1
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Zhao H, Young N, Kalchschmidt J, Lieberman J, El Khattabi L, Casellas R, Asturias FJ. Structure of mammalian Mediator complex reveals Tail module architecture and interaction with a conserved core. Nat Commun 2021; 12:1355. [PMID: 33649303 PMCID: PMC7921410 DOI: 10.1038/s41467-021-21601-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 02/01/2021] [Indexed: 01/04/2023] Open
Abstract
The Mediator complex plays an essential and multi-faceted role in regulation of RNA polymerase II transcription in all eukaryotes. Structural analysis of yeast Mediator has provided an understanding of the conserved core of the complex and its interaction with RNA polymerase II but failed to reveal the structure of the Tail module that contains most subunits targeted by activators and repressors. Here we present a molecular model of mammalian (Mus musculus) Mediator, derived from a 4.0 Å resolution cryo-EM map of the complex. The mammalian Mediator structure reveals that the previously unresolved Tail module, which includes a number of metazoan specific subunits, interacts extensively with core Mediator and has the potential to influence its conformation and interactions.
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Affiliation(s)
- Haiyan Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO, USA
| | - Natalie Young
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO, USA
| | | | | | - Laila El Khattabi
- Institut Cochin Laboratoire de Cytogénétique Constitutionnelle Pré et Post Natale, Paris, France
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD, USA.,Center for Cancer Research, NCI, NIH, Bethesda, MD, USA
| | - Francisco J Asturias
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO, USA.
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2
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Bester SM, Wei G, Zhao H, Adu-Ampratwum D, Iqbal N, Courouble VV, Francis AC, Annamalai AS, Singh PK, Shkriabai N, Van Blerkom P, Morrison J, Poeschla EM, Engelman AN, Melikyan GB, Griffin PR, Fuchs JR, Asturias FJ, Kvaratskhelia M. Structural and mechanistic bases for a potent HIV-1 capsid inhibitor. Science 2020; 370:360-364. [PMID: 33060363 PMCID: PMC7831379 DOI: 10.1126/science.abb4808] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 08/25/2020] [Indexed: 12/11/2022]
Abstract
The potent HIV-1 capsid inhibitor GS-6207 is an investigational principal component of long-acting antiretroviral therapy. We found that GS-6207 inhibits HIV-1 by stabilizing and thereby preventing functional disassembly of the capsid shell in infected cells. X-ray crystallography, cryo-electron microscopy, and hydrogen-deuterium exchange experiments revealed that GS-6207 tightly binds two adjoining capsid subunits and promotes distal intra- and inter-hexamer interactions that stabilize the curved capsid lattice. In addition, GS-6207 interferes with capsid binding to the cellular HIV-1 cofactors Nup153 and CPSF6 that mediate viral nuclear import and direct integration into gene-rich regions of chromatin. These findings elucidate structural insights into the multimodal, potent antiviral activity of GS-6207 and provide a means for rationally developing second-generation therapies.
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Affiliation(s)
- Stephanie M Bester
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Guochao Wei
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Haiyan Zhao
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Daniel Adu-Ampratwum
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Naseer Iqbal
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Valentine V Courouble
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Ashwanth C Francis
- Department of Pediatrics, Infectious Diseases, Emory University, Atlanta, GA 30322, USA
| | - Arun S Annamalai
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Parmit K Singh
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Nikoloz Shkriabai
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Peter Van Blerkom
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - James Morrison
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Eric M Poeschla
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Gregory B Melikyan
- Department of Pediatrics, Infectious Diseases, Emory University, Atlanta, GA 30322, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - James R Fuchs
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Francisco J Asturias
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA.
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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3
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El Khattabi L, Zhao H, Kalchschmidt J, Young N, Jung S, Van Blerkom P, Kieffer-Kwon P, Kieffer-Kwon KR, Park S, Wang X, Krebs J, Tripathi S, Sakabe N, Sobreira DR, Huang SC, Rao SSP, Pruett N, Chauss D, Sadler E, Lopez A, Nóbrega MA, Aiden EL, Asturias FJ, Casellas R. A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers. Cell 2019; 178:1145-1158.e20. [PMID: 31402173 PMCID: PMC7533040 DOI: 10.1016/j.cell.2019.07.011] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 05/24/2019] [Accepted: 07/09/2019] [Indexed: 12/11/2022]
Abstract
While Mediator plays a key role in eukaryotic transcription, little is known about its mechanism of action. This study combines CRISPR-Cas9 genetic screens, degron assays, Hi-C, and cryoelectron microscopy (cryo-EM) to dissect the function and structure of mammalian Mediator (mMED). Deletion analyses in B, T, and embryonic stem cells (ESC) identified a core of essential subunits required for Pol II recruitment genome-wide. Conversely, loss of non-essential subunits mostly affects promoters linked to multiple enhancers. Contrary to current models, however, mMED and Pol II are dispensable to physically tether regulatory DNA, a topological activity requiring architectural proteins. Cryo-EM analysis revealed a conserved core, with non-essential subunits increasing structural complexity of the tail module, a primary transcription factor target. Changes in tail structure markedly increase Pol II and kinase module interactions. We propose that Mediator's structural pliability enables it to integrate and transmit regulatory signals and act as a functional, rather than an architectural bridge, between promoters and enhancers.
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Affiliation(s)
| | - Haiyan Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora CO 80045, USA
| | | | - Natalie Young
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora CO 80045, USA
| | - Seolkyoung Jung
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Peter Van Blerkom
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora CO 80045, USA
| | | | | | - Solji Park
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Xiang Wang
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Jordan Krebs
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | | | - Noboru Sakabe
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Débora R Sobreira
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Su-Chen Huang
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Suhas S P Rao
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Daniel Chauss
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Erica Sadler
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Andrea Lopez
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Marcelo A Nóbrega
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Francisco J Asturias
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora CO 80045, USA.
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA; Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA.
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4
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Yu X, Veesler D, Campbell MG, Barry ME, Asturias FJ, Barry MA, Reddy VS. Cryo-EM structure of human adenovirus D26 reveals the conservation of structural organization among human adenoviruses. Sci Adv 2017; 3:e1602670. [PMID: 28508067 PMCID: PMC5425241 DOI: 10.1126/sciadv.1602670] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/09/2017] [Indexed: 05/17/2023]
Abstract
Human adenoviruses (HAdVs) cause acute respiratory, ocular, and gastroenteric diseases and are also frequently used as gene and vaccine delivery vectors. Unlike the archetype human adenovirus C5 (HAdV-C5), human adenovirus D26 (HAdV-D26) belongs to species-D HAdVs, which target different cellular receptors, and is differentially recognized by immune surveillance mechanisms. HAdV-D26 is being championed as a lower seroprevalent vaccine and oncolytic vector in preclinical and human clinical studies. To understand the molecular basis for their distinct biological properties and independently validate the structures of minor proteins, we determined the first structure of species-D HAdV at 3.7 Å resolution by cryo-electron microscopy. All the hexon hypervariable regions (HVRs), including HVR1, have been identified and exhibit a distinct organization compared to those of HAdV-C5. Despite the differences in the arrangement of helices in the coiled-coil structures, protein IX molecules form a continuous hexagonal network on the capsid exterior. In addition to the structurally conserved region (3 to 300) of IIIa, we identified an extra helical domain comprising residues 314 to 390 that further stabilizes the vertex region. Multiple (two to three) copies of the cleaved amino-terminal fragment of protein VI (pVIn) are observed in each hexon cavity, suggesting that there could be ≥480 copies of VI present in HAdV-D26. In addition, a localized asymmetric reconstruction of the vertex region provides new details of the three-pronged "claw hold" of the trimeric fiber and its interactions with the penton base. These observations resolve the previous conflicting assignments of the minor proteins and suggest the likely conservation of their organization across different HAdVs.
