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Ma L, Zhang X, Li C, Ma X, Zhao X, Zhao X, Zhang P, Zhu X. A U2 snRNP-specific protein, U2A', is involved in stress response and drug resistance in Cryptococcus deneoformans. Biochimie 2024; 220:179-187. [PMID: 37806618 DOI: 10.1016/j.biochi.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 08/14/2023] [Accepted: 10/06/2023] [Indexed: 10/10/2023]
Abstract
The spliceosome, a large complex containing five conserved small ribonucleoprotein particles (snRNPs) U1, U2, U4, U5 and U6, plays important roles in precursor messenger RNA splicing. However, the function and mechanism of the spliceosomal snRNPs have not been thoroughly studied in the pathogenic yeast Cryptococcus deneoformans. In this study, we identified a U2A' homologous protein as a component of the cryptococcal U2 snRNP, which was encoded by the LEA1 gene. Using the "suicide" CRISPR-Cas9 tool, we deleted the LEA1 gene in C. deneoformans JEC21 strain and obtained the disruption mutant lea1Δ. The mutant showed a hypersensitivity to 0.03 % sodium dodecyl sulfate, as well as disordered chitin distribution in cell wall observed with Calcofluor White staining, which collectively illustrated the function of U2A' in maintenance of cell wall integrity. Further examination showed that lea1Δ displayed a decreased tolerance to lower or elevated temperatures, osmotic pressure and oxidative stress. The lea1Δ still exhibited susceptibility to geneticin and 5-flucytosine, and increased resistance to ketoconazole. Even, the mutant had a reduced capsule, and the virulence of lea1Δ in the Galleria mellonella model was decreased. Our results indicate that the U2A'-mediated RNA-processing has a particular role in the processing of gene products involved in response to stresses and virulence.
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Affiliation(s)
- Lan Ma
- Beijing Key Laboratory of Genetic Engineering Drug and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xueqing Zhang
- Beijing Key Laboratory of Genetic Engineering Drug and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Chenxi Li
- Beijing Key Laboratory of Genetic Engineering Drug and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xiaoyu Ma
- Beijing Key Laboratory of Genetic Engineering Drug and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xuan Zhao
- Beijing Key Laboratory of Genetic Engineering Drug and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xueru Zhao
- Henan Provincial People's Hospital, Zhengzhou, 450003, China
| | - Ping Zhang
- Beijing Key Laboratory of Genetic Engineering Drug and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Xudong Zhu
- Beijing Key Laboratory of Genetic Engineering Drug and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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2
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Liu Y, Tian Y, Wang LX, Fan T, Zhang J, Chen MX, Liu YG. Phylogeny and conservation of plant U2A/U2A', a core splicing component in U2 spliceosomal complex. PLANTA 2021; 255:25. [PMID: 34940917 DOI: 10.1007/s00425-021-03752-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/09/2021] [Indexed: 06/14/2023]
Abstract
This study systematically identifies 112 U2A genes from 80 plant species by combinatory bioinformatics analysis, which is important for understanding their phylogenetic history, expression profiles and for predicting specific functions. In eukaryotes, a pre-mRNA can generate multiple transcripts by removing certain introns and joining corresponding exons, thus greatly expanding the transcriptome and proteome diversity. The spliceosome is a mega-Dalton ribonucleoprotein (RNP) complex that is essential for the process of splicing. In spliceosome components, the U2 small nuclear ribonucleoprotein (U2 snRNP) forms the pre-spliceosome by association with the branch site. An essential component that promotes U2 snRNP assembly, named U2A, has been extensively identified in humans, yeast and nematodes. However, studies examining U2A genes in plants are scarce. In this study, we performed a comprehensive analysis and identified a total of 112 U2A genes from 80 plant species representing dicots, monocots, mosses and algae. Comparisons of the gene structures, protein domains, and expression patterns of 112 U2A genes indicated that the conserved functions were likely retained by plant U2A genes and important for responses to internal and external stimuli. In addition, analysis of alternative transcripts and splice sites of U2A genes indicated that the fifth intron contained a conserved alternative splicing event that might be important for its molecular function. Our work provides a general understanding of this splicing factor family in terms of genes and proteins, and it will serve as a fundamental resource that will contribute to further mechanistic characterization in plants.
