151
|
Routsias JG, Tzioufas AG, Moutsopoulos HM. The clinical value of intracellular autoantigens B-cell epitopes in systemic rheumatic diseases. Clin Chim Acta 2004; 340:1-25. [PMID: 14734193 DOI: 10.1016/j.cccn.2003.10.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A hallmark of autoimmune diseases is the production of autoantibodies against intracellular autoantigens. Although their pathogenetic and their etiologic relationship are not fully understood, these autoantibodies are important tools for establishing the diagnosis, classification and prognosis of autoimmune diseases. Systemic rheumatic diseases are among the most complex disorders because their clinical presentation and constellation of findings are in part reflected by the wide spectrum of autoantibodies found in the sera of patients suffering from these disorders. These autoantibodies usually target large complexes consisting of protein antigens noncovalently associated with (ribo)-nucleic acid(s), like the spliceosome or Ro/La-RNPs. In this review, we first address the main characteristics and the clinical value of several autoantibodies, with respect to their diagnostic sensitivity and specificity. Subsequently, we provide a brief overview of the antigenic determinant types that have been identified on the corresponding autoantigens. The antibody targets of autontigens include primary, secondary, tertiary and quarternary structure epitopes, as well as cryptotopes, neoepitopes and mimotopes. We next focus on antigenic structures corresponding to B-cell epitopes with high disease specificity and sensitivity for all the major autoantigens in systemic autoimmunity including the Ro/La and U1 ribonucleoprotein complexes and the Ku70/80, ribosomal P, DNA topoisomerase I, filaggrin, Jo-1 and PM/SCl-100 autoantigens. These epitopes, defined at the peptide level, can be chemically synthesized and engineered for the development of new inexpensive and easier to perform assays and the improvement of the methods for autoantibody detection. Specific examples of newly developed assays that incorporate (i) epitopes with high disease specificity and sensitivity, (ii) modified epitopes, (iii) conformational epitopes and (iv) complementary epitopes are discussed in detail. Finally, we examine the potential of combining these synthetic epitopes for future development of multiplex diagnostic tests based on miniaturized autoantigen arrays.
Collapse
Affiliation(s)
- John G Routsias
- Department of Pathophysiology, School of Medicine, University of Athens, 75, M Asias St., 11527 Athens, Greece
| | | | | |
Collapse
|
152
|
Zeiner GM, Foldynová S, Sturm NR, Lukes J, Campbell DA. SmD1 is required for spliced leader RNA biogenesis. EUKARYOTIC CELL 2004; 3:241-4. [PMID: 14871954 PMCID: PMC329508 DOI: 10.1128/ec.3.1.241-244.2004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2003] [Accepted: 12/10/2003] [Indexed: 11/20/2022]
Abstract
The Sm-binding site of the kinetoplastid spliced leader RNA has been implicated in accurate spliced leader RNA maturation and trans-splicing competence. In Trypanosoma brucei, RNA interference-mediated knockdown of SmD1 caused defects in spliced leader RNA maturation, displaying aberrant 3'-end formation, partial formation of cap 4, and overaccumulation in the cytoplasm; U28 pseudouridylation was unaffected.
Collapse
Affiliation(s)
- Gusti M Zeiner
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095-1489, USA
| | | | | | | | | |
Collapse
|
153
|
Nicholson WV, Malladi R. Correlation-based methods of automatic particle detection in electron microscopy images with smoothing by anisotropic diffusion. J Microsc 2004; 213:119-28. [PMID: 14731293 DOI: 10.1111/j.1365-2818.2004.01286.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two methods of correlation-based automatic particle detection in electron microscopy images are compared - computing a cross-correlation function or a local correlation coefficient vs. azimuthally averaged reference projections (either from a model or from experimental particle images). The ability of smoothing images by anisotropic diffusion to improve the performance of particle detection is also considered. Anisotropic diffusion is an effective method of preprocessing that enhances the edges and overall shape of particles while reducing noise. It is found that anisotropic diffusion improves particle detection by a local correlation coefficient when projections from a high-resolution reconstruction are used as references. When references from experimental particle images are used, a cross-correlation function shows a more marked improvement in particle detection in images smoothed by anisotropic diffusion.
Collapse
Affiliation(s)
- W V Nicholson
- School of Biomedical Sciences, University of Leeds, Worsley Building, Leeds LS2 9JT, UK.
| | | |
Collapse
|
154
|
Greidinger EL, Foecking MF, Magee J, Wilson L, Ranatunga S, Ortmann RA, Hoffman RW. A Major B Cell Epitope Present on the Apoptotic but Not the Intact Form of the U1-70-kDa Ribonucleoprotein Autoantigen. THE JOURNAL OF IMMUNOLOGY 2003; 172:709-16. [PMID: 14688384 DOI: 10.4049/jimmunol.172.1.709] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Apoptotically modified forms of autoantigens have been hypothesized to participate in lupus immunopathogenesis. This study identifies a major B cell epitope present on the apoptotic but not the intact form of the U1-70-kDa ribonucleoprotein lupus autoantigen (70k). Human autoimmune sera with strong recognition of apoptotic 70k and minimal recognition of intact 70k were identified and tested for reactivity to truncated forms of 70k by immunoblot and ELISA. Patient sera that preferentially recognized apoptotic 70k were specific for an epitope dependent on residues 180-205 of the protein. This epitope was also recognized by 19 of 28 (68%) intact anti-70k-positive autoimmune human sera with Abs also recognizing apoptotic but not the intact form 70k, but only 1 of 9 (11%) intact 70k-positive sera without such Abs (Fisher's exact, p = 0.0055). Immunization of HLA-DR4-transgenic C57BL/6 mice with a peptide containing this epitope induced anti-70k immunity in 13 of 15 mice, including Abs recognizing apoptotic but not intact forms of autoantigens in 12 of 15 mice. Anti-70k responder mice also developed spreading of immunity to epitopes on the endogenous form of 70k, and proliferative lung lesions consistent with those described in patients with anti-70k autoimmunity. Thus, a major epitope in the B cell response to U1-70 kDa localizes to the RNA binding domain of the molecule, overlaps with the most common T cell epitope in the anti-70k response, and is not present on the intact form of the 70k molecule. Immunization of mice against this epitope induces an immune response with features seen in human anti-70k autoimmune disease.
