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Borao S, Vega M, Boronat S, Hidalgo E, Hümmer S, Ayté J. A systematic screen identifies Saf5 as a link between splicing and transcription in fission yeast. PLoS Genet 2024; 20:e1011316. [PMID: 38833506 PMCID: PMC11178228 DOI: 10.1371/journal.pgen.1011316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 06/14/2024] [Accepted: 05/23/2024] [Indexed: 06/06/2024] Open
Abstract
Splicing is an important step of gene expression regulation in eukaryotes, as there are many mRNA precursors that can be alternatively spliced in different tissues, at different cell cycle phases or under different external stimuli. We have developed several integrated fluorescence-based in vivo splicing reporter constructs that allow the quantification of fission yeast splicing in vivo on intact cells, and we have compared their splicing efficiency in a wild type strain and in a prp2-1 (U2AF65) genetic background, showing a clear dependency between Prp2 and a consensus signal at 5' splicing site (5'SS). To isolate novel genes involved in regulated splicing, we have crossed the reporter showing more intron retention with the Schizosaccharomyces pombe knock out collection. Among the candidate genes involved in the regulation of splicing, we have detected strong splicing defects in two of the mutants -Δcwf12, a member of the NineTeen Complex (NTC) and Δsaf5, a methylosome subunit that acts together with the survival motor neuron (SMN) complex in small nuclear ribonucleoproteins (snRNP) biogenesis. We have identified that strains with mutations in cwf12 have inefficient splicing, mainly when the 5'SS differs from the consensus. However, although Δsaf5 cells also have some dependency on 5'SS sequence, we noticed that when one intron of a given pre-mRNA was affected, the rest of the introns of the same pre-mRNA had high probabilities of being also affected. This observation points Saf5 as a link between transcription rate and splicing.
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Affiliation(s)
- Sonia Borao
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona, Spain
| | - Montserrat Vega
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona, Spain
| | - Susanna Boronat
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona, Spain
| | - Elena Hidalgo
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona, Spain
| | - Stefan Hümmer
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona, Spain
| | - José Ayté
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona, Spain
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Ruan M, Wang H, Zhu M, Sun R, Shi J, Wang Q, Chen Y, Wang Y, Wang D. Heterozygous pathogenic variants in CWF19L1 in a Chinese family with spinocerebellar ataxia, autosomal recessive 17. J Clin Lab Anal 2022; 36:e24767. [PMID: 36357319 PMCID: PMC9757004 DOI: 10.1002/jcla.24767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/27/2022] [Accepted: 10/31/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND CWF19L1 is responsible for spinocerebellar ataxia, autosomal recessive 17, which presents with cerebellar ataxia, and atrophy. Here, we report novel compound heterozygous variants of CWF19L1 in a Chinese family with progressive ataxia and mental retardation of unknown etiology by analyzing clinical characteristics and genetic variations. METHODS Clinical profiles and genomic DNA extracts of family members were collected. Whole-exome and Sanger sequencing were performed to detect associated genetic variants. Pathogenicity prediction and conservation analysis of the identified variants were performed using bioinformatics tools. RESULTS We identified heterozygous variants at the invariant +2 position (c.1555_c.1557delGAG in exon 14 and c.1070G > T in exon 11) of the CWF19L1 gene. Two novel heterozygous variants of the CWF19L1 gene were identified in the CWF19L1 gene associated with autosomal recessive cerebellar ataxia. CONCLUSION Our results suggest that CWF19L1 variants may be a novel cause of recessive ataxia with developmental delay. Whole-exome sequencing is an efficient tool for screening variants associated with the disease. This case report may help diagnose and identify the causes of other ataxias, leading to novel therapies, especially in China. This finding enriches the variant spectrum of the CWF19L1 gene and lays the foundation for future studies on the correlation between genotype and phenotype.
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Affiliation(s)
- Miaohua Ruan
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Hongwei Wang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Mianmian Zhu
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Rongyue Sun
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jiamin Shi
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Qiu Wang
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yuan Chen
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yihong Wang
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Dan Wang
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Willet AH, Igarashi MG, Chen JS, Bhattacharjee R, Ren L, Cullati SN, Elmore ZC, Roberts-Galbraith RH, Johnson AE, Beckley JR, Gould KL. Phosphorylation in the intrinsically disordered region of F-BAR protein Imp2 regulates its contractile ring recruitment. J Cell Sci 2021; 134:271847. [PMID: 34279633 DOI: 10.1242/jcs.258645] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 07/12/2021] [Indexed: 11/20/2022] Open
Abstract
The F-BAR protein Imp2 is an important contributor to cytokinesis in the fission yeast, Schizosaccharomyces pombe. Because cell cycle regulated phosphorylation of the central intrinsically disordered region (IDR) of the Imp2 paralog, Cdc15, controls Cdc15 oligomerization state, localization, and ability to bind protein partners, we investigated whether Imp2 is similarly phosphoregulated. We found that Imp2 is endogenously phosphorylated on 28 sites within its IDR with the bulk of phosphorylation being constitutive. In vitro, casein kinase 1 (CK1) Hhp1 and Hhp2 can phosphorylate 17 sites and Cdk1 the remaining 11 sites. Mutations that prevent Cdk1 phosphorylation result in precocious Imp2 recruitment to the cell division site, and mutations designed to mimic these phosphorylation events delay Imp2 CR accumulation. Mutations that eliminated CK1 phosphorylation sites allowed CR sliding, and phosphomimetic substitutions at these sites reduced Imp2 protein levels and slowed CR constriction. Thus, like Cdc15, the Imp2 IDR is phosphorylated at many sites by multiple kinases. In contrast to Cdc15, for which phosphorylation plays a major cell cycle regulatory role, Imp2 phosphorylation is primarily constitutive with milder effects on localization and function.
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Affiliation(s)
- Alaina H Willet
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Maya G Igarashi
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Jun-Song Chen
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Rahul Bhattacharjee
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Liping Ren
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Sierra N Cullati
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Zachary C Elmore
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Rachel H Roberts-Galbraith
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Alyssa E Johnson
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Janel R Beckley
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Kathleen L Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
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4
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Zheng Q, Chen X, Qiao C, Wang M, Chen W, Luan X, Yan Y, Shen C, Fang J, Hu X, Zheng B, Wu Y, Yu J. Somatic CG6015 mediates cyst stem cell maintenance and germline stem cell differentiation via EGFR signaling in Drosophila testes. Cell Death Discov 2021; 7:68. [PMID: 33824283 PMCID: PMC8024382 DOI: 10.1038/s41420-021-00452-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/21/2021] [Accepted: 03/18/2021] [Indexed: 11/09/2022] Open
Abstract
Stem cell niche is regulated by intrinsic and extrinsic factors. In the Drosophila testis, cyst stem cells (CySCs) support the differentiation of germline stem cells (GSCs). However, the underlying mechanisms remain unclear. In this study, we found that somatic CG6015 is required for CySC maintenance and GSC differentiation in a Drosophila model. Knockdown of CG6015 in CySCs caused aberrant activation of dpERK in undifferentiated germ cells in the Drosophila testis, and disruption of key downstream targets of EGFR signaling (Dsor1 and rl) in CySCs results in a phenotype resembling that of CG6015 knockdown. CG6015, Dsor1, and rl are essential for the survival of Drosophila cell line Schneider 2 (S2) cells. Our data showed that somatic CG6015 regulates CySC maintenance and GSC differentiation via EGFR signaling, and inhibits aberrant activation of germline dpERK signals. These findings indicate regulatory mechanisms of stem cell niche homeostasis in the Drosophila testis.
