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A single helix repression domain is functional across diverse eukaryotes. Proc Natl Acad Sci U S A 2022; 119:e2206986119. [PMID: 36191192 PMCID: PMC9564828 DOI: 10.1073/pnas.2206986119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The corepressor TOPLESS (TPL) and its paralogs coordinately regulate a large number of genes critical to plant development and immunity. As in many members of the larger pan-eukaryotic Tup1/TLE/Groucho corepressor family, TPL contains a Lis1 Homology domain (LisH), whose function is not well understood. We have previously found that the LisH in TPL-and specifically the N-terminal 18 amino acid alpha-helical region (TPL-H1)-can act as an autonomous repression domain. We hypothesized that homologous domains across diverse LisH-containing proteins could share the same function. To test that hypothesis, we built a library of H1s that broadly sampled the sequence and evolutionary space of LisH domains, and tested their activity in a synthetic transcriptional repression assay in Saccharomyces cerevisiae. Using this approach, we found that repression activity was highly conserved and likely the ancestral function of this motif. We also identified key residues that contribute to repressive function. We leveraged this new knowledge for two applications. First, we tested the role of mutations found in somatic cancers on repression function in two human LisH-containing proteins. Second, we validated function of many of our repression domains in plants, confirming that these sequences should be of use to synthetic biology applications across many eukaryotes.
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2
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Reyes AA, Fishbain S, He Y. Structural and functional analysis of the SET3 histone deacetylase complex. Acta Crystallogr F Struct Biol Commun 2022; 78:113-118. [PMID: 35234136 PMCID: PMC8900736 DOI: 10.1107/s2053230x22000553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/16/2022] [Indexed: 11/10/2022] Open
Abstract
The SET3 complex (SET3C) is a seven-subunit histone deacetylase complex that is capable of transcriptional regulation. Methylated histone 3 marks recruit SET3C to the nucleosome, and the SET3C catalytic subunits deacetylate the histone 3 and 4 tails. There is very limited structural knowledge of the SET3C subunits, with most subunits having unknown structures or functions. Here, a catalytically active SET3 complex was endogenously purified from Saccharomyces cerevisiae and utilized for negative-stain electron microscopy (EM) to determine an apo model for the holo complex. The negative-stain EM 3D model revealed a three-lobe architecture, with each lobe extending from a central point.
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Affiliation(s)
- Alexis A. Reyes
- Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois, USA
| | - Susan Fishbain
- Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Yuan He
- Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, Illinois, USA
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3
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Willison KR. The substrate specificity of eukaryotic cytosolic chaperonin CCT. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0192. [PMID: 29735743 DOI: 10.1098/rstb.2017.0192] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2018] [Indexed: 12/22/2022] Open
Abstract
The cytosolic chaperonin CCT (chaperonin containing TCP-1) is an ATP-dependent double-ring protein machine mediating the folding of members of the eukaryotic cytoskeletal protein families. The actins and tubulins are obligate substrates of CCT because they are completely dependent on CCT activity to reach their native states. Genetic and proteomic analysis of the CCT interactome in the yeast Saccharomyces cerevisiae revealed a CCT network of approximately 300 genes and proteins involved in many fundamental biological processes. We classified network members into sets such as substrates, CCT cofactors and CCT-mediated assembly processes. Many members of the 7-bladed propeller family of proteins are commonly found tightly bound to CCT isolated from human and plant cells and yeasts. The anaphase promoting complex (APC/C) cofactor propellers, Cdh1p and Cdc20p, are also obligate substrates since they both require CCT for folding and functional activation. In vitro translation analysis in prokaryotic and eukaryotic cell extracts of a set of yeast propellers demonstrates their highly differential interactions with CCT and GroEL (another chaperonin). Individual propeller proteins have idiosyncratic interaction modes with CCT because they emerged independently with neo-functions many times throughout eukaryotic evolution. We present a toy model in which cytoskeletal protein biogenesis and folding flux through CCT couples cell growth and size control to time dependent cell cycle mechanisms.This article is part of a discussion meeting issue 'Allostery and molecular machines'.
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Affiliation(s)
- Keith R Willison
- Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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4
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Genome Wide Analysis of WD40 Proteins in Saccharomyces cerevisiae and Their Orthologs in Candida albicans. Protein J 2019; 38:58-75. [PMID: 30511317 DOI: 10.1007/s10930-018-9804-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The WD40 domain containing proteins are present in the lower organisms (Monera) to higher complex metazoans with involvement in diverse cellular processes. The WD40 repeats fold into β propeller structure due to which the proteins harbouring WD40 domains function as scaffold by offering platform for interactions, bring together diverse cellular proteins to form a single complex for mediating downstream effects. Multiple functions of WD40 domain containing proteins in lower eukaryote as in Fungi have been reported with involvement in vegetative and reproductive growth, virulence etc. In this article insilico analysis of the WDR proteins in the budding yeast Saccharomyces cerevisiae was performed. By WDSP software 83 proteins in S. cerevisiae were identified with at least one WD40 motif. WD40 proteins with 6 or more WD40 motifs were considered for further studies. The WD40 proteins in yeast which are involved in various biological processes show distribution on all chromosomes (16 chromosomes in yeast) except chromosome 1. Besides the WD40 domain some of these proteins also contain other protein domains which might be responsible for the diversity in the functions of WD40 proteins in the budding yeast. These proteins in budding yeast were analysed by DAVID and Blast2Go software for functional and domains categorization. Candida albicans, an opportunistic fungal pathogen also have orthologs of these WD40 proteins with possible similar functions. This is the first time genome wide analysis of WD40 proteins in lower eukaryote i.e. budding yeast. This data may be useful in further study of the functional diversity of yeast proteomes.
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Tsui C, Inouye C, Levy M, Lu A, Florens L, Washburn MP, Tjian R. dCas9-targeted locus-specific protein isolation method identifies histone gene regulators. Proc Natl Acad Sci U S A 2018; 115:E2734-E2741. [PMID: 29507191 PMCID: PMC5866577 DOI: 10.1073/pnas.1718844115] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eukaryotic gene regulation is a complex process, often coordinated by the action of tens to hundreds of proteins. Although previous biochemical studies have identified many components of the basal machinery and various ancillary factors involved in gene regulation, numerous gene-specific regulators remain undiscovered. To comprehensively survey the proteome directing gene expression at a specific genomic locus of interest, we developed an in vitro nuclease-deficient Cas9 (dCas9)-targeted chromatin-based purification strategy, called "CLASP" (Cas9 locus-associated proteome), to identify and functionally test associated gene-regulatory factors. Our CLASP method, coupled to mass spectrometry and functional screens, can be efficiently adapted for isolating associated regulatory factors in an unbiased manner targeting multiple genomic loci across different cell types. Here, we applied our method to isolate the Drosophila melanogaster histone cluster in S2 cells to identify several factors including Vig and Vig2, two proteins that bind and regulate core histone H2A and H3 mRNA via interaction with their 3' UTRs.
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Affiliation(s)
- Chiahao Tsui
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
| | - Carla Inouye
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
| | - Michaella Levy
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Andrew Lu
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, CA 94720
| | | | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160
| | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, CA 94720;
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
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Structure of the Arabidopsis TOPLESS corepressor provides insight into the evolution of transcriptional repression. Proc Natl Acad Sci U S A 2017; 114:8107-8112. [PMID: 28698367 DOI: 10.1073/pnas.1703054114] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Transcriptional repression involves a class of proteins called corepressors that link transcription factors to chromatin remodeling complexes. In plants such as Arabidopsis thaliana, the most prominent corepressor is TOPLESS (TPL), which plays a key role in hormone signaling and development. Here we present the crystallographic structure of the Arabidopsis TPL N-terminal region comprising the LisH and CTLH (C-terminal to LisH) domains and a newly identified third region, which corresponds to a CRA domain. Comparing the structure of TPL with the mammalian TBL1, which shares a similar domain structure and performs a parallel corepressor function, revealed that the plant TPLs have evolved a new tetramerization interface and unique and highly conserved surface for interaction with repressors. Using site-directed mutagenesis, we validated those surfaces in vitro and in vivo and showed that TPL tetramerization and repressor binding are interdependent. Our results illustrate how evolution used a common set of protein domains to create a diversity of corepressors, achieving similar properties with different molecular solutions.
