chapter 12 part 3 Flashcards
what happens under heat stress
alternative sigma factors are used to activate expression of specialized heat stress response genes
what do heat shock genes encode
proteins that protect cells from certain types of heat-induced damage
what does heat shock response in bacteria require?
expression of an alternative sigma factor that changes the promoter-recognition ability of the RNA polymerase core enzyme
what gene encodes the sigma factor 32?
rpoH
what does the sigma factor 32 recognize?
promoters that contain G-C rich sequences at the -10 position
(instead of the usual A-T rish sequence of the Pribnow box)
what is the promoter for rpoH recognized by?
sigma 70 containing RNA polymerase when the temperature is elevated
what is also elevated during the heat shock response?
third sigma factor 24
-also re3cognizes rpoH gene promoter
what else happens when there is high temperature in heat response?
change in chaperone proteins
what do chaperone proteins normally do?
several chaperones bind to the small amount of sigma 32 present in the cell to inhibit it from forming holoenzyme RNA polymerase & targets it for degradation by the proteasome
what happens to chaperone proteins at high temperature
the chaperones release sigma 32 leaving it free to join RNA polymerase
-the chaperones are redirected to heat-damaged proteins
what is more commonly used: transcriptional regulation of translational regulation?
transcriptional regulation
what do translation repressor proteins bind?
mRNAs near the Shine-Dalgarno sequence
what do translation repressor proteins do?
they interfere with interaction between the mRNA & the 16s rRNA in the small subunit to precent translation of these bound mRNAs
what do complementary antisense RNA do?
block mRNA translation
what does the binding of complementary antisense RNA and antisense RNA do?
creates a double-stranded region of the message
what is IS10 regulation
antisense RNA regulation
how many & what are the promoters that the IS10 sequence contains?
there are 2
-PIN: relatively weak & controls transcription of the transposase
-POUT: much stronger
what does pOUT promoter do?
its embedded in the transposase gene
-directs transcription of an antisense RNA complimentary to part of the transposase mRNA
where is most transposase mRNA bound?
to antisense RNA, so that very little transposase is made, & transpostion is relatively rare
what is a riboswitch
occurs when an mRNA binds a small regulatory molecule
what can riboswitches do?
-regulate transciption
-affect translation
-can alter mRNA stability
what do riboswitches regulate?
transcription of the thiamin (thi) operon, which codes for proteins of the biosynthetic pathway for thiamin pyrophosphate (TPP) production
riboswitch mRNA in Bacillus substilis
Low TPP concentration
–TPP wont bind to riboswitch ..leads to antitermination stem loop formation & transcription of operon genes
High TPP concentration
–TPP will bind to riboswitch… generates termination stem loop followed by poly-U sequence
—PREVENTS TRANSCRIPTION
does riboswitch is bacillus subitilis affect transcription or translation?
transcription
riboswitch of mRNA in E.coli
Low TPP
-shine dalgarno antisequestor stem loop is formed
-start codon may initiate translation of the operon mRNA
High TPP
-tpp binds to riboswitch which makes mRNA stem loop that prevents shine-dalgarno sequence & start codon from initiating translation
-PREVENTS TRANSLARION
in e. coli, TPP proudction by the thiMD operon is regulated by a riboswitch at the level of _________.
translation
in B. subtilus, which gene codes for enzyme glutamine:fructose-6-phosphate amidotransferase
glm6
what is involved in production of GlcN6P?
glm6 which encodes for enzyme glutamine:fructose-6-phosphate amidotransferase
what happens when there are low concentrations of GlcN6P?
glmS is expressed
what happens when GlcN6P is high?
GlcN6P binds to riboswitch sequence in the glmS mRNA, inducing mRNA cleavage & preventing translation
-AFFECTS mRNA STABILITY
what are the requirements for successful phage infection?
-genetic regulatory switches must be controlled by phage gene expression to redirect action of host genes
-phage gene expression must initiate a sequence of events leading the host cell to participate in expression of phage genetic info (most clearly seen in lambda phage, which can undergo lytic or lysogenic cycle)
what is the lambda genome composed of?