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Affiliation(s)
- Yue Liu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Shenzhen Institutes of Advanced Technology, Shenzhen Institute of Synthetic Biology, Chinese Academy of Sciences, Shenzhen, 518055, People's Republic of China
| | - Yuan Tian
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
| | - Lan-Xiang Wang
- Guangdong Provincial Key Laboratory of Seed and Seedling Health Management Technology, Guangdong Province, Shenzhen Noposion Agrochemical Co. Ltd, Shenzhen, 518102, China
- Shenzhen Institutes of Advanced Technology, Shenzhen Institute of Synthetic Biology, Chinese Academy of Sciences, Shenzhen, 518055, People's Republic of China
| | - Tao Fan
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Mo-Xian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China.
- Guangdong Provincial Key Laboratory of Seed and Seedling Health Management Technology, Guangdong Province, Shenzhen Noposion Agrochemical Co. Ltd, Shenzhen, 518102, China.
- Shenzhen Institutes of Advanced Technology, Shenzhen Institute of Synthetic Biology, Chinese Academy of Sciences, Shenzhen, 518055, People's Republic of China.
| | - Ying-Gao Liu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China.
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3
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Fish L, Khoroshkin M, Navickas A, Garcia K, Culbertson B, Hänisch B, Zhang S, Nguyen HCB, Soto LM, Dermit M, Mardakheh FK, Molina H, Alarcón C, Najafabadi HS, Goodarzi H. A prometastatic splicing program regulated by SNRPA1 interactions with structured RNA elements. Science 2021; 372:eabc7531. [PMID: 33986153 PMCID: PMC8238114 DOI: 10.1126/science.abc7531] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 04/01/2021] [Indexed: 12/14/2022]
Abstract
Aberrant alternative splicing is a hallmark of cancer, yet the underlying regulatory programs that control this process remain largely unknown. Here, we report a systematic effort to decipher the RNA structural code that shapes pathological splicing during breast cancer metastasis. We discovered a previously unknown structural splicing enhancer that is enriched near cassette exons with increased inclusion in highly metastatic cells. We show that the spliceosomal protein small nuclear ribonucleoprotein polypeptide A' (SNRPA1) interacts with these enhancers to promote cassette exon inclusion. This interaction enhances metastatic lung colonization and cancer cell invasion, in part through SNRPA1-mediated regulation of PLEC alternative splicing, which can be counteracted by splicing modulating morpholinos. Our findings establish a noncanonical regulatory role for SNRPA1 as a prometastatic splicing enhancer in breast cancer.
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Affiliation(s)
- Lisa Fish
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Matvei Khoroshkin
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Albertas Navickas
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kristle Garcia
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Bruce Culbertson
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Benjamin Hänisch
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Steven Zhang
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hoang C B Nguyen
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Larisa M Soto
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- McGill Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Maria Dermit
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Faraz K Mardakheh
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Henrik Molina
- Proteome Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Claudio Alarcón
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Hamed S Najafabadi
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- McGill Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
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van der Feltz C, Hoskins AA. Structural and functional modularity of the U2 snRNP in pre-mRNA splicing. Crit Rev Biochem Mol Biol 2019; 54:443-465. [PMID: 31744343 DOI: 10.1080/10409238.2019.1691497] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The U2 small nuclear ribonucleoprotein (snRNP) is an essential component of the spliceosome, the cellular machine responsible for removing introns from precursor mRNAs (pre-mRNAs) in all eukaryotes. U2 is an extraordinarily dynamic splicing factor and the most frequently mutated in cancers. Cryo-electron microscopy (cryo-EM) has transformed our structural and functional understanding of the role of U2 in splicing. In this review, we synthesize these and other data with respect to a view of U2 as an assembly of interconnected functional modules. These modules are organized by the U2 small nuclear RNA (snRNA) for roles in spliceosome assembly, intron substrate recognition, and protein scaffolding. We describe new discoveries regarding the structure of U2 components and how the snRNP undergoes numerous conformational and compositional changes during splicing. We specifically highlight large scale movements of U2 modules as the spliceosome creates and rearranges its active site. U2 serves as a compelling example for how cellular machines can exploit the modular organization and structural plasticity of an RNP.