Collapse
MESH Headings
- Animals
- Apoptosis/genetics
- Apoptosis/immunology
- Autoantibodies/biosynthesis
- Autoantibodies/blood
- Autoantigens/administration & dosage
- Autoantigens/genetics
- Autoantigens/immunology
- Autoantigens/metabolism
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- Epitope Mapping
- Epitopes, B-Lymphocyte/administration & dosage
- Epitopes, B-Lymphocyte/genetics
- Epitopes, B-Lymphocyte/immunology
- Epitopes, B-Lymphocyte/metabolism
- Humans
- Immune Sera/metabolism
- Jurkat Cells
- Lupus Erythematosus, Cutaneous/immunology
- Lupus Erythematosus, Cutaneous/pathology
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Transgenic
- Protein Structure, Tertiary
- RNA-Binding Proteins/administration & dosage
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/immunology
- Ribonucleoprotein, U1 Small Nuclear/administration & dosage
- Ribonucleoprotein, U1 Small Nuclear/genetics
- Ribonucleoprotein, U1 Small Nuclear/immunology
- Ribonucleoprotein, U1 Small Nuclear/metabolism
- Vaccination
Collapse
Affiliation(s)
- Eric L Greidinger
- Division of Rheumatology, University of Miami, Miami, FL 33136, USA.
| | | | | | | | | | | | | |
Collapse
|
155
|
Rivera-Calzada A, Robertson D, MacFadyen JR, Boskovic J, Isacke CM, Llorca O. Three-dimensional interplay among the ligand-binding domains of the urokinase-plasminogen-activator-receptor-associated protein, Endo180. EMBO Rep 2003; 4:807-12. [PMID: 12856000 PMCID: PMC1326338 DOI: 10.1038/sj.embor.embor898] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2003] [Revised: 06/10/2003] [Accepted: 06/11/2003] [Indexed: 11/09/2022] Open
Abstract
Endo180, also known as the urokinase plasminogen activator receptor (uPAR)-associated protein (uPARAP), is one of the four members of the mannose receptor family, and is implicated in extracellular-matrix remodelling through its interactions with collagens, sugars and uPAR. The extracellular portion of Endo180 contains an amino-terminal cysteine-rich domain, a single fibronectin type II domain and eight C-type lectin-like domains. We have purified a soluble version of Endo180 and analysed it by single-particle electron microscopy to obtain a three-dimensional structure of the N-terminal part of the protein at a resolution of 17 A and reveal, for the first time, the interactions between non-adjacent domains in the mannose receptor family. We show that for Endo180, the cysteine-rich domain contacts the second C-type lectin-like domain, thus providing structural insight into how modulation of its several ligand interactions may regulate Endo180 receptor function.
Collapse
MESH Headings
- Animals
- COS Cells
- Crystallography, X-Ray
- Humans
- Image Processing, Computer-Assisted
- Kinetics
- Lectins, C-Type/chemistry
- Ligands
- Mannose Receptor
- Mannose-Binding Lectins/chemistry
- Membrane Glycoproteins/chemistry
- Membrane Glycoproteins/isolation & purification
- Membrane Glycoproteins/metabolism
- Microscopy, Electron
- Models, Molecular
- Protein Binding
- Protein Conformation
- Protein Structure, Tertiary
- Receptors, Cell Surface/chemistry
- Receptors, Mitogen/chemistry
- Receptors, Mitogen/isolation & purification
- Receptors, Mitogen/metabolism
- Receptors, Urokinase Plasminogen Activator
Collapse
Affiliation(s)
- Angel Rivera-Calzada
- Centro de Investigaciones Biológicas, Consejo
Superior de Investigaciones Científicas, Ramiro de Maeztu 9, Campus Universidad
Complutense, 28040 Madrid, Spain
| | - David Robertson
- The Breakthrough Toby Robins Breast Cancer
Research Centre, Institute of Cancer Research, Chester Beatty
Laboratories, 237 Fulham Road, London
SW3 6JB, UK
| | - John R. MacFadyen
- The Breakthrough Toby Robins Breast Cancer
Research Centre, Institute of Cancer Research, Chester Beatty
Laboratories, 237 Fulham Road, London
SW3 6JB, UK
| | - Jasminka Boskovic
- Centro de Investigaciones Biológicas, Consejo
Superior de Investigaciones Científicas, Ramiro de Maeztu 9, Campus Universidad
Complutense, 28040 Madrid, Spain
| | - Clare M. Isacke
- The Breakthrough Toby Robins Breast Cancer
Research Centre, Institute of Cancer Research, Chester Beatty
Laboratories, 237 Fulham Road, London
SW3 6JB, UK
| | - Oscar Llorca
- Centro de Investigaciones Biológicas, Consejo
Superior de Investigaciones Científicas, Ramiro de Maeztu 9, Campus Universidad
Complutense, 28040 Madrid, Spain
| |
Collapse
|
156
|
Sauter C, Basquin J, Suck D. Sm-like proteins in Eubacteria: the crystal structure of the Hfq protein from Escherichia coli. Nucleic Acids Res 2003; 31:4091-8. [PMID: 12853626 PMCID: PMC167641 DOI: 10.1093/nar/gkg480] [Citation(s) in RCA: 164] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Hfq protein was discovered in Escherichia coli in the early seventies as a host factor for the Qbeta phage RNA replication. During the last decade, it was shown to be involved in many RNA processing events and remote sequence homology indicated a link to spliceosomal Sm proteins. We report the crystal structure of the E.coli Hfq protein showing that its monomer displays a characteristic Sm-fold and forms a homo-hexamer, in agreement with former biochemical data. Overall, the structure of the E.coli Hfq ring is similar to the one recently described for Staphylococcus aureus. This confirms that bacteria contain a hexameric Sm-like protein which is likely to be an ancient and less specialized form characterized by a relaxed RNA binding specificity. In addition, we identified an Hfq ortholog in the archaeon Methanococcus jannaschii which lacks a classical Sm/Lsm gene. Finally, a detailed structural comparison shows that the Sm-fold is remarkably well conserved in bacteria, Archaea and Eukarya, and represents a universal and modular building unit for oligomeric RNA binding proteins.
Collapse
Affiliation(s)
- Claude Sauter
- European Molecular Biology Laboratory, Structural and Computational Biology Programme, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | | | | |
Collapse
|
157
|
Sander B, Golas MM, Stark H. Automatic CTF correction for single particles based upon multivariate statistical analysis of individual power spectra. J Struct Biol 2003; 142:392-401. [PMID: 12781666 DOI: 10.1016/s1047-8477(03)00072-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Three-dimensional electron cryomicroscopy of randomly oriented single particles is a method that is suitable for the determination of three-dimensional structures of macromolecular complexes at molecular resolution. However, the electron-microscopical projection images are modulated by a contrast transfer function (CTF) that prevents the calculation of three-dimensional reconstructions of biological complexes at high resolution from uncorrected images. We describe here an automated method for the accurate determination and correction of the CTF parameters defocus, twofold astigmatism and amplitude-contrast proportion from single-particle images. At the same time, the method allows the frequency-dependent signal decrease (B factor) and the non-convoluted background signal to be estimated. The method involves the classification of the power spectra of single-particle images into groups with similar CTF parameters; this is done by multivariate statistical analysis (MSA) and hierarchically ascending classification (HAC). Averaging over several power spectra generates class averages with enhanced signal-to-noise ratios. The correct CTF parameters can be deduced from these class averages by applying an iterative correlation procedure with theoretical CTF functions; they are then used to correct the raw images. Furthermore, the method enables the tilt axis of the sample holder to be determined and allows the elimination of individual poor-quality images that show high drift or charging effects.
Collapse
Affiliation(s)
- B Sander
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | | |
Collapse
|
158
|
Golas MM, Sander B, Will CL, Lührmann R, Stark H. Molecular architecture of the multiprotein splicing factor SF3b. Science 2003; 300:980-4. [PMID: 12738865 DOI: 10.1126/science.1084155] [Citation(s) in RCA: 216] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The splicing factor SF3b is a multiprotein complex essential for the accurate excision of introns from pre-messenger RNA. As an integral component of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP, SF3b is involved in the recognition of the pre-messenger RNA's branch site within the major and minor spliceosomes. We have determined the three-dimensional structure of the human SF3b complex by single-particle electron cryomicroscopy at a resolution of less than 10 angstroms, allowing identification of protein domains with known structural folds. The best fit of a modeled RNA-recognition motif indicates that the protein p14 is located in the central cavity of the complex. The 22 tandem helical repeats of the protein SF3b155 are located in the outer shell of the complex enclosing p14.
