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Christophe Romier - One of the best experts on this subject based on the ideXlab platform.
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tfiid taf6 taf9 complex formation involves the heat repeat containing c terminal domain of taf6 and is modulated by taf5 protein
Journal of Biological Chemistry, 2012Co-Authors: Elisabeth Scheer, Laszlo Tora, Frédéric Delbac, Dino Moras, Christophe RomierAbstract:The general transcription factor TFIID recognizes specifically the core promoter of genes transcribed by eukaryotic RNA polymerase II, nucleating the assembly of the preinitiation complex at the transcription start site. However, the understanding in molecular terms of TFIID assembly and function remains poorly understood. Histone Fold motifs have been shown to be extremely important for the heterodimerization of many TFIID subunits. However, these subunits display several evolutionary conserved noncanonical features when compared with Histones, including additional regions whose role is unknown. Here we show that the conserved additional C-terminal region of TFIID subunit TAF6 can be divided into two domains: a small middle domain (TAF6M) and a large C-terminal domain (TAF6C). Our crystal structure of the TAF6C domain from Antonospora locustae at 1.9 Å resolution reveals the presence of five conserved HEAT repeats. Based on these data, we designed several mutants that were introduced into full-length human TAF6. Surprisingly, the mutants affect the interaction between TAF6 and TAF9, suggesting that the formation of the complex between these two TFIID subunits do not only depend on their Histone Fold motifs. In addition, the same mutants affect even more strongly the interaction between TAF6 and TAF9 in the context of a TAF5-TAF6-TAF9 complex. Expression of these mutants in HeLa cells reveals that most of them are unstable, suggesting their poor incorporation within endogenous TFIID. Taken together, our results suggest that the conserved additional domains in Histone Fold-containing subunits of TFIID and of co-activator SAGA are important for the assembly of these complexes.
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functional analysis of the tfiid specific yeast taf4 ytafii48 reveals an unexpected organization of its Histone Fold domain
Journal of Biological Chemistry, 2002Co-Authors: Sylvie Thuault, Anthony P Weil, Sebastiaan Werten, Christophe Romier, Yann-gaël Gangloff, Steven L Sanders, Jay Kirchner, Irwin DavidsonAbstract:Abstract Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain Histone-Fold domains (HFDs). The C-terminal region of the TFIID-specific yTAF4 (yTAFII48) containing the HFD shares strong sequence similarity with Drosophila(d)TAF4 (dTAFII110) and human TAF4 (hTAFII135). A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. Temperature-sensitive mutations in the yTAF4 HFD α2 helix or the CCTD can be suppressed upon overexpression of yTAF12 (yTAFII68). Moreover, coexpression in Escherichia coli indicates direct yTAF4-yTAF12 heterodimerization optimally requires both the yTAF4 HFD and CCTD. The x-ray crystal structure of the orthologous hTAF4-hTAF12 Histone-like heterodimer indicates that the α3 region within the predicted TAF4 HFD is unstructured and does not correspond to thebona fide α3 helix. Our functional and biochemical analysis of yTAF4, rather provides strong evidence that the HFD α3 helix of the TAF4 family lies within the CCTD. These results reveal an unexpected and novel HFD organization in which the α3 helix is separated from the α2 helix by an extended loop containing a conserved functional domain.
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Crystal Structure of a Subcomplex of Human Transcription Factor TFIID Formed by TATA Binding Protein-Associated Factors Htaf4 (Htaf(II)135) and Htaf12 (Htaf(II)20).
Journal of Biological Chemistry, 2002Co-Authors: Sebastiaan Werten, Christophe Romier, Yann-gaël Gangloff, Sylvie Thuault, Irwin Davidson, Andre Mitschler, Dino MorasAbstract:Abstract The crystal structure is presented of a complex formed by the interacting domains from two subunits of the general transcription factor TFIID, the human TATA binding protein-associated factors hTAF4 (hTAFII135) and hTAF12 (hTAFII20). In agreement with predictions, hTAF12 forms a Histone Fold that is very similar to that of Histone H2B, yet unexpected differences are observed between the structures of the hTAF12 interaction domain of hTAF4 and Histone H2A. Most importantly, the hTAF4 fragment forms only the first two helices of a classical Histone Fold, which are followed by a 26-residue disordered region. This indicates that either full-length TAF4 contains an unusually long connecting loop between its second and third helix, and this helix is not required for stable interaction with TAF12, or that TAF4 represents a novel class of partial Histone Fold motifs. Structural models and structure-based sequence alignments support a role for TAF4b and hSTAF42/yADA1 as alternative partners for TAF12 and are consistent with the formation of nucleosome-like Histone-Fold octamers through interaction of TAF12 with a TAF6–TAF9 tetramer, yet argue against involvement of TAF12-containing Histone-Fold pairs in DNA binding.