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Affiliation(s)
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
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5
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Weber G, DeKoster GT, Holton N, Hall KB, Wahl MC. Molecular principles underlying dual RNA specificity in the Drosophila SNF protein. Nat Commun 2018; 9:2220. [PMID: 29880797 PMCID: PMC5992148 DOI: 10.1038/s41467-018-04561-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 05/02/2018] [Indexed: 12/22/2022] Open
Abstract
The first RNA recognition motif of the Drosophila SNF protein is an example of an RNA binding protein with multi-specificity. It binds different RNA hairpin loops in spliceosomal U1 or U2 small nuclear RNAs, and only in the latter case requires the auxiliary U2A' protein. Here we investigate its functions by crystal structures of SNF alone and bound to U1 stem-loop II, U2A' or U2 stem-loop IV and U2A', SNF dynamics from NMR spectroscopy, and structure-guided mutagenesis in binding studies. We find that different loop-closing base pairs and a nucleotide exchange at the tips of the loops contribute to differential SNF affinity for the RNAs. U2A' immobilizes SNF and RNA residues to restore U2 stem-loop IV binding affinity, while U1 stem-loop II binding does not require such adjustments. Our findings show how U2A' can modulate RNA specificity of SNF without changing SNF conformation or relying on direct RNA contacts.
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Affiliation(s)
- Gert Weber
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustraße 6, D-14195, Berlin, Germany. .,Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489, Berlin, Germany.
| | - Gregory T DeKoster
- Department of Biochemistry and Molecular Biophysics, Washington University Medical School, St. Louis, Missouri, 63110, USA
| | - Nicole Holton
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustraße 6, D-14195, Berlin, Germany
| | - Kathleen B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University Medical School, St. Louis, Missouri, 63110, USA.
| | - Markus C Wahl
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustraße 6, D-14195, Berlin, Germany. .,Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489, Berlin, Germany.
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6
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Co-evolution of SNF spliceosomal proteins with their RNA targets in trans-splicing nematodes. Genetica 2016; 144:487-96. [PMID: 27450547 DOI: 10.1007/s10709-016-9918-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 07/15/2016] [Indexed: 10/21/2022]
Abstract
Although the mechanism of pre-mRNA splicing has been well characterized, the evolution of spliceosomal proteins is poorly understood. The U1A/U2B″/SNF family (hereafter referred to as the SNF family) of RNA binding spliceosomal proteins participates in both the U1 and U2 small interacting nuclear ribonucleoproteins (snRNPs). The highly constrained nature of this system has inhibited an analysis of co-evolutionary trends between the proteins and their RNA binding targets. Here we report accelerated sequence evolution in the SNF protein family in Phylum Nematoda, which has allowed an analysis of protein:RNA co-evolution. In a comparison of SNF genes from ecdysozoan species, we found a correlation between trans-splicing species (nematodes) and increased phylogenetic branch lengths of the SNF protein family, with respect to their sister clade Arthropoda. In particular, we found that nematodes (~70-80 % of pre-mRNAs are trans-spliced) have experienced higher rates of SNF sequence evolution than arthropods (predominantly cis-spliced) at both the nucleotide and amino acid levels. Interestingly, this increased evolutionary rate correlates with the reliance on trans-splicing by nematodes, which would alter the role of the SNF family of spliceosomal proteins. We mapped amino acid substitutions to functionally important regions of the SNF protein, specifically to sites that are predicted to disrupt protein:RNA and protein:protein interactions. Finally, we investigated SNF's RNA targets: the U1 and U2 snRNAs. Both are more divergent in nematodes than arthropods, suggesting the RNAs have co-evolved with SNF in order to maintain the necessarily high affinity interaction that has been characterized in other species.
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7
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Rapid RNA-ligand interaction analysis through high-information content conformational and stability landscapes. Nat Commun 2015; 6:8898. [PMID: 26638992 PMCID: PMC4686816 DOI: 10.1038/ncomms9898] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 10/07/2015] [Indexed: 01/22/2023] Open
Abstract
The structure and biological properties of RNAs are a function of changing cellular conditions, but comprehensive, simultaneous investigation of the effect of multiple interacting environmental variables is not easily achieved. We have developed an efficient, high-throughput method to characterize RNA structure and thermodynamic stability as a function of multiplexed solution conditions using Förster resonance energy transfer (FRET). In a single FRET experiment using conventional quantitative PCR instrumentation, 19,400 conditions of MgCl2, ligand and temperature are analysed to generate detailed empirical conformational and stability landscapes of the cyclic diguanylate (c-di-GMP) riboswitch. The method allows rapid comparison of RNA structure modulation by cognate and non-cognate ligands. Landscape analysis reveals that kanamycin B stabilizes a non-native, idiosyncratic conformation of the riboswitch that inhibits c-di-GMP binding. This demonstrates that allosteric control of folding, rather than direct competition with cognate effectors, is a viable approach for pharmacologically targeting riboswitches and other structured RNA molecules. The structure and biological properties of RNAs are a function of changing cellular conditions. Here, Baird et al. report a high-throughput Förster resonance energy transfer (FRET) method to rapidly compare RNA structure modulation by cognate and non-cognate ligands across multiplexed solution conditions.