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Studies of recombinant TWA1 reveal constitutive dimerization. Biosci Rep 2017; 37:BSR20160401. [PMID: 27920276 PMCID: PMC5234100 DOI: 10.1042/bsr20160401] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 11/25/2016] [Accepted: 12/05/2016] [Indexed: 01/06/2023] Open
Abstract
The mammalian muskelin/RanBP9/C-terminal to LisH (CTLH) complex and the Saccharomyces cerevisiae glucose-induced degradation (GID) complex are large, multi-protein complexes that each contain a RING E3 ubiquitin ligase. The yeast GID complex acts to degrade a key enzyme of gluconeogenesis, fructose 1,6-bisphosphatase, under conditions of abundant fermentable carbon sources. However, the assembly and functions of the mammalian complex remain poorly understood. A striking feature of these complexes is the presence of multiple proteins that contain contiguous lissencephaly-1 homology (LisH), CTLH and C-terminal CT11-RanBP9 (CRA) domains. TWA1/Gid8, the smallest constituent protein of these complexes, consists only of LisH, CTLH and CRA domains and is highly conserved in eukaryotes. Towards better knowledge of the role of TWA1 in these multi-protein complexes, we established a method for bacterial expression and purification of mouse TWA1 that yields tag-free, recombinant TWA1 in quantities suitable for biophysical and biochemical studies. CD spectroscopy of recombinant TWA1 indicated a predominantly α-helical protein. Gel filtration chromatography, size-exclusion chromatography (SEC) with multi-angle light scattering (SEC-MALS) and native PAGE demonstrated a propensity of untagged TWA1 to form stable dimers and, to a lesser extent, higher order oligomers. TWA1 has a single cysteine residue, Cys139, yet the dimeric form was preserved when TWA1 was purified in the presence of the reducing agent tris(2-carboxyethyl)phosphine (TCEP). These findings have implications for understanding the molecular role of TWA1 in the yeast GID complex and related multi-protein E3 ubiquitin ligases identified in other eukaryotes.
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Heinen CA, Jongejan A, Watson PJ, Redeker B, Boelen A, Boudzovitch-Surovtseva O, Forzano F, Hordijk R, Kelley R, Olney AH, Pierpont ME, Schaefer GB, Stewart F, van Trotsenburg ASP, Fliers E, Schwabe JWR, Hennekam RC. A specific mutation in TBL1XR1 causes Pierpont syndrome. J Med Genet 2016; 53:330-7. [PMID: 26769062 PMCID: PMC4853543 DOI: 10.1136/jmedgenet-2015-103233] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 12/14/2015] [Indexed: 12/30/2022]
Abstract
Background The combination of developmental delay, facial characteristics, hearing loss and abnormal fat distribution in the distal limbs is known as Pierpont syndrome. The aim of the present study was to detect and study the cause of Pierpont syndrome. Methods We used whole-exome sequencing to analyse four unrelated individuals with Pierpont syndrome, and Sanger sequencing in two other unrelated affected individuals. Expression of mRNA of the wild-type candidate gene was analysed in human postmortem brain specimens, adipose tissue, muscle and liver. Expression of RNA in lymphocytes in patients and controls was additionally analysed. The variant protein was expressed in, and purified from, HEK293 cells to assess its effect on protein folding and function. Results We identified a single heterozygous missense variant, c.1337A>C (p.Tyr446Cys), in transducin β-like 1 X-linked receptor 1 (TBL1XR1) as disease-causing in all patients. TBL1XR1 mRNA expression was demonstrated in pituitary, hypothalamus, white and brown adipose tissue, muscle and liver. mRNA expression is lower in lymphocytes of two patients compared with the four controls. The mutant TBL1XR1 protein assembled correctly into the nuclear receptor corepressor (NCoR)/ silencing mediator for retinoid and thyroid receptors (SMRT) complex, suggesting a dominant-negative mechanism. This contrasts with loss-of-function germline TBL1XR1 deletions and other TBL1XR1 mutations that have been implicated in autism. However, autism is not present in individuals with Pierpont syndrome. Conclusions This study identifies a specific TBL1XR1 mutation as the cause of Pierpont syndrome. Deletions and other mutations in TBL1XR1 can cause autism. The marked differences between Pierpont patients with the p.Tyr446Cys mutation and individuals with other mutations and whole gene deletions indicate a specific, but as yet unknown, disease mechanism of the TBL1XR1 p.Tyr446Cys mutation.
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Affiliation(s)
- Charlotte A Heinen
- Department of Endocrinology and Metabolism, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands Department of Paediatric Endocrinology, Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Aldo Jongejan
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Peter J Watson
- Department of Biochemistry, Henry Wellcome Laboratories of Structural Biology, University of Leicester, Leicester, UK
| | - Bert Redeker
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Anita Boelen
- Department of Endocrinology and Metabolism, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Olga Boudzovitch-Surovtseva
- Department of Endocrinology and Metabolism, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Roel Hordijk
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Richard Kelley
- Division of Metabolism, Kennedy Krieger Institute, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ann H Olney
- Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Centre, Omaha, Nebraska, USA
| | - Mary Ella Pierpont
- Division of Genetics, Children's Hospitals and Clinics of Minnesota, University of Minnesota, Minneapolis, Minnesota, USA
| | - G Bradley Schaefer
- Division of Medical Genetics, Arkansas Children's Hospital, Little Rock, Arkansas, USA
| | - Fiona Stewart
- Division of Medical Genetics, Belfast City Hospital, Belfast, Ireland
| | - A S Paul van Trotsenburg
- Department of Paediatric Endocrinology, Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Eric Fliers
- Department of Endocrinology and Metabolism, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - John W R Schwabe
- Department of Biochemistry, Henry Wellcome Laboratories of Structural Biology, University of Leicester, Leicester, UK
| | - Raoul C Hennekam
- Department of Paediatrics, Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
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9
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Structure of the WD40 domain of SCAP from fission yeast reveals the molecular basis for SREBP recognition. Cell Res 2015; 25:401-11. [PMID: 25771684 PMCID: PMC4387560 DOI: 10.1038/cr.2015.32] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 01/20/2015] [Accepted: 01/20/2015] [Indexed: 12/31/2022] Open
Abstract
The sterol regulatory element-binding protein (SREBP) and SREBP cleavage-activating protein (SCAP) are central players in the SREBP pathway, which control the cellular lipid homeostasis. SCAP binds to SREBP through their carboxyl (C) domains and escorts SREBP from the endoplasmic reticulum to the Golgi upon sterol depletion. A conserved pathway, with the homologues of SREBP and SCAP being Sre1 and Scp1, was identified in fission yeast Schizosaccharomyces pombe. Here we report the in vitro reconstitution of the complex between the C domains of Sre1 and Scp1 as well as the crystal structure of the WD40 domain of Scp1 at 2.1 Å resolution. The structure reveals an eight-bladed β-propeller that exhibits several distinctive features from a canonical WD40 repeat domain. Structural and biochemical characterization led to the identification of two Scp1 elements that are involved in Sre1 recognition, an Arg/Lys-enriched surface patch on the top face of the WD40 propeller and a 30-residue C-terminal tail. The structural and biochemical findings were corroborated by in vivo examinations. These studies serve as a framework for the mechanistic understanding and further functional characterization of the SREBP and SCAP proteins in fission yeast and higher organisms.
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10
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Terzo EA, Lyons SM, Poulton JS, Temple BRS, Marzluff WF, Duronio RJ. Distinct self-interaction domains promote Multi Sex Combs accumulation in and formation of the Drosophila histone locus body. Mol Biol Cell 2015; 26:1559-74. [PMID: 25694448 PMCID: PMC4395134 DOI: 10.1091/mbc.e14-10-1445] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 02/12/2015] [Indexed: 11/11/2022] Open
Abstract
The Drosophila Multi Sex Combs (Mxc) protein is necessary for the recruitment of histone mRNA biosynthetic factors to the histone locus body (HLB). Mxc contains multiple domains required for HLB assembly and histone mRNA biosynthesis. Two N-terminal domains of Mxc are essential for promoting HLB assembly via a self-interaction. Nuclear bodies (NBs) are structures that concentrate proteins, RNAs, and ribonucleoproteins that perform functions essential to gene expression. How NBs assemble is not well understood. We studied the Drosophila histone locus body (HLB), a NB that concentrates factors required for histone mRNA biosynthesis at the replication-dependent histone gene locus. We coupled biochemical analysis with confocal imaging of both fixed and live tissues to demonstrate that the Drosophila Multi Sex Combs (Mxc) protein contains multiple domains necessary for HLB assembly. An important feature of this assembly process is the self-interaction of Mxc via two conserved N-terminal domains: a LisH domain and a novel self-interaction facilitator (SIF) domain immediately downstream of the LisH domain. Molecular modeling suggests that the LisH and SIF domains directly interact, and mutation of either the LisH or the SIF domain severely impairs Mxc function in vivo, resulting in reduced histone mRNA accumulation. A region of Mxc between amino acids 721 and 1481 is also necessary for HLB assembly independent of the LisH and SIF domains. Finally, the C-terminal 195 amino acids of Mxc are required for recruiting FLASH, an essential histone mRNA-processing factor, to the HLB. We conclude that multiple domains of the Mxc protein promote HLB assembly in order to concentrate factors required for histone mRNA biosynthesis.