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Affiliation(s)
- Xiaodi Yu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David Veesler
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Melody G. Campbell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mary E. Barry
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN 55902, USA
| | - Francisco J. Asturias
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael A. Barry
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN 55902, USA
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55902, USA
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55902, USA
| | - Vijay S. Reddy
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Corresponding author.
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5
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Tsai KL, Yu X, Gopalan S, Chao TC, Zhang Y, Florens L, Washburn MP, Murakami K, Conaway RC, Conaway JW, Asturias FJ. Mediator structure and rearrangements required for holoenzyme formation. Nature 2017; 544:196-201. [PMID: 28241144 DOI: 10.1038/nature21393] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 12/28/2016] [Indexed: 12/12/2022]
Abstract
The conserved Mediator co-activator complex has an essential role in the regulation of RNA polymerase II transcription in all eukaryotes. Understanding the structure and interactions of Mediator is crucial for determining how the complex influences transcription initiation and conveys regulatory information to the basal transcription machinery. Here we present a 4.4 Å resolution cryo-electron microscopy map of Schizosaccharomyces pombe Mediator in which conserved Mediator subunits are individually resolved. The essential Med14 subunit works as a central backbone that connects the Mediator head, middle and tail modules. Comparison with a 7.8 Å resolution cryo-electron microscopy map of a Mediator-RNA polymerase II holoenzyme reveals that changes in the structure of Med14 facilitate a large-scale Mediator rearrangement that is essential for holoenzyme formation. Our study suggests that access to different conformations and crosstalk between structural elements are essential for the Mediator regulation mechanism, and could explain the capacity of the complex to integrate multiple regulatory signals.
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Affiliation(s)
- Kuang-Lei Tsai
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla California, USA
| | - Xiaodi Yu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla California, USA
| | - Sneha Gopalan
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Ti-Chun Chao
- Department of Pediatrics and Institute for Genomic Medicine, University of California San Diego School of Medicine, La Jolla, California, USA
| | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, Missouri, USA.,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City Kansas, USA
| | - Kenji Murakami
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, Missouri, USA.,Department of Biochemistry &Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, Kansas City, Missouri, USA.,Department of Biochemistry &Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Francisco J Asturias
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla California, USA
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6
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Sato S, Tomomori-Sato C, Tsai KL, Yu X, Sardiu M, Saraf A, Washburn MP, Florens L, Asturias FJ, Conaway RC, Conaway JW. Role for the MED21-MED7 Hinge in Assembly of the Mediator-RNA Polymerase II Holoenzyme. J Biol Chem 2016; 291:26886-26898. [PMID: 27821593 DOI: 10.1074/jbc.m116.756098] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/03/2016] [Indexed: 11/06/2022] Open
Abstract
Mediator plays an integral role in activation of RNA polymerase II (Pol II) transcription. A key step in activation is binding of Mediator to Pol II to form the Mediator-Pol II holoenzyme. Here, we exploit a combination of biochemistry and macromolecular EM to investigate holoenzyme assembly. We identify a subset of human Mediator head module subunits that bind Pol II independent of other subunits and thus probably contribute to a major Pol II binding site. In addition, we show that binding of human Mediator to Pol II depends on the integrity of a conserved "hinge" in the middle module MED21-MED7 heterodimer. Point mutations in the hinge region leave core Mediator intact but lead to increased disorder of the middle module and markedly reduced affinity for Pol II. These findings highlight the importance of Mediator conformation for holoenzyme assembly.
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Affiliation(s)
- Shigeo Sato
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | | | - Kuang-Lei Tsai
- the Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California 92037, and
| | - Xiaodi Yu
- the Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California 92037, and
| | - Mihaela Sardiu
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Anita Saraf
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Michael P Washburn
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110.,the Departments of Pathology and Laboratory Medicine and
| | - Laurence Florens
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Francisco J Asturias
- the Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California 92037, and
| | - Ronald C Conaway
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110.,Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160
| | - Joan W Conaway
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110, .,Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160
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7
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Ando N, Li H, Brignole EJ, Thompson S, McLaughlin MI, Page JE, Asturias FJ, Stubbe J, Drennan CL. Allosteric Inhibition of Human Ribonucleotide Reductase by dATP Entails the Stabilization of a Hexamer. Biochemistry 2016; 55:373-81. [PMID: 26727048 PMCID: PMC4722859 DOI: 10.1021/acs.biochem.5b01207] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Ribonucleotide
reductases (RNRs) are responsible for all de novo
biosynthesis of DNA precursors in nature by catalyzing the conversion
of ribonucleotides to deoxyribonucleotides. Because of its essential
role in cell division, human RNR is a target for a number of anticancer
drugs in clinical use. Like other class Ia RNRs, human RNR requires
both a radical-generation subunit (β) and nucleotide-binding
subunit (α) for activity. Because of their complex dependence
on allosteric effectors, however, the active and inactive quaternary
forms of many class Ia RNRs have remained in question. Here, we present
an X-ray crystal structure of the human α subunit in the presence
of inhibiting levels of dATP, depicting a ring-shaped hexamer (α6) where the active sites line the inner hole. Surprisingly,
our small-angle X-ray scattering (SAXS) results indicate that human
α forms a similar hexamer in the presence of ATP, an activating
effector. In both cases, α6 is assembled from dimers
(α2) without a previously proposed tetramer intermediate
(α4). However, we show with SAXS and electron microscopy
that at millimolar ATP, the ATP-induced α6 can further
interconvert with higher-order filaments. Differences in the dATP-
and ATP-induced α6 were further examined by SAXS
in the presence of the β subunit and by activity assays as a
function of ATP or dATP. Together, these results suggest that dATP-induced
α6 is more stable than the ATP-induced α6 and that stabilization of this ring-shaped configuration
provides a mechanism to prevent access of the β subunit to the
active site of α.
