Regulation after initiation
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Transcript of Regulation after initiation
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Regulation after initiation
Antitermination of transcription:
Attenuation in biosynthetic operons: trp
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lac regulatory region
Repressor
TATAATUV5 mutation, up
Promoter OperatorActivator binding site
+11+1-10-35-52-72
TTTACA TATGTT
RNA polymerase
'
cAMP-CAP
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The CTD of the alpha subunit of RNA Pol can interact with activators
Class I promoters:CAP binding sites upstream of -35, E.g. centered at -62, -83, -93.
Class II promoters:CAP binding sites centered at -42, Overlaps -35 box.
CTD
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Binding of repressor blocks transcription from pR but activates pRM
oR1oR2
-10-35
-10 -35
oR3
cro N
PR
PRM
2 dimers of Repressor, bound cooperatively
RNA Pol
= operator
-10-35 = promoter
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Antitermination occurs at two stages in the life cycle
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Immediate early transcription
Transcription by E. coli RNA polymerase initiates at strongpromoters PR , PR’, and PL , and terminates at t’s.
6S RNA
oR
Pint oL PL PRM PR PRE PR‘tR3
tL1 tR1 tR2 t6S
attint
xisred
gam
cIII N cI cro cII O P Q S R A…J
N Cro
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Antitermination by N protein leads to early gene expression
Pint PL PRM PR PRE PR‘tR3
tL1 tR1 tR2 t6S
attint
xisred
gam
cIII N cI cro cII O P Q S R A…J
N N N
N protein Cro
6S RNA
CIII
Recombination proteins
CII
Replication proteins
Q protein
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Lytic cascade: Cro turns off cI, Q protein action leads to late gene expression
oR
Pint oL PL PRM PR PRE PR‘tR3
tL1 tR1 tR2 t6S
attint
xisred
gam
cIII N cI cro cII O P Q S R A…J
Cro Cro Q
Lytic functionsReplication proteins
Viral head & tail proteins
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Review of -dependent termination of transcription
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Termination of transcription in E. coli: Rho-dependent site
5' ...AUCGCUACCUCAUAUCCGCACCUCCUCAAACGCUACCUCGACCAGAAAGGCGUCUCUU
Termination occurs at one of these 3 nucleotides.
• Little sequence specificity: rich in C, poor in G.• Requires action of rho ( ) in vitro and in vivo.• Many (most?) genes in E. coli have rho-dependent
terminators.
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Model for
action of rho factor
'
αρ-dependent site
Structure in RNA that causes pausing
ρ hexamer binds to protein-free RNA and moves along it.
RNA polymerase pauses at the
ρ-dependent terminator site,
and ρ catches up
ρ unwinds the RNA-DNA hybrid and transcription terminates
RNA polymerase transcribes along the
template, and ρ moves along the RNA.
ρ
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Components needed for antitermination
• Sites on DNA– nut sites (N utilization sites) for N protein, qut sites for
Q protein– Are found within the transcription unit– nut sites are 17 bp sequences with dyad symmetry
• Proteins– Antiterminators: N protein and Q protein encoded by – Host proteins (encoded by E. coli)
• Nus A (encoded by nusA, N-utilization substance)• Rho protein
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Arrangement of nut sites in transcription units
cIN
tL1
cIII...
cro
tR1
cII O P
tR2
Q
...
nutL
nutR
immediate
early txn
delayed
early txn (N
present)
immediate
early txn
delayed
early txn (N
present)
PR
PL
PL
PR
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N plus Nus
factors block rho
action
N NusA
-dependent site
RNA polymerase does NOT pause at
the ρ-dependent terminator site, and
ρ never catches up
Transcription continues past the terminator
ρ RNA polymerase (with N and NusA
transcribes along the template, and .moves along the RNA
)
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NusG and elongation
• NusG is another E. coli protein needed for lambda N to prevent termination
• Homolog of a family of proteins involved in elongation in prokaryotes and eukaryotes
• Eukaryotic DSIF– DRB-sensitivity inducing factor (Flies and mammals)
• DRB is a drug that blocks transcriptional elongation
– Two subunits• 160 kDa, homolog to yeast Spt5• 14 kDa, homolog to yeast Spt4
– Implicated in positive and negative control of elongation
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Regulation of E. coli trp operon by attenuation of transcription
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Organization of the E. coli trp operon
t
leaderattenuator
trpE trpD trpC trpB trpA t’p,o
Chorismicacid
tryptophan
N
CH2 CH COOH
NH2
COOH
OH
O C
CH2
COOH
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The trp operon is regulated in part by an apo-repressor
ttrpE trpD trpC trpB trpA t’p,o
p trpEo
+ trp
Apo-repressor Repressor(with trp bound)
p trpEo
Operon OFF
Operon ON
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The trp operon is also regulated by attenuation
1 27 54 70 90 114 126 140
AUG UGGUGG UGA txnpause attenuatortrp trp
Leader peptide:14 amino acids, 2 are trp
Rho-independent terminatorof transcription.Conditional :Terminates in high [trp],Allows readthrough inlow [trp]
tleader atten. trpE trpD trpC trpB trpA t’p,o
RNA
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Termination of transcription in E. coli: Rho-independent site
G UUA
GA
GUA
G
UA
GGCCUUG
ACAA
GCCCUAA
CG
A
5' ...
CCG
G
AUA
AC
GUUUCGGGAUU U U U U ...3'
G+C rich region in stem
Run of U's 3' to stem-loop
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How attenuation works in trp
• The [trp] determines the [trp-tRNA].• The [trp-tRNA] determines whether a translating
ribosome will add trp to the leader peptide.• If trp is added:
– The ribosome moves on to the translation stop codon.– This places the attenuator in a secondary structure that
causes termination of transcription (OFF).
• If trp is not added: – A different secondary structure forms in the leader RNA – Allows readthrough transcription into the structural
genes (ON).
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Basic components for attenuation in trp
translation secondary structures [trp-tRNA] of trpL formed in RNA Attenuator OperonHigh complete 3-4 stem terminate txn OFFLow stalls at 2-3 stem allow read- ON
trp codons through txn
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Requirements for attenuation in trp operon
• Simultaneous transcription and translation.
• A segment of RNA that can serve as a terminator because of its base-paired (secondary) structure.
• An alternative secondary structure in the RNA that does not allow termination of transcription.
• Does NOT need an additional protein, such as a repressor.
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Alternative base-paired structures in leader RNA
1 27 54 70 90 114 126 140
AUG UGGUGG UGA txnpause
attenuatortrp trp
1 2 3 4
1 2
3 4
12 3
4Terminationof transcription
No termination
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Progress of ribosome determines secondary structure of trp leader RNA
High [trp], terminationof transcription
Low [trp],No termination
2
3 4UGGUGG UGA
attenuator
trp trp
1
ribosome
12 3
4UGGUGG
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Examples of mutational analysis of trp
• Translation of trp leader is needed for regulation– Mutation of AUG prevents transcription past the
attenuator– Without translation, the 1:2 and 3:4 stem-loops form,
and thus causing termination
• Specific secondary structures are needed– Mutations that decrease the number of base pairs in the
3:4 stem-loop increase expression (less termination) in high [trp].
– Compensatory mutations that restore the wild-type number of base pairs allow termination in high [trp].
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Many biosynthetic operons are regulated by attenuation
• Amino acid biosynthetic operons
• E.g., his, phe, leu, thr, ilv
• In each case, a short leader RNA and polypeptide precede the structural genes. This leader polypeptide is rich in the amino acid that is the product of the pathway.