Transcript Clues and consequences of DNA bending in transcription

El papel de la curvatura de
DNA en la regulación
Clues and consequences of DNA
bending in transcription
• Nature of DNA bending. Bendability vs curved DNA
• Clues of DNA bending
– Inducer/ inhibitor of protein-DNA interactions
– Catalyst of protein-protein interactions
– DNA chaperones
• Consequences of DNA bending
– Channeling signals through promoter architecture
– Helping response-amplification signals
– Avoiding transcriptional promiscuity
• DNA bending: A new signal-transduction mechanism?
Curved DNA
Wedge model
Structural discontinuities
model
Bendability
• Bendability: the ability of specific short
sequences
conformations
to
assume
that
preferentially
accommodate
the
deformation associated with protein-induced
bending.
Bendability vs curved DNA
• Curved DNA is deformed even in the absence of
external forces, thereby resulting in a very rigid
structure.
• Bendable DNA allows a mixture of many different
conformational states, the equilibrium of which can be
displaced toward one specific form by external forces
such as proteins interacting with them.
Protein-mediated DNA bending
• Neutralization of charges in
the DNA backbone
• Setting up extended proteinDNA contacts
• Intercalation of protein side
chains in the minor groove
Bend DNA is important for
DNA-protein interactions
• CAP: Correlation between bendability of CAP site
and the affinity of the protein (Gartenberg and
Crothers, 1988)
• Bacterial s70-RNA polymerase induces a strong
bend in the promoter upon binding (Pérez-Martín and
Espinosa, 1994)
• TBP and holo-TFIID bend DNA (Starr et al., 1995)
Clues of DNA bending in
transcription
• Inducer/ inhibitor of protein-DNA interactions
• Catalyst of protein-protein interactions
• DNA chaperones
DNA bending as an inducer or
inhibitor of DNA-protein interactions
• Structural synergy:
– Pre-curved CAP DNA binding sites
– HMG1 and the human progesterone receptor
• Structural inhibition:
– Out of phase RepA-induced bends
Structural synergy at the CAPbinding sites (Kahn and Crothers, 1992)
Structural synergy between
HMG1 and PR (Oñate et al., 1994)
HMG1
PR
Structural inhibition
(Pérez-Martín and
Espinosa, 1991)
RNApol+ RepA
RNApol
RNApol
RNApol
Clues of DNA bending in
transcription
• Inducer/ inhibitor of protein-DNA interactions
• Catalyst of protein-protein interactions
• DNA chaperones
DNA bending as a catalyst of
protein-protein interactions
• Short distances:
Free energy
– bendability: XylR
enhancer
– extra factors: LEF1 enhancer
• Long distances:
– IHF
|
10
|
100
|
1000
Distance (bp)
– histones
XylR enhancer
(Pérez-Martín and de
Lorenzo, 1996)
30 bp
ATP
Bendable DNA
LEF-1 enhancer in TCRa (Giese et al.,
1992)
ATF/CREB
LEF-1
Ets-1
PEBP2a
DNA bending as a catalyst of
protein-protein interactions
• Short distances:
Free energy
– bendability: XylR
enhancer
– extra factors: LEF1 enhancer
• Long distances:
– IHF
|
10
|
100
|
1000
Distance (bp)
– histones
IHF at Pu promoter (Pérez-Martín and
de Lorenzo, 1996)
>200 bp
XylR
s54-RNAP
IHF
s54-RNAP
Nucleosome positioning at the Drosophila
hsp26 promoter (Thomas and Elgin, 1988)
-400
HSTF-box GAGA-box
nucleosome
-300
-200
-100
GAGA-box HSTF-box
RNApolII
TATA box
Clues of DNA bending in
transcription
• Inducer/ inhibitor of protein-DNA interactions
• Catalyst of protein-protein interactions
• DNA chaperones
DNA chaperones (Travers, 1994)
• DNA chaperones are DNA-bending proteins that
stabilize an otherwise loose structure in a
particular conformation which sustains the
assembly of additional proteins into a higherorder complex, being displaced away from the
DNA in the final assembly.
DNA chaperones: HMG1 and PR
(Oñate et al., 1994)
PR
HMG1
DNA chaperones: HU at Ps promoter
(Pérez-Martín and de Lorenzo, 1995)
s54-RNAP
HU
s54-RNAP
s54-RNAP
Consequences of DNA bending in
transcription
• Channeling signals through promoter
architecture
• Helping response-amplification signals
• Avoiding transcriptional promiscuity
Channeling signals through
promoter architecture
• Co-activation
– CAP and MalT
– nucleosome in Xenopus vitellogenin B1 promoter
• Anti-repression
– CAP in ParaBAD
• Anti-induction
– YY1 in c-fos promoter
– IHF in nac promoter
Co-activation: MalT and CAP at PmalEPmalK in E.coli (Richet et al., 1991)
PmalE
RNApol
CAP
MalT
RNApol
PmalK
cAMP
Maltose
Co-activation: Xenopus vitellogenin B1
promoter (Schild et al., 1993)
Cell-type
Hormone
NF1
HNF3
Oestrogen
receptor
RNApolII
Anti-repression: AraC and CAP at ParaBAD
in E.coli (Lobell and Schleif, 1991)
AraC
RNApol
RNApol
RNApol
cAMP
CAP
Arabinose
Anti-induction: YY1 at the c- fos
promoter (Natesan and Gilman, 1993)
cAMP
YY1
RNApolII
CREBP
Cell status
Anti-induction: Nac at the nac promoter
from K. aerogenes (Feng et al., 1995)
Nitrogen
status
Nac levels
NtrC
Nac
HU
Pnac
RNApol
Consequences of DNA bending in
transcription
• Channeling signals through promoter
architecture
• Helping response-amplification signals
• Avoiding transcriptional promiscuity
DNA bending in
response-amplification mechanisms
Pe
O1
IHF
O2
O3
O1
RNApol
Pe
O2
LYSIS
O3
LYSOGENY
Stimulation of lysis/lisogeny of phage Mu by
DNA bending (Goosen, van de Putte, 1995)
Consequences of DNA bending in
transcription
• Channeling signals through promoter
architecture
• Helping response-amplification signals
• Avoiding transcriptional promiscuity
DNA bending and transcriptional
promiscuity
?
?
• Mechanisms to suppress non-specific
activation at enhancers: restrictors
Restrictor: a new role of IHF in Pu
promoter (Pérez-Martín and de Lorenzo,
1995)
XylR
IHF
s54-RNAP
IHF
s54-RNAP
+IHF
s54-RNAP
-IHF
Clues and consequences of DNA
bending in transcription
DNA bending: A new signaltransduction mechanism?
Characteristics of signaltransduction mechanisms
• Integration of signals
• Amplification of signals
• Specificity of signals
Integration of signals
Kinase1
SignalA
Kinase2
SignalB
Kinase3
SignalC
Characteristics of signaltransduction mechanisms
• Integration of signals
• Amplification of signals
• Specificity of signals
Amplification of signals
Kinase1
Kinase2
Kinase2
Kinase3 Kinase3 Kinase3 Kinase3
Characteristics of signaltransduction mechanisms
• Integration of signals
• Amplification of signals
• Specificity of signals
Specificity of signals
(Scaffolding)
SignalA
SignalB
Kinase1
Kinase1
Kinase2
Kinase2
Kinase3
Kinase3
Designing promoters “ a la carte”
Specificity
Integration
Amplification