MT2 Flashcards
1
Q
What was the first virus discovered?
A
Tobacco mosaic virus
2
Q
Phage P1 belongs to which family?
A
Myoviridae
3
Q
What is the morphology of Geminiviridae?
A
Two icosahedral capsids stuck together. Have ssDNA circular genome
4
Q
What is the morphology of the phage T4 capsid?
A
Oblate icosahedral
5
Q
Which two non-virion proteins make up the baculovirus occlusion body?
A
Polyhedrin and P10 protein
6
Q
An example of an insect virus family with a segmented dsDNA genome?
A
Polydnaviridae
7
Q
What taxonomic group is Nidovirales in?
A
Order
8
Q
What taxonomic group is Torovirinae in?
A
subfamily
9
Q
What type of genome does Maize Streak Mosaic virus have?
A
ssDNA circular genome
10
Q
The family of viroids that replicate in a plastid is called?
A
Avsunviroidae
11
Q
What enzyme does Avsunviroidae use to circularize their genomes?
A
tRNA ligase
12
Q
What two phenotypes are produced in infected insects?
A
- Budded Virus - responsible for systemic infection.
2. Occlusion derived virus - responsible for spreading the virus from one host to another
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
14
Q
Name some ways in which genetically enhanced Baculoviiruses for biocontrol have been produced.
A
- Cloned BT toxins
- Cloned Scorpion toxins
- Cloned mite paralytic toxins
- viral enhancing factor
- genes for moulting hormones
- genes that inactivate hormones
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.
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
17
Q
What three proteins are coded in the Tobacco mosaic virus genome?
A
Coat protein, movement protein, and replicase
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
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.
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.
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.
22
Q
What are some types of anti-phage mechanisms bacteria have?
A
- Mutation is one but not the best solution.
2. Restriction modifications
23
Q
Virology is the study of…
A
viruses
24
Q
Viruses of Archaea have genomes made of ___ with the vast majority having which form of that nucleic acid ____.
A
- DNA
2. double-stranded
25
Two examples of virophages are?
1. Zamilon
2. Sputnik
3. Mavirus
26
What virus does Zamilon infect?
Mimivirus
27
What virus does Sputnik infect?
Mimivirus
28
Excision of a lambda prophage from an E. coli genome requires which two proteins/enzymes?
Integrase and exicisionase
29
An example of a pararetrovirus?
Cauliflower mosaic virus
30
What is the name of the family to which viruses that are symbionts of parasitoid wasps belong?
Polydnaviridae
31
What viroid replicates in the nucleus?
Pospiviroidae
32
What enzyme does Pospivoidae use to circularize their genomes?
DNA ligase I
33
The insect viruses that have been exploited the most for biological control belong to?
Baculoviridae
34
Name three defence systems archaea and bacteria have that enable them to survive phage infection.
1. Any of abortive infection
2. CRISPR-Cas
3. Restriction/modification systems
4. Modifying or mutating receptor genes.
35
Define Abortive Infection System
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
36
Define occlusion body
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.
37
Define Viroid
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.
38
Define Lysogenic Conversion
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.
39
Define Prophage
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.
40
Define Polintons
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.
41
What are some ways in which plant viruses can be transmitted from one plant to another?
Arthropods, vegetation propagation of plants, mechanical damage, and occasionally in seeds.
42
What is required for plant viruses to infect their hosts?
Damage to plant cell wall and often membrane such as wounds, insect bites, etc.
43
How do viruses move in plants?
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.
44
How would you distinguish Lambda and T4 in E. coli petri plates?
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.
45
T/F - Lambda is a temperate phage
True
46
Describe morphology of T4
It has a rigid tail which contracts and its head is a prolate icosahedron.
47
Describe morphology of Lambda
Long non-contractile tail and a regular icosahedron head.
48
T/F - T4 phage can transduce DNA
False, cannot mediate generalized transduction but mutants of T4 can
49
T/F - Lambda can transduce DNA
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).
50
T/F - T4 phage DNA won't digest with most common restriction enzymes
True
51
How would you distinguish T4 and Lambda?
Using plates, qPCR, or gel electrophoresis (T4 has a larger genome that does not get digested by restriction enzymes).