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Affiliation(s)
- Qianwen Zheng
- Department of Gynecology, the Affiliated Hospital of Jiangsu University, Jiangsu University, 212001, Zhenjiang, Jiangsu, P.R. China
| | - Xia Chen
- Department of Gynecology, the Affiliated Hospital of Jiangsu University, Jiangsu University, 212001, Zhenjiang, Jiangsu, P.R. China
| | - Chen Qiao
- Department of Clinical Pharmacy, the Affiliated Hospital of Jiangsu University, Jiangsu University, 212001, Zhenjiang, Jiangsu, P.R. China
| | - Min Wang
- Department of Gynecology, the Affiliated Hospital of Jiangsu University, Jiangsu University, 212001, Zhenjiang, Jiangsu, P.R. China
| | - Wanyin Chen
- Department of Gynecology, the Affiliated Hospital of Jiangsu University, Jiangsu University, 212001, Zhenjiang, Jiangsu, P.R. China
| | - Xiaojin Luan
- Department of Gynecology, the Affiliated Hospital of Jiangsu University, Jiangsu University, 212001, Zhenjiang, Jiangsu, P.R. China
| | - Yidan Yan
- Department of Gynecology, the Affiliated Hospital of Jiangsu University, Jiangsu University, 212001, Zhenjiang, Jiangsu, P.R. China
| | - Cong Shen
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, 215002, Suzhou, Jiangsu, P.R. China
| | - Jie Fang
- Department of Gynecology, the Affiliated Hospital of Jiangsu University, Jiangsu University, 212001, Zhenjiang, Jiangsu, P.R. China
| | - Xing Hu
- Department of Gynecology, the Affiliated Hospital of Jiangsu University, Jiangsu University, 212001, Zhenjiang, Jiangsu, P.R. China
| | - Bo Zheng
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, 215002, Suzhou, Jiangsu, P.R. China.
| | - Yibo Wu
- Human Reproductive and Genetic Center, Affiliated Hospital of Jiangnan University, 214062, Wuxi, Jiangsu, P.R. China.
| | - Jun Yu
- Department of Gynecology, the Affiliated Hospital of Jiangsu University, Jiangsu University, 212001, Zhenjiang, Jiangsu, P.R. China.
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Abstract
The HIV-1 Rev protein is a nuclear export factor for unspliced and incompletely spliced HIV-1 RNAs. Without Rev, these intron-retaining RNAs are trapped in the nucleus. A genome-wide screen identified nine proteins of the spliceosome, which all enhanced expression from the HIV-1 unspliced RNA after CRISPR/Cas knockdown. Depletion of DHX38, WDR70, and four proteins of the Prp19-associated complex (ISY1, BUD31, XAB2, and CRNKL1) resulted in a more than 20-fold enhancement of unspliced HIV-1 RNA levels in the cytoplasm. Targeting of CRNKL1, DHX38, and BUD31 affected nuclear export efficiencies of the HIV-1 unspliced RNA to a much larger extent than splicing. Transcriptomic analyses further revealed that CRNKL1 also suppresses cytoplasmic levels of a subset of cellular mRNAs, including some with selectively retained introns. Thus, CRNKL1-dependent nuclear retention is a novel cellular mechanism for the regulation of cytoplasmic levels of intron-retaining HIV-1 mRNAs, which HIV-1 may have harnessed to direct its complex splicing pattern.IMPORTANCE To regulate its complex splicing pattern, HIV-1 uses the adaptor protein Rev to shuttle unspliced or partially spliced mRNA from the nucleus to the cytoplasm. In the absence of Rev, these RNAs are retained in the nucleus, but it is unclear why. Here we identify cellular proteins whose depletion enhances cytoplasmic levels of the HIV-1 unspliced RNA. Depletion of one of them, CRNKL1, also increases cytoplasmic levels of a subset of intron-retaining cellular mRNA, suggesting that CRNKL1-dependent nuclear retention may be a basic cellular mechanism exploited by HIV-1.
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Depletion of the MFAP1/SPP381 Splicing Factor Causes R-Loop-Independent Genome Instability. Cell Rep 2020; 28:1551-1563.e7. [PMID: 31390568 PMCID: PMC6693559 DOI: 10.1016/j.celrep.2019.07.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 03/18/2019] [Accepted: 07/01/2019] [Indexed: 01/19/2023] Open
Abstract
THO/TREX is a conserved complex with a role in messenger ribonucleoprotein biogenesis that links gene expression and genome instability. Here, we show that human THO interacts with MFAP1 (microfibrillar-associated protein 1), a spliceosome-associated factor. Interestingly, MFAP1 depletion impairs cell proliferation and genome integrity, increasing γH2AX foci and DNA breaks. This phenotype is not dependent on either transcription or RNA-DNA hybrids. Mutations in the yeast orthologous gene SPP381 cause similar transcription-independent genome instability, supporting a conserved role. MFAP1 depletion has a wide effect on splicing and gene expression in human cells, determined by transcriptome analyses. MFAP1 depletion affects a number of DNA damage response (DDR) genes, which supports an indirect role of MFAP1 on genome integrity. Our work defines a functional interaction between THO and RNA processing and argues that splicing factors may contribute to genome integrity indirectly by regulating the expression of DDR genes rather than by a direct role.
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7
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Barbosa RL, da Cunha JPC, Menezes AT, Melo RDFP, Elias MC, Silber AM, Coltri PP. Proteomic analysis of Trypanosoma cruzi spliceosome complex. J Proteomics 2020; 223:103822. [PMID: 32422275 DOI: 10.1016/j.jprot.2020.103822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 05/01/2020] [Accepted: 05/11/2020] [Indexed: 11/17/2022]
Abstract
The unicellular protists of the group Kinetoplastida include the genera Leishmania and Trypanosoma, which are pathogens of invertebrate and vertebrate animals. Despite their medical and economical importance, critical aspects of their biology such as specific molecular characteristics of gene expression regulation are just beginning to be deciphered. Gene expression regulation also depends on post-transcriptional processing steps, such as the trans-splicing process. Despite being widely used in trypanosomes, trans-splicing is a rare event in other eukaryotes. We sought to describe the protein composition of spliceosomes in epimastigotes of T. cruzi, the etiological agent of Chagas disease. We used two TAP-tagged proteins to affinity purify spliceosomes and analyzed their composition by mass spectrometry. Among the 115 identified proteins we detected conserved spliceosome components, as Sm and LSm proteins, RNA helicases, U2- and U5-snRNP specific proteins. Importantly, by comparing our data with proteomic data of human and T. brucei spliceosome complexes, we observed a core group of proteins common to all spliceosomes. By using amino acid sequence comparisons, we identified RNA-associated proteins that might be involved with splicing regulation in T. cruzi, namely the orthologous of WDR33, PABPCL1 and three different HNRNPs. Data are available via ProteomeXchange with identifier PXD018776.
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Affiliation(s)
- Rosicler L Barbosa
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Julia Pinheiro Chagas da Cunha
- Special Laboratory of Cell Cycle, Center of Toxins, Immune Response and Cell Signalling (CeTICS), Butantan Institute, São Paulo 05503-900, Brazil
| | - Arthur T Menezes
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Raíssa de F P Melo
- Laboratory of Biochemistry of Tryps - LaBTryps. Department of Parasitology, Institute for Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Maria Carolina Elias
- Special Laboratory of Cell Cycle, Center of Toxins, Immune Response and Cell Signalling (CeTICS), Butantan Institute, São Paulo 05503-900, Brazil
| | - Ariel M Silber
- Laboratory of Biochemistry of Tryps - LaBTryps. Department of Parasitology, Institute for Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Patricia P Coltri
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil.