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nf y recruitment of tfiid multiple interactions with Histone Fold tafiis
Journal of Biological Chemistry, 2002Co-Authors: Mattia Frontini, Laszlo Tora, Christophe Romier, Irwin Davidson, Dino Moras, Carol Imbriano, Alberto Disilvio, Brendan Bell, Alessia Bogni, Roberto MantovaniAbstract:The nuclear factor y (NF-Y) trimer and TFIID contain Histone Fold subunits, and their binding to the CCAAT and Initiator elements of the major histocompatibility complex class II Ea promoter is required for transcriptional activation. Using agarose-electrophoretic mobility shift assay we found that NF-Y increases the affinity of holo-TFIID for Ea in a CCAAT- and Inr-dependent manner. We began to dissect the interplay between NF-Y- and TBP-associated factors PO1II (TAFIIs)-containing Histone Fold domains in protein-protein interactions and transfections. hTAFII20, hTAFII28, and hTAFII18-hTAFII28 bind to the NF-Y B-NF-YC Histone Fold dimer; hTAFII80 and hTAFII31-hTAFII80 interact with the trimer but not with the NF-YB-NF-YC dimer. The Histone Fold α2 helix of hTAFII80 is not required for NF-Y association, as determined by interactions with the naturally occurring splice variant hTAFII80δ. Expression of hTAFII28 and hTAFII18 in mouse cells significantly and specifically reduced NF-Y activation in GAL4-based experiments, whereas hTAFII20 and hTAFII135 increased it. These results indicate that NF-Y (i) recruits purified holo-TFIID in vitro and (ii) can associate multiple TAFIIs, potentially accommodating different core promoter architectures.
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the tfiid components human taf ii 140 and drosophila bip2 taf ii 155 are novel metazoan homologues of yeast taf ii 47 containing a Histone Fold and a phd finger
Molecular and Cellular Biology, 2001Co-Authors: Yann-gaël Gangloff, Laszlo Tora, Christophe Romier, Sylvie Thuault, Lucie Carre, Jeanchristophe Pointud, Selen C Muratoglu, Marjorie Brand, Jeanlouis Couderc, Irwin DavidsonAbstract:The RNA polymerase II transcription factor TFIID comprises the TATA binding protein (TBP) and a set of TBP-associated factors (TAFIIs). TFIID has been extensively characterized for yeast, Drosophila, and humans, demonstrating a high degree of conservation of both the amino acid sequences of the constituent TAFIIs and overall molecular organization. In recent years, it has been assumed that all the metazoan TAFIIs have been identified, yet no metazoan homologues of yeast TAFII47 (yTAFII47) and yTAFII65 are known. Both of these yTAFIIs contain a Histone Fold domain (HFD) which selectively heterodimerizes with that of yTAFII25. We have cloned a novel mouse protein, TAFII140, containing an HFD and a plant homeodomain (PHD) finger, which we demonstrated by immunoprecipitation to be a mammalian TFIID component. TAFII140 shows extensive sequence similarity to Drosophila BIP2 (dBIP2) (dTAFII155), which we also show to be a component of Drosophila TFIID. These proteins are metazoan homologues of yTAFII47 as their HFDs selectively heterodimerize with dTAFII24 and human TAFII30, metazoan homologues of yTAFII25. We further show that yTAFII65 shares two domains with the Drosophila Prodos protein, a recently described potential dTAFII. These conserved domains are critical for yTAFII65 function in vivo. Our results therefore identify metazoan homologues of yTAFII47 and yTAFII65.
Dino Moras - One of the best experts on this subject based on the ideXlab platform.