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8
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McCusker CD, Athippozhy A, Diaz-Castillo C, Fowlkes C, Gardiner DM, Voss SR. Positional plasticity in regenerating Amybstoma mexicanum limbs is associated with cell proliferation and pathways of cellular differentiation. BMC DEVELOPMENTAL BIOLOGY 2015; 15:45. [PMID: 26597593 PMCID: PMC4657325 DOI: 10.1186/s12861-015-0095-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 11/16/2015] [Indexed: 01/07/2023]
Abstract
Background The endogenous ability to dedifferentiate, re-pattern, and re-differentiate adult cells to repair or replace damaged or missing structures is exclusive to only a few tetrapod species. The Mexican axolotl is one example of these species, having the capacity to regenerate multiple adult structures including their limbs by generating a group of progenitor cells, known as the blastema, which acquire pattern and differentiate into the missing tissues. The formation of a limb regenerate is dependent on cells in the connective tissues that retain memory of their original position in the limb, and use this information to generate the pattern of the missing structure. Observations from recent and historic studies suggest that blastema cells vary in their potential to pattern distal structures during the regeneration process; some cells are plastic and can be reprogrammed to obtain new positional information while others are stable. Our previous studies showed that positional information has temporal and spatial components of variation; early bud (EB) and apical late bud (LB) blastema cells are plastic while basal-LB cells are stable. To identify the potential cellular and molecular basis of this variation, we compared these three cell populations using histological and transcriptional approaches. Results Histologically, the basal-LB sample showed greater tissue organization than the EB and apical-LB samples. We also observed that cell proliferation was more abundant in EB and apical-LB tissue when compared to basal-LB and mature stump tissue. Lastly, we found that genes associated with cellular differentiation were expressed more highly in the basal-LB samples. Conclusions Our results characterize histological and transcriptional differences between EB and apical-LB tissue compared to basal-LB tissue. Combined with our results from a previous study, we hypothesize that the stability of positional information is associated with tissue organization, cell proliferation, and pathways of cellular differentiation. Electronic supplementary material The online version of this article (doi:10.1186/s12861-015-0095-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Antony Athippozhy
- Department of Biology, Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, 40506, USA.
| | - Carlos Diaz-Castillo
- Department of Developmental and Cellular Biology, University of California, Irvine, CA, 92602, USA.
| | - Charless Fowlkes
- Donald Bren School of Information and Computer Science, University of California, Irvine, CA, 92602, USA.
| | - David M Gardiner
- Department of Developmental and Cellular Biology, University of California, Irvine, CA, 92602, USA.
| | - S Randal Voss
- Department of Biology, Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, 40506, USA.
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9
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Abstract
One of the great challenges to structural biologists lies in explaining the complexities of the spliceosome – a ribosome-sized molecular machine that is assembled in a step-wise manner and is responsible for pre-mRNA splicing. The spliceosome is both fascinating and difficult to work with, because of its dynamic nature. At each discrete step of splicing tens of proteins come and go orchestrating the functional transition through massive structural rearrangements. The retention and splicing complex (RES) is an important splicing factor interacting with pre-mRNA at the onset of the first transesterification reaction. RES is a specific splicing factor for a number of genes and is important for controlling pre-mRNA retention in the nucleus. RES is a 71 kDa heterotrimer composed of the 3 proteins Pml1p, Bud13p and Snu17p. We solved the 3-dimensional structure of the core of the RES complex as well as the 2 dimers, Snu17p-Bud13p and Snu17p-Pml1p. Further biophysical analysis revealed an astounding cooperativity that governs the assembly of this trimeric complex as well as its interaction with pre-mRNA. The more than 100-fold cooperativity originates from the progressive rigidification of Snu17p upon coupled binding-and-folding of protein regions, which are disordered in the unbound state. Our work highlights the role of cooperativity in the spliceosome and poses new questions about the structure and assembly of the spliceosome.