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Cipakova I, Jurcik M, Rubintova V, Borbova M, Mikolaskova B, Jurcik J, Bellova J, Barath P, Gregan J, Cipak L. Identification of proteins associated with splicing factors Ntr1, Ntr2, Brr2 and Gpl1 in the fission yeast Schizosaccharomyces pombe. Cell Cycle 2019; 18:1532-1536. [PMID: 31219728 PMCID: PMC6619935 DOI: 10.1080/15384101.2019.1632126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 05/24/2019] [Accepted: 05/30/2019] [Indexed: 01/12/2023] Open
Abstract
The spliceosome is a complex molecular machine assembled from many components, which catalyzes the removal of introns from mRNA precursors. Our previous study revealed that the Nrl1 (NRDE-2 like 1) protein associates with spliceosome proteins and regulates pre-mRNA splicing and homologous recombination-dependent R-loop formation in the fission yeast Schizosaccharomyces pombe. Here, we identify proteins associated with splicing factors Ntr1, Ntr2, Brr2 and Gpl1, a poorly characterized G-patch domain-containing protein required for efficient splicing. This work provides new evidence that Nrl1 and splicing factors physically interact and reveals additional insights into the protein interaction network of the spliceosome. We discuss implications of these findings in the light of recent progress in our understanding of how Nrl1 and splicing factors ensure genome stability.
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Affiliation(s)
- Ingrid Cipakova
- Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Matus Jurcik
- Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Veronika Rubintova
- Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Marianna Borbova
- Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Barbora Mikolaskova
- Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jan Jurcik
- Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jana Bellova
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Peter Barath
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Juraj Gregan
- Advanced Microscopy Facility, VBCF and Department of Chromosome Biology, MFPL, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Lubos Cipak
- Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Bratislava, Slovakia
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Burke JE, Longhurst AD, Merkurjev D, Sales-Lee J, Rao B, Moresco JJ, Yates JR, Li JJ, Madhani HD. Spliceosome Profiling Visualizes Operations of a Dynamic RNP at Nucleotide Resolution. Cell 2019; 173:1014-1030.e17. [PMID: 29727661 DOI: 10.1016/j.cell.2018.03.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/19/2018] [Accepted: 03/07/2018] [Indexed: 11/28/2022]
Abstract
Tools to understand how the spliceosome functions in vivo have lagged behind advances in the structural biology of the spliceosome. Here, methods are described to globally profile spliceosome-bound pre-mRNA, intermediates, and spliced mRNA at nucleotide resolution. These tools are applied to three yeast species that span 600 million years of evolution. The sensitivity of the approach enables the detection of canonical and non-canonical events, including interrupted, recursive, and nested splicing. This application of statistical modeling uncovers independent roles for the size and position of the intron and the number of introns per transcript in substrate progression through the two catalytic stages. These include species-specific inputs suggestive of spliceosome-transcriptome coevolution. Further investigations reveal the ATP-dependent discard of numerous endogenous substrates after spliceosome assembly in vivo and connect this discard to intron retention, a form of splicing regulation. Spliceosome profiling is a quantitative, generalizable global technology used to investigate an RNP central to eukaryotic gene expression.
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Affiliation(s)
- Jordan E Burke
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Adam D Longhurst
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daria Merkurjev
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jade Sales-Lee
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Beiduo Rao
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James J Moresco
- Department of Molecular Medicine, the Scripps Research Institute, La Jolla, CA, USA
| | - John R Yates
- Department of Molecular Medicine, the Scripps Research Institute, La Jolla, CA, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA.
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10
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Genome-Wide Identification and Characterization of WD40 Protein Genes in the Silkworm, Bombyx mori. Int J Mol Sci 2018; 19:ijms19020527. [PMID: 29425159 PMCID: PMC5855749 DOI: 10.3390/ijms19020527] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 01/27/2018] [Accepted: 02/06/2018] [Indexed: 12/18/2022] Open
Abstract
WD40 proteins are scaffolding molecules in protein-protein interactions and play crucial roles in fundamental biological processes. Genome-wide characterization of WD40 proteins in animals has been conducted solely in humans. We retrieved 172 WD40 protein genes in silkworm (BmWD40s) and identified these genes in 7 other insects, 9 vertebrates and 5 nematodes. Comparative analysis revealed that the WD40 protein gene family underwent lineage-specific expansions during animal evolution, but did not undergo significant expansion during insect evolution. The BmWD40s were categorized into five clusters and 12 classes according to the phylogenetic classification and their domain architectures, respectively. Sequence analyses indicated that tandem and segmental duplication played minor roles in producing the current number of BmWD40s, and domain recombination events of multi-domain BmWD40s might have occurred mainly after gene duplication events. Gene Ontology (GO) analysis revealed that a higher proportion of BmWD40s was involved in processes, such as binding, transcription-regulation and cellular component biogenesis, compared to all silkworm genes annotated in GO. Microarray-based analysis demonstrated that many BmWD40s had tissue-specific expression and exhibited high and/or sex-related expression during metamorphosis. These findings contribute to a better understanding of the evolution of the animal WD40 protein family and assist the study of the functions of BmWD40s.
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11
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Rai SK, Sangesland M, Lee M, Esnault C, Cui Y, Chatterjee AG, Levin HL. Host factors that promote retrotransposon integration are similar in distantly related eukaryotes. PLoS Genet 2017; 13:e1006775. [PMID: 29232693 PMCID: PMC5741268 DOI: 10.1371/journal.pgen.1006775] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 12/22/2017] [Accepted: 11/07/2017] [Indexed: 12/14/2022] Open
Abstract
Retroviruses and Long Terminal Repeat (LTR)-retrotransposons have distinct patterns of integration sites. The oncogenic potential of retrovirus-based vectors used in gene therapy is dependent on the selection of integration sites associated with promoters. The LTR-retrotransposon Tf1 of Schizosaccharomyces pombe is studied as a model for oncogenic retroviruses because it integrates into the promoters of stress response genes. Although integrases (INs) encoded by retroviruses and LTR-retrotransposons are responsible for catalyzing the insertion of cDNA into the host genome, it is thought that distinct host factors are required for the efficiency and specificity of integration. We tested this hypothesis with a genome-wide screen of host factors that promote Tf1 integration. By combining an assay for transposition with a genetic assay that measures cDNA recombination we could identify factors that contribute differentially to integration. We utilized this assay to test a collection of 3,004 S. pombe strains with single gene deletions. Using these screens and immunoblot measures of Tf1 proteins, we identified a total of 61 genes that promote integration. The candidate integration factors participate in a range of processes including nuclear transport, transcription, mRNA processing, vesicle transport, chromatin structure and DNA repair. Two candidates, Rhp18 and the NineTeen complex were tested in two-hybrid assays and were found to interact with Tf1 IN. Surprisingly, a number of pathways we identified were found previously to promote integration of the LTR-retrotransposons Ty1 and Ty3 in Saccharomyces cerevisiae, indicating the contribution of host factors to integration are common in distantly related organisms. The DNA repair factors are of particular interest because they may identify the pathways that repair the single stranded gaps flanking the sites of strand transfer following integration of LTR retroelements. Retroviruses and retrotransposons are genetic elements that propagate by integrating into chromosomes of eukaryotic cells. Genetic disorders are being treated with retrovirus-based vectors that integrate corrective genes into the chromosomes of patients. Unfortunately, the vectors can alter expression of adjacent genes and depending on the position of integration, cancer genes can be induced. It is therefore essential that we understand how integration sites are selected. Interestingly, different retroviruses and retrotransposons have different profiles of integration sites. While specific proteins have been identified that select target sites, it’s not known what other cellular factors promote integration. In this paper, we report a comprehensive screen of host factors that promote LTR-retrotransposon integration in the widely-studied yeast, Schizosaccharomyces pombe. Unexpectedly, we found a wide range of pathways and host factors participate in integration. And importantly, we found the cellular processes that promote integration relative to recombination in S. pombe are the same that drive integration of LTR-retrotransposons in the distantly related yeast Saccharomyces cerevisiae. This suggests a specific set of cellular pathways are responsible for integration in a wide range of eukaryotic hosts.