Collapse
Affiliation(s)
- Monika M Golas
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | | | | | | |
Collapse
|
159
|
Collins BM, Cubeddu L, Naidoo N, Harrop SJ, Kornfeld GD, Dawes IW, Curmi PMG, Mabbutt BC. Homomeric ring assemblies of eukaryotic Sm proteins have affinity for both RNA and DNA. Crystal structure of an oligomeric complex of yeast SmF. J Biol Chem 2003; 278:17291-8. [PMID: 12618433 DOI: 10.1074/jbc.m211826200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sm and Sm-like proteins are key components of small ribonucleoproteins involved in many RNA and DNA processing pathways. In eukaryotes, these complexes contain seven unique Sm or Sm-like (Lsm) proteins assembled as hetero-heptameric rings, whereas in Archaea and bacteria six or seven-membered rings are made from only a single polypeptide chain. Here we show that single Sm and Lsm proteins from yeast also have the capacity to assemble into homo-oligomeric rings. Formation of homo-oligomers by the spliceosomal small nuclear ribonucleoprotein components SmE and SmF preclude hetero-interactions vital to formation of functional small nuclear RNP complexes in vivo. To better understand these unusual complexes, we have determined the crystal structure of the homomeric assembly of the spliceosomal protein SmF. Like its archaeal/bacterial homologs, the SmF complex forms a homomeric ring but in an entirely novel arrangement whereby two heptameric rings form a co-axially stacked dimer via interactions mediated by the variable loops of the individual SmF protein chains. Furthermore, we demonstrate that the homomeric assemblies of yeast Sm and Lsm proteins are capable of binding not only to oligo(U) RNA but, in the case of SmF, also to oligo(dT) single-stranded DNA.
Collapse
Affiliation(s)
- Brett M Collins
- Cambridge Institute for Medical Research, University of Cambridge, Department of Clinical Biochemistry, Hills Road, Cambridge CB2 2XY, United Kingdom
| | | | | | | | | | | | | | | |
Collapse
|
160
|
Mura C, Phillips M, Kozhukhovsky A, Eisenberg D. Structure and assembly of an augmented Sm-like archaeal protein 14-mer. Proc Natl Acad Sci U S A 2003; 100:4539-44. [PMID: 12668760 PMCID: PMC404694 DOI: 10.1073/pnas.0538042100] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/31/2002] [Indexed: 11/18/2022] Open
Abstract
To better understand the roles of Sm proteins in forming the cores of many RNA-processing ribonucleoproteins, we determined the crystal structure of an atypical Sm-like archaeal protein (SmAP3) in which the conserved Sm domain is augmented by a previously uncharacterized, mixed alpha/beta C-terminal domain. The structure reveals an unexpected SmAP3 14-mer that is perforated by a cylindrical pore and is bound to 14 cadmium (Cd(2+)) ions. Individual heptamers adopt either "apical" or "equatorial" conformations that chelate Cd(2+) differently. SmAP3 forms supraheptameric oligomers (SmAP3)(n = 7,14,28) in solution, and assembly of the asymmetric 14-mer is modulated by differential divalent cation-binding in apical and equatorial subunits. Phylogenetic and sequence analyses substantiate SmAP3s as a unique subset of SmAPs. These results distinguish SmAP3s from other Sm proteins and provide a model for the structure and properties of Sm proteins >100 residues in length, e.g., several human Sm proteins.
Collapse
Affiliation(s)
- Cameron Mura
- Howard Hughes Medical Institute, Molecular Biology Institute, and Department of Energy Institute for Genomics and Proteomics, 201 Boyer Hall Molecular Biology Institute, University of California, Box 951570, Los Angeles, CA 90095-1570, USA
| | | | | | | |
Collapse
|
161
|
Mura C, Kozhukhovsky A, Gingery M, Phillips M, Eisenberg D. The oligomerization and ligand-binding properties of Sm-like archaeal proteins (SmAPs). Protein Sci 2003; 12:832-47. [PMID: 12649441 PMCID: PMC2323858 DOI: 10.1110/ps.0224703] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Intron splicing is a prime example of the many types of RNA processing catalyzed by small nuclear ribonucleoprotein (snRNP) complexes. Sm proteins form the cores of most snRNPs, and thus to learn principles of snRNP assembly we characterized the oligomerization and ligand-binding properties of Sm-like archaeal proteins (SmAPs) from Pyrobaculum aerophilum (Pae) and Methanobacterium thermautotrophicum (Mth). Ultracentrifugation shows that Mth SmAP1 is exclusively heptameric in solution, whereas Pae SmAP1 forms either disulfide-bonded 14-mers or sub-heptameric states (depending on the redox potential). By electron microscopy, we show that Pae and Mth SmAP1 polymerize into bundles of well ordered fibers that probably form by head-to-tail stacking of heptamers. The crystallographic results reported here corroborate these findings by showing heptamers and 14-mers of both Mth and Pae SmAP1 in four new crystal forms. The 1.9 A-resolution structure of Mth SmAP1 bound to uridine-5'-monophosphate (UMP) reveals conserved ligand-binding sites. The likely RNA binding site in Mth agrees with that determined for Archaeoglobus fulgidus (Afu) SmAP1. Finally, we found that both Pae and Mth SmAP1 gel-shift negatively supercoiled DNA. These results distinguish SmAPs from eukaryotic Sm proteins and suggest that SmAPs have a generic single-stranded nucleic acid-binding activity.
Collapse
Affiliation(s)
- Cameron Mura
- Howard Hughes Medical Institute, Molecular Biology Institute, Los Angeles, California 90095-1570, USA
| | | | | | | | | |
Collapse
|
162
|
McConnell TS, Lokken RP, Steitz JA. Assembly of the U1 snRNP involves interactions with the backbone of the terminal stem of U1 snRNA. RNA (NEW YORK, N.Y.) 2003; 9:193-201. [PMID: 12554862 PMCID: PMC1370385 DOI: 10.1261/rna.2136103] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Nucleotide analog interference mapping (NAIM) is a powerful method for identifying RNA functional groups involved in protein-RNA interactions. We examined particles assembled on modified U1 small nuclear RNAs (snRNAs) in vitro and detected two categories of interferences. The first class affects the stability of two higher-order complexes and comprises changes in two adenosines, A65 and A70, in the loop region previously identified as the binding site for the U1 small nuclear ribonucleoprotein (snRNP)-specific U1A protein. Addition of an exocyclic amine to position 2 of A65 interferes strongly with protein binding, whereas removal or modification of the exocyclic amine at position 6 makes little difference. Modifications of A70 exhibit the opposite effects: Additions at position 2 are permitted, but modification of the exocyclic amine at position 6 significantly inhibits protein binding. These interactions, critical for U1A-U1 snRNA recognition in the context of in vitro snRNP assembly, are consistent with previous structural studies of the isolated protein with the RNA hairpin containing the U1A binding site. The second category of interferences affects all partially assembled U1-protein complexes by decreasing the stability of Sm core protein associations. Interestingly, most strong interferences occur at phosphates in the terminal stem-loop region of U1, rather than in the Sm binding site. These data argue that interactions with the phosphate backbone of the terminal stem loop are essential for the stable association of Sm core proteins with the U1 snRNA. We suggest that the stem loop of all Sm snRNAs may act as a clamp to hold the ring of Sm proteins in place.
