Section 2 pt 3 Flashcards
cll is a transcriptional regulator. It activates expression of __ (the repressor) and __ (integrate)
cl
int
cl protein function:
turns off all the replication and lysis genes, activates its own expression
integrase
protein recombines the genome into the host genome
Integration happens by recombination between the __ (attachment phage) and the ___(attachment bacterium) sites which are homologues sequences in the two DNA molecules
attP
attB
The organization of genes integrated is different than that in the linear virion form.
Genes that were next to each other in the circular form are now at opposite ends
cl, the only gene expressed and the only protein made in the lysogenic state.
cl is a ____-_____ protein that is only able to bind DNA as a dimer (binds to diff sites w diff affinities)
DNA-binding
regulatory proteins that bind to DNA will bind to their recognition sequences and variants of them at different affinity
SO occupancy of the sequences depends of concentration of the protein
Low amount of protein: only strong sites bound
A lot of protein: all sites bound
cl binds to 6 different sites on DNA: operators: (3) ________ which overlap promotors: (2) _____________
and operators: (3)________ which overlap promotor: (1)________
OR1,2,3 overlap PR and PRM
OL1.2.3 overlap PL
when there is ___ _____, PR and PL are left free and active so it allows for late gene expression Replication, structural, lysis
no cl
when there is __ ___ ___, all 6 sites are occupied and PRM, PR, PL are all off so no expression
a lot of cl
when there is cl, the cl proteins on the two sets of O sequences interact forming ____ _______ and makes the binding even stronger
DNA loops around
preference for binding of cl is OR1>OR2>OR3 where ____ and ____ adjacent dimers interact and have a synergistic cooperate binding effect even stronger
OR1 and OR2
The _____ is the weakest of all 6Os, last to be occupied and it overlaps PRM “Promotor for Repressor Maintenance”
OR3
if cl levels decrease OR3 is the first to be vacant, frees up ____ and activates cl transcription
PRM
This cells cell in lysogenic state
cells carrying lambda integrated as a prophage are protected from super-infection by other lambda particles (and similar things) as there is a lot of ___ protein that can prevent expression of all incoming phage genes
cl
lambda (and other prophages) can be included to enter lytic cycle by _____ of the cl protien from its DNA and prevention of its binding
HOW??
REMOVAL OF cl protein TO ENTER LYTIC
induction of the lytic cycle occurs when the cl protein is degraded by the bacterial protease ____
RecA
cleaves and inactivates cl preventing its binding to DNA
how does RecA work: (2 things)
- happens in response to hosts SOS response (bacteria response to stress such as DNA damaging agents)
- cleaves and inactivates cl preventing its binding to DNA
RecA is normally a _______ _____ but in response to DNA damage it becomes active as a protease
recombination enzyme
RecA targets cellular repressors and removes them especially ______ which triggers the SOS response
LexA
LexA normally inhibits expression of _____ _____ so when its removed all the DNA damage stress genes get expressed
stress genes
LexA and cl look alike so RecA recognizes it by mistake and it is a way the phage co-opted the cell’s damage control system as a cue for activating its lytic replication AKA:
things are going bad for this cell lets get out
removal of cl repressor exposes PR and allows for transcription of cro protein
Right promotor
Cro turns on expression of early lytic genes and inhibits ___ transcription
cl
upon induction ______ occurs, where the phages genome comes out of its integrated into the cells chromosome state into a circle
excision
integration requires ____ and excision requires __ and ____ both are translated from the mRNA at the end of the integrated genome
int
int and xis (excisionsase)
The genome must be in circular excised from for the lytic pathway to :(2 things)
- replicate the DNA
- express late genes
During the lytic cycle: Integration into the host genome is prevented by a phenomenon called _____
retroregulation
Retroregulation: anti termination by N allows PL transcription to proceed past int and xis to ____
sib
sib does not encode a protein, so what does it do?
has a sequence that gets targeted by the cellular RNase enzymes, which degrade the mRNA in a 3’ to 5’ direction
due to sib, more xis gets translated before the RNase makes it to it as compared to int, this disproportionate ratio keeps lambda DNA out of the chromosome ONLY WHEN
its in the excised circular form
when its inside the chromosome to begin with, sib isn’t downstream of int cuz of the attp, so int and xis get transcribed to allow excision, then sib prevents int translation so that the genome can’t reintegrate
why must the genome be In circular form for the lytic cycle?
- cuz the structure gene promoter is at the other end of the linear version of the genome that is inside visions
- cuz the mechanism for DNA replication for phage lambda is the rolling circle replication of a long concatemer that joins at cos sites
phage genomes are made up of sets of genes called _____ that are located together and transcribed together, each having diff functions
modules
phages can be put together from modules with _______ evolutionary backgrounds (mix and match modules A&B blue and red)
different
exchangeable modules are _______ than complete structural or functional units
smaller
Plasmid prophages:
(ex P1)
temperate phages that do not integrate into the bacterial genome but rather exist as circular plasmid prophages
Plasmid prophages: because its not actually integrated into the genome it does tricks to get passed down to daughter cells: (2tricks)
- has partition genes that make each daughter cell get 1 copy
- plasmid addiction module that kills the cell if plasmid is lost (HOW?)
how does plasmid addiction module work in plasmid prophages?
has two proteins
Doc: toxin protein (STABLE alone)
PhD: toxin inhibitor (unstable)
if plasmid goes away PhD degrades and the stable doc protein gets freed to kill the cell
Another plasmid prophage: N15 half of its genome like lambda but the other half is very diff allows it to exist as a ____ plasmid and replicate as a ______ plasmid
exist as linear
replicate as circular
Linear DNA circularizes at cos sites after entering the cell then ____
circular form re-linearizes but with different organization than in the virus particle
(linearized DNA in host cell has hairpin ends called telomeres)
Satellite phages (ex. P4)
depend on another phage for replication
P4 can only replicate in a cell thats also infected by P2 integrated into its genome as a prophage
P4:
- Does not _____
- turns off _____ and activates just
- makes a protein ___
- Does not encode its own structural or lysis genes
- P2 prophage genes and activates just the late lytic genes
- sid “side determination” that alters the structure of P2 cased to make the head smaller that only packages P4
P4 is a _____ and a satellite prophage as it integrates into host genome if P2 is not there (waits for it to come infect a P4 lysogen so that P4 becomes activated
temperate
SaPIs are
Staphylococcus aureus pathogenicity islands
diff SaPIs are present in diff Staphylococcus aureus strains to encode various _____ factors that contribute to bacterial pathogenicity
virulence
SaPIs are normally not active but they are induced for replication by ______ _____ that have a protein that induces SaPIs to make a protein that hijacks the phage capsid protein and packaging machinery (makes phages with shrunken heads and SaPI DNA)
replicating phages
lysed cell releases SaPIs ____ _____and some of the original helper phage ____ _____
smaller heads
larger heads
released SaPI can
1- go and infect other cells
2- Integrate SaPI DNA into cells genome (recombination at att sites like lambda)
3- SaPI inactive for replication until helper gene comes
Results in transfer of virulence factors from cell to cell
SaPI encode repressor protein that keeps them inactive ____ (acts as sensor to see if helper is there)
when helper phage comes, it encodes the antirepressor protien and SaPI is activated
Stl
SaPI proteins inhibit
helper Phage gene replication
shrink the head
alter the terminase packaging enzymes so that SaPI genes get packaged
SaPIs were the first to be discovered, now there is a lot of PICIs “___”
phage-inducible chromosomal islands