52
T/F - No archaeal viruses with an RNA genome have been isolated yet, but there is evidence from metagenomic studies that they might exist
True
53
T/F - Archaeal viruses can have ssDNA genomes
True
54
What family does T7 belong to and why?
Autographivirdae since it encodes RNA polymerase on its genome
55
T/F - T4 packages its genome by a headful mechanism
True
56
T/F - T4 encodes a DNA ligase and its own RNA polymerase
False, encodes DNA ligase and not RNA polymerase
57
T/F - T4 is a temperate phage
False
58
T/F - T4 genome is circular
False, it is linear but is circularly permuted
59
T/F - T4 packages more than its entire genome in the head
True - terminal redundancy
60
What is the repressor protein of phage Lambda that shuts down transcription when it is in its prophage state
C1
61
What is the transcriptional activator of Lambda that induces transcription of the gene for the repressor protein?
CII
62
How does T4 modify its genome?
Glycosylation of one of the four nucleotides in its genome and using hydroxymethylcytosine instead of cytosine in the DNA.
63
T/F - All archaeal viruses lyse their host cells
False
64
Describe T7
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
TF - DNA concatemers are formed during T7 replication
True. Depends on the transcription by viral RNA pol and occurs during DNA packaging into preformed proheads.
66
What are the special features of T7 phages?
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
How does T7 enter?
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
What cleaves the DNA concatemers in T7?
Terminase or maturation proteins while its being packaged.
69
Describe Myoviridae
dsDNA genome phages with rigid contractile tails.
Includes T-even phages, Mu, and P1
70
Describe P1 phages
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
Describe Mu
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
Describe T4
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
What enzymes does T4 use?
DNa ligase, polynucleotide kinase, lysozyme, RNA ligase, and DNA pol
74
T/F - There are no RNA cultured archaeal viruses
True, only metagenomic evidence
75
Describe Siphoviridae
Phages with long, flexible non-contractile tails.
Examples includes Lambda.
Linear dsDNA genome
Non-enveloped with icosahedral capsid (T=7).
76
Describe Lambda
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
T/F - Lambda uses rolling circle during replication
True
78
What circularizes the Lambda DNA
cos sequences
79
What gene if deleted would prevent the Lambda phage from entering the lytic cycle
Integrase gene
80
What gene if deleted would permanently make the Lambda phage virulent?
CI repressor gene
81
T/F - T2 is not a temperate phage
True
82
T7 has a genome that ends with....
double stranded direct repeats
83
T/F - Lambda uses headful packaging
False, T4 types use this
84
What recognizes the packaging signals in Lamda?
phage terminase
85
What are the antiterminators in Lamda?
N and Q
86
How does Lamda inject its DNA?
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
What does Q do in Lambda?
It activates the late genes which are the structural and cell lysis genes (its an early gene)
88
What does CI repressor regulate?
Three nearby promoters: Pl, Pr, and Prm.
Switches from lytic to lysogenic state.
89
What can lead to prophage induction?
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
Define RecA
A enzyme used by the Lambda phage.
It binds to ssDNA and acts as a coprotease to CI.
91
What does CIII do in the Lambda phage?
It enhances the stability of CII
92
How does Lamdba insert its DNA into the bacterial chromosome?
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
How does Lambda cause cell lysis?
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
Describe Lambda's DNA packaging and Virion Assembly process
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
What are some ways bacteria protect themselves from phages?
1. Mutation of receptors
2. Superinfection exclusion and immunity (lysogeny)
3. Restriction/modification systems
4. Abortive infection systems (Abi)
5. CRISPRS and CAS
96
Define superinfection immunity`
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
Define superinfection exclusion
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
Define restriction/modification systems
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
Define CRISPR
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
Define Cas
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
Define spacers
Region of non-coding DNA between genes. Incorporation of foreign DNA into the cell's gene which alters their genome.
102
Define protospacers
The specific sequence in foreign DNA that gets incorporated into the host's DNA making it the spacer.
Has PAM sequence with it
103
Define protospacer adjacent motifs (PAMs)
Short DNA sequence (2-6 b.p) that follows the DNA region (protospacer) targeted for cleavage by the CRISPR system.