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Affiliation(s)
- Sudhir Kumar Rai
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Maya Sangesland
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Michael Lee
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Caroline Esnault
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Yujin Cui
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Atreyi Ghatak Chatterjee
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Henry L. Levin
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
- * E-mail:
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12
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Scheres SH, Nagai K. CryoEM structures of spliceosomal complexes reveal the molecular mechanism of pre-mRNA splicing. Curr Opin Struct Biol 2017; 46:130-139. [PMID: 28888105 DOI: 10.1016/j.sbi.2017.08.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 07/26/2017] [Accepted: 08/07/2017] [Indexed: 01/09/2023]
Abstract
The spliceosome is an intricate molecular machine which catalyses the removal of introns from eukaryotic mRNA precursors by two trans-esterification reactions (branching and exon ligation) to produce mature mRNA with uninterrupted protein coding sequences. The structures of the spliceosome in several key states determined by electron cryo-microscopy have greatly advanced our understanding of its molecular mechanism. The catalytic RNA core is formed during the activation of the fully assembled B to Bact complex and remains largely unchanged throughout the splicing cycle. RNA helicases and step specific factors regulate docking and undocking of the substrates (branch site and 3' splice site) to the single RNA-based active site to catalyse the two trans-esterification reactions.
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Affiliation(s)
- Sjors Hw Scheres
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
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13
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Interconnections Between RNA-Processing Pathways Revealed by a Sequencing-Based Genetic Screen for Pre-mRNA Splicing Mutants in Fission Yeast. G3-GENES GENOMES GENETICS 2016; 6:1513-23. [PMID: 27172183 PMCID: PMC4889648 DOI: 10.1534/g3.116.027508] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Pre-mRNA splicing is an essential component of eukaryotic gene expression and is highly conserved from unicellular yeasts to humans. Here, we present the development and implementation of a sequencing-based reverse genetic screen designed to identify nonessential genes that impact pre-mRNA splicing in the fission yeast Schizosaccharomyces pombe, an organism that shares many of the complex features of splicing in higher eukaryotes. Using a custom-designed barcoding scheme, we simultaneously queried ∼3000 mutant strains for their impact on the splicing efficiency of two endogenous pre-mRNAs. A total of 61 nonessential genes were identified whose deletions resulted in defects in pre-mRNA splicing; enriched among these were factors encoding known or predicted components of the spliceosome. Included among the candidates identified here are genes with well-characterized roles in other RNA-processing pathways, including heterochromatic silencing and 3ʹ end processing. Splicing-sensitive microarrays confirm broad splicing defects for many of these factors, revealing novel functional connections between these pathways.
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Evers C, Kaufmann L, Seitz A, Paramasivam N, Granzow M, Karch S, Fischer C, Hinderhofer K, Gdynia G, Elsässer M, Pinkert S, Schlesner M, Bartram CR, Moog U. Exome sequencing reveals a novelCWF19L1mutation associated with intellectual disability and cerebellar atrophy. Am J Med Genet A 2016; 170:1502-9. [DOI: 10.1002/ajmg.a.37632] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 03/07/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Christina Evers
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
| | - Lilian Kaufmann
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
| | - Angelika Seitz
- Department of Neuroradiology; University Hospital Heidelberg; Heidelberg Germany
| | - Nagarajan Paramasivam
- Division of Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Heidelberg Germany
- Medical Faculty Heidelberg; Heidelberg University; Germany
| | - Martin Granzow
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
| | - Stephanie Karch
- Center for Child and Adolescent Medicine, Pediatric Neurology; Heidelberg University Hospital; Heidelberg Germany
| | - Christine Fischer
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
| | | | - Georg Gdynia
- Institute of Pathology; University of Heidelberg; Heidelberg Germany
- German Cancer Research Center; Clinical Cooperation Unit Molecular Tumor Pathology; Heidelberg Germany
| | - Michael Elsässer
- Department of Obstetrics and Gynecology, Prenatal Medicine; University Hospital Heidelberg; Heidelberg Germany
| | - Stefan Pinkert
- Genomics and Proteomics Core Facility (GPCF); High Throughput Sequencing, German Cancer Research Center (DKFZ); Heidelberg Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | - Claus R. Bartram
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
| | - Ute Moog
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
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15
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Wang C, Dong X, Han L, Su XD, Zhang Z, Li J, Song J. Identification of WD40 repeats by secondary structure-aided profile-profile alignment. J Theor Biol 2016; 398:122-9. [PMID: 27021623 DOI: 10.1016/j.jtbi.2016.03.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 01/20/2016] [Accepted: 03/16/2016] [Indexed: 12/31/2022]
Abstract
A WD40 protein typically contains four or more repeats of ~40 residues ended with the Trp-Asp dipeptide, which folds into β-propellers with four β strands in each repeat. They often function as scaffolds for protein-protein interactions and are involved in numerous fundamental biological processes. Despite their important functional role, the "velcro" closure of WD40 propellers and the diversity of WD40 repeats make their identification a difficult task. Here we develop a new WD40 Repeat Recognition method (WDRR), which uses predicted secondary structure information to generate candidate repeat segments, and further employs a profile-profile alignment to identify the correct WD40 repeats from candidate segments. In particular, we design a novel alignment scoring function that combines dot product and BLOSUM62, thereby achieving a great balance of sensitivity and accuracy. Taking advantage of these strategies, WDRR could effectively reduce the false positive rate and accurately identify more remote homologous WD40 repeats with precise repeat boundaries. We further use WDRR to re-annotate the Pfam families in the β-propeller clan (CL0186) and identify a number of WD40 repeat proteins with high confidence across nine model organisms. The WDRR web server and the datasets are available at http://protein.cau.edu.cn/wdrr/.
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Affiliation(s)
- Chuan Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China; Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.
| | - Xiaobao Dong
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Lei Han
- Center for Cancer Molecular Diagnosis, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.
| | - Xiao-Dong Su
- State Key Laboratory of Protein and Plant Gene Research and Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China.
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Jinyan Li
- Advanced Analytics Institute and Centre for Health Technologies, University of Technology Sydney, 81 Broadway, Sydney, NSW 2007, Australia.
| | - Jiangning Song
- National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Faculty of Medicine, Monash University, Melbourne, VIC 3800, Australia; Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia.
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16
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CryoEM structures of two spliceosomal complexes: starter and dessert at the spliceosome feast. Curr Opin Struct Biol 2016; 36:48-57. [PMID: 26803803 PMCID: PMC4830896 DOI: 10.1016/j.sbi.2015.12.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 12/21/2015] [Indexed: 12/31/2022]
Abstract
Recent advances in cryoEM are revolutionizing our understanding of how molecular machines function. The structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP has been revealed. The structure of Schizosaccharomyces pombe U2.U6.U5 spliceosomal complex has been revealed. These structures greatly advanced our understanding of the mechanism of pre-mRNA splicing.
