular genome

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4
Q

What is the morphology of the phage T4 capsid?

A

Oblate icosahedral

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5
Q

Which two non-virion proteins make up the baculovirus occlusion body?

A

Polyhedrin and P10 protein

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6
Q

An example of an insect virus family with a segmented dsDNA genome?

A

Polydnaviridae

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7
Q

What taxonomic group is Nidovirales in?

A

Order

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8
Q

What taxonomic group is Torovirinae in?

A

subfamily

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9
Q

What type of genome does Maize Streak Mosaic virus have?

A

ssDNA circular genome

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10
Q

The family of viroids that replicate in a plastid is called?

A

Avsunviroidae

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11
Q

What enzyme does Avsunviroidae use to circularize their genomes?

A

tRNA ligase

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12
Q

What two phenotypes are produced in infected insects?

A
  1. Budded Virus - responsible for systemic infection.

2. Occlusion derived virus - responsible for spreading the virus from one host to another

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13
Q

What are virus-like particles (VLPs)?

A

molecules that closely resemble viruses but are non-infectious as they contain no viral genetic material. They can be synthesized from engineered Baculoviruses that express capsid proteins of other viruses

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14
Q

Name some ways in which genetically enhanced Baculoviiruses for biocontrol have been produced.

A
  1. Cloned BT toxins
  2. Cloned Scorpion toxins
  3. Cloned mite paralytic toxins
  4. viral enhancing factor
  5. genes for moulting hormones
  6. genes that inactivate hormones
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15
Q

Name a plant virus that requires multiple particles containing different genome segments to infect its plant host.

A

Can say these: cucumber mosaic virus, tobacco rattle virus, alfalfa mosaic virus, etc.

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16
Q

Which Cauliflower mosaic virus protein allows its 35S RNA to be translated as a polycistronic mRNA?

A

TAV protein, protein 6, or Orf 6

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17
Q

What three proteins are coded in the Tobacco mosaic virus genome?

A

Coat protein, movement protein, and replicase

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18
Q

Define Cas9

A

Cas9 is a CRISPR-associated protein found in type II crispr-cas system. It is a large protein involved in complexing with crRNAs and tracRNA to recognize and bind to protospacers, and working in concert with RNAse III, to cut them

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19
Q

Define viral movement protein

A

A viral movement protein is a protein encoded on the genome of a plant virus that is used for either long-distance movement through vascular bundles or cell-cell movement through plasmodesmata.

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20
Q

Define RexAB

A

RexAB are proteins encoded by the rexAB genes on phage Lambda. These genes are expressed when Lambda is in the prophage state, and produce proteins that by an abortive infection mechanism will kill the cell or stop its growth when a T4 or T4 like phage infects the cell. The mechanism of action is formation of a depolarizing membrane channel by RexB when the phage’s proteins are detected by RexA.

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21
Q

Define Holin

A

It is a common phage protein involved in cell lysis. It is synthesized late in the infection, inserts into the cytoplasmic membrane to create pores through which other phage encoded enzymes (lysins and lyzozymes) can access the peptidoglycan and digest it, resulting in cell lysis.

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22
Q

What are some types of anti-phage mechanisms bacteria have?

A
  1. Mutation is one but not the best solution.

2. Restriction modifications

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23
Q

Virology is the study of…

A

viruses

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24
Q

Viruses of Archaea have genomes made of ___ with the vast majority having which form of that nucleic acid ____.

A
  1. DNA

2. double-stranded

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25
Q

Two examples of virophages are?

A
  1. Zamilon
  2. Sputnik
  3. Mavirus
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26
Q

What virus does Zamilon infect?

A

Mimivirus

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27
Q

What virus does Sputnik infect?

A

Mimivirus

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28
Q

Excision of a lambda prophage from an E. coli genome requires which two proteins/enzymes?

A

Integrase and exicisionase

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29
Q

An example of a pararetrovirus?

A

Cauliflower mosaic virus

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30
Q

What is the name of the family to which viruses that are symbionts of parasitoid wasps belong?

A

Polydnaviridae

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31
Q

What viroid replicates in the nucleus?

