The Experts below are selected from a list of 2010 Experts worldwide ranked by ideXlab platform
Patrick Schultz - One of the best experts on this subject based on the ideXlab platform.
-
Molecular structure of promoter-bound yeast TFIID.
Nature Communications, 2018Co-Authors: Olga Kolesnikova, Adam Ben-shem, Jeff Ranish, Patrick Schultz, Gabor PapaiAbstract:Transcription Preinitiation Complex assembly on the promoters of protein encoding genes is nucleated in vivo by TFIID composed of the TATA-box Binding Protein (TBP) and 13 TBP-associate factors (Tafs) providing regulatory and chromatin binding functions. Here we present the cryo-electron microscopy structure of promoter-bound yeast TFIID at a resolution better than 5 A, except for a flexible domain. We position the crystal structures of several subunits and, in combination with cross-linking studies, describe the quaternary organization of TFIID. The compact tri lobed architecture is stabilized by a topologically closed Taf5-Taf6 tetramer. We confirm the unique subunit stoichiometry prevailing in TFIID and uncover a hexameric arrangement of Tafs containing a histone fold domain in the Twin lobe.
-
Molecular structure of promoter-bound yeast TFIID
Nature Communications, 2018Co-Authors: Olga Kolesnikova, Adam Ben-shem, Jeff Ranish, Patrick Schultz, Gabor PapaiAbstract:Transcription Preinitiation Complex assembly begins with the recognition of the gene promoter by the TATA-box Binding Protein-containing TFIID Complex. Here the authors present a Cryo-EM structure of promoter-bound yeast TFIID Complex, providing a detailed view of its subunit organization and promoter DNA contacts. Transcription Preinitiation Complex assembly on the promoters of protein encoding genes is nucleated in vivo by TFIID composed of the TATA-box Binding Protein (TBP) and 13 TBP-associate factors (Tafs) providing regulatory and chromatin binding functions. Here we present the cryo-electron microscopy structure of promoter-bound yeast TFIID at a resolution better than 5 Å, except for a flexible domain. We position the crystal structures of several subunits and, in combination with cross-linking studies, describe the quaternary organization of TFIID. The compact tri lobed architecture is stabilized by a topologically closed Taf5-Taf6 tetramer. We confirm the unique subunit stoichiometry prevailing in TFIID and uncover a hexameric arrangement of Tafs containing a histone fold domain in the Twin lobe.
-
Molecular structure of promoter-bound yeast TFIID
Nature Publishing Group, 2018Co-Authors: Olga Kolesnikova, Jeff Ranish, Patrick Schultz, Adam Ben-shem, Jie Luo, Gabor PapaiAbstract:Transcription Preinitiation Complex assembly begins with the recognition of the gene promoter by the TATA-box Binding Protein-containing TFIID Complex. Here the authors present a Cryo-EM structure of promoter-bound yeast TFIID Complex, providing a detailed view of its subunit organization and promoter DNA contacts
-
Structure, assembly and dynamics of macromolecular Complexes by single particle cryo-electron microscopy
Journal of Nanobiotechnology, 2013Co-Authors: Alexandre Durand, Gabor Papai, Patrick SchultzAbstract:Background Proteins in their majority act rarely as single entities. Multisubunit macromolecular Complexes are the actors in most of the cellular processes. These nanomachines are hold together by weak protein-protein interactions and undergo functionally important conformational changes. TFIID is such a multiprotein Complex acting in eukaryotic Transcription initiation. This Complex is first to be recruited to the promoter of the genes and triggers the formation of the Transcription Preinitiation Complex involving RNA polymerase II which leads to gene Transcription. The exact role of TFIID in this process is not yet understood.
