Bacteriophage Genetics
What is a viral superinfection?
When a cell is infected by a virus, and later on is again infected by a different virus. 1 cell infected by two viruses.
Which enzymes reforms BOB' & POP' sites?
Xis-int
In Campell's model for prophage insertion and excision, the prophage is flanked by two new attachment sites called what?
BOP' & POB'.
The synthesis of intergrase is coupled with what other synthesis?
Coupled with the cl protein repressor synthesis.
What is lysogenization?
A process of infecting bacteria with a temperate phage.
What are the steps of the intergrase reaction?
Melting & reannealing Make first nick, rotate, & join. Make second nick, rotate & join. Synthesis of intergrase is coupled to synthesis of cl protein repressor.
Are T4 and T7 temperate phages?
No.
What process causes a bacterium to be infected via a temperate phage?
Lysogenization.
What occurs in bacteria when they are starved for nutrients?
Bacteria can start to degrade their own mRNA & proteins.
Which bacterium cannot allow for the prophage to escape the cell?
A defective lysogen.
Which bacterium is resistant to superinfections?
A lysogen.
What are the two unique features of a lysogens?
1. Immunity 2. Induction
What is the bacterial attachment site called?
BOB'
Where does the recombination event occur in the lambda phage?
Between lambda and E. coli chromosome.
Where is the lambda prophage inserted on the bacterial genome?
Between the galactose operon and the biotin operon.
What is the role of repressor cI proteins in Lysogens?
Bind to the operator sites of DNA and PREVENT the phage's transcription to occur because RNA polymerase cannot then bind to promoter site. Thus, it "turns off" the prophage so the phage's genes cannot be expressed.
What are the 5 steps of excision of the prophage?
Damage of host cells results in activation of SOS repair. RecA protein is activated to become a proteinase. RecA proteinase cleaves lamda cl repressor De-repression occurs: now early promoters, accessible to RNA Polymerase. Lytic cycle starts.
Which bacteriophage's DNA becomes a plasmid instead of going through the lysogenic cycle?
E. coli's phage P1.
What is the role of E. coli P1? (bacteriophage)
Enters the cell Circularizes Represses 1-2 copies/cell Each daughter cell gets a copy Replication is couple to chromosome replication
What enzyme is used during prophage excision?
Excisionase.
What is the role of Xis?
Forms a complex with intergrase & allows it to recognize BOP & POB. xis-int binds, makes cuts, reforms BOB & POP sites.
Which "robust" enzyme is used during lamnda phage's integration? Which other enzyme does this robust enzyme resemble because of similar function?
Intergrase is the robust enzyme that grabs fragments of DNA & splices them in on the gene like DNA gyrase.
Does intergrase cause a reversible or irreversible reaction?
Irreversible reaction.
What is the physiological processes of lysogen's having immunity against superinfections?
Lysogens contain repressor genes that code for repressor proteins called "cI" repressor proteins. These cl repressor genes turn off the prophage & cause transcription to be inhibited.
What is the lambda phage attachment site called?
POP' Lambda attachment Att Att lambda
The genetic material of a bacteriophage?
Prophage.
What does a depression or prophage induction cause to happen?
Release of the phage DNA (prophage)... Which starts the lytic cycle signal... That causes damage to the host cell DNA.
What does the irreversible reaction of integrase require for it to bind to the att site?
Requires IHF (Integration host factor) binds to att site.
Do phages have a specific site for integration or do some phages just integrate anywhere?
Some phages integrate ANYWHERE! i.e. Mu-mutator
What type of phage has the ability to choose a lytic or lysogenic cycle?
Temperate phage.
What is the main requirement a bacterium must have for a phage to be able to grow?
The bacterium must be actively metabolizing for a phage to grow.
What is called when phage DNA integrates the gene order?
The gene order is said to be "PERMUTATED".
What does the immunity of a lysogen refer to?
The lysogen cannot be RE-INFECTED with phage type that has already been integrated. Thus, it is resistant to viral SUPERINFECTION.
What is a prophage?
The phage DNA.
Which other enzyme is required to work with intergrase?
Type I topoisomerase
What is the most studied inducing agent?
UV light.
Do some phages have more than one attachment sites?
Yes. Some phages have SEVERAL attachment sites.
Which proteins are used to prevent RNA polymerase from binding to the promoter site, which in turn caused transcription to be inhibited?
cI repressor proteins from a lysogen. (By binding to the operator sites).
A bacterium that is harboring a prophage is called what?
A lysogen.
What is a lysogen?
A lysogen is a bacterium that contains a complete set of phage genes. Prophage = phage genes.
What percentage of phages are temperate?
>90%
What is a temperate phage?
A bacteriophage that has the ability to choose a lytic or lysogenic cycle.
What is a defective lysogen?
A bacterium WIHTOUT a complete phage gene set. This bacterium has lost essential genes, so when the phage is released from the bacterium, it is non-viurulent and can't infect other cells, making the phage defective.
What is Induction of a lysogen?
Induction refers to the process of leaving the lysogenic cycle and starting the lytic cycle where the phage genome will be released.
What is the process called when a lysogen exits the lysogenic cycle and reverts back to the lytic cycle?
Induction.
Does the lambda phage prefer one or two sites for integration?
Prefers a single site for integration via the enzyme intergrase.
If a bacterial cell starts to degrade their own mRNA and proteins during a starvation state, what occurs to the phage?
The cell eventually dies, and the phage cannot be produced but may wait years before the phage can find a suitable host again. This is why the lysogenic cycle is advantageous to the bacteriophage.
Where is the "att" site located in the phage?
The center of the phage DNA
What is the product of pL?
The excisionase protein called Xis
What molecule receives an advantage when the lysogen is damaged?
The prophage has an advantage to get out and infect other cells.
What occurs during the viral lysogenic cycle?
The viral phage DNA is injected into the bacteria genome where it replicates it's viral genes as does bacterial genes. It is a latent infection.
What occurs during the brief period of transcription in the lysogenic cycle?
There is a brief period of transcription to produce INTEGRATION ENZYME: which turns off transcription by the repressor.
How is E. coli's phage P1 an exception to the rule of lysogeny?
There is no integration, and the phage DNA become a plasmid.