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tfiid taf6 taf9 complex formation involves the heat repeat containing c terminal domain of taf6 and is modulated by taf5 protein
Journal of Biological Chemistry, 2012Co-Authors: Elisabeth Scheer, Laszlo Tora, Frédéric Delbac, Dino Moras, Christophe RomierAbstract:The general transcription factor TFIID recognizes specifically the core promoter of genes transcribed by eukaryotic RNA polymerase II, nucleating the assembly of the preinitiation complex at the transcription start site. However, the understanding in molecular terms of TFIID assembly and function remains poorly understood. Histone Fold motifs have been shown to be extremely important for the heterodimerization of many TFIID subunits. However, these subunits display several evolutionary conserved noncanonical features when compared with Histones, including additional regions whose role is unknown. Here we show that the conserved additional C-terminal region of TFIID subunit TAF6 can be divided into two domains: a small middle domain (TAF6M) and a large C-terminal domain (TAF6C). Our crystal structure of the TAF6C domain from Antonospora locustae at 1.9 Å resolution reveals the presence of five conserved HEAT repeats. Based on these data, we designed several mutants that were introduced into full-length human TAF6. Surprisingly, the mutants affect the interaction between TAF6 and TAF9, suggesting that the formation of the complex between these two TFIID subunits do not only depend on their Histone Fold motifs. In addition, the same mutants affect even more strongly the interaction between TAF6 and TAF9 in the context of a TAF5-TAF6-TAF9 complex. Expression of these mutants in HeLa cells reveals that most of them are unstable, suggesting their poor incorporation within endogenous TFIID. Taken together, our results suggest that the conserved additional domains in Histone Fold-containing subunits of TFIID and of co-activator SAGA are important for the assembly of these complexes.
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Crystal Structure of a Subcomplex of Human Transcription Factor TFIID Formed by TATA Binding Protein-Associated Factors Htaf4 (Htaf(II)135) and Htaf12 (Htaf(II)20).
Journal of Biological Chemistry, 2002Co-Authors: Sebastiaan Werten, Christophe Romier, Yann-gaël Gangloff, Sylvie Thuault, Irwin Davidson, Andre Mitschler, Dino MorasAbstract:Abstract The crystal structure is presented of a complex formed by the interacting domains from two subunits of the general transcription factor TFIID, the human TATA binding protein-associated factors hTAF4 (hTAFII135) and hTAF12 (hTAFII20). In agreement with predictions, hTAF12 forms a Histone Fold that is very similar to that of Histone H2B, yet unexpected differences are observed between the structures of the hTAF12 interaction domain of hTAF4 and Histone H2A. Most importantly, the hTAF4 fragment forms only the first two helices of a classical Histone Fold, which are followed by a 26-residue disordered region. This indicates that either full-length TAF4 contains an unusually long connecting loop between its second and third helix, and this helix is not required for stable interaction with TAF12, or that TAF4 represents a novel class of partial Histone Fold motifs. Structural models and structure-based sequence alignments support a role for TAF4b and hSTAF42/yADA1 as alternative partners for TAF12 and are consistent with the formation of nucleosome-like Histone-Fold octamers through interaction of TAF12 with a TAF6–TAF9 tetramer, yet argue against involvement of TAF12-containing Histone-Fold pairs in DNA binding.
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nf y recruitment of tfiid multiple interactions with Histone Fold tafiis
Journal of Biological Chemistry, 2002Co-Authors: Mattia Frontini, Laszlo Tora, Christophe Romier, Irwin Davidson, Dino Moras, Carol Imbriano, Alberto Disilvio, Brendan Bell, Alessia Bogni, Roberto MantovaniAbstract:The nuclear factor y (NF-Y) trimer and TFIID contain Histone Fold subunits, and their binding to the CCAAT and Initiator elements of the major histocompatibility complex class II Ea promoter is required for transcriptional activation. Using agarose-electrophoretic mobility shift assay we found that NF-Y increases the affinity of holo-TFIID for Ea in a CCAAT- and Inr-dependent manner. We began to dissect the interplay between NF-Y- and TBP-associated factors PO1II (TAFIIs)-containing Histone Fold domains in protein-protein interactions and transfections. hTAFII20, hTAFII28, and hTAFII18-hTAFII28 bind to the NF-Y B-NF-YC Histone Fold dimer; hTAFII80 and hTAFII31-hTAFII80 interact with the trimer but not with the NF-YB-NF-YC dimer. The Histone Fold α2 helix of hTAFII80 is not required for NF-Y association, as determined by interactions with the naturally occurring splice variant hTAFII80δ. Expression of hTAFII28 and hTAFII18 in mouse cells significantly and specifically reduced NF-Y activation in GAL4-based experiments, whereas hTAFII20 and hTAFII135 increased it. These results indicate that NF-Y (i) recruits purified holo-TFIID in vitro and (ii) can associate multiple TAFIIs, potentially accommodating different core promoter architectures.