Collapse
Affiliation(s)
- Timothy S McConnell
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA
| | | | | |
Collapse
|
163
|
Thore S, Mayer C, Sauter C, Weeks S, Suck D. Crystal structures of the Pyrococcus abyssi Sm core and its complex with RNA. Common features of RNA binding in archaea and eukarya. J Biol Chem 2003; 278:1239-47. [PMID: 12409299 DOI: 10.1074/jbc.m207685200] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. Their proposed function is to mediate RNA-RNA interactions. We present here the crystal structures of Pyrococcus abyssi Sm protein (PA-Sm1) and its complex with a uridine heptamer. The overall structure of the protein complex, a heptameric ring with a central cavity, is similar to that proposed for the eukaryotic Sm core complex and found for other archaeal Sm proteins. RNA molecules bind to the protein at two different sites. They interact specifically inside the ring with three highly conserved residues, defining the uridine-binding pocket. In addition, nucleotides also interact on the surface formed by the N-terminal alpha-helix as well as a conserved aromatic residue in beta-strand 2 of the PA-Sm1 protein. The mutation of this conserved aromatic residue shows the importance of this second site for the discrimination between RNA sequences. Given the high structural homology between archaeal and eukaryotic Sm proteins, the PA-Sm1.RNA complex provides a model for how the small nuclear RNA contacts the Sm proteins in the Sm core. In addition, it suggests how Sm proteins might exert their function as modulators of RNA-RNA interactions.
Collapse
Affiliation(s)
- Stéphane Thore
- Structural Biology Program, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | | | | | | |
Collapse
|
164
|
Förch P, Puig O, Martínez C, Séraphin B, Valcárcel J. The splicing regulator TIA-1 interacts with U1-C to promote U1 snRNP recruitment to 5' splice sites. EMBO J 2002; 21:6882-92. [PMID: 12486009 PMCID: PMC139089 DOI: 10.1093/emboj/cdf668] [Citation(s) in RCA: 185] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2002] [Revised: 10/17/2002] [Accepted: 10/22/2002] [Indexed: 11/12/2022] Open
Abstract
The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site (ss) at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' ss is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' ss. Here we describe a molecular dissection of the activities of TIA-1. RNA recognition motifs (RRMs) 2 and 3 are necessary and sufficient for binding to the pre-mRNA. The non- consensus RRM1 and the C-terminal glutamine-rich (Q) domain are required for association with U1 snRNP and to facilitate its recruitment to 5' ss. Co-precipitation experiments revealed a specific and direct interaction involving the N-terminal region of the U1 protein U1-C and the Q-rich domain of TIA-1, an interaction enhanced by RRM1. The results argue that binding of TIA-1 in the vicinity of a 5' ss helps to stabilize U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator.
Collapse
Affiliation(s)
| | - Oscar Puig
- Gene Expression Programme, European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
Present address: Molecular and Cell Biology Department, University of California at Berkeley, Berkeley, CA, USA Present address: Centre de Regulació Genòmica, Passeig Marítim 37–49, 08003 Barcelona, Spain Present address: CGM-CNRS, Gif sur Yvette, France Corresponding author e-mail:
| | - Concepción Martínez
- Gene Expression Programme, European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
Present address: Molecular and Cell Biology Department, University of California at Berkeley, Berkeley, CA, USA Present address: Centre de Regulació Genòmica, Passeig Marítim 37–49, 08003 Barcelona, Spain Present address: CGM-CNRS, Gif sur Yvette, France Corresponding author e-mail:
| | - Bertrand Séraphin
- Gene Expression Programme, European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
Present address: Molecular and Cell Biology Department, University of California at Berkeley, Berkeley, CA, USA Present address: Centre de Regulació Genòmica, Passeig Marítim 37–49, 08003 Barcelona, Spain Present address: CGM-CNRS, Gif sur Yvette, France Corresponding author e-mail:
| | - Juan Valcárcel
- Gene Expression Programme, European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
Present address: Molecular and Cell Biology Department, University of California at Berkeley, Berkeley, CA, USA Present address: Centre de Regulació Genòmica, Passeig Marítim 37–49, 08003 Barcelona, Spain Present address: CGM-CNRS, Gif sur Yvette, France Corresponding author e-mail:
| |
Collapse
|
165
|
Pitici F, Beveridge DL, Baranger AM. Molecular dynamics simulation studies of induced fit and conformational capture in U1A-RNA binding: do molecular substates code for specificity? Biopolymers 2002; 65:424-35. [PMID: 12434430 DOI: 10.1002/bip.10251] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Molecular dynamics (MD) simulations on stem loop 2 of U1 small nuclear RNA and a construct of the U1A protein were carried out to obtain predictions of the structures for the unbound forms in solution and to elucidate dynamical aspects of induced fit upon binding. A crystal structure of the complex between the U1A protein and stem loop 2 RNA and an NMR structure for the uncomplexed form of the U1A protein are available from Oubridge et al. (Nature, 1994, Vol. 372, pp. 432-438) and Avis et al. (Journal of Molecular Biology, 1996, Vol. 257, pp. 398-411), respectively. As a consequence, U1A-RNA binding is a particularly attractive case for investigations of induced fit in protein-nucleic acid complexation. When combined with the available structural data, the results from simulations indicate that structural adaptation of U1A protein and RNA define distinct mechanisms for induced fit. For the protein, the calculations indicate that induced fit upon binding involves a non-native thermodynamic substate in which the structure is preorganized for binding. In contrast, induced fit of the RNA involves a distortion of the native structure in solution to an unstable form. However, the RNA solution structures predicted from simulation show evidence that structures in which groups of bases are favorably oriented for binding the U1A protein are thermally accessible. These results, which quantify with computational modeling recent proposals on induced fit and conformational capture by Leuillot and Varani (Biochemistry, 2001, Vol. 40, pp. 7947-7956) and by Williamson (Nature Structural Biology, 2000, Vol. 7, pp. 834-837) suggest an important role for intrinsic molecular architecture and substates other than the native form in the specificity of protein-RNA interactions.
Collapse
Affiliation(s)
- Felicia Pitici
- Chemistry Department and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459, USA
| | | | | |
Collapse
|
166
|
Tuite JB, Shiels JC, Baranger AM. Substitution of an essential adenine in the U1A-RNA complex with a non-polar isostere. Nucleic Acids Res 2002; 30:5269-75. [PMID: 12466552 PMCID: PMC137951 DOI: 10.1093/nar/gkf636] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The RNA recognition motif (RRM) binds to single-stranded RNA target sites of diverse sequences and structures. A conserved mode of base recognition by the RRM involves the simultaneous formation of a network of hydrogen bonds with the base functional groups and a stacking interaction between the base and a highly conserved aromatic amino acid. We have investigated the energetic contribution of the functional groups involved in the recognition of an essential adenine, A6, in stem-loop 2 of U1 snRNA by the N-terminal RRM of the U1A protein. Previously, we found that elimination of individual hydrogen bond donors and acceptors on A6 destabilized the complex by 0.8-1.9 kcal/mol, while mutation of the aromatic amino acid (Phe56) that stacks with A6 to Ala destabilized the complex by 5.5 kcal/mol. Here we continue to probe the contribution of A6 to complex stability through mutation of both the RNA and protein. We have removed two hydrogen-bonding functional groups by introducing a U1A mutation, Ser91Ala, and replacing A6 with tubercidin, purine, or 1-deazaadenine. We find that the complex is destabilized an additional 1.2-2.6 kcal/mol by the elimination of the second hydrogen bond donor or acceptor. Surprisingly, deletion of all of the functional groups involved in hydrogen bonds with the U1A protein by substituting adenine with 4-methylindole reduced the binding free energy by only 2.0 kcal/mol. Experiments with U1A proteins containing mutations of Phe56 suggested that improved stacking interactions due to the greater hydrophobicity of 4-methylindole than adenine may be partly responsible for the small destabilization of the complex upon substitution of 4-methylindole for A6. The data imply that hydrophobic interactions can compensate energetically for the disruption of the complex hydrogen-bonding network between nucleotide and protein.