-
Structure, assembly and dynamics of macromolecular Complexes by single particle cryo-electron microscopy
Journal of Nanobiotechnology, 2013Co-Authors: Alexandre Durand, Gabor Papai, Patrick SchultzAbstract:Background Proteins in their majority act rarely as single entities. Multisubunit macromolecular Complexes are the actors in most of the cellular processes. These nanomachines are hold together by weak protein-protein interactions and undergo functionally important conformational changes. TFIID is such a multiprotein Complex acting in eukaryotic Transcription initiation. This Complex is first to be recruited to the promoter of the genes and triggers the formation of the Transcription Preinitiation Complex involving RNA polymerase II which leads to gene Transcription. The exact role of TFIID in this process is not yet understood. Methods Last generation electron microscopes, improved data collection and new image analysis tools made it possible to obtain structural information of biological molecules at atomic resolution. Cryo-electron microscopy of vitrified samples visualizes proteins in a fully hydrated, close to native state. Molecular images are recorded at liquid nitrogen temperature in low electron dose conditions to reduce radiation damage. Digital image analysis of these noisy images aims at improving the signal-to-noise ratio, at separating distinct molecular views and at reconstructing a three-dimensional model of the biological particle. Results Using these methods we showed the early events of an activated Transcription initiation process. We explored the interaction of the TFIID coactivator with the yeast Rap1 activator, the Transcription factor TFIIA and the promoter DNA. We demonstrated that TFIID serves as an assembly platform for transient protein-protein interactions, which are essential for Transcription initiation. Conclusions Recent developments in electron microscopy have provided new insights into the structural organization and the dynamic reorganization of large macromolecular Complexes. Examples of near-atomic resolutions exist but the molecular flexibility of macromolecular Complexes remains the limiting factor in most case. Electron microscopy has the potential to provide both structural and dynamic information of biological assemblies in order to understand the molecular mechanisms of their functions.
Steven Hahn - One of the best experts on this subject based on the ideXlab platform.
-
Position of the general Transcription factor TFIIF within the RNA polymerase II Transcription Preinitiation Complex.
The EMBO Journal, 2009Co-Authors: Jesse Eichner, Hung-ta Chen, Linda Warfield, Steven HahnAbstract:The RNA polymerase (pol) II general Transcription factor TFIIF functions at several steps in Transcription initiation including Preinitiation Complex (PIC) formation and start site selection. We find that two structured TFIIF domains bind Pol II at separate locations far from the active site with the TFIIF dimerization domain on the Pol II lobe and the winged helix domain of the TFIIF small subunit Tfg2 above the Pol II protrusion where it may interact with upstream promoter DNA. Binding of the winged helix to the protrusion is PIC specific. Anchoring of these two structured TFIIF domains at separate sites locates an essential and unstructured region of Tfg2 near the Pol II active site cleft where it may interact with flexible regions of Pol II and the general factor TFIIB to promote initiation and start site selection. Consistent with this mechanism, mutations far from the enzyme active site, which alter the binding of either structured TFIIF domains to Pol II, have similar defects in Transcription start site usage.
-
The positions of TFIIF and TFIIE in the RNA polymerase II Transcription Preinitiation Complex
Nature Structural & Molecular Biology, 2007Co-Authors: Hung-ta Chen, Linda Warfield, Steven HahnAbstract:We incorporated the non-natural photoreactive amino acid p -benzoyl- L -phenylalanine (Bpa) into the RNA polymerase II (Pol II) surface surrounding the central cleft formed by the Rpb1 and Rpb2 subunits. Photo-cross-linking of Preinitiation Complexes (PICs) with these Pol II derivatives and hydroxyl-radical cleavage assays revealed that the TFIIF dimerization domain interacts with the Rpb2 lobe and protrusion domains adjacent to Rpb9, while TFIIE cross-links to the Rpb1 clamp domain on the opposite side of the Pol II central cleft. Mutations in the Rpb2 lobe and protrusion domains alter both Pol II–TFIIF binding and the Transcription start site, a phenotype associated with mutations in TFIIF, Rpb9 and TFIIB. Together with previous biochemical and structural studies, these findings illuminate the structural organization of the PIC and the network of protein-protein interactions involved in Transcription start site selection.