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synergistic transcriptional activation by tata binding protein and htafii28 requires specific amino acids of the htafii28 Histone Fold
Molecular and Cellular Biology, 1999Co-Authors: Anneclaire Lavigne, Christophe Romier, Yann-gaël Gangloff, Dino Moras, Catherine Birck, Olivier Poch, Gabrielle Mengus, Lucie Carre, Irwin DavidsonAbstract:Coexpression of the human TATA-binding protein (TBP)-associated factor 28 (hTAFII28) with the alteredspecificity mutant TBP spm3 synergistically enhances transcriptional activation by the activation function 2 of the nuclear receptors (NRs) for estrogen and vitamin D3 from a reporter plasmid containing a TGTA element in mammalian cells. This synergy is abolished by mutation of specific amino acids in the a2-helix of the Histone Fold in the conserved C-terminal region of hTAFII28. Critical amino acids are found on both the exposed hydrophilic face of this helix and the hydrophobic interface with TAFII18. This a-helix of hTAFII28 therefore mediates multiple interactions required for coactivator activity. We further show that mutation of specific residues in the H1* a-helix of TBP either reduces or increases interactions with hTAFII28. The mutations which reduce interactions with hTAFII28 do not affect functional synergy, whereas the TBP mutation which increases interaction with hTAFII28 is defective in its ability to synergistically enhance activation by NRs. However, this TBP mutant supports activation by other activators and is thus specifically defective for its ability to synergize with hTAFII28.
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human tafii28 and tafii18 interact through a Histone Fold encoded by atypical evolutionary conserved motifs also found in the spt3 family
Cell, 1998Co-Authors: Catherine Birck, Christophe Romier, Irwin Davidson, Olivier Poch, Marc Ruff, Gabrielle Mengus, Anneclaire Lavigne, Dino MorasAbstract:Abstract Determination of the crystal structure of the human TBP-associated factor (hTAF II )28/hTAF II 18 heterodimer shows that these TAF II s form a novel Histone-like pair in the TFIID complex. The Histone Folds in hTAF II 28 and hTAF II 18 were not predicted from their primary sequence, indicating that these TAF II s define a novel family of atypical Histone Fold sequences. The TAF II 18 and TAF II 28 Histone Fold motifs are also present in the N- and C-terminal regions of the SPT3 proteins, suggesting that the Histone Fold in SPT3 may be reconstituted by intramolecular rather than classical intermolecular interactions. The existence of additional Histone-like pairs in both the TFIID and SAGA complexes shows that the Histone Fold is a more commonly used motif for mediating TAF–TAF interactions than previously believed.
Elisabeth Scheer - One of the best experts on this subject based on the ideXlab platform.
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Architecture of TAF11/TAF13/TBP complex suggests novel regulation properties of general transcription factor TFIID
eLife, 2017Co-Authors: Kapil Gupta, Elisabeth Scheer, Aleksandra A Watson, Tiago Baptista, Anna L Chambers, Christine Koehler, Juan Zou, Ima Obong-ebong, Eaazhisai Kandiah, Arturo TembladorAbstract:General transcription factor TFIID is a key component of RNA polymerase II transcription initiation. Human TFIID is a megadalton-sized complex comprising TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). TBP binds to core promoter DNA, recognizing the TATA-box. We identified a ternary complex formed by TBP and the Histone Fold (HF) domain-containing TFIID subunits TAF11 and TAF13. We demonstrate that TAF11/TAF13 competes for TBP binding with TATA-box DNA, and also with the N-terminal domain of TAF1 previously implicated in TATA-box mimicry. In an integrative approach combining crystal coordinates, biochemical analyses and data from cross-linking mass-spectrometry (CLMS), we determine the architecture of the TAF11/TAF13/TBP complex, revealing TAF11/TAF13 interaction with the DNA binding surface of TBP. We identify a highly conserved C-terminal TBP-interaction domain (CTID) in TAF13, which is essential for supporting cell growth. Our results thus have implications for cellular TFIID assembly and suggest a novel regulatory state for TFIID function.