A

Pospiviroidae

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32
Q

What enzyme does Pospivoidae use to circularize their genomes?

A

DNA ligase I

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33
Q

The insect viruses that have been exploited the most for biological control belong to?

A

Baculoviridae

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34
Q

Name three defence systems archaea and bacteria have that enable them to survive phage infection.

A
  1. Any of abortive infection
  2. CRISPR-Cas
  3. Restriction/modification systems
  4. Modifying or mutating receptor genes.
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35
Q

Define Abortive Infection System

A

This is a bacterial or archaeal system which is designed to cause cell death or arrest of growth in a cell. Once the cell has been infected by a phage/virus, it will arrest cell growth or kill the cell. This stops the virus from spreading to other cells of the same strain. Examples include the RexAB system in Lambda prophages or toxIN

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36
Q

Define occlusion body

A

Large crystalline structure (polyhedral) that accumulates in the nucleus of cells infected with certain types of Baculovirus (Nuclear Polyhedrosis viruses) or in the cytoplasm of insect cells infected with cytoplasmic polyhedrosis virus. Made mostly of one protein, polyhedrin. Functions to encase virions and extend their life in the extracellular environment.

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37
Q

Define Viroid

A

Infectious agent that causes plant disease and consists of a single stranded circular RNA molecule exhibiting a great deal of base pairing and secondary structure. Viroids cause on their own and do not require help viruses to replicate.

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38
Q

Define Lysogenic Conversion

A

The presence of a prophafe due to its expression of certain genes in the phage genome, confers a new property on the host bacterium. This can either induce a phenotypic or physiological property. Examples include the RexAB system in Lambda, cholera toxin.

The new property is not related to the biology of the phage itself.

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39
Q

Define Prophage

A

A temperate phage that has not gone into a lytic cycle but has had its DNA incorporated into the host genome either by integration into the chromosome or by independent replication as a plasmid.

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40
Q

Define Polintons

A

Eukaryotic dsDNA transposon that appears to encode viral proteins, though encapsidation has not been observed. Speculated to evolved from Tectivirus tpye entity and to be related to Megavirales and virophages, may have an important link in viral evolution.

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41
Q

What are some ways in which plant viruses can be transmitted from one plant to another?

A

Arthropods, vegetation propagation of plants, mechanical damage, and occasionally in seeds.

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42
Q

What is required for plant viruses to infect their hosts?

A

Damage to plant cell wall and often membrane such as wounds, insect bites, etc.

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43
Q

How do viruses move in plants?

A

They use movement proteins that interact with plasmodesmata to make openings bigger and also coat the viral RNA and hitch it to trafficking systems inside the cell. Either the virus or its genome can pass to adjacent cells. Long distance movement proteins facilitate movement into the vascular bundles (Xylem and phoelem) to spread to distant parts of the plant.

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44
Q

How would you distinguish Lambda and T4 in E. coli petri plates?

A

If you mutate the LamB or maltose outer membrane transporter in which Lambda binds to, it would not allow Lambda to grow and plaque. T4 will be able to. Mutations in the OmpC and LPS (receptors for T4) will allow Lambda to grow but not T4.

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45
Q

T/F - Lambda is a temperate phage

A

True

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46
Q

Describe morphology of T4

A

It has a rigid tail which contracts and its head is a prolate icosahedron.

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47
Q

Describe morphology of Lambda

A

Long non-contractile tail and a regular icosahedron head.

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48
Q

T/F - T4 phage can transduce DNA

A

False, cannot mediate generalized transduction but mutants of T4 can

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49
Q

T/F - Lambda can transduce DNA

A

False, it cannot mediate generalized transduction but can if the genes are adjacent to the attB site and if it excises imprecisely from its prophage state (happens at a low frequency).

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50
Q

T/F - T4 phage DNA won’t digest with most common restriction enzymes

A

True

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51
Q

How would you distinguish T4 and Lambda?

A

Using plates, qPCR, or gel electrophoresis (T4 has a larger genome that does not get digested by restriction enzymes).