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Affiliation(s)
- Esteban A Terzo
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Shawn M Lyons
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - John S Poulton
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Brenda R S Temple
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599
| | - William F Marzluff
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599 Department of Biology, University of North Carolina, Chapel Hill, NC 27599 Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599 Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599 Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599 Department of Biology, University of North Carolina, Chapel Hill, NC 27599 Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599 Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599 Department of Genetics, University of North Carolina, Chapel Hill, NC 27599
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11
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Erzberger JP, Stengel F, Pellarin R, Zhang S, Schaefer T, Aylett CHS, Cimermančič P, Boehringer D, Sali A, Aebersold R, Ban N. Molecular architecture of the 40S⋅eIF1⋅eIF3 translation initiation complex. Cell 2015; 158:1123-1135. [PMID: 25171412 PMCID: PMC4151992 DOI: 10.1016/j.cell.2014.07.044] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 05/29/2014] [Accepted: 07/29/2014] [Indexed: 11/25/2022]
Abstract
Eukaryotic translation initiation requires the recruitment of the large, multiprotein eIF3 complex to the 40S ribosomal subunit. We present X-ray structures of all major components of the minimal, six-subunit Saccharomyces cerevisiae eIF3 core. These structures, together with electron microscopy reconstructions, cross-linking coupled to mass spectrometry, and integrative structure modeling, allowed us to position and orient all eIF3 components on the 40S⋅eIF1 complex, revealing an extended, modular arrangement of eIF3 subunits. Yeast eIF3 engages 40S in a clamp-like manner, fully encircling 40S to position key initiation factors on opposite ends of the mRNA channel, providing a platform for the recruitment, assembly, and regulation of the translation initiation machinery. The structures of eIF3 components reported here also have implications for understanding the architecture of the mammalian 43S preinitiation complex and the complex of eIF3, 40S, and the hepatitis C internal ribosomal entry site RNA. X-ray structures of major yeast eIF3 components and subcomplexes Crosslinking coupled to mass-spectrometry analysis of 40S⋅eIF1⋅eIF3 complex Integrative modeling reveals architecture of 40S⋅eIF1⋅eIF3 complex
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Affiliation(s)
- Jan P Erzberger
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zurich, Switzerland.
| | - Florian Stengel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland
| | - Riccardo Pellarin
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, UCSF MC 2552, Byers Hall Room 503B, 1700 4th Street, San Francisco, CA 94158-2330, USA
| | - Suyang Zhang
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Tanja Schaefer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Christopher H S Aylett
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Peter Cimermančič
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, UCSF MC 2552, Byers Hall Room 503B, 1700 4th Street, San Francisco, CA 94158-2330, USA
| | - Daniel Boehringer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, UCSF MC 2552, Byers Hall Room 503B, 1700 4th Street, San Francisco, CA 94158-2330, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, 8006 Zurich, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zurich, Switzerland.
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Abstract
Human cancer genomes harbour a variety of alterations leading to the deregulation of key pathways in tumour cells. The genomic characterization of tumours has uncovered numerous genes recurrently mutated, deleted or amplified, but gene fusions have not been characterized as extensively. Here we develop heuristics for reliably detecting gene fusion events in RNA-seq data and apply them to nearly 7,000 samples from The Cancer Genome Atlas. We thereby are able to discover several novel and recurrent fusions involving kinases. These findings have immediate clinical implications and expand the therapeutic options for cancer patients, as approved or exploratory drugs exist for many of these kinases. Kinases activated by gene fusions represent potentially important targets for the development of cancer drugs. Here, the authors develop a method for detecting gene fusion events in RNA sequencing data from The Cancer Genome Atlas and identify several novel recurrent fusions involving kinases.
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CRL4-like Clr4 complex in Schizosaccharomyces pombe depends on an exposed surface of Dos1 for heterochromatin silencing. Proc Natl Acad Sci U S A 2014; 111:1795-800. [PMID: 24449894 DOI: 10.1073/pnas.1313096111] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Repressive histone H3 lysine 9 methylation (H3K9me) and its recognition by HP1 proteins are necessary for pericentromeric heterochromatin formation. In Schizosaccharomyces pombe, H3K9me deposition depends on the RNAi pathway. Cryptic loci regulator 4 (Clr4), the only known H3K9 methyltransferase in this organism, is a subunit of the Clr4 methyltransferase complex (CLRC), whose composition is reminiscent of a CRL4 type cullin-RING ubiquitin ligase (CRL) including its cullin Cul4, the RING-box protein Pip1, the DNA damage binding protein 1 homolog Rik1, and the DCAF-like protein delocalization of Swi6 1 (Dos1). Dos2 and Stc1 have been proposed to be part of the complex but do not bear similarity to canonical ubiquitin ligase components. CLRC is an active E3 ligase in vitro, and this activity is necessary for heterochromatin assembly in vivo. The similarity between CLRC and the CRLs suggests that the WD repeat protein Dos1 will act to mediate target recognition and substrate specificity for CLRC. Here, we present a pairwise interaction screen that confirms a CRL4-like subunit arrangement and further identifies Dos2 as a central component of the complex and recruiter of Stc1. We determined the crystal structure of the Dos1 WD repeat domain, revealing an eight-bladed β-propeller fold. Functional mapping of the putative target-binding surface of Dos1 identifies key residues required for heterochromatic silencing, consistent with Dos1's role as the specificity factor for the E3 ubiquitin ligase.
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Janer A, Antonicka H, Lalonde E, Nishimura T, Sasarman F, Brown GK, Brown RM, Majewski J, Shoubridge EA. An RMND1 Mutation causes encephalopathy associated with multiple oxidative phosphorylation complex deficiencies and a mitochondrial translation defect. Am J Hum Genet 2012; 91:737-43. [PMID: 23022098 DOI: 10.1016/j.ajhg.2012.08.020] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 08/03/2012] [Accepted: 08/21/2012] [Indexed: 11/29/2022] Open
Abstract
Mutations in the genes composing the mitochondrial translation apparatus are an important cause of a heterogeneous group of oxidative phosphorylation (OXPHOS) disorders. We studied the index case in a consanguineous family in which two children presented with severe encephalopathy, lactic acidosis, and intractable seizures leading to an early fatal outcome. Blue native polyacrylamide gel electrophoretic (BN-PAGE) analysis showed assembly defects in all of the OXPHOS complexes with mtDNA-encoded structural subunits, and these defects were associated with a severe deficiency in mitochondrial translation. Immunoblot analysis showed reductions in the steady-state levels of several structural subunits of the mitochondrial ribosome. Whole-exome sequencing identified a homozygous missense mutation (c.1250G>A) in an uncharacterized gene, RMND1 (required for meiotic nuclear division 1). RMND1 localizes to mitochondria and behaves as an integral membrane protein. Retroviral expression of the wild-type RMND1 cDNA rescued the biochemical phenotype in subject cells, and siRNA-mediated knockdown of the protein recapitulated the defect. BN-PAGE, gel filtration, and mass spectrometry analyses showed that RMND1 forms a high-molecular-weight and most likely homopolymeric complex (∼240 kDa) that does not assemble in subject fibroblasts but that is rescued by expression of RMND1 cDNA. The p.Arg417Gln substitution, predicted to be in a coiled-coil domain, which is juxtaposed to a transmembrane domain at the extreme C terminus of the protein, does not alter the steady-state level of RMND1 but might prevent protein-protein interactions in this complex. Our results demonstrate that the RMND1 complex is necessary for mitochondrial translation, possibly by coordinating the assembly or maintenance of the mitochondrial ribosome.
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Affiliation(s)
- Alexandre Janer
- Department of Human Genetics, McGill University, 1205 Penfield Avenue, Montréal, QC H3A 1B1, Canada
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15
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Molecular cloning and characterization of the anti-obesity gene adipose in pig. Gene 2012; 509:110-9. [PMID: 23010425 DOI: 10.1016/j.gene.2012.07.087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 07/22/2012] [Accepted: 07/30/2012] [Indexed: 11/20/2022]
Abstract
Obesity has become an epidemic health problem characterized by aberrant energy metabolism. As the major player in energy homeostasis, adipose tissue has a decisive role in the development of obesity. Many genes involved in adipogenesis are also correlated with obesity. Adipose (Adp) has been established as an anti-obesity gene to repress adipogenesis and fat accumulation in mice, which inhibits the transcriptional activity of PPARγ by forming a chromatin remodeling complex with histones and HDAC3. Here, we reported the cloning and characterization of the pig Adp gene. Pig Adp cDNA had an ORF of 2034 nucleotides and was highly conserved among various species. Genomic sequence analysis indicated that pig Adp gene contains 16 exons and 15 introns, spanning more than 60kb on chromosome 6q21-24. The expression of pig Adp was high in testis, lung, kidney and adipose tissues, and relatively low in skeletal muscle. Bioinformatic analysis of 5'-flanking region of Adp has identified several potential binding sites for pivotal transcriptional factors related to both adipocyte differentiation and inflammation, highlighting the significance of Adp in energy metabolism. We have confirmed that KLF6, a positive regulator of adipogenesis, can enhance the promoter activity of Adp and up-regulate its mRNA expression. Taken together, our results would be helpful for further study of Adp regulation in the process of fat accumulation.