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tfiid taf6 taf9 complex formation involves the heat repeat containing c terminal domain of taf6 and is modulated by taf5 protein
Journal of Biological Chemistry, 2012Co-Authors: Elisabeth Scheer, Laszlo Tora, Frédéric Delbac, Dino Moras, Christophe RomierAbstract:The general transcription factor TFIID recognizes specifically the core promoter of genes transcribed by eukaryotic RNA polymerase II, nucleating the assembly of the preinitiation complex at the transcription start site. However, the understanding in molecular terms of TFIID assembly and function remains poorly understood. Histone Fold motifs have been shown to be extremely important for the heterodimerization of many TFIID subunits. However, these subunits display several evolutionary conserved noncanonical features when compared with Histones, including additional regions whose role is unknown. Here we show that the conserved additional C-terminal region of TFIID subunit TAF6 can be divided into two domains: a small middle domain (TAF6M) and a large C-terminal domain (TAF6C). Our crystal structure of the TAF6C domain from Antonospora locustae at 1.9 Å resolution reveals the presence of five conserved HEAT repeats. Based on these data, we designed several mutants that were introduced into full-length human TAF6. Surprisingly, the mutants affect the interaction between TAF6 and TAF9, suggesting that the formation of the complex between these two TFIID subunits do not only depend on their Histone Fold motifs. In addition, the same mutants affect even more strongly the interaction between TAF6 and TAF9 in the context of a TAF5-TAF6-TAF9 complex. Expression of these mutants in HeLa cells reveals that most of them are unstable, suggesting their poor incorporation within endogenous TFIID. Taken together, our results suggest that the conserved additional domains in Histone Fold-containing subunits of TFIID and of co-activator SAGA are important for the assembly of these complexes.
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the nuclear import of taf10 is regulated by one of its three Histone Fold domain containing interaction partners
Molecular and Cellular Biology, 2005Co-Authors: Evi Soutoglou, Elisabeth Scheer, Mate A Demeny, Giulia Fienga, Paolo Sassonecorsi, Laszlo ToraAbstract:TFIID, comprising the TATA box binding protein (TBP) and 13 TBP-associated factors (TAFs), plays a role in nucleation in the assembly of the RNA polymerase II preinitiation complexes on protein-encoding genes. TAFs are shared among other transcription regulatory complexes (e.g., SAGA, TBP-free TAF-containing complex [TFTC], STAGA, and PCAF/GCN5). Human TAF10, a subunit of both TFIID and TFTC, has three Histone Fold-containing interaction partners: TAF3, TAF8, and SPT7Like (SPT7L). In human cells, exogenously expressed TAF10 remains rather cytoplasmic and leptomycin B does not affect this localization. By using fluorescent fusion proteins, we show that TAF10 does not have an intrinsic nuclear localization signal (NLS) and needs one of its three interaction partners to be transported into the nucleus. When the NLS sequences of either TAF8 or SPT7L are mutated, TAF10 remains cytoplasmic, but a heterologous NLS can drive TAF10 into the nucleus. Experiments using fluorescence recovery after photobleaching show that TAF10 does not associate with any cytoplasmic partner but that once transported into the nucleus it binds to nuclear structures. TAF10 binding to importin β in vitro is dependent on the coexpression of either TAF8 or TAF3, but not SPT7L. The cytoplasmic-nuclear transport of TAF10 is naturally observed during the differentiation of adult male germ cells. Thus, here we describe a novel role of the three mammalian interacting partners in the nuclear localization of TAF10, and our data suggest that a complex network of regulated cytoplasmic associations may exist among these factors and that this network is important for the composition of different TFIID and TFTC-type complexes in the nucleus.
Laszlo Tora - One of the best experts on this subject based on the ideXlab platform.
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tfiid taf6 taf9 complex formation involves the heat repeat containing c terminal domain of taf6 and is modulated by taf5 protein
Journal of Biological Chemistry, 2012Co-Authors: Elisabeth Scheer, Laszlo Tora, Frédéric Delbac, Dino Moras, Christophe RomierAbstract:The general transcription factor TFIID recognizes specifically the core promoter of genes transcribed by eukaryotic RNA polymerase II, nucleating the assembly of the preinitiation complex at the transcription start site. However, the understanding in molecular terms of TFIID assembly and function remains poorly understood. Histone Fold motifs have been shown to be extremely important for the heterodimerization of many TFIID subunits. However, these subunits display several evolutionary conserved noncanonical features when compared with Histones, including additional regions whose role is unknown. Here we show that the conserved additional C-terminal region of TFIID subunit TAF6 can be divided into two domains: a small middle domain (TAF6M) and a large C-terminal domain (TAF6C). Our crystal structure of the TAF6C domain from Antonospora locustae at 1.9 Å resolution reveals the presence of five conserved HEAT repeats. Based on these data, we designed several mutants that were introduced into full-length human TAF6. Surprisingly, the mutants affect the interaction between TAF6 and TAF9, suggesting that the formation of the complex between these two TFIID subunits do not only depend on their Histone Fold motifs. In addition, the same mutants affect even more strongly the interaction between TAF6 and TAF9 in the context of a TAF5-TAF6-TAF9 complex. Expression of these mutants in HeLa cells reveals that most of them are unstable, suggesting their poor incorporation within endogenous TFIID. Taken together, our results suggest that the conserved additional domains in Histone Fold-containing subunits of TFIID and of co-activator SAGA are important for the assembly of these complexes.