The spliceosome is formed on pre-mRNA substrates from five small nuclear ribonucleoprotein particles (U1, U2, U4/U6 and U5 snRNPs), and numerous non-snRNP factors. Saccharomyces cerevisiae U4/U6.U5 tri-snRNP comprises U5 snRNA, U4/U6 snRNA duplex and approximately 30 proteins and represents a substantial part of the spliceosome before activation. Schizosaccharomyces pombe U2.U6.U5 spliceosomal complex is a post-catalytic intron lariat spliceosome containing U2 and U5 snRNPs, NTC (nineteen complex), NTC-related proteins (NTR), U6 snRNA, and an RNA intron lariat. Two recent papers describe near-complete atomic structures of these complexes based on cryoEM single-particle analysis. The U4/U6.U5 tri-snRNP structure provides crucial insight into the activation mechanism of the spliceosome. The U2.U6.U5 complex reveals the striking architecture of NTC and NTR and important features of the group II intron-like catalytic RNA core remaining after spliced mRNA is released. These two structures greatly advance our understanding of the mechanism of pre-mRNA splicing.
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17
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Bayne EH, Bijos DA, White SA, de Lima Alves F, Rappsilber J, Allshire RC. A systematic genetic screen identifies new factors influencing centromeric heterochromatin integrity in fission yeast. Genome Biol 2015; 15:481. [PMID: 25274039 PMCID: PMC4210515 DOI: 10.1186/s13059-014-0481-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Indexed: 12/20/2022] Open
Abstract
Background Heterochromatin plays important roles in the regulation and stability of eukaryotic genomes. Both heterochromatin components and pathways that promote heterochromatin assembly, including RNA interference, RNAi, are broadly conserved between the fission yeast Schizosaccharomyces pombe and humans. As a result, fission yeast has emerged as an important model system for dissecting mechanisms governing heterochromatin integrity. Thus far, over 50 proteins have been found to contribute to heterochromatin assembly at fission yeast centromeres. However, previous studies have not been exhaustive, and it is therefore likely that further factors remain to be identified. Results To gain a more complete understanding of heterochromatin assembly pathways, we have performed a systematic genetic screen for factors required for centromeric heterochromatin integrity. In addition to known RNAi and chromatin modification components, we identified several proteins with previously undescribed roles in heterochromatin regulation. These included both known and newly characterised splicing-associated proteins, which are required for proper processing of centromeric transcripts by the RNAi pathway, and COP9 signalosome components Csn1 and Csn2, whose role in heterochromatin assembly can be explained at least in part by a role in the Ddb1-dependent degradation of the heterochromatin regulator Epe1. Conclusions This work has revealed new factors involved in RNAi-directed heterochromatin assembly in fission yeast. Our findings support and extend previous observations that implicate components of the splicing machinery as a platform for RNAi, and demonstrate a novel role for the COP9 signalosome in heterochromatin regulation. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0481-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elizabeth H Bayne
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JR, UK.
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18
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Ianiri G, Idnurm A. Essential gene discovery in the basidiomycete Cryptococcus neoformans for antifungal drug target prioritization. mBio 2015; 6:e02334-14. [PMID: 25827419 PMCID: PMC4453551 DOI: 10.1128/mbio.02334-14] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 03/04/2015] [Indexed: 12/28/2022] Open
Abstract
UNLABELLED Fungal diseases represent a major burden to health care globally. As with other pathogenic microbes, there is a limited number of agents suitable for use in treating fungal diseases, and resistance to these agents can develop rapidly. Cryptococcus neoformans is a basidiomycete fungus that causes cryptococcosis worldwide in both immunocompromised and healthy individuals. As a basidiomycete, it diverged from other common pathogenic or model ascomycete fungi more than 500 million years ago. Here, we report C. neoformans genes that are essential for viability as identified through forward and reverse genetic approaches, using an engineered diploid strain and genetic segregation after meiosis. The forward genetic approach generated random insertional mutants in the diploid strain, the induction of meiosis and sporulation, and selection for haploid cells with counterselection of the insertion event. More than 2,500 mutants were analyzed, and transfer DNA (T-DNA) insertions in several genes required for viability were identified. The genes include those encoding the thioredoxin reductase (Trr1), a ribosome assembly factor (Rsa4), an mRNA-capping component (Cet1), and others. For targeted gene replacement, the C. neoformans homologs of 35 genes required for viability in ascomycete fungi were disrupted, meiosis and sporulation were induced, and haploid progeny were evaluated for their ability to grow on selective media. Twenty-one (60%) were found to be required for viability in C. neoformans. These genes are involved in mitochondrial translation, ergosterol biosynthesis, and RNA-related functions. The heterozygous diploid mutants were evaluated for haploinsufficiency on a number of perturbing agents and drugs, revealing phenotypes due to the loss of one copy of an essential gene in C. neoformans. This study expands the knowledge of the essential genes in fungi using a basidiomycete as a model organism. Genes that have no mammalian homologs and are essential in both Cryptococcus and ascomycete human pathogens would be ideal for the development of antifungal drugs with broad-spectrum activity. IMPORTANCE Fungal infections are very common in humans but may be neglected due to misdiagnosis and inattention. Cryptococcus neoformans is a yeast that infects mainly immunocompromised people, causing high mortality rates in developing countries. The fungus infects the lungs, crosses the blood-brain barrier, and invades the cerebrospinal fluid, causing fatal meningitis. C. neoformans infections are treated with amphotericin B, flucytosine, and azoles, all developed decades ago. However, problems with antifungal agents highlight the urgent need for more-effective drugs to treat C. neoformans and other invasive fungal infections. These issues include the negative side effects of amphotericin B, the spontaneous resistance of C. neoformans to azoles, and the inefficacy of the echinocandin antifungals. In this study, we report the identification of C. neoformans essential genes as targets for the development of novel antifungals. Because of the level of evolutionary divergence between C. neoformans and the ascomycetes, a subset of these genes is likely essential in all fungi. Genes identified in this study represent an excellent starting point for the future development of new antifungals by pharmaceutical companies.
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Ambrósio DL, Badjatia N, Günzl A. The spliceosomal PRP19 complex of trypanosomes. Mol Microbiol 2015; 95:885-901. [PMID: 25524563 DOI: 10.1111/mmi.12910] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2014] [Indexed: 02/05/2023]
Abstract
In trypanosomes, mRNAs are processed by spliced leader (SL) trans splicing, in which a capped SL, derived from SL RNA, is spliced onto the 5' end of each mRNA. This process is mediated by the spliceosome, a large and dynamic RNA-protein machinery consisting of small nuclear ribonucleoproteins (snRNPs) and non-snRNP proteins. Due to early evolutionary divergence, the amino acid sequences of trypanosome splicing factors exhibit limited similarity to those of their eukaryotic orthologs making their bioinformatic identification challenging. Most of the ~ 60 protein components that have been characterized thus far are snRNP proteins because, in contrast to individual snRNPs, purification of intact spliceosomes has not been achieved yet. Here, we characterize the non-snRNP PRP19 complex of Trypanosoma brucei. We identified a complex that contained the core subunits PRP19, CDC5, PRL1, and SPF27, as well as PRP17, SKIP and PPIL1. Three of these proteins were newly annotated. The PRP19 complex was associated primarily with the activated spliceosome and, accordingly, SPF27 silencing blocked the first splicing step. Interestingly, SPF27 silencing caused an accumulation of SL RNA with a hypomethylated cap that closely resembled the defect observed previously upon depletion of the cyclin-dependent kinase CRK9, indicating that both proteins may function in spliceosome activation.