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Affiliation(s)
| | | | | | | | | | | | - Francisco J Asturias
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , La Jolla, California 92037, United States
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8
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Tsai KL, Tomomori-Sato C, Sato S, Conaway RC, Conaway JW, Asturias FJ. Subunit Architecture and Functional Modular Rearrangements of the Transcriptional Mediator Complex. Cell 2014; 158:463. [PMID: 28915369 DOI: 10.1016/j.cell.2014.06.036] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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Tsai KL, Tomomori-Sato C, Sato S, Conaway RC, Conaway JW, Asturias FJ. Subunit architecture and functional modular rearrangements of the transcriptional mediator complex. Cell 2014; 157:1430-1444. [PMID: 24882805 DOI: 10.1016/j.cell.2014.05.015] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 04/18/2014] [Accepted: 05/10/2014] [Indexed: 11/16/2022]
Abstract
The multisubunit Mediator, comprising ∼30 distinct proteins, plays an essential role in gene expression regulation by acting as a bridge between DNA-binding transcription factors and the RNA polymerase II (RNAPII) transcription machinery. Efforts to uncover the Mediator mechanism have been hindered by a poor understanding of its structure, subunit organization, and conformational rearrangements. By overcoming biochemical and image analysis hurdles, we obtained accurate EM structures of yeast and human Mediators. Subunit localization experiments, docking of partial X-ray structures, and biochemical analyses resulted in comprehensive mapping of yeast Mediator subunits and a complete reinterpretation of our previous Mediator organization model. Large-scale Mediator rearrangements depend on changes at the interfaces between previously described Mediator modules, which appear to be facilitated by factors conducive to transcription initiation. Conservation across eukaryotes of Mediator structure, subunit organization, and RNA polymerase II interaction suggest conservation of fundamental aspects of the Mediator mechanism.
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Affiliation(s)
- Kuang-Lei Tsai
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | - Shigeo Sato
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Biochemistry & Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Biochemistry & Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Francisco J Asturias
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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10
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Aye Y, Brignole EJ, Long MJC, Chittuluru J, Drennan CL, Asturias FJ, Stubbe J. Clofarabine targets the large subunit (α) of human ribonucleotide reductase in live cells by assembly into persistent hexamers. ACTA ACUST UNITED AC 2014; 19:799-805. [PMID: 22840768 DOI: 10.1016/j.chembiol.2012.05.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 05/19/2012] [Accepted: 05/24/2012] [Indexed: 11/30/2022]
Abstract
Clofarabine (ClF) is a drug used in the treatment of leukemia. One of its primary targets is human ribonucleotide reductase (hRNR), a dual-subunit, (α(2))(m)(β(2))(n), regulatory enzyme indispensable in de novo dNTP synthesis. We report that, in live mammalian cells, ClF targets hRNR by converting its α-subunit into kinetically stable hexamers. We established mammalian expression platforms that enabled isolation of functional α and characterization of its altered oligomeric associations in response to ClF treatment. Size exclusion chromatography and electron microscopy documented persistence of in-cell-assembled-α(6). Our data validate hRNR as an important target of ClF, provide evidence that in vivo α's quaternary structure can be perturbed by a nonnatural ligand, and suggest small-molecule-promoted, persistent hexamerization as a strategy to modulate hRNR activity. These studies lay foundations for documentation of RNR oligomeric state within a cell.
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Affiliation(s)
- Yimon Aye
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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11
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Lai YT, Tsai KL, Sawaya MR, Asturias FJ, Yeates TO. Structure and flexibility of nanoscale protein cages designed by symmetric self-assembly. J Am Chem Soc 2013; 135:7738-43. [PMID: 23621606 DOI: 10.1021/ja402277f] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Designing protein molecules that self-assemble into complex architectures is an outstanding goal in the area of nanobiotechnology. One design strategy for doing this involves genetically fusing together two natural proteins, each of which is known to form a simple oligomer on its own (e.g., a dimer or trimer). If two such components can be fused in a geometrically predefined configuration, that designed subunit can, in principle, assemble into highly symmetric architectures. Initial experiments showed that a 12-subunit tetrahedral cage, 16 nm in diameter, could be constructed following such a procedure [Padilla, J. E.; et al. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 2217; Lai, Y. T.; et al. Science 2012, 336, 1129]. Here we characterize multiple crystal structures of protein cages constructed in this way, including cages assembled from two mutant forms of the same basic protein subunit. The flexibilities of the designed assemblies and their deviations from the target model are described, along with implications for further design developments.
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Affiliation(s)
- Yen-Ting Lai
- Department of Bioengineering, University of California, Los Angeles, California 90095, USA
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12
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Tsai KL, Sato S, Tomomori-Sato C, Conaway RC, Conaway JW, Asturias FJ. A conserved Mediator-CDK8 kinase module association regulates Mediator-RNA polymerase II interaction. Nat Struct Mol Biol 2013; 20:611-9. [PMID: 23563140 PMCID: PMC3648612 DOI: 10.1038/nsmb.2549] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 02/26/2013] [Indexed: 01/24/2023]
Abstract
The CDK8 kinase module (CKM) is a conserved, dissociable Mediator subcomplex whose component subunits were genetically linked to the RNA polymerase II (RNAPII) carboxy-terminal domain (CTD) and individually recognized as transcriptional repressors before Mediator was identified as a preeminent complex in eukaryotic transcription regulation. We used macromolecular electron microscopy and biochemistry to investigate the subunit organization, structure, and Mediator interaction of the Saccharomyces cerevisiae CKM. We found that interaction of the CKM with Mediator’s Middle module interferes with CTD-dependent RNAPII binding to a previously unknown Middle module CTD-binding site targeted early on in a multi-step holoenzyme formation process. Taken together, our results reveal the basis for CKM repression, clarify the origin of the connection between CKM subunits and the CTD, and suggest that a combination of competitive interactions and conformational changes that facilitate holoenzyme formation underlie the Mediator mechanism.
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Affiliation(s)
- Kuang-Lei Tsai
- Department of Cell Biology, Scripps Research Institute, La Jolla, California, USA
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13
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Minnihan EC, Ando N, Brignole EJ, Olshansky L, Chittuluru J, Asturias FJ, Drennan CL, Nocera DG, Stubbe J. Generation of a stable, aminotyrosyl radical-induced α2β2 complex of Escherichia coli class Ia ribonucleotide reductase. Proc Natl Acad Sci U S A 2013; 110:3835-40. [PMID: 23431160 PMCID: PMC3593893 DOI: 10.1073/pnas.1220691110] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ribonucleotide reductase (RNR) catalyzes the conversion of nucleoside diphosphates to deoxynucleoside diphosphates (dNDPs). The Escherichia coli class Ia RNR uses a mechanism of radical propagation by which a cysteine in the active site of the RNR large (α2) subunit is transiently oxidized by a stable tyrosyl radical (Y•) in the RNR small (β2) subunit over a 35-Å pathway of redox-active amino acids: Y122• ↔ [W48?] ↔ Y356 in β2 to Y731 ↔ Y730 ↔ C439 in α2. When 3-aminotyrosine (NH2Y) is incorporated in place of Y730, a long-lived NH2Y730• is generated in α2 in the presence of wild-type (wt)-β2, substrate, and effector. This radical intermediate is chemically and kinetically competent to generate dNDPs. Herein, evidence is presented that NH2Y730• induces formation of a kinetically stable α2β2 complex. Under conditions that generate NH2Y730•, binding between Y730NH2Y-α2 and wt-β2 is 25-fold tighter (Kd = 7 nM) than for wt-α2
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Affiliation(s)
| | - Nozomi Ando
- Departments of Chemistry and
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139; and
| | - Edward J. Brignole
- Departments of Chemistry and
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139; and
| | | | | | | | - Catherine L. Drennan
- Departments of Chemistry and
- Biology, and
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139; and
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14
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Cai G, Chaban YL, Imasaki T, Kovacs JA, Calero G, Penczek PA, Takagi Y, Asturias FJ. Interaction of the mediator head module with RNA polymerase II. Structure 2012; 20:899-910. [PMID: 22579255 DOI: 10.1016/j.str.2012.02.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Revised: 02/24/2012] [Accepted: 02/28/2012] [Indexed: 02/09/2023]
Abstract
Mediator, a large (21 polypeptides, MW ∼1 MDa) complex conserved throughout eukaryotes, plays an essential role in control of gene expression by conveying regulatory signals that influence the activity of the preinitiation complex. However, the precise mode of interaction between Mediator and RNA polymerase II (RNAPII), and the mechanism of regulation by Mediator remain elusive. We used cryo-electron microscopy and reconstituted in vitro transcription assays to characterize a transcriptionally-active complex including the Mediator Head module and components of a minimum preinitiation complex (RNAPII, TFIIF, TFIIB, TBP, and promoter DNA). Our results reveal how the Head interacts with RNAPII, affecting its conformation and function.