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52
Q

T/F - No archaeal viruses with an RNA genome have been isolated yet, but there is evidence from metagenomic studies that they might exist

A

True

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53
Q

T/F - Archaeal viruses can have ssDNA genomes

A

True

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54
Q

What family does T7 belong to and why?

A

Autographivirdae since it encodes RNA polymerase on its genome

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55
Q

T/F - T4 packages its genome by a headful mechanism

A

True

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56
Q

T/F - T4 encodes a DNA ligase and its own RNA polymerase

A

False, encodes DNA ligase and not RNA polymerase

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57
Q

T/F - T4 is a temperate phage

A

False

58
Q

T/F - T4 genome is circular

A

False, it is linear but is circularly permuted

59
Q

T/F - T4 packages more than its entire genome in the head

A

True - terminal redundancy

60
Q

What is the repressor protein of phage Lambda that shuts down transcription when it is in its prophage state

A

C1

61
Q

What is the transcriptional activator of Lambda that induces transcription of the gene for the repressor protein?

A

CII

62
Q

How does T4 modify its genome?

A

Glycosylation of one of the four nucleotides in its genome and using hydroxymethylcytosine instead of cytosine in the DNA.

63
Q

T/F - All archaeal viruses lyse their host cells

A

False

64
Q

Describe T7

A

It is a bacteriophage that has a linear dsDNA genome.

It is an icosahedron with T=7.

Receptor is LPS

It has a short non-contractile tail belonging to Podoviridae.

New group is called Autographivirdae as it encodes its own RNA pol.

Its genome is organized based on its order of expression and has terminal direct repeats.

Similar to P22, but proteins encoded are similar to Lambda.

65
Q

TF - DNA concatemers are formed during T7 replication

A

True. Depends on the transcription by viral RNA pol and occurs during DNA packaging into preformed proheads.

66
Q

What are the special features of T7 phages?

A
  1. Overcome host restriction/modification –> inactivating host endonucleases to avoid viral DNA degradation.
  2. F-restriction –> lack of ability to replicate in the presence of the F- factor (Abi).
  3. Experimental evolutionary studies –> useful model for the study of microbial evolution.
  4. Viral RNA pol is used widely for gene expression experiments.
67
Q

How does T7 enter?

A
  1. DNA is injected by tail.
  2. DNA is spooled in by cellular RNA polymerase
  3. DNA is spooled in by T7 RNA polymerase (it takes over).
68
Q

What cleaves the DNA concatemers in T7?

A

Terminase or maturation proteins while its being packaged.

69
Q

Describe Myoviridae

A

dsDNA genome phages with rigid contractile tails.

Includes T-even phages, Mu, and P1

70
Q

Describe P1 phages

A

dsDNA with rigid contractile tails.

Icosahedral head (T=7)

Lysogenic

Replicates like a plasmid but does not integrate into the genome.

Receptor is LPS

71
Q

Describe Mu

A

Similar to P1 (cannot tell apart)

Linear dsDNA genome with a rigid contractile tail

Replicates like a transposon where it has non-specific integration into the host genome.

Binds to LPS (receptor)

Lysogenic

Can mutate every time it jumps and makes a new copy of itself while jumping

72
Q

Describe T4

A

Studied the most in the Myoviridae family.

Capsid is a distorted icosahedron –> prolate icosahedron.

Linear dsDNA genome

Rigid contractile tail

Bigger than T7

Genomes are circularly permuted.

Receptors are LPS and OmpC.

Has 8 tRNA genes

73
Q

What enzymes does T4 use?

A

DNa ligase, polynucleotide kinase, lysozyme, RNA ligase, and DNA pol

74
Q

T/F - There are no RNA cultured archaeal viruses

A

True, only metagenomic evidence

75
Q

Describe Siphoviridae

A

Phages with long, flexible non-contractile tails.

Examples includes Lambda.

Linear dsDNA genome

Non-enveloped with icosahedral capsid (T=7).

76
Q

Describe Lambda

A

linear dsDNA genome

Icosahedral capsid with T=7

Non-enveloped

Flexible long non-contractile tail.

Temperate phage

LamB (maltose outer membrane transporter) is the receptor

Discovered by Ether Lederberg.