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16
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Wu XH, Wang Y, Zhuo Z, Jiang F, Wu YD. Identifying the hotspots on the top faces of WD40-repeat proteins from their primary sequences by β-bulges and DHSW tetrads. PLoS One 2012; 7:e43005. [PMID: 22916195 PMCID: PMC3419727 DOI: 10.1371/journal.pone.0043005] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 07/16/2012] [Indexed: 11/19/2022] Open
Abstract
The analysis of 36 available crystal structures of WD40 repeat proteins reveals widespread existence of a beta-bulge formed at the beginning of strand a and the end of strand b, termed as WDb–a bulge: among a total of 259 WD40 blades, there are 243 such β-bulges. The R1 positions in these WDb–a bulges have fair distributions of Arg, His, Ile, Leu, Lys, Met, Phe, Trp, Tyr and Val residues. These residues protrude on the top face of the WD40 proteins and can serve as hotspots for protein-protein interactions. An analysis of 29 protein complexes formed by 17 WD proteins reveals that these R1 residues, along with two other residues (R1-2 and D-1), are indeed widely involved in protein-protein interactions. Interestingly, these WDb–a bulges can be easily identified by the 4-amino acid sequences of (V, L, I), R1, R2, (V, L, I), along with some other significant amino acids. Thus, the hotspots of WD40 proteins on the top face can be readily predicted based on the primary sequences of the proteins. The literature-reported mutagenesis studies for Met30, MDV1, Tup11, COP1 and SPA1, which crystal structures are not available, can be readily understood based on the feature-based method. Applying the method, the twelve potential hotspots on the top face of Tup11 from S. japonicas have been identified. Our ITC measurements confirm seven of them, Tyr382, Arg284, Tyr426, Tyr508, Leu559, Lys575 and Ile601, are essential for recognizing Fep1. The ITC measurements further convinced that the feature-based method provides accurate prediction of hotspots on the top face.
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Affiliation(s)
- Xian-Hui Wu
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, People’s Republic of China
- * E-mail: (XHW); (YDW)
| | - Yang Wang
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, People’s Republic of China
| | - Zhu Zhuo
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, People’s Republic of China
| | - Fan Jiang
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, People’s Republic of China
| | - Yun-Dong Wu
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, People’s Republic of China
- College of Chemistry, Peking University, Beijing, People’s Republic of China
- * E-mail: (XHW); (YDW)
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17
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Lim YM, Hayashi S, Tsuda L. Ebi/AP-1 suppresses pro-apoptotic genes expression and permits long-term survival of Drosophila sensory neurons. PLoS One 2012; 7:e37028. [PMID: 22666340 PMCID: PMC3364243 DOI: 10.1371/journal.pone.0037028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 04/11/2012] [Indexed: 12/23/2022] Open
Abstract
Sensory organs are constantly exposed to physical and chemical stresses that collectively threaten the survival of sensory neurons. Failure to protect stressed neurons leads to age-related loss of neurons and sensory dysfunction in organs in which the supply of new sensory neurons is limited, such as the human auditory system. Transducin β-like protein 1 (TBL1) is a candidate gene for ocular albinism with late-onset sensorineural deafness, a form of X-linked age-related hearing loss. TBL1 encodes an evolutionarily conserved F-box–like and WD40 repeats–containing subunit of the nuclear receptor co-repressor/silencing mediator for retinoid and thyroid hormone receptor and other transcriptional co-repressor complexes. Here we report that a Drosophila homologue of TBL1, Ebi, is required for maintenance of photoreceptor neurons. Loss of ebi function caused late-onset neuronal apoptosis in the retina and increased sensitivity to oxidative stress. Ebi formed a complex with activator protein 1 (AP-1) and was required for repression of Drosophila pro-apoptotic and anti-apoptotic genes expression. These results suggest that Ebi/AP-1 suppresses basal transcription levels of apoptotic genes and thereby protects sensory neurons from degeneration.
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Affiliation(s)
- Young-Mi Lim
- Animal Models of Aging, National Center for Geriatrics and Gerontology, Gengo, Obu, Aichi, Japan
| | - Shigeo Hayashi
- Laboratory for Morphogenetic Signaling, RIKEN Center for Developmental Biology, Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo, Japan
- Department of Biology, Kobe University Graduate School of Science, Kobe, Hyogo, Japan
| | - Leo Tsuda
- Animal Models of Aging, National Center for Geriatrics and Gerontology, Gengo, Obu, Aichi, Japan
- * E-mail:
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18
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Watson PJ, Fairall L, Schwabe JW. Nuclear hormone receptor co-repressors: structure and function. Mol Cell Endocrinol 2012; 348:440-9. [PMID: 21925568 PMCID: PMC3315023 DOI: 10.1016/j.mce.2011.08.033] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 08/17/2011] [Accepted: 08/25/2011] [Indexed: 01/22/2023]
Abstract
Co-repressor proteins, such as SMRT and NCoR, mediate the repressive activity of unliganded nuclear receptors and other transcription factors. They appear to act as intrinsically disordered "hub proteins" that integrate the activities of a range of transcription factors with a number of histone modifying enzymes. Although these co-repressor proteins are challenging targets for structural studies due to their largely unstructured character, a number of structures have recently been determined of co-repressor interaction regions in complex with their interacting partners. These have yielded considerable insight into the mechanism of assembly of these complexes, the structural basis for the specificity of the interactions and also open opportunities for targeting these interactions therapeutically.
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19
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Causier B, Ashworth M, Guo W, Davies B. The TOPLESS interactome: a framework for gene repression in Arabidopsis. PLANT PHYSIOLOGY 2012; 158:423-38. [PMID: 22065421 PMCID: PMC3252085 DOI: 10.1104/pp.111.186999] [Citation(s) in RCA: 365] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 11/04/2011] [Indexed: 05/17/2023]
Abstract
Transcription factors activate or repress target gene expression or switch between activation and repression. In animals and yeast, Groucho/Tup1 corepressor proteins are recruited by diverse transcription factors to induce context-specific transcriptional repression. Two groups of Groucho/Tup1-like corepressors have been described in plants. LEUNIG and LEUNIG_HOMOLOG constitute one group and TOPLESS (TPL) and the four TPL-related (TPR) corepressors form the other. To discover the processes in which TPL and the TPR corepressors operate, high-throughput yeast two-hybrid approaches were used to identify interacting proteins. We found that TPL/TPR corepressors predominantly interact directly with specific transcription factors, many of which were previously implicated in transcriptional repression. The interacting transcription factors reveal that the TPL/TPR family has been coopted multiple times to modulate gene expression in diverse processes, including hormone signaling, stress responses, and the control of flowering time, for which we also show biological validation. The interaction data suggest novel mechanisms for the involvement of TPL/TPR corepressors in auxin and jasmonic acid signaling. A number of short repression domain (RD) sequences have previously been identified in Arabidopsis (Arabidopsis thaliana) transcription factors. All known RD sequences were enriched among the TPL/TPR interactors, and novel TPL-RD interactions were identified. We show that the presence of RD sequences is essential for TPL/TPR recruitment. These data provide a framework for TPL/TPR-dependent transcriptional repression. They allow for predictions about new repressive transcription factors, corepressor interactions, and repression mechanisms and identify a wide range of plant processes that utilize TPL/TPR-mediated gene repression.
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20
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Chen CKM, Chan NL, Wang AHJ. The many blades of the β-propeller proteins: conserved but versatile. Trends Biochem Sci 2011; 36:553-61. [PMID: 21924917 DOI: 10.1016/j.tibs.2011.07.004] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 07/14/2011] [Accepted: 07/18/2011] [Indexed: 11/20/2022]
Abstract
The β-propeller is a highly symmetrical structure with 4-10 repeats of a four-stranded antiparallel β-sheet motif. Although β-propeller proteins with different blade numbers all adopt disc-like shapes, they are involved in a diverse set of functions, and defects in this family of proteins have been associated with human diseases. However, it has remained ambiguous how variations in blade number could alter the function of β-propellers. In addition to the regularly arranged β-propeller topology, a recently discovered β-pinwheel propeller has been found. Here, we review the structural and functional diversity of β-propeller proteins, including β-pinwheels, as well as recent advances in the typical and atypical propeller structures.