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Affiliation(s)
- Gang Cai
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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15
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Zimanyi CM, Ando N, Brignole EJ, Asturias FJ, Stubbe J, Drennan CL. Tangled up in knots: structures of inactivated forms of E. coli class Ia ribonucleotide reductase. Structure 2012; 20:1374-83. [PMID: 22727814 PMCID: PMC3459064 DOI: 10.1016/j.str.2012.05.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 05/16/2012] [Accepted: 05/17/2012] [Indexed: 11/19/2022]
Abstract
Ribonucleotide reductases (RNRs) provide the precursors for DNA biosynthesis and repair and are successful targets for anticancer drugs such as clofarabine and gemcitabine. Recently, we reported that dATP inhibits E. coli class Ia RNR by driving formation of RNR subunits into α4β4 rings. Here, we present the first X-ray structure of a gemcitabine-inhibited E. coli RNR and show that the previously described α4β4 rings can interlock to form an unprecedented (α4β4)2 megacomplex. This complex is also seen in a higher-resolution dATP-inhibited RNR structure presented here, which employs a distinct crystal lattice from that observed in the gemcitabine-inhibited case. With few reported examples of protein catenanes, we use data from small-angle X-ray scattering and electron microscopy to both understand the solution conditions that contribute to concatenation in RNRs as well as present a mechanism for the formation of these unusual structures.
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Affiliation(s)
- Christina M. Zimanyi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Nozomi Ando
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Edward J. Brignole
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Catherine L. Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
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16
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Yang Z, Fang J, Chittuluru J, Asturias FJ, Penczek PA. Iterative stable alignment and clustering of 2D transmission electron microscope images. Structure 2012; 20:237-47. [PMID: 22325773 DOI: 10.1016/j.str.2011.12.007] [Citation(s) in RCA: 194] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 12/06/2011] [Accepted: 12/14/2011] [Indexed: 11/30/2022]
Abstract
Identification of homogeneous subsets of images in a macromolecular electron microscopy (EM) image data set is a critical step in single-particle analysis. The task is handled by iterative algorithms, whose performance is compromised by the compounded limitations of image alignment and K-means clustering. Here we describe an approach, iterative stable alignment and clustering (ISAC) that, relying on a new clustering method and on the concepts of stability and reproducibility, can extract validated, homogeneous subsets of images. ISAC requires only a small number of simple parameters and, with minimal human intervention, can eliminate bias from two-dimensional image clustering and maximize the quality of group averages that can be used for ab initio three-dimensional structural determination and analysis of macromolecular conformational variability. Repeated testing of the stability and reproducibility of a solution within ISAC eliminates heterogeneous or incorrect classes and introduces critical validation to the process of EM image clustering.
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Affiliation(s)
- Zhengfan Yang
- Department of Biochemistry and Molecular Biology, University of Texas-Houston Medical School, 6431 Fannin Street, MSB 6.218, Houston, TX 77030, USA
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17
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Takagi Y, Imasaki T, Cai G, Tsai KL, Yamada K, Berger I, Asturias FJ. Architecture of the Mediator Head Module. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.1585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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18
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Ando N, Brignole EJ, Zimanyi CM, Funk MA, Yokoyama K, Asturias FJ, Stubbe J, Drennan CL. Structural interconversions modulate activity of Escherichia coli ribonucleotide reductase. Proc Natl Acad Sci U S A 2011; 108:21046-51. [PMID: 22160671 PMCID: PMC3248520 DOI: 10.1073/pnas.1112715108] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Essential for DNA biosynthesis and repair, ribonucleotide reductases (RNRs) convert ribonucleotides to deoxyribonucleotides via radical-based chemistry. Although long known that allosteric regulation of RNR activity is vital for cell health, the molecular basis of this regulation has been enigmatic, largely due to a lack of structural information about how the catalytic subunit (α(2)) and the radical-generation subunit (β(2)) interact. Here we present the first structure of a complex between α(2) and β(2) subunits for the prototypic RNR from Escherichia coli. Using four techniques (small-angle X-ray scattering, X-ray crystallography, electron microscopy, and analytical ultracentrifugation), we describe an unprecedented α(4)β(4) ring-like structure in the presence of the negative activity effector dATP and provide structural support for an active α(2)β(2) configuration. We demonstrate that, under physiological conditions, E. coli RNR exists as a mixture of transient α(2)β(2) and α(4)β(4) species whose distributions are modulated by allosteric effectors. We further show that this interconversion between α(2)β(2) and α(4)β(4) entails dramatic subunit rearrangements, providing a stunning molecular explanation for the allosteric regulation of RNR activity in E. coli.