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Affiliation(s)
- Piotr Wysoczanski
- a Department for NMR-based Structural Biology ; Max Planck Institute for Biophysical Chemistry ; Am Fassberg 11, Göttingen , Germany
| | - Markus Zweckstetter
- a Department for NMR-based Structural Biology ; Max Planck Institute for Biophysical Chemistry ; Am Fassberg 11, Göttingen , Germany.,b German Center for Neurodegenerative Diseases (DZNE) ; Göttingen , Germany.,c Center for Nanoscale Microscopy and Molecular Physiology of the Brain; University Medical Center ; Göttingen , Germany
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10
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Abstract
The action of the spliceosome depends on the stepwise cooperative assembly and disassembly of its components. Very strong cooperativity was observed for the RES (Retention and Splicing) hetero-trimeric complex where the affinity from binary to tertiary interactions changes more than 100-fold and affects RNA binding. The RES complex is involved in splicing regulation and retention of not properly spliced pre-mRNA with its three components—Snu17p, Pml1p and Bud13p—giving rise to the two possible intermediate dimeric complexes Pml1p-Snu17p and Bud13p-Snu17p. Here we determined the three-dimensional structure and dynamics of the Pml1p-Snu17p and Bud13p-Snu17p dimers using liquid state NMR. We demonstrate that localized as well as global changes occur along the RES trimer assembly pathway. The stepwise rigidification of the Snu17p structure following the binding of Pml1p and Bud13p provides a basis for the strong cooperative nature of RES complex assembly.
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Affiliation(s)
- Piotr Wysoczanski
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Markus Zweckstetter
- 1] Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany [2] German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany [3] Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center, 37073 Göttingen, Germany
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11
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Zhao H, Piszczek G, Schuck P. SEDPHAT--a platform for global ITC analysis and global multi-method analysis of molecular interactions. Methods 2015; 76:137-148. [PMID: 25477226 PMCID: PMC4380758 DOI: 10.1016/j.ymeth.2014.11.012] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 11/19/2014] [Accepted: 11/20/2014] [Indexed: 01/02/2023] Open
Abstract
Isothermal titration calorimetry experiments can provide significantly more detailed information about molecular interactions when combined in global analysis. For example, global analysis can improve the precision of binding affinity and enthalpy, and of possible linkage parameters, even for simple bimolecular interactions, and greatly facilitate the study of multi-site and multi-component systems with competition or cooperativity. A pre-requisite for global analysis is the departure from the traditional binding model, including an 'n'-value describing unphysical, non-integral numbers of sites. Instead, concentration correction factors can be introduced to account for either errors in the concentration determination or for the presence of inactive fractions of material. SEDPHAT is a computer program that embeds these ideas and provides a graphical user interface for the seamless combination of biophysical experiments to be globally modeled with a large number of different binding models. It offers statistical tools for the rigorous determination of parameter errors, correlations, as well as advanced statistical functions for global ITC (gITC) and global multi-method analysis (GMMA). SEDPHAT will also take full advantage of error bars of individual titration data points determined with the unbiased integration software NITPIC. The present communication reviews principles and strategies of global analysis for ITC and its extension to GMMA in SEDPHAT. We will also introduce a new graphical tool for aiding experimental design by surveying the concentration space and generating simulated data sets, which can be subsequently statistically examined for their information content. This procedure can replace the 'c'-value as an experimental design parameter, which ceases to be helpful for multi-site systems and in the context of gITC.
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Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Grzegorz Piszczek
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA.
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12
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Wysoczański P, Schneider C, Xiang S, Munari F, Trowitzsch S, Wahl MC, Lührmann R, Becker S, Zweckstetter M. Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex. Nat Struct Mol Biol 2014; 21:911-8. [PMID: 25218446 DOI: 10.1038/nsmb.2889] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 08/15/2014] [Indexed: 02/08/2023]
Abstract
The precursor mRNA (pre-mRNA) retention and splicing (RES) complex is a spliceosomal complex that is present in yeast and humans and is important for RNA splicing and retention of unspliced pre-mRNA. Here, we present the solution NMR structure of the RES core complex from Saccharomyces cerevisiae. Complex formation leads to an intricate folding of three components-Snu17p, Bud13p and Pml1p-that stabilizes the RNA-recognition motif (RRM) fold of Snu17p and increases binding affinity in tertiary interactions between the components by more than 100-fold compared to that in binary interactions. RES interacts with pre-mRNA within the spliceosome, and through the assembly of the RES core complex RNA binding efficiency is increased. The three-dimensional structure of the RES core complex highlights the importance of cooperative folding and binding in the functional organization of the spliceosome.
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Affiliation(s)
- Piotr Wysoczański
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Cornelius Schneider
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - ShengQi Xiang
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Francesca Munari
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Simon Trowitzsch
- 1] Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. [2]
| | - Markus C Wahl
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Markus Zweckstetter
- 1] Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. [2] German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany. [3] Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center, Göttingen, Germany
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