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Affiliation(s)
- Cammy K-M Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
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21
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Oberoi J, Fairall L, Watson PJ, Yang JC, Czimmerer Z, Kampmann T, Goult BT, Greenwood JA, Gooch JT, Kallenberger BC, Nagy L, Neuhaus D, Schwabe JW. Structural basis for the assembly of the SMRT/NCoR core transcriptional repression machinery. Nat Struct Mol Biol 2011; 18:177-84. [PMID: 21240272 PMCID: PMC3232451 DOI: 10.1038/nsmb.1983] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2009] [Accepted: 11/08/2010] [Indexed: 11/08/2022]
Abstract
Eukaryotic transcriptional repressors function by recruiting large coregulatory complexes that target histone deacetylase enzymes to gene promoters and enhancers. Transcriptional repression complexes, assembled by the corepressor NCoR and its homolog SMRT, are crucial in many processes, including development and metabolic physiology. The core repression complex involves the recruitment of three proteins, HDAC3, GPS2 and TBL1, to a highly conserved repression domain within SMRT and NCoR. We have used structural and functional approaches to gain insight into the architecture and biological role of this complex. We report the crystal structure of the tetrameric oligomerization domain of TBL1, which interacts with both SMRT and GPS2, and the NMR structure of the interface complex between GPS2 and SMRT. These structures, together with computational docking, mutagenesis and functional assays, reveal the assembly mechanism and stoichiometry of the corepressor complex.
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Affiliation(s)
- Jasmeen Oberoi
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester. LE1 9HN
- MRC-Laboratory of Molecular Biology, Hills Road, Cambridge. CB2 0QH
| | - Louise Fairall
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester. LE1 9HN
| | - Peter J. Watson
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester. LE1 9HN
| | - Ji-Chun Yang
- MRC-Laboratory of Molecular Biology, Hills Road, Cambridge. CB2 0QH
| | - Zsolt Czimmerer
- Apoptosis and Genomics Research Group of the Hungarian Academy of Sciences, Department of Biochemistry and Molecular Biology, Life Sciences Building, Medical and Health Science Center, University of Debrecen, Debrecen, Egyetem ter 1. H-4032 Hungary
| | - Thorsten Kampmann
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester. LE1 9HN
| | - Benjamin T. Goult
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester. LE1 9HN
| | - Jacquie A. Greenwood
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester. LE1 9HN
| | - John T. Gooch
- MRC-Laboratory of Molecular Biology, Hills Road, Cambridge. CB2 0QH
| | | | - Laszlo Nagy
- Apoptosis and Genomics Research Group of the Hungarian Academy of Sciences, Department of Biochemistry and Molecular Biology, Life Sciences Building, Medical and Health Science Center, University of Debrecen, Debrecen, Egyetem ter 1. H-4032 Hungary
| | - David Neuhaus
- MRC-Laboratory of Molecular Biology, Hills Road, Cambridge. CB2 0QH
| | - John W.R. Schwabe
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester. LE1 9HN
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22
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Noinaj N, Fairman JW, Buchanan SK. The crystal structure of BamB suggests interactions with BamA and its role within the BAM complex. J Mol Biol 2011; 407:248-60. [PMID: 21277859 DOI: 10.1016/j.jmb.2011.01.042] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 01/14/2011] [Accepted: 01/17/2011] [Indexed: 01/17/2023]
Abstract
Escherichia coli BamB is the largest of four lipoproteins in the β-barrel assembly machinery (BAM) complex. It interacts with the periplasmic domain of BamA, an integral outer membrane protein (OMP) essential for OMP biogenesis. Although BamB is not essential, it serves an important function in the BAM complex, significantly increasing the folding efficiency of some OMPs in vivo and in vitro. To learn more about the BAM complex, we solved structures of BamB in three different crystal forms. BamB crystallized in space groups P2(1)3, I222, and P2(1)2(1)2(1), with one molecule per asymmetric unit in each case. Crystals from the space group I222 diffracted to 1. 65-Å resolution. BamB forms an eight-bladed β-propeller with a central pore and is shaped like a doughnut. A DALI search revealed that BamB shares structural homology to several eukaryotic proteins containing WD40 repeat domains, which commonly have β-propeller folds and often serve as scaffolding proteins within larger multi-protein complexes that carry out signal transduction, cell division, and chemotaxis. Using mutagenesis data from previous studies, we docked BamB onto a BamA structural model and assessed known and possible interactions between these two proteins. Our data suggest that BamB serves as a scaffolding protein within the BAM complex by optimally orienting the flexible periplasmic domain of BamA for interaction with other BAM components and chaperones. This may facilitate integration of newly synthesized OMPs into the outer membrane.
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Affiliation(s)
- Nicholas Noinaj
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-8030, USA
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23
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Kim KH, Paetzel M. Crystal structure of Escherichia coli BamB, a lipoprotein component of the β-barrel assembly machinery complex. J Mol Biol 2010; 406:667-78. [PMID: 21168416 DOI: 10.1016/j.jmb.2010.12.020] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 12/07/2010] [Accepted: 12/09/2010] [Indexed: 01/20/2023]
Abstract
In Gram-negative bacteria, the BAM (β-barrel assembly machinery) complex catalyzes the essential process of assembling outer membrane proteins. The BAM complex in Escherichia coli consists of five proteins: one β-barrel membrane protein, BamA, and four lipoproteins, BamB, BamC, BamD, and BamE. Despite their role in outer membrane protein biogenesis, there is currently a lack of functional and structural information on the lipoprotein components of the BAM complex. Here, we report the first crystal structure of BamB, the largest and most functionally characterized lipoprotein component of the BAM complex. The crystal structure shows that BamB has an eight-bladed β-propeller structure, with four β-strands making up each blade. Mapping onto the structure the residues previously shown to be important for BamA interaction reveals that these residues, despite being far apart in the amino acid sequence, are localized to form a continuous solvent-exposed surface on one side of the β-propeller. Found on the same side of the β-propeller is a cluster of residues conserved among BamB homologs. Interestingly, our structural comparison study suggests that other proteins with a BamB-like fold often participate in protein or ligand binding, and that the binding interface on these proteins is located on the surface that is topologically equivalent to where the conserved residues and the residues that are important for BamA interaction are found on BamB. Our structural and bioinformatic analyses, together with previous biochemical data, provide clues to where the BamA and possibly a substrate interaction interface may be located on BamB.
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Affiliation(s)
- Kelly H Kim
- Department of Molecular Biology and Biochemistry, Simon Fraser University, South Science Building, 8888 University Drive, Burnaby, British Columbia, Canada
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24
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Galland N, Michels PAM. Comparison of the peroxisomal matrix protein import system of different organisms. Exploration of possibilities for developing inhibitors of the import system of trypanosomatids for anti-parasite chemotherapy. Eur J Cell Biol 2010; 89:621-37. [PMID: 20435370 DOI: 10.1016/j.ejcb.2010.04.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Revised: 03/28/2010] [Accepted: 04/06/2010] [Indexed: 10/19/2022] Open
Abstract
In recent decades, research on peroxisome biogenesis has been particularly boosted since the role of these organelles in metabolism became unraveled. Indeed in plants, yeasts and fungi, peroxisomes play an important role in the adaptation of metabolism during developmental processes and/or altered environmental conditions. In mammals their importance is illustrated by the fact that several severe human inherited diseases have been identified as peroxisome biogenesis disorders (PBD). Particularly interesting are the glycosomes - peroxisome-like organelles in trypanosomatids where the major part of the glycolytic pathway is sequestered - because it was demonstrated that proper compartmentalization of matrix proteins inside glycosomes is essential for the parasite. Although the overall process of peroxisome biogenesis seems well conserved between species, careful study of the literature reveals nonetheless many differences at various steps. In this review, we present a comparison of the first two steps of peroxisome biogenesis - receptor loading and docking at the peroxisomal membrane - in yeasts, mammals, plants and trypanosomatids and highlight major differences in the import process between species despite the conservation of (some of) the proteins involved. Some of the unique features of the process as it occurs in trypanosomatids will be discussed with regard to the possibilities for exploiting them for the development of compounds that could specifically disturb interactions between trypanosomatid peroxins. This strategy could eventually lead to the discovery of drugs against the diseases caused by these parasites.