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Affiliation(s)
- Nozomi Ando
- Howard Hughes Medical Institute
- Department of Chemistry, and
| | - Edward J. Brignole
- Howard Hughes Medical Institute
- Department of Chemistry, and
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037
| | | | | | | | | | - JoAnne Stubbe
- Howard Hughes Medical Institute
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; and
| | - Catherine L. Drennan
- Howard Hughes Medical Institute
- Department of Chemistry, and
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; and
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19
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Chittuluru JR, Chaban Y, Monnet-Saksouk J, Carrozza MJ, Sapountzi V, Selleck W, Huang J, Utley RT, Cramet M, Allard S, Cai G, Workman JL, Fried MG, Tan S, Côté J, Asturias FJ. Structure and nucleosome interaction of the yeast NuA4 and Piccolo-NuA4 histone acetyltransferase complexes. Nat Struct Mol Biol 2011; 18:1196-203. [PMID: 21984211 PMCID: PMC3210417 DOI: 10.1038/nsmb.2128] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 07/27/2011] [Indexed: 11/09/2022]
Abstract
We have used electron microscopy (EM) and biochemistry to characterize the structure and nucleosome core particle (NCP) interaction of NuA4, an essential yeast histone acetyltransferase (HAT) complex conserved throughout eukaryotes. The ATM-related Tra1 subunit, shared with the SAGA coactivator, forms a large domain joined to a second portion that accommodates the Piccolo catalytic subcomplex and other NuA4 subunits. EM analysis of an NuA4–NCP complex shows the NCP bound at NuA4's periphery. EM characterization of Piccolo and Piccolo–NCP provided further information about subunit organization and confirmed that histone acetylation requires minimal contact with the NCP. A small conserved region at the N-terminus of Piccolo subunit Epl1 is essential for NCP interaction, whereas subunit Yng2 apparently positions Piccolo for efficient acetylation of H4 or H2A tails. Taken together, these results provide an understanding of NuA4 subunit organization and NCP interactions.
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20
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Imasaki T, Calero G, Cai G, Tsai KL, Yamada K, Cardelli F, Erdjument-Bromage H, Tempst P, Berger I, Kornberg GL, Asturias FJ, Kornberg RD, Takagi Y. Architecture of the Mediator head module. Nature 2011; 475:240-3. [PMID: 21725323 DOI: 10.1038/nature10162] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 04/28/2011] [Indexed: 01/14/2023]
Abstract
Mediator is a key regulator of eukaryotic transcription, connecting activators and repressors bound to regulatory DNA elements with RNA polymerase II (Pol II). In the yeast Saccharomyces cerevisiae, Mediator comprises 25 subunits with a total mass of more than one megadalton (refs 5, 6) and is organized into three modules, called head, middle/arm and tail. Our understanding of Mediator assembly and its role in regulating transcription has been impeded so far by limited structural information. Here we report the crystal structure of the essential Mediator head module (seven subunits, with a mass of 223 kilodaltons) at a resolution of 4.3 ångströms. Our structure reveals three distinct domains, with the integrity of the complex centred on a bundle of ten helices from five different head subunits. An intricate pattern of interactions within this helical bundle ensures the stable assembly of the head subunits and provides the binding sites for general transcription factors and Pol II. Our structural and functional data suggest that the head module juxtaposes transcription factor IIH and the carboxy-terminal domain of the largest subunit of Pol II, thereby facilitating phosphorylation of the carboxy-terminal domain of Pol II. Our results reveal architectural principles underlying the role of Mediator in the regulation of gene expression.
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Affiliation(s)
- Tsuyoshi Imasaki
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, USA
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21
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Opalka N, Brown J, Lane WJ, Twist KAF, Landick R, Asturias FJ, Darst SA. Complete structural model of Escherichia coli RNA polymerase from a hybrid approach. PLoS Biol 2010; 8. [PMID: 20856905 PMCID: PMC2939025 DOI: 10.1371/journal.pbio.1000483] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Accepted: 08/04/2010] [Indexed: 11/25/2022] Open
Abstract
A combination of structural approaches yields a complete atomic model of the highly biochemically characterized Escherichia coli RNA polymerase, enabling fuller exploitation of E. coli as a model for understanding transcription. The Escherichia coli transcription system is the best characterized from a biochemical and genetic point of view and has served as a model system. Nevertheless, a molecular understanding of the details of E. coli transcription and its regulation, and therefore its full exploitation as a model system, has been hampered by the absence of high-resolution structural information on E. coli RNA polymerase (RNAP). We use a combination of approaches, including high-resolution X-ray crystallography, ab initio structural prediction, homology modeling, and single-particle cryo-electron microscopy, to generate complete atomic models of E. coli core RNAP and an E. coli RNAP ternary elongation complex. The detailed and comprehensive structural descriptions can be used to help interpret previous biochemical and genetic data in a new light and provide a structural framework for designing experiments to understand the function of the E. coli lineage-specific insertions and their role in the E. coli transcription program. Transcription, or the synthesis of RNA from DNA, is one of the most important processes in the cell. The central enzyme of transcription is the DNA-dependent RNA polymerase (RNAP), a large, macromolecular assembly consisting of at least five subunits. Historically, much of our fundamental information on the process of transcription has come from genetic and biochemical studies of RNAP from the model bacterium Escherichia coli. More recently, major breakthroughs in our understanding of the mechanism of action of RNAP have come from high resolution crystal structures of various bacterial, archaebacterial, and eukaryotic enzymes. However, all of our high-resolution bacterial RNAP structures are of enzymes from the thermophiles Thermus aquaticus or T. thermophilus, organisms with poorly characterized transcription systems. It has thus far proven impossible to obtain a high-resolution structure of E. coli RNAP, which has made it difficult to relate the large collection of genetic and biochemical data on RNAP function directly to the available structural information. Here, we used a combination of approaches—high-resolution X-ray crystallography of E. coli RNAP fragments, ab initio structure prediction, homology modeling, and single-particle cryo-electron microscopy—to generate complete atomic models of E. coli RNAP. Our detailed and comprehensive structural models provide the heretofore missing structural framework for understanding the function of the highly characterized E. coli RNAP.
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Affiliation(s)
- Natacha Opalka
- The Rockefeller University, New York, New York, United States of America
| | - Jesse Brown
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - William J. Lane
- Department of Pathology, Brigham & Women's Hospital, Boston, Massachusetts, United States of America
| | | | - Robert Landick
- Departments of Biochemistry and Bacteriology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Francisco J. Asturias
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail: (FJA); (SAD)
| | - Seth A. Darst
- The Rockefeller University, New York, New York, United States of America
- * E-mail: (FJA); (SAD)
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22
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Asturias FJ, Cai G, Imasaki T, Yamada K, Cardelli F, Takagi Y. Mediator Structure and Interaction with the Basal Transcription Machinery. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.679.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Gang Cai
- Department of Cell BiologyThe Scripps Research InsituteLa JollaCA
| | - Tsuyoshi Imasaki
- Department of Biochemistry and Molecular BiologyIndiana University School of MedicineIndianapolisIN
| | - Kentaro Yamada
- Department of Biochemistry and Molecular BiologyIndiana University School of MedicineIndianapolisIN
| | - Francesco Cardelli
- Department of Biochemistry and Molecular BiologyIndiana University School of MedicineIndianapolisIN
| | - Yuichiro Takagi
- Department of Biochemistry and Molecular BiologyIndiana University School of MedicineIndianapolisIN
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23
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24
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Cai G, Imasaki T, Yamada K, Cardelli F, Takagi Y, Asturias FJ. Mediator head module structure and functional interactions. Nat Struct Mol Biol 2010; 17:273-9. [PMID: 20154708 DOI: 10.1038/nsmb.1757] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Accepted: 12/03/2009] [Indexed: 11/09/2022]
Abstract
We used single-particle electron microscopy to characterize the structure and subunit organization of the Mediator Head module that controls Mediator-RNA polymerase II (RNAPII) and Mediator-promoter interactions. The Head module adopts several conformations differing in the position of a movable jaw formed by the Med18-Med20 subcomplex. We also characterized, by structural, biochemical and genetic means, the interactions of the Head module with TATA-binding protein (TBP) and RNAPII subunits Rpb4 and Rpb7. TBP binds near the Med18-Med20 attachment point and stabilizes an open conformation of the Head module. Rpb4 and Rpb7 bind between the Head jaws, establishing contacts essential for yeast-cell viability. These results, and consideration of the structure of the Mediator-RNAPII holoenzyme, shed light on the stabilization of the pre-initiation complex by Mediator and suggest how Mediator might influence initiation by modulating polymerase conformation and interaction with promoter DNA.