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the nuclear import of taf10 is regulated by one of its three Histone Fold domain containing interaction partners
Molecular and Cellular Biology, 2005Co-Authors: Evi Soutoglou, Elisabeth Scheer, Mate A Demeny, Giulia Fienga, Paolo Sassonecorsi, Laszlo ToraAbstract:TFIID, comprising the TATA box binding protein (TBP) and 13 TBP-associated factors (TAFs), plays a role in nucleation in the assembly of the RNA polymerase II preinitiation complexes on protein-encoding genes. TAFs are shared among other transcription regulatory complexes (e.g., SAGA, TBP-free TAF-containing complex [TFTC], STAGA, and PCAF/GCN5). Human TAF10, a subunit of both TFIID and TFTC, has three Histone Fold-containing interaction partners: TAF3, TAF8, and SPT7Like (SPT7L). In human cells, exogenously expressed TAF10 remains rather cytoplasmic and leptomycin B does not affect this localization. By using fluorescent fusion proteins, we show that TAF10 does not have an intrinsic nuclear localization signal (NLS) and needs one of its three interaction partners to be transported into the nucleus. When the NLS sequences of either TAF8 or SPT7L are mutated, TAF10 remains cytoplasmic, but a heterologous NLS can drive TAF10 into the nucleus. Experiments using fluorescence recovery after photobleaching show that TAF10 does not associate with any cytoplasmic partner but that once transported into the nucleus it binds to nuclear structures. TAF10 binding to importin β in vitro is dependent on the coexpression of either TAF8 or TAF3, but not SPT7L. The cytoplasmic-nuclear transport of TAF10 is naturally observed during the differentiation of adult male germ cells. Thus, here we describe a novel role of the three mammalian interacting partners in the nuclear localization of TAF10, and our data suggest that a complex network of regulated cytoplasmic associations may exist among these factors and that this network is important for the composition of different TFIID and TFTC-type complexes in the nucleus.
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mapping Histone Fold tafs within yeast tfiid
The EMBO Journal, 2002Co-Authors: Claire Leurent, Anthony P Weil, Laszlo Tora, Steven L Sanders, Christine Ruhlmann, Veronique Mallouh, Doris B Kirschner, Patrick SchultzAbstract:The transcription factor TFIID is a large multiprotein complex, composed of the TATA box-binding protein (TBP) and 14 TBP-associated factors (TAFs), which plays a key role in the regulation of gene expression by RNA polymerase II. The three-dimensional structure of yeast (y) TFIID, determined at ∼3 nm resolution by electron microscopy and image analysis, resembles a molecular clamp formed by three major lobes connected by thin linking domains. The yTFIID is structurally similar to the human factor although the clamp appears more closed in the yeast complex, probably reflecting the conformational flexibility of the structure. Immunolabelling experiments showed that nine TAFs that contain the Histone Fold structural motif were located in three distinct substructures of TFIID. The distribution of these TAFs showed that the previously reported pair-wise interactions between Histone Fold domain (HFD)-containing TAFs are likely to occur in the native yTFIID complex. Most of the HFD-containing TAFs have been found in two distinct lobes, thus revealing an unexpected and novel molecular organization of TFIID.
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nf y recruitment of tfiid multiple interactions with Histone Fold tafiis
Journal of Biological Chemistry, 2002Co-Authors: Mattia Frontini, Laszlo Tora, Christophe Romier, Irwin Davidson, Dino Moras, Carol Imbriano, Alberto Disilvio, Brendan Bell, Alessia Bogni, Roberto MantovaniAbstract:The nuclear factor y (NF-Y) trimer and TFIID contain Histone Fold subunits, and their binding to the CCAAT and Initiator elements of the major histocompatibility complex class II Ea promoter is required for transcriptional activation. Using agarose-electrophoretic mobility shift assay we found that NF-Y increases the affinity of holo-TFIID for Ea in a CCAAT- and Inr-dependent manner. We began to dissect the interplay between NF-Y- and TBP-associated factors PO1II (TAFIIs)-containing Histone Fold domains in protein-protein interactions and transfections. hTAFII20, hTAFII28, and hTAFII18-hTAFII28 bind to the NF-Y B-NF-YC Histone Fold dimer; hTAFII80 and hTAFII31-hTAFII80 interact with the trimer but not with the NF-YB-NF-YC dimer. The Histone Fold α2 helix of hTAFII80 is not required for NF-Y association, as determined by interactions with the naturally occurring splice variant hTAFII80δ. Expression of hTAFII28 and hTAFII18 in mouse cells significantly and specifically reduced NF-Y activation in GAL4-based experiments, whereas hTAFII20 and hTAFII135 increased it. These results indicate that NF-Y (i) recruits purified holo-TFIID in vitro and (ii) can associate multiple TAFIIs, potentially accommodating different core promoter architectures.