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Affiliation(s)
- Nathalie Galland
- Research Unit for Tropical Diseases, de Duve Institute, Brussels, Belgium
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25
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Wu XH, Chen RC, Gao Y, Wu YD. The effect of Asp-His-Ser/Thr-Trp tetrad on the thermostability of WD40-repeat proteins. Biochemistry 2010; 49:10237-45. [PMID: 20939513 DOI: 10.1021/bi101321y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We recently found that Asp-His-Ser/Thr-Trp hydrogen-bonded tetrads are widely and uniquely present in the WD40-repeat proteins. WDR5 protein is a seven WD40-repeat propeller with five such tetrads. To explore the effect of the tetrad on the structure and stability of WD40-repeat proteins, the wild-type WDR5 and its seven mutants involving the substitutions of tetrad residues have been isolated. The crystal structures of the wild-type WDR5 and its three WDR5 mutants have been determined by X-ray diffraction method. The mutations of the tetrad residues are found not to change the basic structural features. The denaturing profiles of the wild type and the seven mutants with the use of denaturant guanidine hydrochloride have been studied by circular dichroism spectroscopy to determine the folding free energies of these proteins. The folding free energies of the wild type and the S62A, S146A, S188A, D192E, W330F, W330Y, and D324E mutants are measured to be about -11.6, -2.7, -3.1, -2.9, -3.6, -7.1, -7.0, and -7.5 kcal/mol, respectively. These suggest that (1) the hydrogen bonds in these hydrogen bond networks are unusually strong; (2) each hydrogen-bonded tetrad provides over 12 kcal/mol stability to the protein; thus, the removal of any single tetrad would cause unfolding of the protein; (3) since there are five tetrads, the protein must be in a highly unstable state without the tetrads, which might be related to its biological functions.
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Affiliation(s)
- Xian-Hui Wu
- School of Chemical Biology and Biotechnology, Laboratory of Chemical Genomics, Shenzhen Graduate School of Peking University, Shenzhen 518055, China
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26
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Ding SL, Liu W, Iliuk A, Ribot C, Vallet J, Tao A, Wang Y, Lebrun MH, Xu JR. The tig1 histone deacetylase complex regulates infectious growth in the rice blast fungus Magnaporthe oryzae. THE PLANT CELL 2010; 22:2495-508. [PMID: 20675574 PMCID: PMC2929099 DOI: 10.1105/tpc.110.074302] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Magnaporthe oryzae is the most damaging fungal pathogen of rice (Oryza sativa). In this study, we characterized the TIG1 transducin beta-like gene required for infectious growth and its interacting genes that are required for plant infection in this model phytopathogenic fungus. Tig1 homologs in yeast and mammalian cells are part of a conserved histone deacetylase (HDAC) transcriptional corepressor complex. The tig1 deletion mutant was nonpathogenic and defective in conidiogenesis. It had an increased sensitivity to oxidative stress and failed to develop invasive hyphae in plant cells. Using affinity purification and coimmunoprecipitation assays, we identified several Tig1-associated proteins, including two HDACs that are homologous to components of the yeast Set3 complex. Functional analyses revealed that TIG1, SET3, SNT1, and HOS2 were core components of the Tig1 complex in M. oryzae. The set3, snt1, and hos2 deletion mutants displayed similar defects as those observed in the tig1 mutant, but deletion of HST1 or HOS4 had no detectable phenotypes. Deletion of any of these core components of the Tig1 complex resulted in a significant reduction in HDAC activities. Our results showed that TIG1, like its putative yeast and mammalian orthologs, is one component of a conserved HDAC complex that is required for infectious growth and conidiogenesis in M. oryzae and highlighted that chromatin modification is an essential regulatory mechanism during plant infection.
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Affiliation(s)
- Sheng-Li Ding
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Wende Liu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Anton Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Cecile Ribot
- Université Lyon-1, Centre National de la Recherche Scientifique, Bayer CropScience, 69263 Lyon Cedex 09, France
| | - Julie Vallet
- Université Lyon-1, Centre National de la Recherche Scientifique, Bayer CropScience, 69263 Lyon Cedex 09, France
| | - Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Yang Wang
- College of Plant Protection and Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Marc-Henri Lebrun
- Université Lyon-1, Centre National de la Recherche Scientifique, Bayer CropScience, 69263 Lyon Cedex 09, France
- Institut National de la Recherche Agronomique, 78850 Thiverval-Grignon, France
| | - Jin-Rong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
- College of Plant Protection and Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Address correspondence to
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27
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Mss11, a transcriptional activator, is required for hyphal development in Candida albicans. EUKARYOTIC CELL 2009; 8:1780-91. [PMID: 19734367 DOI: 10.1128/ec.00190-09] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Candida albicans undergoes a morphological transition from yeast to hyphae in response to a variety of stimuli and growth conditions. We previously isolated a LisH domain containing transcription factor Flo8, which is essential for hyphal development in C. albicans. To search the putative binding partner of Flo8 in C. albicans, we identified C. albicans Mss11, a functional homolog of Saccharomyces cerevisiae Mss11, which also contains a LisH motif at its N terminus. C. albicans Mss11 can interact with Flo8 via the LisH motif by in vivo coimmunoprecipitation. The results of a chromatin immunoprecipitation (ChIP) assay showed that more Mss11 and Flo8 proteins bound to the upstream activating sequence region of HWP1 promoter in hyphal cells than in yeast cells, and the increased binding of each of these two proteins responding to hyphal induction was dependent on the other. Overexpression of MSS11 enhanced filamentous growth. Deletion of MSS11 caused a profound defect in hyphal development and the induction of hypha-specific genes. Our data suggest that Mss11 functions as an activator in hyphal development of C. albicans. Furthermore, overexpression of FLO8 can bypass the requirement of Mss11 in filamentous formation, whereas overexpression of MSS11 failed to promote hyphae growth in flo8 mutants. In summary, we show that the expression level of MSS11 increases during hyphal induction, and the enhanced expression of MSS11 may contribute to cooperative binding of Mss11 and Flo8 to the HWP1 promoter.
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Ding S, Mehrabi R, Koten C, Kang Z, Wei Y, Seong K, Kistler HC, Xu JR. Transducin beta-like gene FTL1 is essential for pathogenesis in Fusarium graminearum. EUKARYOTIC CELL 2009; 8:867-76. [PMID: 19377037 PMCID: PMC2698311 DOI: 10.1128/ec.00048-09] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Accepted: 04/01/2009] [Indexed: 11/20/2022]
Abstract
Fusarium head blight caused by Fusarium graminearum is an important disease of wheat and barley. In a previous study, we identified several mutants with reduced virulence by insertional mutagenesis. A transducin beta-like gene named FTL1 was disrupted in one of these nonpathogenic mutants. FTL1 is homologous to Saccharomyces cerevisiae SIF2, which is a component of the Set3 complex involved in late stages of ascospore formation. The Delta ftl1 mutant was significantly reduced in conidiation and failed to cause typical disease symptoms. It failed to colonize the vascular tissues of rachis or cause necrosis on the rachis of inoculated wheat heads. The Delta ftl1 mutant also was defective in spreading from infected anthers to ovaries and more sensitive than the wild type to plant defensins MsDef1 and osmotin. However, the activation of two mitogen-activated protein kinases, Mgv1 and Gpmk1, production of deoxynivalenol, and expression of genes known to be important for plant infection in F. graminearum were not affected, indicating that the defect of the Delta ftl1 mutant in plant infection is unrelated to known virulence factors in this pathogen and may involve novel mechanisms. The Delta ftl1 deletion mutant was significantly reduced in histone deacetylation, and many members of the yeast Set3 complex are conserved in F. graminearum. FTL1 appears to be a component of this well-conserved protein complex that plays a critical role in the penetration and colonization of wheat tissues.
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Affiliation(s)
- Shengli Ding
- Department of Botany and Plant Pathology, 915 West State Street, Lilly Hall, Purdue University, West Lafayette, IN 47907, USA
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Phylogenetic, structural and functional relationships between WD- and Kelch-repeat proteins. Subcell Biochem 2008; 48:6-19. [PMID: 18925367 DOI: 10.1007/978-0-387-09595-0_2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The beta-propeller domain is a widespread protein organizational motif. Typically, beta-propeller proteins are encoded by repeated sequences where each repeat unit corresponds to a twisted beta-sheet structural motif; these beta-sheets are arranged in a circle around a central axis to generate the beta-propeller structure. Two superfamilies of beta-propeller proteins, the WD-repeat and Kelch-repeat families, exhibit similarities not only in structure, but, remarkably, also in the types of molecular functions they perform. While it is unlikely that WD and Kelch repeats evolved from a common ancestor, their evolution into diverse families of similar function may reflect the evolutionary advantages of the stable core beta-propeller fold. In this chapter, we examine the relationships between these two widespread protein families, emphasizing recently published work relating to the structure and function of both Kelch and WD-repeat proteins.
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Abstract
The WD-repeat-containing proteins form a very large family that is diverse in both its function and domain structure. Within all these proteins the WD-repeat domains are thought to have two common features: the domain folds into a beta propeller; and the domains form a platform without any catalytic activity on which multiple protein complexes assemble reversibly. The fact that these proteins play such key roles in the formation of protein-protein complexes in nearly all the major pathways and organelles unique to eukaryotic cells has two important implications. It supports both their ancient and proto eukaryotic origins and supports a likely association with many genetic diseases.
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Affiliation(s)
- Temple F Smith
- BioMolecular Engineering Research Center, College of Engineering, Boston University, 36 Cummington Street, Boston, MA 02215, USA.