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Affiliation(s)
- Gang Cai
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, USA
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25
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Cai G, Imasaki T, Takagi Y, Asturias FJ. Mediator structural conservation and implications for the regulation mechanism. Structure 2009; 17:559-67. [PMID: 19368889 DOI: 10.1016/j.str.2009.01.016] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Revised: 01/29/2009] [Accepted: 01/30/2009] [Indexed: 11/27/2022]
Abstract
Mediator, the multisubunit complex that plays an essential role in the regulation of transcription initiation in all eukaryotes, was isolated using an affinity purification protocol that yields pure material suitable for structural analysis. Conformational sorting of yeast Mediator single-particle images characterized the inherent flexibility of the complex and made possible calculation of a cryo-EM reconstruction. Comparison of free and RNA polymerase II (RNAPII) -associated yeast Mediator reconstructions demonstrates that intrinsic flexibility allows structural modules to reorganize and establish a complex network of contacts with RNAPII. We demonstrate that, despite very low sequence homology, the structures of human and yeast Mediators are surprisingly similar and the structural rearrangement that enables interaction of yeast Mediator with RNAPII parallels the structural rearrangement triggered by interaction of human Mediator with a nuclear receptor. This suggests that the topology and structural dynamics of Mediator constitute important elements of a conserved regulation mechanism.
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Affiliation(s)
- Gang Cai
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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26
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Shaikh TR, Gao H, Baxter WT, Asturias FJ, Boisset N, Leith A, Frank J. SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. Nat Protoc 2009; 3:1941-74. [PMID: 19180078 DOI: 10.1038/nprot.2008.156] [Citation(s) in RCA: 351] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This protocol describes the reconstruction of biological molecules from the electron micrographs of single particles. Computation here is performed using the image-processing software SPIDER and can be managed using a graphical user interface, termed the SPIDER Reconstruction Engine. Two approaches are described to obtain an initial reconstruction: random-conical tilt and common lines. Once an existing model is available, reference-based alignment can be used, a procedure that can be iterated. Also described is supervised classification, a method to look for homogeneous subsets when multiple known conformations of the molecule may coexist.
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Affiliation(s)
- Tanvir R Shaikh
- Wadsworth Center, Empire State Plaza, Albany, New York 12201-0509, USA
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27
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Brignole EJ, Smith S, Asturias FJ. Conformational flexibility of metazoan fatty acid synthase enables catalysis. Nat Struct Mol Biol 2009; 16:190-7. [PMID: 19151726 PMCID: PMC2653270 DOI: 10.1038/nsmb.1532] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Accepted: 11/14/2008] [Indexed: 11/09/2022]
Abstract
The metazoan cytosolic fatty acid synthase (FAS) contains all of the enzymes required for de novo fatty acid biosynthesis covalently linked around two reaction chambers. Although the three-dimensional architecture of FAS has been mostly defined, it is unclear how reaction intermediates can transfer between distant catalytic domains. Using single-particle EM, we have identified a near continuum of conformations consistent with a remarkable flexibility of FAS. The distribution of conformations was influenced by the presence of substrates and altered by different catalytic mutations, suggesting a direct correlation between conformation and specific enzymatic activities. We interpreted three-dimensional reconstructions by docking high-resolution structures of individual domains, and they show that the substrate-loading and condensation domains dramatically swing and swivel to access substrates within either reaction chamber. Concomitant rearrangement of the beta-carbon-processing domains synchronizes acyl chain reduction in one chamber with acyl chain elongation in the other.
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Affiliation(s)
- Edward J Brignole
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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28
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Fuxreiter M, Tompa P, Simon I, Uversky VN, Hansen JC, Asturias FJ. Malleable machines take shape in eukaryotic transcriptional regulation. Nat Chem Biol 2008; 4:728-37. [PMID: 19008886 DOI: 10.1038/nchembio.127] [Citation(s) in RCA: 168] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Transcriptional control requires the spatially and temporally coordinated action of many macromolecular complexes. Chromosomal proteins, transcription factors, co-activators and components of the general transcription machinery, including RNA polymerases, often use structurally or stoichiometrically ill-defined regions for interactions that convey regulatory information in processes ranging from chromatin remodeling to mRNA processing. Determining the functional significance of intrinsically disordered protein regions and developing conceptual models of their action will help to illuminate their key role in transcription regulation. Complexes comprising disordered regions often display short recognition elements embedded in flexible and sequentially variable environments that can lead to structural and functional malleability. This provides versatility to recognize multiple targets having different structures, facilitate conformational rearrangements and physically communicate with many partners in response to environmental changes. All these features expand the capacities of ordered complexes and give rise to efficient regulatory mechanisms.
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Affiliation(s)
- Monika Fuxreiter
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Karolina ut 29, H-1113, H-1518 Budapest, Hungary.
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29
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Yang C, Penczek PA, Leith A, Asturias FJ, Ng EG, Glaeser RM, Frank J. The parallelization of SPIDER on distributed-memory computers using MPI. J Struct Biol 2006; 157:240-9. [PMID: 16859923 DOI: 10.1016/j.jsb.2006.05.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Revised: 05/30/2006] [Accepted: 05/31/2006] [Indexed: 10/24/2022]
Abstract
We describe the strategies and implementation details we employed to parallelize the SPIDER software package on distributed-memory parallel computers using the message passing interface (MPI). The MPI-enabled SPIDER preserves the interactive command line and batch interface used in the sequential version of SPIDER, thus does not require users to modify their existing batch programs. We show the excellent performance of the MPI-enabled SPIDER when it is used to perform multi-reference alignment and 3-D reconstruction operations on a number of different computing platforms. We point out some performance issues when the MPI-enabled SPIDER is used for a complete 3-D projection matching refinement run, and propose several ways to further improve the parallel performance of SPIDER on distributed-memory machines.
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Affiliation(s)
- Chao Yang
- Lawrence Berkeley National Laboratory, Computational Research Division, Berkeley, CA 94720, USA.
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Abstract
Mammalian fatty acid synthase (FAS) is a homodimeric, multifunctional polypeptide which comprises two full sets of catalytic subunits that carry out fatty acid synthesis. A recently published X-ray structure of FAS reveals, for the first time, the organization of all active sites involved in acyl chain elongation and provides a structural framework for interpretation of extensive functional studies. Further analysis with techniques capable of providing information about single molecule conformations will eventually provide a more complete understanding of FAS.