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the tfiid components human taf ii 140 and drosophila bip2 taf ii 155 are novel metazoan homologues of yeast taf ii 47 containing a Histone Fold and a phd finger
Molecular and Cellular Biology, 2001Co-Authors: Yann-gaël Gangloff, Laszlo Tora, Christophe Romier, Sylvie Thuault, Lucie Carre, Jeanchristophe Pointud, Selen C Muratoglu, Marjorie Brand, Jeanlouis Couderc, Irwin DavidsonAbstract:The RNA polymerase II transcription factor TFIID comprises the TATA binding protein (TBP) and a set of TBP-associated factors (TAFIIs). TFIID has been extensively characterized for yeast, Drosophila, and humans, demonstrating a high degree of conservation of both the amino acid sequences of the constituent TAFIIs and overall molecular organization. In recent years, it has been assumed that all the metazoan TAFIIs have been identified, yet no metazoan homologues of yeast TAFII47 (yTAFII47) and yTAFII65 are known. Both of these yTAFIIs contain a Histone Fold domain (HFD) which selectively heterodimerizes with that of yTAFII25. We have cloned a novel mouse protein, TAFII140, containing an HFD and a plant homeodomain (PHD) finger, which we demonstrated by immunoprecipitation to be a mammalian TFIID component. TAFII140 shows extensive sequence similarity to Drosophila BIP2 (dBIP2) (dTAFII155), which we also show to be a component of Drosophila TFIID. These proteins are metazoan homologues of yTAFII47 as their HFDs selectively heterodimerize with dTAFII24 and human TAFII30, metazoan homologues of yTAFII25. We further show that yTAFII65 shares two domains with the Drosophila Prodos protein, a recently described potential dTAFII. These conserved domains are critical for yTAFII65 function in vivo. Our results therefore identify metazoan homologues of yTAFII47 and yTAFII65.
Roberto Mantovani - One of the best experts on this subject based on the ideXlab platform.
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CONSTANS imparts DNA sequence specificity to the Histone Fold NF-YB/NF-YC dimer
The Plant cell, 2017Co-Authors: Nerina Gnesutta, Roderick W Kumimoto, Ben F Holt, Swadhin Swain, Matteo Chiara, Chamindika L. Siriwardana, David S. Horner, Roberto MantovaniAbstract:Nuclear Factor Y (NF-Y) is a heterotrimeric transcription factor that binds CCAAT elements. The NF-Y trimer is composed of a Histone Fold Domain (HFD) dimer (NF-YB/NF-YC) and NF-YA, which confers DNA sequence specificity. NF-YA shares a conserved domain with the CONSTANS, CONSTANS-LIKE, TOC1 (CCT) proteins. We show that CONSTANS (CO/B-BOX PROTEIN1 BBX1), a master flowering regulator, forms a trimer with Arabidopsis thaliana NF-YB2/NF-YC3 to efficiently bind the CORE element of the FLOWERING LOCUS T promoter. We term this complex NF-CO. Using saturation mutagenesis, electrophoretic mobility shift assays, and RNA-sequencing profiling of co, nf-yb, and nf-yc mutants, we identify CCACA elements as the core NF-CO binding site. CO physically interacts with the same HFD surface required for NF-YA association, as determined by mutations in NF-YB2 and NF-YC9, and tested in vitro and in vivo. The co-7 mutation in the CCT domain, corresponding to an NF-YA arginine directly involved in CCAAT recognition, abolishes NF-CO binding to DNA. In summary, a unifying molecular mechanism of CO function relates it to the NF-YA paradigm, as part of a trimeric complex imparting sequence specificity to HFD/DNA interactions. It is likely that members of the large CCT family participate in similar complexes with At-NF-YB and At-NF-YC, broadening HFD combinatorial possibilities in terms of trimerization, DNA binding specificities, and transcriptional regulation.