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Affiliation(s)
- Daniela L Ambrósio
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT, 06030-6403, USA
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Burns R, Majczenko K, Xu J, Peng W, Yapici Z, Dowling JJ, Li JZ, Burmeister M. Homozygous splice mutation in CWF19L1 in a Turkish family with recessive ataxia syndrome. Neurology 2014; 83:2175-82. [PMID: 25361784 PMCID: PMC4276403 DOI: 10.1212/wnl.0000000000001053] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 09/02/2014] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE To elucidate the genetic cause of a rare recessive ataxia presented by 2 siblings from a consanguineous Turkish family with a nonprogressive, congenital ataxia with mental retardation of unknown etiology. METHODS Whole-exome sequencing was combined with homozygosity mapping, linkage, and expression analysis to identify candidate genes, confirmed by Sanger sequencing. Reverse transcription-PCR and immunoblotting were used to determine the functional consequences of the gene variant. A zebrafish model was developed using morpholino-mediated knockdown. RESULTS We identified a homozygous mutation at the invariant +1 position (c.964+1G>A) in intron 9 of the CWF19L1 (complexed with cdc5 protein 19-like 1) gene. This mutation is absent in >6,500 European and African American individuals and 200 Turkish control DNAs. The mutation causes exon skipping, reduction in messenger RNA levels, and protein loss in cell lines of affected individuals. Morpholino-mediated knockdown in a zebrafish model demonstrates that loss of the evolutionarily highly conserved CWF19L1, whose normal biological function is unknown, alters cerebellar morphology and causes movement abnormalities. CONCLUSIONS Our results suggest that CWF19L1 mutations may be a novel cause of recessive ataxia with developmental delay. Our research may help with diagnosis, especially in Turkey, identify causes of other ataxias, and may lead to novel therapies.
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Affiliation(s)
- Randi Burns
- From the Program in Cellular and Molecular Biology (R.B., M.B.), Molecular & Behavioral Neuroscience Institute (R.B., K.M., M.B.), Departments of Human Genetics (J.X., W.P., J.Z.L., M.B.), Neurology (J.J.D.), Pediatrics (J.J.D.), and Psychiatry (M.B.), University of Michigan Medical Center, Ann Arbor; and Department of Neurology (Z.Y.), Division of Child Neurology, Istanbul Faculty of Medicine, Istanbul University, Turkey. J.J.D. is currently affiliated with the Division of Neurology and Program of Genetics and Genome Biology, Hospital for Sick Children, Departments of Pediatrics and Molecular Genetics, University of Toronto, Canada
| | - Karen Majczenko
- From the Program in Cellular and Molecular Biology (R.B., M.B.), Molecular & Behavioral Neuroscience Institute (R.B., K.M., M.B.), Departments of Human Genetics (J.X., W.P., J.Z.L., M.B.), Neurology (J.J.D.), Pediatrics (J.J.D.), and Psychiatry (M.B.), University of Michigan Medical Center, Ann Arbor; and Department of Neurology (Z.Y.), Division of Child Neurology, Istanbul Faculty of Medicine, Istanbul University, Turkey. J.J.D. is currently affiliated with the Division of Neurology and Program of Genetics and Genome Biology, Hospital for Sick Children, Departments of Pediatrics and Molecular Genetics, University of Toronto, Canada
| | - Jishu Xu
- From the Program in Cellular and Molecular Biology (R.B., M.B.), Molecular & Behavioral Neuroscience Institute (R.B., K.M., M.B.), Departments of Human Genetics (J.X., W.P., J.Z.L., M.B.), Neurology (J.J.D.), Pediatrics (J.J.D.), and Psychiatry (M.B.), University of Michigan Medical Center, Ann Arbor; and Department of Neurology (Z.Y.), Division of Child Neurology, Istanbul Faculty of Medicine, Istanbul University, Turkey. J.J.D. is currently affiliated with the Division of Neurology and Program of Genetics and Genome Biology, Hospital for Sick Children, Departments of Pediatrics and Molecular Genetics, University of Toronto, Canada
| | - Weiping Peng
- From the Program in Cellular and Molecular Biology (R.B., M.B.), Molecular & Behavioral Neuroscience Institute (R.B., K.M., M.B.), Departments of Human Genetics (J.X., W.P., J.Z.L., M.B.), Neurology (J.J.D.), Pediatrics (J.J.D.), and Psychiatry (M.B.), University of Michigan Medical Center, Ann Arbor; and Department of Neurology (Z.Y.), Division of Child Neurology, Istanbul Faculty of Medicine, Istanbul University, Turkey. J.J.D. is currently affiliated with the Division of Neurology and Program of Genetics and Genome Biology, Hospital for Sick Children, Departments of Pediatrics and Molecular Genetics, University of Toronto, Canada
| | - Zuhal Yapici
- From the Program in Cellular and Molecular Biology (R.B., M.B.), Molecular & Behavioral Neuroscience Institute (R.B., K.M., M.B.), Departments of Human Genetics (J.X., W.P., J.Z.L., M.B.), Neurology (J.J.D.), Pediatrics (J.J.D.), and Psychiatry (M.B.), University of Michigan Medical Center, Ann Arbor; and Department of Neurology (Z.Y.), Division of Child Neurology, Istanbul Faculty of Medicine, Istanbul University, Turkey. J.J.D. is currently affiliated with the Division of Neurology and Program of Genetics and Genome Biology, Hospital for Sick Children, Departments of Pediatrics and Molecular Genetics, University of Toronto, Canada
| | - James J Dowling
- From the Program in Cellular and Molecular Biology (R.B., M.B.), Molecular & Behavioral Neuroscience Institute (R.B., K.M., M.B.), Departments of Human Genetics (J.X., W.P., J.Z.L., M.B.), Neurology (J.J.D.), Pediatrics (J.J.D.), and Psychiatry (M.B.), University of Michigan Medical Center, Ann Arbor; and Department of Neurology (Z.Y.), Division of Child Neurology, Istanbul Faculty of Medicine, Istanbul University, Turkey. J.J.D. is currently affiliated with the Division of Neurology and Program of Genetics and Genome Biology, Hospital for Sick Children, Departments of Pediatrics and Molecular Genetics, University of Toronto, Canada
| | - Jun Z Li
- From the Program in Cellular and Molecular Biology (R.B., M.B.), Molecular & Behavioral Neuroscience Institute (R.B., K.M., M.B.), Departments of Human Genetics (J.X., W.P., J.Z.L., M.B.), Neurology (J.J.D.), Pediatrics (J.J.D.), and Psychiatry (M.B.), University of Michigan Medical Center, Ann Arbor; and Department of Neurology (Z.Y.), Division of Child Neurology, Istanbul Faculty of Medicine, Istanbul University, Turkey. J.J.D. is currently affiliated with the Division of Neurology and Program of Genetics and Genome Biology, Hospital for Sick Children, Departments of Pediatrics and Molecular Genetics, University of Toronto, Canada
| | - Margit Burmeister
- From the Program in Cellular and Molecular Biology (R.B., M.B.), Molecular & Behavioral Neuroscience Institute (R.B., K.M., M.B.), Departments of Human Genetics (J.X., W.P., J.Z.L., M.B.), Neurology (J.J.D.), Pediatrics (J.J.D.), and Psychiatry (M.B.), University of Michigan Medical Center, Ann Arbor; and Department of Neurology (Z.Y.), Division of Child Neurology, Istanbul Faculty of Medicine, Istanbul University, Turkey. J.J.D. is currently affiliated with the Division of Neurology and Program of Genetics and Genome Biology, Hospital for Sick Children, Departments of Pediatrics and Molecular Genetics, University of Toronto, Canada.