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Affiliation(s)
- Francisco J Asturias
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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Asturias FJ, Cheung IK, Sabouri N, Chilkova O, Wepplo D, Johansson E. Structure of Saccharomyces cerevisiae DNA polymerase epsilon by cryo-electron microscopy. Nat Struct Mol Biol 2005; 13:35-43. [PMID: 16369485 DOI: 10.1038/nsmb1040] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Accepted: 11/17/2005] [Indexed: 11/08/2022]
Abstract
The structure of the multisubunit yeast DNA polymerase epsilon (Pol epsilon) was determined to 20-A resolution using cryo-EM and single-particle image analysis. A globular domain comprising the catalytic Pol2 subunit is flexibly connected to an extended structure formed by subunits Dpb2, Dpb3 and Dpb4. Consistent with the reported involvement of the latter in interaction with nucleic acids, the Dpb portion of the structure directly faces a single cleft in the Pol2 subunit that seems wide enough to accommodate double-stranded DNA. Primer-extension experiments reveal that Pol epsilon processivity requires a minimum length of primer-template duplex that corresponds to the dimensions of the extended Dpb structure. Together, these observations suggest a mechanism for interaction of Pol epsilon with DNA that might explain how the structure of the enzyme contributes to its intrinsic processivity.
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Affiliation(s)
- Francisco J Asturias
- Department of Structural Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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32
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Abstract
Biochemical evidence suggesting that the predominant form of Mediator in the yeast Saccharomyces cerevisiae might be one in which the complex is associated with RNA polymerase II to form a holoenzyme has led to the proposition of a holoenzyme-based model for transcription initiation. We report that polymerase-free Mediator, isolated early on during a whole-cell extract fractionation protocol, is in fact the most abundant form of the Mediator complex. The existence of free Mediator would make possible independent recruitment of Mediator and RNA polymerase II to the pre-initiation complex. This is in agreement with reports from in vivo studies of time and spatial independence of Mediator and RNA polymerase II promoter interaction, with current models of pre-initiation complex structure in which promoter DNA upstream of the transcription start site is positioned between Mediator and polymerase, and with the proposed role of Mediator as the major component of the Scaffold complex involved in transcription reinitiation.
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Affiliation(s)
- Yuichiro Takagi
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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33
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Abstract
Mediator, a macromolecular complex comprising approximately 20 different protein components, is largely responsible for the tight control of transcription that underpins cell development, differentiation, and maintenance in eukaryotes from yeast to human. In the past five years, macromolecular electron microscopy has been used to characterize the structure of Mediator, and of the complexes it forms with other components of the transcription machinery. The results reveal how Mediator interacts with RNA polymerase II, and suggest that regulatory information could be conveyed through changes in Mediator conformation that would influence the transcription initiation process.
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Affiliation(s)
- James Z Chadick
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road CB227, La Jolla, CA 92037, USA
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34
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Asturias FJ, Chadick JZ, Cheung IK, Stark H, Witkowski A, Joshi AK, Smith S. Structure and molecular organization of mammalian fatty acid synthase. Nat Struct Mol Biol 2005; 12:225-32. [PMID: 15711565 DOI: 10.1038/nsmb899] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2004] [Accepted: 01/19/2005] [Indexed: 11/09/2022]
Abstract
De novo synthesis of fatty acids in the cytosol of animal cells is carried out by the multifunctional, homodimeric fatty acid synthase (FAS). Cryo-EM analysis of single FAS particles imaged under conditions that limit conformational variability, combined with gold labeling of the N termini and structural analysis of the FAS monomers, reveals two coiled monomers in an overlapping arrangement. Comparison of dimeric FAS structures related to different steps in the fatty acid synthesis process indicates that only limited local rearrangements are required for catalytic interaction among different functional domains. Monomer coiling probably contributes to FAS efficiency and provides a structural explanation for the reported activity of a FAS monomer dimerized to a catalytically inactive partner. The new FAS structure provides a new paradigm for understanding the architecture of FAS and the related modular polyketide synthases.
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Affiliation(s)
- Francisco J Asturias
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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35
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Witkowski A, Ghosal A, Joshi AK, Witkowska HE, Asturias FJ, Smith S. Head-to-Head Coiled Arrangement of the Subunits of the Animal Fatty Acid Synthase. ACTA ACUST UNITED AC 2004; 11:1667-76. [PMID: 15610851 DOI: 10.1016/j.chembiol.2004.09.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2004] [Revised: 09/25/2004] [Accepted: 09/30/2004] [Indexed: 10/26/2022]
Abstract
The role of the beta-ketoacyl synthase domains in dimerization of the 2505 residue subunits of the multifunctional animal FAS has been evaluated by a combination of crosslinking and characterization of several truncated forms of the protein. Polypeptides containing only the N-terminal 971 residues can form dimers, but polypeptides lacking only the N-terminal 422 residue beta-ketoacyl synthase domain cannot. FAS subunits can be crosslinked with spacer lengths as short as 6 A, via cysteine residues engineered near the N terminus of the full-length polypeptides. The proximity of the N-terminal beta-ketoacyl synthase domains and their essential role in dimerization is consistent with a revised model for the FAS in which a head-to-head arrangement of two coiled subunits facilitates functional interactions between the dimeric beta-ketoacyl synthase and the acyl carrier protein domains of either subunit.
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Affiliation(s)
- Andrzej Witkowski
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, California 94609, USA
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37
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Bourbon HM, Aguilera A, Ansari AZ, Asturias FJ, Berk AJ, Bjorklund S, Blackwell TK, Borggrefe T, Carey M, Carlson M, Conaway JW, Conaway RC, Emmons SW, Fondell JD, Freedman LP, Fukasawa T, Gustafsson CM, Han M, He X, Herman PK, Hinnebusch AG, Holmberg S, Holstege FC, Jaehning JA, Kim YJ, Kuras L, Leutz A, Lis JT, Meisterernest M, Naar AM, Nasmyth K, Parvin JD, Ptashne M, Reinberg D, Ronne H, Sadowski I, Sakurai H, Sipiczki M, Sternberg PW, Stillman DJ, Strich R, Struhl K, Svejstrup JQ, Tuck S, Winston F, Roeder RG, Kornberg RD. A Unified Nomenclature for Protein Subunits of Mediator Complexes Linking Transcriptional Regulators to RNA Polymerase II. Mol Cell 2004; 14:553-7. [PMID: 15175151 DOI: 10.1016/j.molcel.2004.05.011] [Citation(s) in RCA: 218] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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38
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Abstract
Recent X-ray and cryo-electron microscopy studies have provided information about the basal eukaryotic transcription machinery and about Mediator, the complex involved in transcription regulation during initiation. On the basis of this structural information, a model describing the minimal transcription complex and its interaction with Mediator has been proposed. The model provides insight into the possible mechanisms of transcription initiation and regulation.