Has terminal fibres

Part of Siphoviridae

77
Q

T/F - Lambda uses rolling circle during replication

A

True

78
Q

What circularizes the Lambda DNA

A

cos sequences

79
Q

What gene if deleted would prevent the Lambda phage from entering the lytic cycle

A

Integrase gene

80
Q

What gene if deleted would permanently make the Lambda phage virulent?

A

CI repressor gene

81
Q

T/F - T2 is not a temperate phage

A

True

82
Q

T7 has a genome that ends with….

A

double stranded direct repeats

83
Q

T/F - Lambda uses headful packaging

A

False, T4 types use this

84
Q

What recognizes the packaging signals in Lamda?

A

phage terminase

85
Q

What are the antiterminators in Lamda?

A

N and Q

86
Q

How does Lamda inject its DNA?

A

DNA is injected through the tail and into the cell using mannose permease in which the DNA circularizes using cos sequences and host RNA pol begins transcription.

87
Q

What does Q do in Lambda?

A

It activates the late genes which are the structural and cell lysis genes (its an early gene)

88
Q

What does CI repressor regulate?

A

Three nearby promoters: Pl, Pr, and Prm.

Switches from lytic to lysogenic state.

89
Q

What can lead to prophage induction?

A

UV and mitomycin C (antibiotic) by damaging the DNA which will cause cleavage of the CI repressor leading to the lytic cycle.

Leads to the activation of SOS genes that will activate RecA.

90
Q

Define RecA

A

A enzyme used by the Lambda phage.

It binds to ssDNA and acts as a coprotease to CI.

91
Q

What does CIII do in the Lambda phage?

A

It enhances the stability of CII

92
Q

How does Lamdba insert its DNA into the bacterial chromosome?

A
  1. Int binds to attP and IHF creating an intasome which then binds to attB.
  2. A site-specific recombination event occurs in which inserts the Lambda DNA
93
Q

How does Lambda cause cell lysis?

A
  1. Protein R attacks peptidoglycan.
  2. Protein S (holin) forms a pore in the cytoplasmic membrane in which provides a route for Protein R.
  3. Protein Rz and Rz1 encode Spanins that span the periplasm which links and fuses the inner membrane to the outer membrane. This generates huge gaps in the cell envelope, completing cell lysis.
94
Q

Describe Lambda’s DNA packaging and Virion Assembly process

A
  1. uses scaffolding proteins to form procapsid which is not included in the mature capsid.
  2. DNA is inserted into the prohead shell through a rolling circle mechanism that generates concatemeric DNA.
  3. Terminase nicks DNA which separates the cohesive ends remaining bound to the end of DNA at cosB (cos site).

**ATP is used to generate capsid.

95
Q

What are some ways bacteria protect themselves from phages?

A
  1. Mutation of receptors
  2. Superinfection exclusion and immunity (lysogeny)
  3. Restriction/modification systems
  4. Abortive infection systems (Abi)
  5. CRISPRS and CAS
96
Q

Define superinfection immunity`

A

Cells become resistant to phage infection by having phage DNA integrated into the genome where other related phages cannot infect the cell.

The new phage DNA gets inside the cell but does not infect the cell.

97
Q

Define superinfection exclusion

A

When phage DNA is integrated into the bacterial chromosome, not letting new phages get into the cell.

Broader specificity in which unrelated phages won’t infect the cell

98
Q

Define restriction/modification systems

A

Type I - methylation, recognition, restriction (cleavage) all work together to prevent infection. Cleavage is not site specific.

Type II - Most useful in cloning. Site specific which cleavage occurs at a recognition site. Separate methylase and cleavage enzyme.

Type IV - attach methylated DNA.

99
Q

Define CRISPR

A

Clustered regularly interspaced short palindromic repeats.

40-50% in bacteria and 90% in archaea

Function in association with Cas proteins to serve an immunity system against foreign DNA/RNA

100
Q

Define Cas

A

CRISPR-associated proteins.

Microbial adaptive immune system against viruses and plasmids.

Induces cellular apoptosis and proliferation.

Provide enzymatic machinery required for acquisition for new spacers from and targeting invading elements.