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Liu Z, Karmarkar V. Groucho/Tup1 family co-repressors in plant development. TRENDS IN PLANT SCIENCE 2008; 13:137-44. [PMID: 18314376 DOI: 10.1016/j.tplants.2007.12.005] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Revised: 12/05/2007] [Accepted: 12/14/2007] [Indexed: 05/23/2023]
Abstract
Transcription repression is emerging as a key regulatory mechanism underlying cell fate specification and body patterning in both animals and plants. In animals and fungi, the Groucho (Gro)/Tup1 family co-repressors generate the repressed chromatin state in genetic loci that control major developmental decisions ranging from dorsal-ventral patterning to eye development. In higher plants, information about the Gro/Tup1 co-repressors is beginning to emerge. Several recent publications have revealed both conserved and unique structural and mechanistic features of plant Gro/Tup1 co-repressors, including LEUNIG (LUG), TOPLESS (TPL) and WUSCHEL-INTERACTING PROTEINS (WSIPs). These co-repressors regulate key developmental processes in floral organ identity specification, embryo apical-basal fate determination, and stem cell maintenance at the shoot apex.
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Affiliation(s)
- Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
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Choi HK, Choi KC, Kang HB, Kim HC, Lee YH, Haam S, Park HG, Yoon HG. Function of multiple Lis-Homology domain/WD-40 repeat-containing proteins in feed-forward transcriptional repression by silencing mediator for retinoic and thyroid receptor/nuclear receptor corepressor complexes. Mol Endocrinol 2008; 22:1093-104. [PMID: 18202150 DOI: 10.1210/me.2007-0396] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Lis-homology (LisH) motifs are involved in protein dimerization, and the discovery of the conserved N-terminal LisH domain in transducin beta-like protein 1 and its receptor (TBL1 and TBLR1) led us to examine the role of this domain in transcriptional repression. Here we show that multiple beta-transducin (WD-40) repeat-containing proteins interact to form oligomers in solution and that oligomerization depends on the presence of the LisH domain in each protein. Repression of transcription, as assayed using Gal4 fusion proteins, also depended on the presence of the LisH domain, suggesting that oligomerization is a prerequisite for efficient transcriptional repression. Furthermore, we show that the LisH domain is responsible for the binding to the hypoacetylated histone H4 tail and for stable chromatin targeting by the nuclear receptor corepressor complex. Mutations in conserved residues in the LisH motif of TBL1 and TBLR1 block histone binding, oligomerization, and transcriptional repression, supporting the functional importance of the LisH motif in transcriptional repression. Our results indicate that another WD-40 protein, TBL3, also preferentially binds to the N-terminal domain of TBL1 and TBLR1, and forms oligomers with other WD-40 proteins. Finally, we observed that the WD-40 proteins RbAp46 and RbAp48 of the sin3A corepressor complex failed to dimerize. We also found the specific interaction UbcH/E2 with TBL1, but not RbAp46/48. Altogether, our results thus indicate that the presence of multiple LisH/WD-40 repeat containing proteins is exclusive to nuclear receptor corepressor/ silencing mediator for retinoic and thyroid receptor complexes compared with other class 1 histone deacetylase-containing corepessor complexes.
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Affiliation(s)
- Hyo-Kyoung Choi
- Department of Biochemistry and Molecular Biology, Center for Chronic Metabolic Disease Research, Yonsei University College of Medicine, Seoul 120-752, South Korea
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Suh JM, Zeve D, McKay R, Seo J, Salo Z, Li R, Wang M, Graff JM. Adipose is a conserved dosage-sensitive antiobesity gene. Cell Metab 2007; 6:195-207. [PMID: 17767906 PMCID: PMC2587167 DOI: 10.1016/j.cmet.2007.08.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2007] [Revised: 05/30/2007] [Accepted: 08/06/2007] [Indexed: 01/04/2023]
Abstract
Adipose (Adp) is an evolutionarily conserved gene isolated from naturally occurring obese flies homozygous for an adp mutation. Here we show that the anti-obesity function of Adp (worm Y73E7A.9, fly adp, and murine Wdtc1) is conserved from worms to mammals. Further, Adp appears to inhibit fat formation in a dosage-sensitive manner. Adp heterozygous flies and Adp heterozygous mutant mice are obese and insulin resistant, as are mice that express a dominant negative form of Adp in fat cells. Conversely, fat-restricted Adp transgenic mice are lean and display improved metabolic profiles. A transient transgenic increase in Adp activity in adult fly fat tissues reduces fat accumulation, indicating therapeutic potential. ADP may elicit these anti-adipogenic functions by regulating chromatin dynamics and gene transcription, as it binds both histones and HDAC3 and inhibits PPARgamma activity. Thus Adp appears to be involved in an ancient pathway that regulates fat accumulation.
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Affiliation(s)
- Jae Myoung Suh
- Department of Developmental Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, NB5.118, Dallas, TX 75390-9133, USA
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Napetschnig J, Blobel G, Hoelz A. Crystal structure of the N-terminal domain of the human protooncogene Nup214/CAN. Proc Natl Acad Sci U S A 2007; 104:1783-8. [PMID: 17264208 PMCID: PMC1794303 DOI: 10.1073/pnas.0610828104] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Indexed: 12/31/2022] Open
Abstract
The mammalian nuclear pore complex (NPC) is an approximately 120-MDa proteinaceous assembly consisting of approximately 30 proteins and is the sole gate in the nuclear envelope. The human protooncogene Nup214 was first identified as a target for chromosomal translocation involved in leukemogenesis. Nup214 is located on the cytoplasmic face of the NPC and is implicated in anchoring the cytoplasmic filaments of the NPC and recruiting the RNA helicase Ddx19. Here, we present the crystal structure of the human Nup214 N-terminal domain at 1.65-A resolution. The structure reveals a seven-bladed beta-propeller followed by a 30-residue C-terminal extended peptide segment, which folds back onto the beta-propeller and binds to its bottom face. The beta-propeller repeats lack any recognizable sequence motif and are distinguished by extensive insertions between the canonical beta-strands. We propose a mechanism by which the C-terminal peptide extension is involved in NPC assembly.
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Affiliation(s)
- Johanna Napetschnig
- Laboratory of Cell Biology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021
| | - Günter Blobel
- Laboratory of Cell Biology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021
| | - André Hoelz
- Laboratory of Cell Biology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021
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Galland N, Demeure F, Hannaert V, Verplaetse E, Vertommen D, Van der Smissen P, Courtoy PJ, Michels PAM. Characterization of the role of the receptors PEX5 and PEX7 in the import of proteins into glycosomes of Trypanosoma brucei. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2007; 1773:521-35. [PMID: 17320990 DOI: 10.1016/j.bbamcr.2007.01.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2006] [Revised: 12/20/2006] [Accepted: 01/11/2007] [Indexed: 10/23/2022]
Abstract
Peroxins 5 and 7 are receptors for protein import into the peroxisomal matrix. We studied the involvement of these peroxins in the biogenesis of glycosomes in the protozoan parasite Trypanosoma brucei. Glycosomes are peroxisome-like organelles in which a major part of the glycolytic pathway is sequestered. We here report the characterization of the T. brucei homologue of PEX7 and provide several data strongly suggesting that it can bind to PEX5. Depletion of PEX5 or PEX7 by RNA interference had a severe effect on the growth of both the bloodstream-form of the parasite, that relies entirely on glycolysis for its ATP supply, and the procyclic form representative of the parasite living in the tsetse-fly midgut and in which also other metabolic pathways play a prominent role. The role of the two receptors in import of glycosomal matrix proteins with different types of peroxisome/glycosome-targeting signals (PTS) was analyzed by immunofluorescence and subcellular fractionation studies. Knocking down the expression of either receptor gene resulted, in procyclic cells, in the mislocalization of proteins with both a type 1 or 2 targeting motif (PTS1, PTS2) located at the C- and N-termini, respectively, and proteins with a sequence-internal signal (I-PTS) to the cytosol. Electron microscopy confirmed the apparent integrity of glycosomes in these procyclic cells. In bloodstream-form trypanosomes, PEX7 depletion seemed to affect only the subcellular distribution of PTS2-proteins. Western blot analysis suggested that, in both life-cycle stages of the trypanosome, the levels of both receptors are controlled in a coordinated fashion, by a mechanism that remains to be determined. The observation that both PEX5 and PEX7 are essential for the viability of the parasite indicates that the respective branches of the glycosome-import pathway in which each receptor acts might be interesting drug targets.