48 kb of linear double-stranded DNA, encoding nearly 60 genes
what does the lambda genome circularize by?
joining of the two single-stranded cohesive (cos) ends of about 12 nucleotides in length
what is the lambda genome organized as?
a series of operons
-expression of some operons begins immediately after circularization
immediate early genes
expressed shortly after circularizarion
delayed early genes
expressed after immediate early genes
late genes
expressed later in the infection cycle
what are the immediate early genes?
N & cro proteins which compete for control of a genetic switch
-determines whether the phage enters the lytic or lysogenic cycle
what are the two promoters where transcription begins?
PR- rightward transcription of EARLY GENES needed to establish LYTIC cycle by transcribing CRO protein (a repressor)
PL- leftward transcription of PROMOTER needed to establish the LYSOGENIC cycle by transcribing the N protein (an antiterminator)
what does the N protein do?
blocks transcription termination allowing expression of delayed early & late genes
what does regulation for lysogeny begin with?
protein N binding to three transcription terminating DNA sequences: tL, tR1, & tR2
what does tL do when unbound?
acts to block leftward transcription beyond N
what does tR1 & tR2 do when unbound?
prevents rightward transcription beyond cro & three other early genes (cII & others)
when bound by N, what continues?
transcription continues since N protein is an antiterminator
-this allows expression of delayed early genes (integrase, cII, cIII, & cI
what are produced by leftward transcription?
integrase & cIII protein
what is produced by rightward transcription?
protein cII
what is protein cII stabilized by?
binding to cIII
what does the cII/cIII complex do?
promoter PRE to initiate leftward transcription of the cI gene
-it ALSO binds to Pl to produce additional integrase protein
-THIS STIMULATES LYSOGENY
what is the cI gene also called?
lambda repressor protein
what does the genetic switch for lysis or lysogeny depend on?
a balance between cro protein & lambda repressor (cI gene product)
what are the operator sequences?
OR1, OR2, OR3
-these are between PRM & PR
what does entry into the lytic cycle require?
transcription of late genes, regulated by late promoters & late operators
-these are genes rightward of PR
how many base pairs are each of the target sequences for the operator sequences?
17-bp for binding either cro or lambda repressor
what is the order of operators for cro as it increases?
OR3, OR2, OR1
what does cro protein bound at the operator sequence do?
it blocks access of RNA polymerase at the PRM preventing production of lambda repressor (cI)
what does PRM mean
promoter of repressor maintenance
what does cro binding stimulate?
transcription from pR enhancing transcription of cro
what does Q encode
Q protein which is a positive regulator of transcription of late genes rightward of PR
what do late genes include
those needed for production of head & tail proteins & those required for host cell lysis
what is the order in which the dimerized lambda repressor binds to the operator sequences?
OR1, OR2, then OR3
-it functions as a dimer & spans the 17 bp of DNA at each operator sequence
what does lambda repressor protein bound at the operator initiate?
positive control at PRM leading to continuous transcription of cI, maintaining repression, it also activates integrase
would a large number of phages favor lytic or lysogenic cycle?
lysogenic
-prevents wiping out all the host cells in a population
would DNA damage to the host such as UV radiation favor lytic or lysogenic cycle?
lytic cycle
if the host cell population is actively growing, would lytic or lysogenic cycle be favored?
lytic cycle
-new phage can easily find new hosts
-cII protein is degraded by proteases
if the host cell population is growing poorly, would the lytic or lysogenic cycle be favored?
lysogenic
-prophage can remain silent until conditions for continued infection reappear
is lysogeny permanent?
no, its a semi-permanent state
what is the process that brings lysogeny to an end?
induction
-it is like a switch & triggered by DNA damage (UV light or other extracellular conditions) that activates DNA repair
what protein is part of the DNA repair cascade & what is its role?
RecA
-its role is to activate recombination
what type of activity does RecA have & what is it activated by?
protease activity that is activated by UV light damage to DNA
what does RecA do?
it targets the lambda repressor monomores & cleaves off the C terminus
-the OR1, OR2, & OR3 sequences are exposed & positive regulation of ci & negative regulation of cro end
after RecA does its thing, what happens?
cro protein can now bind to the exposed operators
-this leads to expression of Xis which produces enzyme excisionase
what does excisionase do?
removes the lysogen from its integrated location
-this event triggers the resumption of the lytic cycle