-
The positions of TFIIF and TFIIE in the RNA polymerase II Transcription Preinitiation Complex
Nature Structural & Molecular Biology, 2007Co-Authors: Hung-ta Chen, Linda Warfield, Steven HahnAbstract:The non-natural photoreactive amino acid p-Benzoyl-L-Phenylalanine (Bpa) was incorporated into the RNA polymerase (Pol) II surface surrounding the central cleft formed by the Rpb1 and Rpb2 subunits. Photocrosslinking of Preinitiation Complexes (PICs) with these Pol II derivatives and hydroxyl radical cleavage assays revealed that the TFIIF dimerization domain interacts with the Rpb2 lobe and protrusion domains adjacent to Rpb9 while TFIIE crosslinks to the Rpb1 clamp domain on the opposite side of the Pol II central cleft. Mutations in the Rpb2 lobe and protrusion domains were found to alter both Pol II-TFIIF binding and the Transcription start site, a phenotype associated with mutations in TFIIF, Rpb9, and TFIIB. In combination with previous biochemical and structural studies, these new findings illuminate the structural organization of the PIC and reveal a network of protein-protein interactions involved in Transcription start site selection.
-
A DNA-tethered cleavage probe reveals the path for promoter DNA in the yeast Preinitiation Complex
Nature Structural & Molecular Biology, 2006Co-Authors: Gail Miller, Steven HahnAbstract:To directly map the position of promoter DNA within the RNA polymerase II (Pol II) Transcription Preinitiation Complex (PIC), FeBABE was tethered to specific sites within the HIS4 promoter and used to map exposed surfaces of Pol II and the general Transcription factors in proximity to DNA. Our results distinguish between previously proposed models for PIC structure and demonstrate that downstream promoter DNA is positioned over the central cleft of Pol II, with DNA upstream of TATA extending toward the Pol II subunit Rpb3. Also mapped were segments of TFIIB, TFIIE, TFIIF and TFIIH in proximity to promoter DNA. DNA downstream of the Transcription bubble maps to a path between the two helicase subdomains of the TFIIH subunit Rad25 (also called XPB). Together, our results show how the general factors and Pol II converge on promoter DNA within the PIC.
-
Mapping the Location of TFIIB within the RNA Polymerase II Transcription Preinitiation Complex: A Model for the Structure of the PIC
Cell, 2004Co-Authors: Hung-ta Chen, Steven HahnAbstract:Biochemical probes positioned on the surface of the general Transcription factor TFIIB were used to probe the architecture of the RNA polymerase II (Pol II) Transcription Preinitiation Complex (PIC). In PICs, the TFIIB linker and core domains are positioned over the central cleft and wall of Pol II. This positioning is not observed in the smaller Pol II-TFIIB Complex. These results lead to a new model for the structure of the PIC, which agrees with most previously documented protein-DNA interactions within Pol II and archaea PICs. Specific interaction of the TFIIB core domain with Pol II positions and orients the promoter DNA over the Pol II central cleft, and TBP-DNA bending leads to bending of the promoter around the surface of Pol II. The TFIIF subunit Tfg1 was found in close proximity to the TFIIB B finger, linker, and core domains, suggesting that these two factors closely cooperate during initiation.
Gabor Papai - One of the best experts on this subject based on the ideXlab platform.
-
Molecular structure of promoter-bound yeast TFIID.
Nature Communications, 2018Co-Authors: Olga Kolesnikova, Adam Ben-shem, Jeff Ranish, Patrick Schultz, Gabor PapaiAbstract:Transcription Preinitiation Complex assembly on the promoters of protein encoding genes is nucleated in vivo by TFIID composed of the TATA-box Binding Protein (TBP) and 13 TBP-associate factors (Tafs) providing regulatory and chromatin binding functions. Here we present the cryo-electron microscopy structure of promoter-bound yeast TFIID at a resolution better than 5 A, except for a flexible domain. We position the crystal structures of several subunits and, in combination with cross-linking studies, describe the quaternary organization of TFIID. The compact tri lobed architecture is stabilized by a topologically closed Taf5-Taf6 tetramer. We confirm the unique subunit stoichiometry prevailing in TFIID and uncover a hexameric arrangement of Tafs containing a histone fold domain in the Twin lobe.