101
Q

Define spacers

A

Region of non-coding DNA between genes. Incorporation of foreign DNA into the cell’s gene which alters their genome.

102
Q

Define protospacers

A

The specific sequence in foreign DNA that gets incorporated into the host’s DNA making it the spacer.

Has PAM sequence with it

103
Q

Define protospacer adjacent motifs (PAMs)

A

Short DNA sequence (2-6 b.p) that follows the DNA region (protospacer) targeted for cleavage by the CRISPR system.

104
Q

Define bacteriophage insensitive mutants

A

Bacterial mutants of phage-sensitive bacteria that due to their mutation, are now phage-resistant where sensitivity and resistance are both determined on a per phage-type basis.

Achieved through mutation in bacterial-surface molecules that interfere with phage-attachment.

Non-CRISPR mediated pathway

105
Q

What are the steps in CRISPR?

A
  1. Protospacer and PAM are present in foreign DNA in which cleavage occurs at the front of the protospacer and end, leaving out PAM. Mediated by Cas1 and Cas2.
  2. Sequence is integrated into host DNA forming the spacer.
  3. crRNA is made with the help of a cascade + Cas3 which when foreign DNA enters its able to cleave it and provide host with immunity.
106
Q

Type II CRISPR is what?

A

CRISPR-Cas9

107
Q

What are some anti-CRISPR mechanisms phages use?

A
  1. mutation in protospacer sequence or PAM
  2. Anti-CRISPR protein in phage genome such as anti-Cas9
  3. Phage has its own CRISPR system that encodes its own CRISPR-Cas complexes
108
Q

Define defense island

A

Contain abundant antiviral genes that function together between different types of antiviral systems with overlap to maintain homeostasis.

Basically genes that defend against phage infection

109
Q

Define viperin

A

interferon induced cellular protein that is conserved in animals which inhibits the replication of multiple viruses by acting as a chain terminator fir viral RNA pol.

110
Q

Define retron

A

DNA sequence found in genome of bacteria that codes for reverse transcriptase and a unique ssDNA/RNA hybrid.

111
Q

What is the Virus-First Hypothesis?

A

Virus pre-dates cells which contributed to the rise of cellular life.

112
Q

What is the reduction hypothesis?

A

Viruses are reduced forms of parasitic organisms as they need cells to replicate.

113
Q

What is the Escape Hypothesis?

A

Viruses were once part of genes of host cells that escaped and got new genes via horizontal gene transfer.

114
Q

Define Giant Viruses

A

belong to the phylum Nucleocytoviricota and all have dsDNA.

Includes chlorovirus, mimivirus, gammaentomopoxvirus, pithovirus, and pandoravirus.

115
Q

Chlorovirus

A

Linear dsDNA with inner membrane of an icosahedral capsid.

Has inverted repeats.

Infects chlorella which is a symbiont of paramecium

116
Q

Mimivirus

A

Linear dsDNA which has inner membrane and spikes on surface.

icosahedral

infects acanthamoebae polyphage

117
Q

Gammaentomopxvirus

A

linear dsDNA

enveloped with ovoid structure

Hosts are insects

118
Q

Pithovirus

A

circular dsDNA

oval shaped with one opening at end

forms virion factory

Host is amoeba

biggest in size

119
Q

Pandoravirus

A

linear dsDNA

no capsid

host amoeba

Largest genome size

120
Q

Define virophages

A

small, dsDNA viral phages that require co-infect of another virus.

Typically infect giant viruses

May improve recovery and survival of host.

Have parasitic effect.

All grouped in Lavidaviridae

Zamilon and Sputnik

121
Q

Sputnik

A

First virophage discovered.

dsDNA

Depends on mimivirus infection which is packaged inside of it to infect amoeba

122
Q

Define Pathogen Derived Resistance

A

Use of genetic elements from pathogen’s own genome to confer resistance in an otherwise susceptible host via genetic engineering.

123
Q

Tobacco mosaic virus

A

Rod that is rigid

+ssRNA genome

1st virus discovered

causes mosaic mottling and discolouration of leaves.