Collapse
Affiliation(s)
- Jacob B Tuite
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA
| | | | | |
Collapse
|
167
|
Comolli LR, Ulyanov NB, Soto AM, Marky LA, James TL, Gmeiner WH. NMR structure of the 3' stem-loop from human U4 snRNA. Nucleic Acids Res 2002; 30:4371-9. [PMID: 12384583 PMCID: PMC137124 DOI: 10.1093/nar/gkf560] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The NMR structure of the 3' stem-loop (3'SL) from human U4 snRNA was determined to gain insight into the structural basis for conservation of this stem-loop sequence from vertebrates. 3'SL sequences from human, rat, mouse and chicken U4 snRNA each consist of a 7 bp stem capped by a UACG tetraloop. No high resolution structure has previously been reported for a UACG tetraloop. The UACG tetraloop portion of the 3'SL was especially well defined by the NMR data, with a total of 92 NOE-derived restraints (about 15 per residue), including 48 inter-residue restraints (about 8 per residue) for the tetraloop and closing C-G base pair. Distance restraints were derived from NOESY spectra using MARDIGRAS with random error analysis. Refinement of the 20mer RNA hairpin structure was carried out using the programs DYANA and miniCarlo. In the UACG tetraloop, U and G formed a base pair stabilized by two hydrogen bonds, one between the 2'-hydroxyl proton of U and carbonyl oxygen of G, another between the imino proton of G and carbonyl oxygen O2 of U. In addition, the amino group of C formed a hydrogen bond with the phosphate oxygen of A. G adopted a syn orientation about the glycosidic bond, while the sugar puckers of A and C were either C2'-endo or flexible. The conformation of the UACG tetraloop was, overall, similar to that previously reported for UUCG tetraloops, another member of the UNCG class of tetraloops. The presence of an A, rather than a U, at the variable position, however, presents a distinct surface for interaction of the 3'SL tetraloop with either RNA or protein residues that may stabilize interactions important for active spliceosome formation. Such tertiary interactions may explain the conservation of the UACG tetraloop motif in 3'SL sequences from U4 snRNA in vertebrates.
Collapse
Affiliation(s)
- Luis R Comolli
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94143, USA
| | | | | | | | | | | |
Collapse
|
168
|
Abstract
The RNA recognition motif (RRM) is one of the most common RNA binding domains. There have been few investigations of small molecule inhibitors of RRM-RNA complexes, although these inhibitors could be valuable tools for probing biological processes involving RRM-RNA complexes and would have the potential to be effective drugs. In this paper, the inhibition by small molecules of the complex formed between the N-terminal RRM of the U1A protein and stem loop 2 of U1 snRNA has been investigated. An aminoacridine derivative has been found to promote dissociation of the U1A-stem loop 2 RNA complex with an IC(50) value of 1 microM. Fluorescence experiments indicate that two aminoacridine ligands bind to each RNA target site. RNase A footprinting suggests that one binding site may be near the base pair that closes the loop and the other may be in a more flexible region of the loop. The addition of the aminoacridine derivative to stem loop 2 RNA increases the susceptibility of other portions of the loop to digestion by RNase A, which implies that binding of the ligand changes the conformation or dynamics of the stem loop target site. Either direct binding to the RNA or indirect alteration of the structure or dynamics of the loop would be likely to inhibit binding of the U1A protein to this RNA.
Collapse
Affiliation(s)
- Alicia Y Gayle
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA
| | | |
Collapse
|
169
|
Zhou Z, Sim J, Griffith J, Reed R. Purification and electron microscopic visualization of functional human spliceosomes. Proc Natl Acad Sci U S A 2002; 99:12203-7. [PMID: 12215496 PMCID: PMC129422 DOI: 10.1073/pnas.182427099] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2002] [Accepted: 07/18/2002] [Indexed: 11/18/2022] Open
Abstract
Pre-mRNA splicing takes place in a large and highly dynamic complex known as the spliceosome. Here we report the optimization of a maltose-binding protein (MBP) affinity-purification method to isolate functional spliceosomes for electron microscopic analysis. Visualization of the spliceosome preparations revealed distinct 40-60 nm particles. Immunogold-conjugated antibodies to spliceosome components specifically label these particles, which are eliminated by treatment with either RNase or protease. Moreover, spliceosomes assembled on two different pre-mRNAs are indistinguishable. This first visualization of purified functional spliceosomes assembled in vitro reveals striking structural features, including one or more central cavities and multiple elongate lobes.
Collapse
Affiliation(s)
- Zhaolan Zhou
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | | | | | | |
Collapse
|
170
|
Frank J. Single-particle imaging of macromolecules by cryo-electron microscopy. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2002; 31:303-19. [PMID: 11988472 DOI: 10.1146/annurev.biophys.31.082901.134202] [Citation(s) in RCA: 248] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cryo-electron microscopy (cryo-EM) of biological molecules in single-particle (i.e., unordered, nonaggregated) form is a new approach to the study of molecular assemblies, which are often too large and flexible to be amenable to X-ray crystallography. New insights into biological function on the molecular level are expected from cryo-EM applied to the study of such complexes "trapped" at different stages of their conformational changes and dynamical interactions. Important molecular machines involved in the fundamental processes of transcription, mRNA splicing, and translation are examples for successful applications of the new technique, combined with structural knowledge gained by conventional techniques of structure determination, such as X-ray crystallography and NMR.
Collapse
Affiliation(s)
- Joachim Frank
- Howard Hughes Medical Institute, Health Research Inc at the Wadsworth Center, State University of New York at Albany, Empire State Plaza, P.O. Box 509, Albany, NY 12201-0509, USA.
| |
Collapse
|
171
|
Schumacher MA, Pearson RF, Møller T, Valentin-Hansen P, Brennan RG. Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein. EMBO J 2002; 21:3546-56. [PMID: 12093755 PMCID: PMC126077 DOI: 10.1093/emboj/cdf322] [Citation(s) in RCA: 340] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In prokaryotes, Hfq regulates translation by modulating the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences. To elucidate the mechanisms of target recognition and translation regulation by Hfq, we determined the crystal structures of the Staphylococcus aureus Hfq and an Hfq-RNA complex to 1.55 and 2.71 A resolution, respectively. The structures reveal that Hfq possesses the Sm-fold previously observed only in eukaryotes and archaea. However, unlike these heptameric Sm proteins, Hfq forms a homo-hexameric ring. The Hfq-RNA structure reveals that the single-stranded hepta-oligoribonucleotide binds in a circular conformation around a central basic cleft, whereby Tyr42 residues from adjacent subunits stack with six of the bases, and Gln8, outside the Sm motif, provides key protein-base contacts. Such binding suggests a mechanism for Hfq function.