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Cromar G, Wong KC, Loughran N, On T, Song H, Xiong X, Zhang Z, Parkinson J. New tricks for "old" domains: how novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM. Genome Biol Evol 2014; 6:2897-917. [PMID: 25323955 PMCID: PMC4224354 DOI: 10.1093/gbe/evu228] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2014] [Indexed: 12/15/2022] Open
Abstract
The extracellular matrix (ECM) is a defining characteristic of metazoans and consists of a meshwork of self-assembling, fibrous proteins, and their functionally related neighbours. Previous studies, focusing on a limited number of gene families, suggest that vertebrate complexity predominantly arose through the duplication and subsequent modification of retained, preexisting ECM genes. These genes provided the structural underpinnings to support a variety of specialized tissues, as well as a platform for the organization of spatio-temporal signaling and cell migration. However, the relative contributions of ancient versus novel domains to ECM evolution have not been quantified across the full range of ECM proteins. Here, utilizing a high quality list comprising 324 ECM genes, we reveal general and clade-specific domain combinations, identifying domains of eukaryotic and metazoan origin recruited into new roles in approximately two-third of the ECM proteins in humans representing novel vertebrate proteins. We show that, rather than acquiring new domains, sampling of new domain combinations has been key to the innovation of paralogous ECM genes during vertebrate evolution. Applying a novel framework for identifying potentially important, noncontiguous, conserved arrangements of domains, we find that the distinct biological characteristics of the ECM have arisen through unique evolutionary processes. These include the preferential recruitment of novel domains to existing architectures and the utilization of high promiscuity domains in organizing the ECM network around a connected array of structural hubs. Our focus on ECM proteins reveals that distinct types of proteins and/or the biological systems in which they operate have influenced the types of evolutionary forces that drive protein innovation. This emphasizes the need for rigorously defined systems to address questions of evolution that focus on specific systems of interacting proteins.
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Affiliation(s)
- Graham Cromar
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Ka-Chun Wong
- Department of Computer Science, University of Toronto, Ontario, Canada Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Ontario, Canada
| | - Noeleen Loughran
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tuan On
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Hongyan Song
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Xuejian Xiong
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Zhaolei Zhang
- Department of Molecular Genetics, University of Toronto, Ontario, Canada Department of Computer Science, University of Toronto, Ontario, Canada Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Ontario, Canada Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada
| | - John Parkinson
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada Department of Molecular Genetics, University of Toronto, Ontario, Canada Department of Biochemistry, University of Toronto, Ontario, Canada
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22
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Collier SE, Voehler M, Peng D, Ohi R, Gould KL, Reiter NJ, Ohi MD. Structural and functional insights into the N-terminus of Schizosaccharomyces pombe Cdc5. Biochemistry 2014; 53:6439-51. [PMID: 25263959 PMCID: PMC4204884 DOI: 10.1021/bi5008639] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
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The
spliceosome is a dynamic macromolecular machine composed of
five small nuclear ribonucleoparticles (snRNPs), the NineTeen Complex
(NTC), and other proteins that catalyze the removal of introns mature
to form the mature message. The NTC, named after its founding member Saccharomyces cerevisiae Prp19, is a conserved spliceosome
subcomplex composed of at least nine proteins. During spliceosome
assembly, the transition to an active spliceosome correlates with
stable binding of the NTC, although the mechanism of NTC function
is not understood. Schizosaccharomyces pombe Cdc5, a core subunit of the NTC, is an essential protein required
for pre-mRNA splicing. The highly conserved Cdc5 N-terminus contains
two canonical Myb (myeloblastosis) repeats (R1 and R2) and a third
domain (D3) that was previously classified as a Myb-like repeat. Although
the N-terminus of Cdc5 is required for its function, how R1, R2, and
D3 each contribute to functionality is unclear. Using a combination
of yeast genetics, structural approaches, and RNA binding assays,
we show that R1, R2, and D3 are all required for the function of Cdc5
in cells. We also show that the N-terminus of Cdc5 binds RNA in vitro. Structural and functional analyses of Cdc5-D3
show that, while this domain does not adopt a Myb fold, Cdc5-D3 preferentially
binds double-stranded RNA. Our data suggest that the Cdc5 N-terminus
interacts with RNA structures proposed to be near the catalytic core
of the spliceosome.
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Affiliation(s)
- Scott E Collier
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center , Nashville, Tennessee 37232, United States
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23
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Garrey SM, Katolik A, Prekeris M, Li X, York K, Bernards S, Fields S, Zhao R, Damha MJ, Hesselberth JR. A homolog of lariat-debranching enzyme modulates turnover of branched RNA. RNA (NEW YORK, N.Y.) 2014; 20:1337-48. [PMID: 24919400 PMCID: PMC4105757 DOI: 10.1261/rna.044602.114] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Turnover of the branched RNA intermediates and products of pre-mRNA splicing is mediated by the lariat-debranching enzyme Dbr1. We characterized a homolog of Dbr1 from Saccharomyces cerevisiae, Drn1/Ygr093w, that has a pseudo-metallophosphodiesterase domain with primary sequence homology to Dbr1 but lacks essential active site residues found in Dbr1. Whereas loss of Dbr1 results in lariat-introns failing broadly to turnover, loss of Drn1 causes low levels of lariat-intron accumulation. Conserved residues in the Drn1 C-terminal CwfJ domains, which are not present in Dbr1, are required for efficient intron turnover. Drn1 interacts with Dbr1, components of the Nineteen Complex, U2 snRNA, branched intermediates, and products of splicing. Drn1 enhances debranching catalyzed by Dbr1 in vitro, but does so without significantly improving the affinity of Dbr1 for branched RNA. Splicing carried out in in vitro extracts in the absence of Drn1 results in an accumulation of branched splicing intermediates and products released from the spliceosome, likely due to less active debranching, as well as the promiscuous release of cleaved 5'-exon. Drn1 enhances Dbr1-mediated turnover of lariat-intermediates and lariat-intron products, indicating that branched RNA turnover is regulated at multiple steps during splicing.
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Affiliation(s)
- Stephen M Garrey
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Adam Katolik
- Department of Chemistry, McGill University, Montreal, Quebec H3A 2K6, Canada
| | - Mantas Prekeris
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Xueni Li
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Kerri York
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Sarah Bernards
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA Department of Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec H3A 2K6, Canada
| | - Jay R Hesselberth
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
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24
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Kallgren SP, Andrews S, Tadeo X, Hou H, Moresco JJ, Tu PG, Yates JR, Nagy PL, Jia S. The proper splicing of RNAi factors is critical for pericentric heterochromatin assembly in fission yeast. PLoS Genet 2014; 10:e1004334. [PMID: 24874881 PMCID: PMC4038458 DOI: 10.1371/journal.pgen.1004334] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 03/06/2014] [Indexed: 11/19/2022] Open
Abstract
Heterochromatin preferentially assembles at repetitive DNA elements, playing roles in transcriptional silencing, recombination suppression, and chromosome segregation. The RNAi machinery is required for heterochromatin assembly in a diverse range of organisms. In fission yeast, RNA splicing factors are also required for pericentric heterochromatin assembly, and a prevailing model is that splicing factors provide a platform for siRNA generation independently of their splicing activity. Here, by screening the fission yeast deletion library, we discovered four novel splicing factors that are required for pericentric heterochromatin assembly. Sequencing total cellular RNAs from the strongest of these mutants, cwf14Δ, showed intron retention in mRNAs of several RNAi factors. Moreover, introducing cDNA versions of RNAi factors significantly restored pericentric heterochromatin in splicing mutants. We also found that mutations of splicing factors resulted in defective telomeric heterochromatin assembly and mis-splicing the mRNA of shelterin component Tpz1, and that replacement of tpz1+ with its cDNA partially rescued heterochromatin defects at telomeres in splicing mutants. Thus, proper splicing of RNAi and shelterin factors contributes to heterochromatin assembly at pericentric regions and telomeres.