-
Molecular structure of promoter-bound yeast TFIID
Nature Communications, 2018Co-Authors: Olga Kolesnikova, Adam Ben-shem, Jeff Ranish, Patrick Schultz, Gabor PapaiAbstract:Transcription Preinitiation Complex assembly begins with the recognition of the gene promoter by the TATA-box Binding Protein-containing TFIID Complex. Here the authors present a Cryo-EM structure of promoter-bound yeast TFIID Complex, providing a detailed view of its subunit organization and promoter DNA contacts. Transcription Preinitiation Complex assembly on the promoters of protein encoding genes is nucleated in vivo by TFIID composed of the TATA-box Binding Protein (TBP) and 13 TBP-associate factors (Tafs) providing regulatory and chromatin binding functions. Here we present the cryo-electron microscopy structure of promoter-bound yeast TFIID at a resolution better than 5 Å, except for a flexible domain. We position the crystal structures of several subunits and, in combination with cross-linking studies, describe the quaternary organization of TFIID. The compact tri lobed architecture is stabilized by a topologically closed Taf5-Taf6 tetramer. We confirm the unique subunit stoichiometry prevailing in TFIID and uncover a hexameric arrangement of Tafs containing a histone fold domain in the Twin lobe.
-
Molecular structure of promoter-bound yeast TFIID
Nature Publishing Group, 2018Co-Authors: Olga Kolesnikova, Jeff Ranish, Patrick Schultz, Adam Ben-shem, Jie Luo, Gabor PapaiAbstract:Transcription Preinitiation Complex assembly begins with the recognition of the gene promoter by the TATA-box Binding Protein-containing TFIID Complex. Here the authors present a Cryo-EM structure of promoter-bound yeast TFIID Complex, providing a detailed view of its subunit organization and promoter DNA contacts
-
Structure, assembly and dynamics of macromolecular Complexes by single particle cryo-electron microscopy
Journal of Nanobiotechnology, 2013Co-Authors: Alexandre Durand, Gabor Papai, Patrick SchultzAbstract:Background Proteins in their majority act rarely as single entities. Multisubunit macromolecular Complexes are the actors in most of the cellular processes. These nanomachines are hold together by weak protein-protein interactions and undergo functionally important conformational changes. TFIID is such a multiprotein Complex acting in eukaryotic Transcription initiation. This Complex is first to be recruited to the promoter of the genes and triggers the formation of the Transcription Preinitiation Complex involving RNA polymerase II which leads to gene Transcription. The exact role of TFIID in this process is not yet understood.
-
Structure, assembly and dynamics of macromolecular Complexes by single particle cryo-electron microscopy
Journal of Nanobiotechnology, 2013Co-Authors: Alexandre Durand, Gabor Papai, Patrick SchultzAbstract:Background Proteins in their majority act rarely as single entities. Multisubunit macromolecular Complexes are the actors in most of the cellular processes. These nanomachines are hold together by weak protein-protein interactions and undergo functionally important conformational changes. TFIID is such a multiprotein Complex acting in eukaryotic Transcription initiation. This Complex is first to be recruited to the promoter of the genes and triggers the formation of the Transcription Preinitiation Complex involving RNA polymerase II which leads to gene Transcription. The exact role of TFIID in this process is not yet understood. Methods Last generation electron microscopes, improved data collection and new image analysis tools made it possible to obtain structural information of biological molecules at atomic resolution. Cryo-electron microscopy of vitrified samples visualizes proteins in a fully hydrated, close to native state. Molecular images are recorded at liquid nitrogen temperature in low electron dose conditions to reduce radiation damage. Digital image analysis of these noisy images aims at improving the signal-to-noise ratio, at separating distinct molecular views and at reconstructing a three-dimensional model of the biological particle. Results Using these methods we showed the early events of an activated Transcription initiation process. We explored the interaction of the TFIID coactivator with the yeast Rap1 activator, the Transcription factor TFIIA and the promoter DNA. We demonstrated that TFIID serves as an assembly platform for transient protein-protein interactions, which are essential for Transcription initiation. Conclusions Recent developments in electron microscopy have provided new insights into the structural organization and the dynamic reorganization of large macromolecular Complexes. Examples of near-atomic resolutions exist but the molecular flexibility of macromolecular Complexes remains the limiting factor in most case. Electron microscopy has the potential to provide both structural and dynamic information of biological assemblies in order to understand the molecular mechanisms of their functions.