Collapse
MESH Headings
- Amino Acid Motifs
- Amino Acid Sequence
- Carrier Proteins/chemistry
- Carrier Proteins/metabolism
- Carrier Proteins/ultrastructure
- Cryoelectron Microscopy
- Crystallography, X-Ray
- Gene Expression Regulation, Bacterial
- Host Factor 1 Protein
- Integration Host Factors
- Macromolecular Substances
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Binding
- Protein Biosynthesis
- Protein Conformation
- Protein Structure, Tertiary
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Bacterial/ultrastructure
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- RNA, Messenger/ultrastructure
- Recombinant Fusion Proteins/chemistry
- Sequence Alignment
- Sequence Homology, Amino Acid
- Staphylococcus aureus/chemistry
- Substrate Specificity
Collapse
Affiliation(s)
| | | | - Thorleif Møller
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, OR 97201-3098, USA and
Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark Corresponding author e-mail:
| | - Poul Valentin-Hansen
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, OR 97201-3098, USA and
Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark Corresponding author e-mail:
| | - Richard G. Brennan
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, OR 97201-3098, USA and
Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark Corresponding author e-mail:
| |
Collapse
|
172
|
Törö I, Basquin J, Teo-Dreher H, Suck D. Archaeal Sm proteins form heptameric and hexameric complexes: crystal structures of the Sm1 and Sm2 proteins from the hyperthermophile Archaeoglobus fulgidus. J Mol Biol 2002; 320:129-42. [PMID: 12079339 DOI: 10.1016/s0022-2836(02)00406-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteins of largely unknown function related to the Sm proteins present in the core domain of eukaryotic small nuclear ribonucleoprotein particles have recently been detected in Archaea. In contrast to eukaryotes, Archaea contain maximally two distinct Sm-related proteins belonging to different subfamilies, we refer to as Sm1 and Sm2. Here we report the crystal structures of the Sm1- and Sm2-type proteins from the hyperthermophilic euryarchaeon Archaeoglobus fulgidus (AF-Sm1 and AF-Sm2) at a resolution of 2.5 and 1.95 A, respectively. While the AF-Sm1 protein forms a heptameric ring structure similar to that found in other archaeal Sm1-type proteins, the AF-Sm2 protein unexpectedly forms a homo-hexamer in the crystals, and, as is evident from the mass spectrometric analysis, also in solution. Both proteins have essentially the same monomer fold and inter-subunit beta-sheet hydrogen bonding giving rise to a similar overall architecture of the doughnut-shaped six and seven-membered rings. In addition, a conserved uracil-binding pocket identified previously in an AF-Sm1/RNA complex, suggests a common RNA-binding mode for the AF-Sm1 and AF-Sm2 proteins, in line with solution studies showing preferential binding to U-rich oligonucleotides for both proteins. Clear differences are however seen in the charge distribution within the two structures. The rough faces of the rings, i.e. the faces not containing the base binding pockets, have opposite charges in the two structures, being predominantly positive in AF-Sm1 and negative in AF-Sm2. Differences in the ionic interactions between subunits provide an explanation for the distinctly different oligomerisation behaviour of the AF-Sm1 and AF-Sm2 proteins and of Sm1- and Sm2-type proteins in general, as well as the stability of their complexes. Implications for the functions of archaeal Sm proteins are being discussed.
Collapse
Affiliation(s)
- Imre Törö
- Structural and Computational Biology Programme, EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | | | | | | |
Collapse
|
173
|
Palfi Z, Lane WS, Bindereif A. Biochemical and functional characterization of the cis-spliceosomal U1 small nuclear RNP from Trypanosoma brucei. Mol Biochem Parasitol 2002; 121:233-43. [PMID: 12034457 DOI: 10.1016/s0166-6851(02)00044-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recent studies in the trypanosome system have revealed that in addition to trans splicing of a short spliced leader (SL) exon, there is also cis splicing of internal introns. It has been suggested that cis splicing requires base-pairing of U1 small nuclear RNA (snRNA) and the 5' splice site. We have cloned the gene for U1 snRNA from Trypanosoma brucei and characterized the U1 snRNP. Based on immunoprecipitation and direct mass-spectrometric protein analysis the U1 snRNP contains the common Sm core found also in the known trans-spliceosomal snRNPs U2, U4/U6, and U5. The 5' end of U1 snRNA in the U1 snRNP is accessible for and functional in specific recognition of the 5' splice site of the poly(A) polymerase intron.
Collapse
Affiliation(s)
- Zsofia Palfi
- Institut für Biochemie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
| | | | | |
Collapse
|
174
|
Ohi MD, Link AJ, Ren L, Jennings JL, McDonald WH, Gould KL. Proteomics analysis reveals stable multiprotein complexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors, and snRNAs. Mol Cell Biol 2002; 22:2011-24. [PMID: 11884590 PMCID: PMC133674 DOI: 10.1128/mcb.22.7.2011-2024.2002] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2001] [Revised: 09/19/2001] [Accepted: 12/20/2001] [Indexed: 11/20/2022] Open
Abstract
Schizosaccharomyces pombe Cdc5p and its Saccharomyces cerevisiae ortholog, Cef1p, are essential Myb-related proteins implicated in pre-mRNA splicing and contained within large multiprotein complexes. Here we describe the tandem affinity purification (TAP) of Cdc5p- and Cef1p-associated complexes. Using transmission electron microscopy, we show that the purified Cdc5p complex is a discrete structure. The components of the S. pombe Cdc5p/S. cerevisiae Cef1p complexes (termed Cwfs or Cwcs, respectively) were identified using direct analysis of large protein complex (DALPC) mass spectrometry (A. J. Link et al., Nat. Biotechnol. 17:676-682, 1999). At least 26 proteins were detected in the Cdc5p/Cef1p complexes. Comparison of the polypeptides identified by S. pombe Cdc5p purification with those identified by S. cerevisiae Cef1p purification indicates that these two yeast complexes are nearly identical in composition. The majority of S. pombe Cwf proteins and S. cerevisiae Cwc proteins are known pre-mRNA splicing factors including core Sm and U2 and U5 snRNP components. In addition, the complex contains the U2, U5, and U6 snRNAs. Previously uncharacterized proteins were also identified, and we provide evidence that several of these novel factors are involved in pre-mRNA splicing. Our data represent the first comprehensive analysis of CDC5-associated proteins in yeasts, describe a discrete highly conserved complex containing novel pre-mRNA splicing factors, and demonstrate the power of DALPC for identification of components in multiprotein complexes.
Collapse
Affiliation(s)
- Melanie D Ohi
- Howard Hughes Medical Institute. Department of Cell Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | | | | | | | | | | |
Collapse
|
175
|
Abstract
The survival of motor neurons (SMN) protein complex functions in the biogenesis of spliceosomal small nuclear ribonucleoprotein particles (snRNPs) and prob ably other RNPs. All spliceosomal snRNPs have a common core of seven Sm proteins. To mediate the assembly of snRNPs, the SMN complex must be able to bring together Sm proteins with U snRNAs. We showed previously that SMN and other components of the SMN complex interact directly with several Sm proteins. Here, we show that the SMN complex also interacts specifically with U1 snRNA. The stem--loop 1 domain of U1 (SL1) is necessary and sufficient for SMN complex binding in vivo and in vitro. Substitution of three nucleotides in the SL1 loop (SL1A3) abolishes SMN interaction, and the corresponding U1 snRNA (U1A3) is impaired in U1 snRNP biogenesis. Microinjection of excess SL1 but not SL1A3 into Xenopus oocytes inhibits SMN complex binding to U1 snRNA and U1 snRNP assembly. These findings indicate that SMN complex interaction with SL1 is sequence-specific and critical for U1 snRNP biogenesis, further supporting the direct role of the SMN complex in RNP biogenesis.