104
Define bacteriophage insensitive mutants
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
What are the steps in CRISPR?
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
Type II CRISPR is what?
CRISPR-Cas9
107
What are some anti-CRISPR mechanisms phages use?
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
Define defense island
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
Define viperin
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
Define retron
DNA sequence found in genome of bacteria that codes for reverse transcriptase and a unique ssDNA/RNA hybrid.
111
What is the Virus-First Hypothesis?
Virus pre-dates cells which contributed to the rise of cellular life.
112
What is the reduction hypothesis?
Viruses are reduced forms of parasitic organisms as they need cells to replicate.
113
What is the Escape Hypothesis?
Viruses were once part of genes of host cells that escaped and got new genes via horizontal gene transfer.
114
Define Giant Viruses
belong to the phylum Nucleocytoviricota and all have dsDNA.
Includes chlorovirus, mimivirus, gammaentomopoxvirus, pithovirus, and pandoravirus.
115
Chlorovirus
Linear dsDNA with inner membrane of an icosahedral capsid.
Has inverted repeats.
Infects chlorella which is a symbiont of paramecium
116
Mimivirus
Linear dsDNA which has inner membrane and spikes on surface.
icosahedral
infects acanthamoebae polyphage
117
Gammaentomopxvirus
linear dsDNA
enveloped with ovoid structure
Hosts are insects
118
Pithovirus
circular dsDNA
oval shaped with one opening at end
forms virion factory
Host is amoeba
biggest in size
119
Pandoravirus
linear dsDNA
no capsid
host amoeba
Largest genome size
120
Define virophages
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
Sputnik
First virophage discovered.
dsDNA
Depends on mimivirus infection which is packaged inside of it to infect amoeba
122
Define Pathogen Derived Resistance
Use of genetic elements from pathogen's own genome to confer resistance in an otherwise susceptible host via genetic engineering.
123
Tobacco mosaic virus
Rod that is rigid
+ssRNA genome
1st virus discovered
causes mosaic mottling and discolouration of leaves.
124
Alfalfa mosaic virus
icosahedral capsid
+ssRNA genome
contains 4 particles to infect
has 3 RNA strands
infects plants
125
Cauliflower mosaic virus
circular dsDNA genome
Icosahedral capsid
pararetrovirus - has a reverse transcriptase.
Aphids transmitted
126
Geminivirus
circular ssDNA genome
have two capsids that are smashed together.
have diff. promoters for each gene
eg. maize streak virus
127
What are the symptoms of plant viruses?
Mosaics
ringspots
dwarf/stunting
leaf roll/curl
128
What are the plant defenses?
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
How do you infect a plant experimentally?
Need to create an abrasion with sandpaper or inject the virus with a needle
130
Define Satellite Virus RNAs
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
Define Viroids
Naked circular ssRNA that has a lot of secondary structure.
Does not encode proteins
These include Popsiviridae and avsunviroidae.
132
Describe Avsunviroidae
Viroid that has naked ssRNA.
Contains hammerhead ribozyme that self-cleaves.
Replicates in chloroplasts
Uses NEP and tRNA ligase in replication`
133
Describe Pospiviroidae
naked ssRNA viroid
has no ribozyme activity, cannot self-cleave
replicates in the nucleus
134
What are the genes and proteins of the Cucumber mosaic virus?
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
What proteins does Cauliflower mosaic virus contain?
Mov, Atf, Vap, CP, Pol, Tav (inclusion bodies). Contains a reverse transcriptase
136
Cauliflower mosaic virus genome contains...
35 S RNA that serves as a polycistronic mRNA which will be reverse transcribed to generate DNA to package into virion
137
Describe Polydnaviridae (Ichnovirus)
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
Describe entomobirnavirus
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
Describe Iridoviridae
linear dsDNA genome
Icosahedral capsid and some are enveloped.
infects invertebrates and ectothermic vertebrates (snakes, lizards, etc).
DNA forms concatemers
140
Describe cytoplasmic polyhedrosis virus
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
Describe Baculoviruses
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
How are Baculoviruses used for gene expression systems?
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.