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Affiliation(s)
- Francisco J Asturias
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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39
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Chung WH, Craighead JL, Chang WH, Ezeokonkwo C, Bareket-Samish A, Kornberg RD, Asturias FJ. RNA Polymerase II/TFIIF Structure and Conserved Organization of the Initiation Complex. Mol Cell 2003; 12:1003-13. [PMID: 14580350 DOI: 10.1016/s1097-2765(03)00387-3] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The structure of an RNA polymerase II/general transcription factor TFIIF complex was determined by cryo-electron microscopy and single particle analysis. Density due to TFIIF was not concentrated in one area but rather was widely distributed across the surface of the polymerase. The largest subunit of TFIIF interacted with the dissociable Rpb4/Rpb7 polymerase subunit complex and with the mobile "clamp." The distribution of the second largest subunit of TFIIF was very similar to that previously reported for the sigma subunit in the bacterial RNA polymerase holoenzyme, consisting of a series of globular domains extending along the polymerase active site cleft. This result indicates that the second TFIIF subunit is a true structural homolog of the bacterial sigma factor and reveals an important similarity of the transcription initiation mechanism between bacteria and eukaryotes. The structure of the RNAPII/TFIIF complex suggests a model for the organization of a minimal transcription initiation complex.
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Affiliation(s)
- Wen-Hsiang Chung
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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40
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Affiliation(s)
- Francisco J Asturias
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, CB227, La Jolla, CA 92037, USA.
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41
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Affiliation(s)
- Francisco J Asturias
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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42
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Abstract
Electron microscopy of the RSC chromatin-remodeling complex reveals a ring of protein densities around a central cavity. The size and shape of the cavity correspond closely to those of a nucleosome. Results of nuclease protection analysis are consistent with nucleosome binding in the cavity. Such binding could explain the ability of RSC to expose nucleosomal DNA in the presence of ATP without loss of associated histones.
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Affiliation(s)
- Francisco J Asturias
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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43
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Abstract
An 18 A resolution structure of the 12-subunit yeast RNA polymerase II (RNAPII) calculated from electron microscope images of single particles preserved in amorphous ice reveals the conformation of the enzyme in solution. The Rpb4/Rpb7 polymerase subunit complex was localized and found to be ideally positioned to determine the path of the nascent RNA transcript. The RNAPII structure suggests a revised mode of interaction with promoter DNA and demonstrates that regulation of RNAPII must involve structural changes that render the enzyme competent for initiation.
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Affiliation(s)
- John L Craighead
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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44
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Dotson MR, Yuan CX, Roeder RG, Myers LC, Gustafsson CM, Jiang YW, Li Y, Kornberg RD, Asturias FJ. Structural organization of yeast and mammalian mediator complexes. Proc Natl Acad Sci U S A 2000; 97:14307-10. [PMID: 11114191 PMCID: PMC18914 DOI: 10.1073/pnas.260489497] [Citation(s) in RCA: 158] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Structures of yeast Mediator complex, of a related complex from mouse cells and of thyroid hormone receptor-associated protein complex from human cells have been determined by three-dimensional reconstruction from electron micrographs of single particles. All three complexes show a division in two parts, a "head" domain and a combined "middle-tail" domain. The head domains of the three complexes appear most similar and interact most closely with RNA polymerase II. The middle-tail domains show the greatest structural divergence and, in the case of the tail domain, may not interact with polymerase at all. Consistent with this structural divergence, analysis of a yeast Mediator mutant localizes subunits that are not conserved between yeast and mammalian cells to the tail domain. Biochemically defined Rgr1 and Srb4 modules of yeast Mediator are then assigned to the middle and head domains.
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Affiliation(s)
- M R Dotson
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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45
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Asturias FJ, Kornberg RD. Protein crystallization on lipid layers and structure determination of the RNA polymerase II transcription initiation complex. J Biol Chem 1999; 274:6813-6. [PMID: 10066729 DOI: 10.1074/jbc.274.11.6813] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- F J Asturias
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
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46
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Abstract
Single particles of the mediator of transcriptional regulation (Mediator) and of RNA polymerase II holoenzyme were revealed by electron microscopy and image processing. Mediator alone appeared compact, but at high pH or in the presence of RNA polymerase II it displayed an extended conformation. Holoenzyme contained Mediator in a fully extended state, partially enveloping the globular polymerase, with points of apparent contact in the vicinity of the polymerase carboxyl-terminal domain and the DNA-binding channel. A similarity in appearance and conformational behavior of yeast and murine complexes indicates a conservation of Mediator structure among eukaryotes.
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Affiliation(s)
- F J Asturias
- Department of Structural Biology, Fairchild Building, Stanford University School of Medicine, Stanford, CA 94305, USA
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47
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Abstract
Two-dimensional (2-D) crystals of yeast RNA polymerase preserved in vitreous ice were studied by electron crystallographic and single-particle techniques. An electron density projection map of the enzyme was calculated from the data, which extended to a resolution of about 12 A, but was unexpectedly weak at resolutions higher than about 20 A. Multivariate statistics analysis revealed a large amount of variability in unit-cell structure in the polymerase crystals, partially related to high mobility of certain polymerase domains. Those same domains were previously identified as being involved in a conformational transition in the enzyme that controls DNA processivity and access to the active center cleft. Electron microscopic studies of other large multiprotein complexes are likely to require similar approaches to those described here.
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Affiliation(s)
- F J Asturias
- Department of Structural Biology, Stanford University School of Medicine, CA 94305-5400, USA.
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48
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Abstract
A new two-dimensional crystal form of yeast RNA polymerase II was obtained in which the conformation of the enzyme appears "open", allowing entry of DNA, as required for the initiation of transcription. By contrast, a previous crystal form contained the enzyme in a "closed" conformation, appropriate for retention of DNA during RNA chain elongation. Interaction with two polymerase subunits, Rpb4 and Rpb7, favors the closed conformation, and binding of general transcription factor TFIIE may do so as well. The effect of Rpb4 and Rpb7, together with previous biochemical evidence, leads to the conclusion that the open to closed transition is a crucial step in the transcription initiation process.
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Affiliation(s)
- F J Asturias
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5400, USA
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49
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Edwards AM, Darst SA, Hemming SA, Asturias FJ, David PR, Kornberg RD. [11] Two-dimensional protein crystals in aid of three-dimensional protein crystal growth. Methods Enzymol 1997; 276:166-171. [DOI: 10.1016/s0076-6879(97)76057-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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50
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Asturias FJ, Kornberg RD. A novel method for transfer of two-dimensional crystals from the air/water interface to specimen grids. EM sample preparation/lipid-layer crystallization. J Struct Biol 1995; 114:60-6. [PMID: 7772418 DOI: 10.1006/jsbi.1995.1005] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Transfer of two-dimensional (2-D) crystals formed on lipid layers by suspension from a wire loop is described. This method gives better recovery and better preservation of 2-D crystals than attained in the past. The method has been applied to crystals of yeast RNA polymerase II to enable their analysis in the frozen hydrated state.
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Affiliation(s)
- F J Asturias
- Department of Cell Biology, Stanford University School of Medicine, California 94305, USA
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