Collapse
Affiliation(s)
| | | | - Gideon Dreyfuss
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6148, USA
Corresponding author e-mail:
| |
Collapse
|
176
|
Kues T, Dickmanns A, Lührmann R, Peters R, Kubitscheck U. High intranuclear mobility and dynamic clustering of the splicing factor U1 snRNP observed by single particle tracking. Proc Natl Acad Sci U S A 2001; 98:12021-6. [PMID: 11593012 PMCID: PMC59825 DOI: 10.1073/pnas.211250098] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Uridine-rich small nuclear ribonucleoproteins (U snRNPs) are components of the splicing machinery that removes introns from precursor mRNA. Like other splicing factors, U snRNPs are diffusely distributed throughout the nucleus and, in addition, are concentrated in distinct nuclear substructures referred to as speckles. We have examined the intranuclear distribution and mobility of the splicing factor U1 snRNP on a single-molecule level. Isolated U1 snRNPs were fluorescently labeled and incubated with digitonin-permeabilized 3T3 cells in the presence of Xenopus egg extract. By confocal microscopy, U1 snRNPs were found to be imported into nuclei, yielding a speckled intranuclear distribution. Employing a laser video-microscope optimized for high sensitivity and high speed, single U1 snRNPs were visualized and tracked at a spatial precision of 35 nm and a time resolution of 30 ms. The single-particle data revealed that U1 snRNPs occurred in small clusters that colocalized with speckles. In the clusters, U1 snRNPs resided for a mean decay time of 84 ms before leaving the optical slice in the direction of the optical axis, which corresponded to a mean effective diffusion coefficient of 1 microm(2)/s. An analysis of the trajectories of single U1 snRNPs revealed that at least three kinetic classes of low, medium, and high mobility were present. Moreover, the mean square displacements of these fractions were virtually independent of time, suggesting arrays of binding sites. The results substantiate the view that nuclear speckles are not rigid structures but highly dynamic domains characterized by a rapid turnover of U1 snRNPs and other splicing factors.
Collapse
Affiliation(s)
- T Kues
- Institut für Medizinische Physik und Biophysik, Westfälische Wilhelms-Universität, Robert-Koch-Strasse 31, D-48149 Münster, Germany
| | | | | | | | | |
Collapse
|
177
|
Pillai RS, Will CL, Lührmann R, Schümperli D, Müller B. Purified U7 snRNPs lack the Sm proteins D1 and D2 but contain Lsm10, a new 14 kDa Sm D1-like protein. EMBO J 2001; 20:5470-9. [PMID: 11574479 PMCID: PMC125645 DOI: 10.1093/emboj/20.19.5470] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2001] [Revised: 07/30/2001] [Accepted: 08/03/2001] [Indexed: 11/13/2022] Open
Abstract
U7 snRNPs were isolated from HeLa cells by biochemical fractionation, followed by affinity purification with a biotinylated oligonucleotide complementary to U7 snRNA. Purified U7 snRNPs lack the Sm proteins D1 and D2, but contain additional polypeptides of 14, 50 and 70 kDa. Microsequencing identified the 14 kDa polypeptide as a new Sm-like protein related to Sm D1 and D3. Like U7 snRNA, this protein, named Lsm10, is enriched in Cajal bodies of the cell nucleus. Its incorporation into U7 snRNPs is largely dictated by the special Sm binding site of U7 snRNA. This novel type of Sm complex, composed of both conventional Sm proteins and the Sm-like Lsm10, is most likely to be important for U7 snRNP function and subcellular localization.
Collapse
Affiliation(s)
- Ramesh S. Pillai
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland, Max Planck Institute of Biophysical Chemistry, Am Fassberg 11, 37070 Göttingen, Germany and Department of Molecular and Cell Biology, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK Corresponding author e-mail:
| | - Cindy L. Will
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland, Max Planck Institute of Biophysical Chemistry, Am Fassberg 11, 37070 Göttingen, Germany and Department of Molecular and Cell Biology, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK Corresponding author e-mail:
| | - Reinhard Lührmann
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland, Max Planck Institute of Biophysical Chemistry, Am Fassberg 11, 37070 Göttingen, Germany and Department of Molecular and Cell Biology, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK Corresponding author e-mail:
| | - Daniel Schümperli
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland, Max Planck Institute of Biophysical Chemistry, Am Fassberg 11, 37070 Göttingen, Germany and Department of Molecular and Cell Biology, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK Corresponding author e-mail:
| | - Berndt Müller
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland, Max Planck Institute of Biophysical Chemistry, Am Fassberg 11, 37070 Göttingen, Germany and Department of Molecular and Cell Biology, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK Corresponding author e-mail:
| |
Collapse
|
178
|
Abstract
Two new methods, single-particle cryo-electron microscopy reconstruction and electron tomography, are increasingly used to visualize molecular machines in vitro and in the cellular context, respectively. Current efforts focus on the development of methods capable of visualizing molecular signatures in the cell, and first progress in this direction has now been made.
Collapse
|
179
|
Abstract
Electron cryomicroscopy methods comprise a rapidly expanding field providing insights into the structure and function of biological macromolecules and their supramolecular assemblies. The 3.8 A resolution structure of the membrane protein aquaporin, a view of the herpesvirus capsid at 8.5 A and the 10 A resolution structure of the spliceosomal U1 small nuclear ribonucleoprotein complex are three outstanding examples emphasizing the versatility of this technique.
Collapse
Affiliation(s)
- V M Unger
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8024, USA.
| |
Collapse
|
180
|
Abstract
Cryo-electron microscopy allows the visualization of macromolecules in their native state. Combined with techniques of three-dimensional reconstruction, cryo-EM images of single molecules can be used to study macromolecular interactions. The ribosome, a large RNA-protein complex with multiple binding interactions, is an excellent test case illustrating the power of these new techniques. Conformational changes during the binding of tRNA and protein factors to the ribosome can now be studied without the interference of crystal packing. Now that the first X-ray structures of ribosomal subunits have become available, conformational changes observed by cryo-EM in different functional states can be traced back to internal rearrangements of the underlying structural framework. Electron microscopy, X-ray crystallography, and modeling should be used together in the endeavor to understand the functioning of the translational machinery.