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Affiliation(s)
- Nathalie Galland
- Research Unit for Tropical Diseases, Christian de Duve Institute of Cellular Pathology and Laboratory of Biochemistry, Université catholique de Louvain, Brussels, Belgium
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Sridhar VV, Surendrarao A, Liu Z. APETALA1 and SEPALLATA3 interact with SEUSS to mediate transcription repression during flower development. Development 2006; 133:3159-66. [PMID: 16854969 DOI: 10.1242/dev.02498] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The transcriptional repression of key regulatory genes is crucial for plant and animal development. Previously, we identified and isolated two Arabidopsis transcription co-repressors LEUNIG(LUG) and SEUSS (SEU) that function together in a putative co-repressor complex to prevent ectopic AGAMOUS(AG) transcription in flowers. Because neither LUG nor SEU possesses a recognizable DNA-binding motif, how they are tethered to specific target promoters remains unknown. Using the yeast two-hybrid assay and a co-immunoprecipitation assay, we showed that APETALA1 (AP1)and SEPALLATA3 (SEP3), both MADS box DNA-binding proteins,interacted with SEU. The AP1-SEU protein-protein interaction was supported by synergistic genetic interactions between ap1 and seu mutations. The role of SEU proteins in bridging the interaction between AP1/SEP3 and LUG to repress target gene transcription was further demonstrated in yeast and plant cells, providing important mechanistic insights into co-repressor function in plants. Furthermore, a direct in vivo association of SEU proteins with the AG cis-regulatory element was shown by chromatin immunoprecipitation. Accordingly, a reporter gene driven by the AG cis-element was able to respond to AP1- and SEP3-mediated transcriptional repression in a transient plant cell system when supplied with SEU and LUG. These results suggest that AP1and SEP3 may serve as the DNA-binding partners of SEU/LUG. Our demonstration of the direct physical interaction between SEU and the C-terminal domain of SEP3 and AP1 suggests that AP1 and SEP3 MADS box proteins may interact with positive, as well as negative, regulatory proteins via their C-terminal domains, to either stimulate or repress their regulatory targets.
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Affiliation(s)
- Vaniyambadi V Sridhar
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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Zhang XM, Chang Q, Zeng L, Gu J, Brown S, Basch RS. TBLR1 regulates the expression of nuclear hormone receptor co-repressors. BMC Cell Biol 2006; 7:31. [PMID: 16893456 PMCID: PMC1555579 DOI: 10.1186/1471-2121-7-31] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2005] [Accepted: 08/07/2006] [Indexed: 12/02/2022] Open
Abstract
Background Transcription is regulated by a complex interaction of activators and repressors. The effectors of repression are large multimeric complexes which contain both the repressor proteins that bind to transcription factors and a number of co-repressors that actually mediate transcriptional silencing either by inhibiting the basal transcription machinery or by recruiting chromatin-modifying enzymes. Results TBLR1 [GenBank: NM024665] is a co-repressor of nuclear hormone transcription factors. A single highly conserved gene encodes a small family of protein molecules. Different isoforms are produced by differential exon utilization. Although the ORF of the predominant form contains only 1545 bp, the human gene occupies ~200 kb of genomic DNA on chromosome 3q and contains 16 exons. The genomic sequence overlaps with the putative DC42 [GenBank: NM030921] locus. The murine homologue is structurally similar and is also located on Chromosome 3. TBLR1 is closely related (79% homology at the mRNA level) to TBL1X and TBL1Y, which are located on Chromosomes X and Y. The expression of TBLR1 overlaps but is distinct from that of TBL1. An alternatively spliced form of TBLR1 has been demonstrated in human material and it too has an unique pattern of expression. TBLR1 and the homologous genes interact with proteins that regulate the nuclear hormone receptor family of transcription factors. In resting cells TBLR1 is primarily cytoplasmic but after perturbation the protein translocates to the nucleus. TBLR1 co-precipitates with SMRT, a co-repressor of nuclear hormone receptors, and co-precipitates in complexes immunoprecipitated by antiserum to HDAC3. Cells engineered to over express either TBLR1 or N- and C-terminal deletion variants, have elevated levels of endogenous N-CoR. Co-transfection of TBLR1 and SMRT results in increased expression of SMRT. This co-repressor undergoes ubiquitin-mediated degradation and we suggest that the stabilization of the co-repressors by TBLR1 occurs because of a novel mechanism that protects them from degradation. Transient over expression of TBLR1 produces growth arrest. Conclusion TBLR1 is a multifunctional co-repressor of transcription. The structure of this family of molecules is highly conserved and closely related co-repressors have been found in all eukaryotic organisms. Regulation of co-repressor expression and the consequent alterations in transcriptional silencing play an important role in the regulation of differentiation.
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Affiliation(s)
- Xin-Min Zhang
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Qing Chang
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Lin Zeng
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Judy Gu
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Stuart Brown
- Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
| | - Ross S Basch
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
- NYU Cancer Institute, New York University Medical Center, New York, NY 10016, USA
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Nikkhah M, Jawad-Alami Z, Demydchuk M, Ribbons D, Paoli M. Engineering of beta-propeller protein scaffolds by multiple gene duplication and fusion of an idealized WD repeat. ACTA ACUST UNITED AC 2006; 23:185-94. [PMID: 16651025 DOI: 10.1016/j.bioeng.2006.02.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2005] [Revised: 01/10/2006] [Accepted: 01/16/2006] [Indexed: 10/24/2022]
Abstract
The ability to design specific amino acid sequences that fold into desired structures is central to engineering novel proteins. Protein design is also a good method to assess our understanding of sequence-structure and structure-function relationships. While beta-sheet structures are important elements of protein architecture, it has traditionally been more difficult to design beta-proteins than alpha-helical proteins. Taking advantage of the tandem repeated sequences that form the structural building blocks in a group of beta-propeller proteins; we have used a consensus design approach to engineer modular and relatively large scaffolds. An idealized WD repeat was designed from a structure-based sequence alignment with a set of structural guidelines. Using a plasmid sequential ligation strategy, artificial concatemeric genes with up to 10 copies of this idealized repeat were then constructed. Corresponding proteins with 4 through to 10 WD repeats were soluble when over-expressed in Escherichia coli. Notably, they were sufficiently stable in vivo surviving attack from endogenous proteases, and maintained a homogeneous, non-aggregated form in vitro. The results show that the beta-propeller scaffold is an attractive platform for future engineering work, particularly in experiments in which directed evolution techniques might improve the stability of the molecules and/or tailor them for a specific function.
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Affiliation(s)
- Maryam Nikkhah
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, England, UK
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Appleton BA, Wu P, Wiesmann C. The crystal structure of murine coronin-1: a regulator of actin cytoskeletal dynamics in lymphocytes. Structure 2006; 14:87-96. [PMID: 16407068 DOI: 10.1016/j.str.2005.09.013] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Revised: 08/19/2005] [Accepted: 09/18/2005] [Indexed: 12/16/2022]
Abstract
Mammalian coronin-1 is preferentially expressed in hematopoietic cells and plays a poorly understood role in the dynamic reorganization of the actin cytoskeleton. Sequence analysis of coronin-1 revealed five WD40 repeats that were predicted to form a beta propeller. They are followed by a 130 residue extension and a 30 residue leucine zipper domain that is responsible for multimerization of the protein. Here, we present the crystal structure of murine coronin-1 without the leucine zipper at 1.75 A resolution. Coronin-1 forms a seven-bladed beta propeller composed of the five predicted WD40 repeats and two additional blades that lack any homology to the canonical WD40 motif. The C-terminal extension adopts an extended conformation, packs tightly against the bottom surface of the propeller, and is likely to be required for the structural stability of the propeller. Analysis of charged and conserved surface residues delineate possible binding sites for F-actin on the beta propeller.
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Affiliation(s)
- Brent A Appleton
- Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080, USA
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Kieffer M, Stern Y, Cook H, Clerici E, Maulbetsch C, Laux T, Davies B. Analysis of the transcription factor WUSCHEL and its functional homologue in Antirrhinum reveals a potential mechanism for their roles in meristem maintenance. THE PLANT CELL 2006; 18:560-73. [PMID: 16461579 PMCID: PMC1383633 DOI: 10.1105/tpc.105.039107] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
One of the most significant features of plant development is the way in which it can be elaborated and modulated throughout the life of the plant, an ability that is conferred by meristems. The Arabidopsis thaliana WUSCHEL gene (WUS), which encodes a homeodomain transcription factor, is required to maintain the stem cells in the shoot apical meristem in an undifferentiated state. The mechanism by which WUS prevents the differentiation of stem cells is unknown. We have characterized a meristem maintenance mutant in Antirrhinum majus and shown that it arises from a defect in the WUS orthologue ROSULATA (ROA). Detailed characterization of a semidominant roa allele revealed an essential role for the conserved C-terminal domain. Expression of either ROA or WUS lacking this domain causes a failure of meristem maintenance. The conserved domain mediates an interaction between WUS and two members of a small family of corepressor-like proteins in Arabidopsis. Our results suggest that WUS functions by recruiting transcriptional corepressors to repress target genes that promote differentiation, thereby ensuring stem cell maintenance.
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Affiliation(s)
- Martin Kieffer
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
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