124
Q

Alfalfa mosaic virus

A

icosahedral capsid

+ssRNA genome

contains 4 particles to infect

has 3 RNA strands

infects plants

125
Q

Cauliflower mosaic virus

A

circular dsDNA genome

Icosahedral capsid

pararetrovirus - has a reverse transcriptase.

Aphids transmitted

126
Q

Geminivirus

A

circular ssDNA genome

have two capsids that are smashed together.

have diff. promoters for each gene

eg. maize streak virus

127
Q

What are the symptoms of plant viruses?

A

Mosaics
ringspots
dwarf/stunting
leaf roll/curl

128
Q

What are the plant defenses?

A

Non-specific –> physical barriers, lectins, protease inhibitors, and chemicals.

Specific - Hypersensitive response that causes localized cell death which quanatines the pathogen and allows the secretion of antimicrobial agents

129
Q

How do you infect a plant experimentally?

A

Need to create an abrasion with sandpaper or inject the virus with a needle

130
Q

Define Satellite Virus RNAs

A

small base RNAs that can either be linear or circular.

Requires a helper virus to replicate.

It is encapsidated into helper protein coat which it allows it to move into other cells.

Modulates disease symptoms to either be more severe or less.

131
Q

Define Viroids

A

Naked circular ssRNA that has a lot of secondary structure.

Does not encode proteins

These include Popsiviridae and avsunviroidae.

132
Q

Describe Avsunviroidae

A

Viroid that has naked ssRNA.

Contains hammerhead ribozyme that self-cleaves.

Replicates in chloroplasts

Uses NEP and tRNA ligase in replication`

133
Q

Describe Pospiviroidae

A

naked ssRNA viroid

has no ribozyme activity, cannot self-cleave

replicates in the nucleus

134
Q

What are the genes and proteins of the Cucumber mosaic virus?

A

Has 3 genomic RNAs that are separately encapsidated.

  1. RNA 1 codes for protein 1a which is part of satellite replication and virus movement.
  2. RNA 2 codes for 2a and 2b protein. 2a is a replicase. 2b is made from sgRNA 4A that is involved in movement.
  3. RNA 3 codes for protei 3a and coat protein. 3a is a movement protein. Coat protein is made from sgRNA 4.
135
Q

What proteins does Cauliflower mosaic virus contain?

A

Mov, Atf, Vap, CP, Pol, Tav (inclusion bodies). Contains a reverse transcriptase

136
Q

Cauliflower mosaic virus genome contains…

A

35 S RNA that serves as a polycistronic mRNA which will be reverse transcribed to generate DNA to package into virion

137
Q

Describe Polydnaviridae (Ichnovirus)

A

segmented, circular supercoiled dsDNA.

each virion contains multiple copies of the genome.

replicates in the calyx cells of the ovary

Symbionts of parasitic wasps –> larvae need viruses to survive in the host organism.

138
Q

Describe entomobirnavirus

A

dsRNA that is in two segments.

never fully isolated in nature, found as a contaminant in lab cultures of drosophila.

e.g. drosophila virus x

139
Q

Describe Iridoviridae

A

linear dsDNA genome

Icosahedral capsid and some are enveloped.

infects invertebrates and ectothermic vertebrates (snakes, lizards, etc).

DNA forms concatemers

140
Q

Describe cytoplasmic polyhedrosis virus

A

dsRNA genome which is in 10 segments.

replicates in the cytoplasm.

makes a polyhedrin network

kills the insect slowly

doesn’t fully uncoat and replication takes place inside capsids

141
Q

Describe Baculoviruses

A

circular dsDNA

occluded in polyhedra or granules made of virus encoded protein –> polyhedrin.

Infects only invertebrates

Forms two phenotypes of virions: budded virus and occlusion derived virus.

142
Q

How are Baculoviruses used for gene expression systems?

A
  1. polyhedrin gene is removed
  2. foreign DNA is cloned downstream of the polyhedrin promoter in a plasmid transfer vector.
  3. insect cells are co-transfected with infections of WT viral DNA and transfer vector.

These recombinant genes are incorporated into progeny virions.

CMMB 421 (2 decks)

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