Collapse
Affiliation(s)
- J Frank
- Howard Hughes Medical Institute, Health Research, Inc. at the Wadsworth Center, Empire State Plaza, Albany, New York 12201-0509, USA
| |
Collapse
|
181
|
Collins BM, Harrop SJ, Kornfeld GD, Dawes IW, Curmi PM, Mabbutt BC. Crystal structure of a heptameric Sm-like protein complex from archaea: implications for the structure and evolution of snRNPs. J Mol Biol 2001; 309:915-23. [PMID: 11399068 DOI: 10.1006/jmbi.2001.4693] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The Sm/Lsm proteins associate with small nuclear RNA to form the core of small nuclear ribonucleoproteins, required for processes as diverse as pre-mRNA splicing, mRNA degradation and telomere formation. The Lsm proteins from archaea are likely to represent the ancestral Sm/Lsm domain. Here, we present the crystal structure of the Lsm alpha protein from the thermophilic archaeon Methanobacterium thermoautotrophicum at 2.0 A resolution. The Lsm alpha protein crystallizes as a heptameric ring comprised of seven identical subunits interacting via beta-strand pairing and hydrophobic interactions. The heptamer can be viewed as a propeller-like structure in which each blade consists of a seven-stranded antiparallel beta-sheet formed from neighbouring subunits. There are seven slots on the inner surface of the heptamer ring, each of which is lined by Asp, Asn and Arg residues that are highly conserved in the Sm/Lsm sequences. These conserved slots are likely to form the RNA-binding site. In archaea, the gene encoding Lsm alpha is located next to the L37e ribosomal protein gene in a putative operon, suggesting a role for the Lsm alpha complex in ribosome function or biogenesis.
Collapse
Affiliation(s)
- B M Collins
- Department of Chemistry, Macquarie University, NSW 2109, Australia
| | | | | | | | | | | |
Collapse
|
182
|
Abstract
Significant advances have been made in elucidating the biogenesis pathway and three-dimensional structure of the UsnRNPs, the building blocks of the spliceosome. U2 and U4/U6*U5 tri-snRNPs functionally associate with the pre-mRNA at an earlier stage of spliceosome assembly than previously thought, and additional evidence supporting UsnRNA-mediated catalysis of pre-mRNA splicing has been presented.
Collapse
MESH Headings
- Animals
- Crystallography
- Humans
- Macromolecular Substances
- Protein Structure, Tertiary/physiology
- Protein Transport/physiology
- RNA Splicing/genetics
- RNA Splicing/physiology
- RNA, Small Nuclear/chemistry
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- Ribonucleoprotein, U1 Small Nuclear/biosynthesis
- Ribonucleoprotein, U1 Small Nuclear/chemistry
- Ribonucleoprotein, U1 Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/biosynthesis
- Ribonucleoproteins, Small Nuclear/chemistry
- Ribonucleoproteins, Small Nuclear/genetics
- Spliceosomes/chemistry
- Spliceosomes/genetics
- Spliceosomes/metabolism
Collapse
Affiliation(s)
- C L Will
- Max Planck Institute of Biophysical Chemistry, Department of Cellular Biochemistry, Am Fassberg 11, 37077 Göttingen, Germany.
| | | |
Collapse
|
183
|
Mura C, Cascio D, Sawaya MR, Eisenberg DS. The crystal structure of a heptameric archaeal Sm protein: Implications for the eukaryotic snRNP core. Proc Natl Acad Sci U S A 2001; 98:5532-7. [PMID: 11331747 PMCID: PMC33247 DOI: 10.1073/pnas.091102298] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sm proteins form the core of small nuclear ribonucleoprotein particles (snRNPs), making them key components of several mRNA-processing assemblies, including the spliceosome. We report the 1.75-A crystal structure of SmAP, an Sm-like archaeal protein that forms a heptameric ring perforated by a cationic pore. In addition to providing direct evidence for such an assembly in eukaryotic snRNPs, this structure (i) shows that SmAP homodimers are structurally similar to human Sm heterodimers, (ii) supports a gene duplication model of Sm protein evolution, and (iii) offers a model of SmAP bound to single-stranded RNA (ssRNA) that explains Sm binding-site specificity. The pronounced electrostatic asymmetry of the SmAP surface imparts directionality to putative SmAP-RNA interactions.
Collapse
Affiliation(s)
- C Mura
- University of California at Los Angeles-Department of Energy Laboratory of Structural Biology and Molecular Medicine, 201 Boyer Hall/Molecular Biology Institute, Box 951570, Los Angeles, CA 90095-1570, USA
| | | | | | | |
Collapse
|
184
|
Törö I, Thore S, Mayer C, Basquin J, Séraphin B, Suck D. RNA binding in an Sm core domain: X-ray structure and functional analysis of an archaeal Sm protein complex. EMBO J 2001; 20:2293-303. [PMID: 11331594 PMCID: PMC125243 DOI: 10.1093/emboj/20.9.2293] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Eukaryotic Sm and Sm-like proteins associate with RNA to form the core domain of ribonucleoprotein particles involved in pre-mRNA splicing and other processes. Recently, putative Sm proteins of unknown function have been identified in Archaea. We show by immunoprecipitation experiments that the two Sm proteins present in Archaeoglobus fulgidus (AF-Sm1 and AF-Sm2) associate with RNase P RNA in vivo, suggesting a role in tRNA processing. The AF-Sm1 protein also interacts specifically with oligouridylate in vitro. We have solved the crystal structures of this protein and a complex with RNA. AF-Sm1 forms a seven-membered ring, with the RNA interacting inside the central cavity on one face of the doughnut-shaped complex. The bases are bound via stacking and specific hydrogen bonding contacts in pockets lined by residues highly conserved in archaeal and eukaryotic Sm proteins, while the phosphates remain solvent accessible. A comparison with the structures of human Sm protein dimers reveals closely related monomer folds and intersubunit contacts, indicating that the architecture of the Sm core domain and RNA binding have been conserved during evolution.
Collapse
Affiliation(s)
| | | | - Claudine Mayer
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Postfach 102209, 69012 Heidelberg, Germany and
Centre de Génétique Moleculaire, CNRS, Avenue De la Terrasse, 91198 Gif sur Yvette Cedex, France Present address: Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris, France Corresponding author e-mail:
S.Thore and C.Mayer contributed equally to this work
| | | | - Bertrand Séraphin
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Postfach 102209, 69012 Heidelberg, Germany and
Centre de Génétique Moleculaire, CNRS, Avenue De la Terrasse, 91198 Gif sur Yvette Cedex, France Present address: Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris, France Corresponding author e-mail:
S.Thore and C.Mayer contributed equally to this work
| | - Dietrich Suck
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Postfach 102209, 69012 Heidelberg, Germany and
Centre de Génétique Moleculaire, CNRS, Avenue De la Terrasse, 91198 Gif sur Yvette Cedex, France Present address: Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris, France Corresponding author e-mail:
S.Thore and C.Mayer contributed equally to this work
| |
Collapse
|
185
|
Abstract
Advances in cryoEM and single-particle reconstruction have led to results at increasingly high resolutions. However, to sustain continuing improvements in resolution it will be necessary to increase the number of particles included in performing the reconstructions. Manual selection of particles, even when assisted by computer preselection, is a bottleneck that will become significant as single-particle reconstructions are scaled up to achieve near-atomic resolutions. This review describes various approaches that have been developed to address the problem of automatic particle selection. The principal conclusions that have been drawn from the results so far are: (1) cross-correlation with a reference image ("matched filtering") is an effective way to identify candidate particles, but it is inherently unable to avoid also selecting false particles; (2) false positives can be eliminated efficiently on the basis of estimates of particle size, density, and texture; (3) successful application of edge detection (or contouring) to particle identification may require improvements over currently available methods; and (4) neural network techniques, while computationally expensive, must also be investigated as a technology for eliminating false particles.
Collapse
Affiliation(s)
- W V Nicholson
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | | |
Collapse
|