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crystal structure of the arabidopsis thaliana l1l nf yc3 Histone Fold dimer reveals specificities of the lec1 family of nf y subunits in plants
Molecular Plant, 2017Co-Authors: Nerina Gnesutta, Roberto Mantovani, Dana Saad, Antonio Chavessanjuan, M NardiniAbstract:The NF-Y transcription factor is a heterotrimer formed by evolutionarily conserved subunits: NF-YA, NF-YB, and NF-YC. NF-YB and NF-YC harbor a Histone Fold domain (HFD), structurally similar to that of nucleosome core Histones, and form a tight dimer (Romier et al., 2003). NF-YA binds to the NF-YB/NF-YC dimer and provides exquisite sequence specificity for recognizing and binding the CCAAT box (Huber et al., 2012; Nardini et al., 2013), an important DNA regulatory element of all eukaryotes (Dolfini et al., 2009).
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the h2a h2b like Histone Fold domain proteins at the crossroad between chromatin and different dna metabolisms
Transcription, 2013Co-Authors: Nerina Gnesutta, M Nardini, Roberto MantovaniAbstract:Core Histones are the building block of chromatin and among the most highly conserved proteins in eukaryotes. The related “deviant” Histones share the Histone-Fold domain, and serve various roles in DNA metabolism. We provide here a structural and functional outlook of H2A/H2B-like deviant Histones in transcription, replication and remodeling.
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ternary complex formation between mads box transcription factors and the Histone Fold protein nf yb
Journal of Biological Chemistry, 2002Co-Authors: Simona Masiero, Roberto Mantovani, Carol Imbriano, Federica Ravasio, Rebecca Favaro, Nilla Pelucchi, Mirella Sari Gorla, Lucia Colombo, Martin M KaterAbstract:MADS-box proteins are transcription factors present in different eukaryotic kingdoms. In contrast to plants, for mammalian and yeast MADS-box proteins ternary complex formation with unrelated transcription factors was reported. We show here the first identification of such ternary interaction in plants. A rice seed-specific NF-YB was identified as partner of OsMADS18 by two-hybrid screening. NF-YB contains a Histone Fold motif, HFM,(1) and is part of the trimeric CCAAT-binding NF-Y complex. OsMADS18, alone or in combination with a natural partner, interacts with OsNF-YB1 through the MADS and I regions. The mouse NF-YB also associates with OsMADS18 in vivo and in vitro as a NF-YB-NF-YC dimer. Other rice MADS-box proteins do not interact in these assays, indicating specificity for the interaction. OsNF-YB1 is capable of heterodimerizing with NF-YC, but not trimerizing with NF-YA, thus precluding CCAAT binding. Mutation of the variant Asp at position 99 of the HFM alpha2-helix into a conserved serine recovers the capacity to interact with NF-YA, but not with DNA. This is the first indication that members of the NF-YB family work through mechanisms independent of the CCAAT box.
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nf y recruitment of tfiid multiple interactions with Histone Fold tafiis
Journal of Biological Chemistry, 2002Co-Authors: Mattia Frontini, Laszlo Tora, Christophe Romier, Irwin Davidson, Dino Moras, Carol Imbriano, Alberto Disilvio, Brendan Bell, Alessia Bogni, Roberto MantovaniAbstract:The nuclear factor y (NF-Y) trimer and TFIID contain Histone Fold subunits, and their binding to the CCAAT and Initiator elements of the major histocompatibility complex class II Ea promoter is required for transcriptional activation. Using agarose-electrophoretic mobility shift assay we found that NF-Y increases the affinity of holo-TFIID for Ea in a CCAAT- and Inr-dependent manner. We began to dissect the interplay between NF-Y- and TBP-associated factors PO1II (TAFIIs)-containing Histone Fold domains in protein-protein interactions and transfections. hTAFII20, hTAFII28, and hTAFII18-hTAFII28 bind to the NF-Y B-NF-YC Histone Fold dimer; hTAFII80 and hTAFII31-hTAFII80 interact with the trimer but not with the NF-YB-NF-YC dimer. The Histone Fold α2 helix of hTAFII80 is not required for NF-Y association, as determined by interactions with the naturally occurring splice variant hTAFII80δ. Expression of hTAFII28 and hTAFII18 in mouse cells significantly and specifically reduced NF-Y activation in GAL4-based experiments, whereas hTAFII20 and hTAFII135 increased it. These results indicate that NF-Y (i) recruits purified holo-TFIID in vitro and (ii) can associate multiple TAFIIs, potentially accommodating different core promoter architectures.