Basic Transcription Part 4 Flashcards
Anti termination by N
- can cause anti termination at both rho-dependent and independent terminators
- binds to hairpin to prevent its formation
site to the right of cro allows
-polymerase to ignore terminator and enter the delayed early genes
Q utilization site (qut site)
- overlaps late promoter PR’
in absence of Q
- RNA polymerase pauses for several seconds at qut site
- then transcribes to the terminator and stops late transcription
In presence of Q
- Q recognized paused complex and binds qut site
- Q inhibits hairpin formation
- Q then binds polymerase and causes it to resume transcription and ignore terminator and continue into late genes
to progress from immediate early to delayed early genes
- requires anti termination by N
to progress from delayed early genes to late genes
- requires anti termination by Q
- at qut site just downstream of Q
- Q is a delayed early gene
cI
- encodes lambda repressor protein
2 promoters control the cI gene
- PRM
- PRE
repressor maintenance
- PRM
- used during lysogeny to provide continual supply of repressor to maintain lysogenic state
- requires the product of its own product for activity - auto regulation
why PRM cannot be be used to establish lysogeny
- because no repressor present to activate it
- instead PRE is used
PRE
- promoter establishment
- located to the right of PR and cro
- directs transcription leftward through cro and then through cI
- allows cI expression before any repressor is available
PRE transcription
- cro usually transcribed rightward from PR
leftward transcription from PRE
- produces antisense product of cro
- sense product of cI
antisense RNA
- helps establish lysogen by binding to cro mRNA
- cannot be translated
promoting lysogeny
- Cro works against lysogeny
- blocking cro promotes lysogeny
CII
- promotes transcription from a leftward promoter (anti-Q) within Q
cII promotes transcription from a leftward promoter (anti-Q) within Q
- promotes Q antisense RNA - blocks production of Q
What is Q required for
- late transcription in lytic phase
- interfering with its synthesis favors lysogeny
cII function
- can stimulate polymerase to bind only PRE, P1, and anti-Q
- but not other promoters
P1
- promoter for integrase for lysogeny
PRE area
- -10 and -35 boxes with no similarities to consensus
cII interaction RNA pol
- cII required for transcription for transcription
- RNA pol can’t bind alone
- cII can’t bind alone
- both proteins can bind and form a stable complex around the promoter
how do cII and RNA pol bind
- bind cooperatively to the promoter on opposite sides of the helix
cIII
- prevents destruction of cII by proteases in the cell (key stop for deciding between lysis or lysogeny)
- works with cII to establish lysogeny by activating PE and P1
lambda repressor binds where to do what
- to both OR and OL
- to turn off further early transcription, interfering with the lytic cycle
why is turning off cro important
- stimulate own synthesis (lambda repressor) by activating PRM
- allows pol to bind further transcribing the repressor which inhibits transcription from left and right
OR division
- divided into three parts
- OR1, OR2, and OR3
- each can bind repressor
OR controls
- leftward transcription of cI
- rightward transcription of cro
repressor binds most tightly to
- OR1
- then OR2
- and least tightly to OR3
how many repressor binding sites in each operator
3
repressor is a
- dimer
- each subunit has 2 domains
first domain of repressor
- DNA binding
second domain of repressor
- involved in repressor-repressor interactions
repressor dimers bound to both OR1 and O2 close to the binding site for RNA pol at PRM
- inhibit RNA pol from binding to PR but help bring in pol to bind to PRM
- prevent transcription from PRE
how the repressors prevent transcription from PRE
- by blocking cII and cIII transcription from PR and PL
what are cII and cIII required for
- required for transcription from PRE
during lysogeny lambda repressor does what
- represses transcription from PL and PR
- stimulates transcription from PRM
polymerase-repressor interactions
- required for activation of transcription from PRM
activation interaction involves
- sigma factor not alpha
lambda repressor interacts with which region of sigma factor
- region 4
- substitutes for weakly recognized -35 box
maintaining lysogeny
- once lysogeny established, a small amount of repressor is required to maintain it
- cII and cIII disappear
race between cro and cI
- if cI wins, lysogeny results
- cro wins, lytic cycle results
cI wins
- cro binds first to OR3 (has highest affinity for)
- cI binds 1, 2, 3
cro wins
- if cro binds OR3 prevents cI binding
- cI transcription from PRM stops
- OR3 overlaps PRM
- cro represses PRM
cII level
- determines lysis or lysogeny
cII will
- activate PRE and help turn on lysogeny program
- work against lysis by making anti-sense cro RNA
in a rich medium
- high protease concentration
- not enough cIII to protect cII
- lysis
most important determinant in lysis versus lysogeny
- concentration of cII
switch from lysogeny to lysis
- mutagenic chemicals can do it
- SOS response
immunity region
- contains cI, OR, OL, and cro
- lysogen are immune to superinfection by a phage with the same control region
- lambda repressor represses new phage DNA from infecting the cell