Mark A Krasnow - One of the best experts on this subject based on the ideXlab platform.
-
differential regulation of Transcription Preinitiation Complex assembly by activator and repressor homeo domain proteins
Genes & Development, 1992Co-Authors: F B Johnson, Mark A KrasnowAbstract:Different eukaryotic Transcription factors can act through the same upstream binding site to differentially regulate target gene expression, but little is known of the underlying mechanisms. Here, we show that Ultrabithorax and even-skipped homeo domain proteins (UBX and EVE) of Drosophila melanogaster exert active and opposite effects on in vitro Transcription when bound to a common site upstream of a core promoter. Both the activator UBX and the repressor EVE affect the extent but not the rate constant of Preinitiation Complex (preIC) formation. Both regulators act early in preIC assembly and are dispensable later
-
Differential regulation of Transcription Preinitiation Complex assembly by activator and repressor homeo domain proteins.
Genes & Development, 1992Co-Authors: F B Johnson, Mark A KrasnowAbstract:Different eukaryotic Transcription factors can act through the same upstream binding site to differentially regulate target gene expression, but little is known of the underlying mechanisms. Here, we show that Ultrabithorax and even-skipped homeo domain proteins (UBX and EVE) of Drosophila melanogaster exert active and opposite effects on in vitro Transcription when bound to a common site upstream of a core promoter. Both the activator UBX and the repressor EVE affect the extent but not the rate constant of Preinitiation Complex (preIC) formation. Both regulators act early in preIC assembly and are dispensable later. Assembling Complexes become resistant to regulation by the bound proteins, but activation by UBX is restored upon ATP or dATP addition, and regulation by both proteins is restored after the addition of all four nucleoside triphosphates and Transcription initiation. The results establish that upstream activators and repressors can function by fundamentally similar mechanisms, by differentially regulating an early step in preIC assembly, leading to formation of functionally distinct Transcription Complexes. A subsequent step renders mature Complexes transiently refractory to activation and repression. Implications for the mechanism of Transcription Complex assembly and turnover and its regulation are discussed, including a new role for ATP in turnover.
F B Johnson - One of the best experts on this subject based on the ideXlab platform.
-
differential regulation of Transcription Preinitiation Complex assembly by activator and repressor homeo domain proteins
Genes & Development, 1992Co-Authors: F B Johnson, Mark A KrasnowAbstract:Different eukaryotic Transcription factors can act through the same upstream binding site to differentially regulate target gene expression, but little is known of the underlying mechanisms. Here, we show that Ultrabithorax and even-skipped homeo domain proteins (UBX and EVE) of Drosophila melanogaster exert active and opposite effects on in vitro Transcription when bound to a common site upstream of a core promoter. Both the activator UBX and the repressor EVE affect the extent but not the rate constant of Preinitiation Complex (preIC) formation. Both regulators act early in preIC assembly and are dispensable later
-
Differential regulation of Transcription Preinitiation Complex assembly by activator and repressor homeo domain proteins.
Genes & Development, 1992Co-Authors: F B Johnson, Mark A KrasnowAbstract:Different eukaryotic Transcription factors can act through the same upstream binding site to differentially regulate target gene expression, but little is known of the underlying mechanisms. Here, we show that Ultrabithorax and even-skipped homeo domain proteins (UBX and EVE) of Drosophila melanogaster exert active and opposite effects on in vitro Transcription when bound to a common site upstream of a core promoter. Both the activator UBX and the repressor EVE affect the extent but not the rate constant of Preinitiation Complex (preIC) formation. Both regulators act early in preIC assembly and are dispensable later. Assembling Complexes become resistant to regulation by the bound proteins, but activation by UBX is restored upon ATP or dATP addition, and regulation by both proteins is restored after the addition of all four nucleoside triphosphates and Transcription initiation. The results establish that upstream activators and repressors can function by fundamentally similar mechanisms, by differentially regulating an early step in preIC assembly, leading to formation of functionally distinct Transcription Complexes. A subsequent step renders mature Complexes transiently refractory to activation and repression. Implications for the mechanism of Transcription Complex assembly and turnover and its regulation are discussed, including a new role for ATP in turnover.