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Affiliation(s)
- Scott P. Kallgren
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Stuart Andrews
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, New York, United States of America
| | - Xavier Tadeo
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Haitong Hou
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - James J. Moresco
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Patricia G. Tu
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Peter L. Nagy
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, New York, United States of America
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
- * E-mail:
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25
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Chen W, Shulha HP, Ashar-Patel A, Yan J, Green KM, Query CC, Rhind N, Weng Z, Moore MJ. Endogenous U2·U5·U6 snRNA complexes in S. pombe are intron lariat spliceosomes. RNA (NEW YORK, N.Y.) 2014; 20:308-20. [PMID: 24442611 PMCID: PMC3923126 DOI: 10.1261/rna.040980.113] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Excision of introns from pre-mRNAs is mediated by the spliceosome, a multi-megadalton complex consisting of U1, U2, U4/U6, and U5 snRNPs plus scores of associated proteins. Spliceosome assembly and disassembly are highly dynamic processes involving multiple stable intermediates. In this study, we utilized a split TAP-tag approach for large-scale purification of an abundant endogenous U2·U5·U6 complex from Schizosaccharomyces pombe. RNAseq revealed this complex to largely contain excised introns, indicating that it is primarily ILS (intron lariat spliceosome) complexes. These endogenous ILS complexes are remarkably resistant to both high-salt and nuclease digestion. Mass spectrometry analysis identified 68, 45, and 43 proteins in low-salt-, high-salt-, and micrococcal nuclease-treated preps, respectively. The protein content of a S. pombe ILS complex strongly resembles that previously reported for human spliced product (P) and Saccharomyces cerevisiae ILS complexes assembled on single pre-mRNAs in vitro. However, the ATP-dependent RNA helicase Brr2 was either substoichiometric in low-salt preps or completely absent from high-salt and MNase preps. Because Brr2 facilitates spliceosome disassembly, its relative absence may explain why the ILS complex accumulates logarithmically growing cultures and the inability of S. pombe extracts to support in vitro splicing.
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Affiliation(s)
- Weijun Chen
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Hennady P. Shulha
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Ami Ashar-Patel
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Jing Yan
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Karin M. Green
- UMMS Proteomics and Mass Spectrometry Facility, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | | | - Nick Rhind
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Zhiping Weng
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Melissa J. Moore
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
- Corresponding authorE-mail
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26
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Chen W, Moore MJ. The spliceosome: disorder and dynamics defined. Curr Opin Struct Biol 2014; 24:141-9. [PMID: 24530854 DOI: 10.1016/j.sbi.2014.01.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 01/07/2014] [Accepted: 01/14/2014] [Indexed: 01/02/2023]
Abstract
Among the many macromolecular machines involved in eukaryotic gene expression, the spliceosome remains one of the most challenging for structural biologists. Defining features of this highly complex apparatus are its excessive number of individual parts, many of which have been evolutionarily selected for regions of structural disorder, and the remarkable compositional and conformation dynamics it must undertake to complete each round of splicing. Here we review recent advances in our understanding of spliceosome structural dynamics stemming from bioinformatics, deep sequencing, high throughput methods for determining protein-protein, protein-RNA and RNA-RNA interaction dynamics, single molecule microscopy and more traditional structural analyses. Together, these tools are rapidly changing our structural appreciation of this remarkably dynamic machine.
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Affiliation(s)
- Weijun Chen
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Pharmacology, RNA and Neuro Therapeutics Institutes, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Melissa J Moore
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Pharmacology, RNA and Neuro Therapeutics Institutes, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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27
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Mojardín L, Botet J, Quintales L, Moreno S, Salas M. New insights into the RNA-based mechanism of action of the anticancer drug 5'-fluorouracil in eukaryotic cells. PLoS One 2013; 8:e78172. [PMID: 24223771 PMCID: PMC3815194 DOI: 10.1371/journal.pone.0078172] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 09/18/2013] [Indexed: 01/23/2023] Open
Abstract
5-Fluorouracil (5FU) is a chemotherapeutic drug widely used in treating a range of advanced, solid tumours and, in particular, colorectal cancer. Here, we used high-density tiling DNA microarray technology to obtain the specific transcriptome-wide response induced by 5FU in the eukaryotic model Schizosaccharomyces pombe. This approach combined with real-time quantitative PCR analysis allowed us to detect splicing defects of a significant number of intron-containing mRNA, in addition to identify some rRNA and tRNA processing defects after 5FU treatment. Interestingly, our studies also revealed that 5FU specifically induced the expression of certain genes implicated in the processing of mRNA, tRNA and rRNA precursors, and in the post-transcriptional modification of uracil residues in RNA. The transcription of several tRNA genes was also significantly induced after drug exposure. These transcriptional changes might represent a cellular response mechanism to counteract 5FU damage since deletion strains for some of these up-regulated genes were hypersensitive to 5FU. Moreover, most of these RNA processing genes have human orthologs that participate in conserved pathways, suggesting that they could be novel targets to improve the efficacy of 5FU-based treatments.
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Affiliation(s)
- Laura Mojardín
- Instituto de Biología Molecular “Eladio Viñuela” (CSIC), Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Universidad Autónoma, Cantoblanco, Madrid, Spain
- * E-mail: (LM); (MS)
| | - Javier Botet
- Instituto de Biología Funcional y Genómica (CSIC/Universidad de Salamanca), Salamanca, Spain
| | - Luis Quintales
- Instituto de Biología Funcional y Genómica (CSIC/Universidad de Salamanca), Salamanca, Spain
| | - Sergio Moreno
- Instituto de Biología Funcional y Genómica (CSIC/Universidad de Salamanca), Salamanca, Spain
| | - Margarita Salas
- Instituto de Biología Molecular “Eladio Viñuela” (CSIC), Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Universidad Autónoma, Cantoblanco, Madrid, Spain
- * E-mail: (LM); (MS)
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28
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Livesay SB, Collier SE, Bitton DA, Bähler J, Ohi MD. Structural and functional characterization of the N terminus of Schizosaccharomyces pombe Cwf10. EUKARYOTIC CELL 2013; 12:1472-89. [PMID: 24014766 PMCID: PMC3837936 DOI: 10.1128/ec.00140-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/03/2013] [Indexed: 01/10/2023]
Abstract
The spliceosome is a dynamic macromolecular machine that catalyzes the removal of introns from pre-mRNA, yielding mature message. Schizosaccharomyces pombe Cwf10 (homolog of Saccharomyces cerevisiae Snu114 and human U5-116K), an integral member of the U5 snRNP, is a GTPase that has multiple roles within the splicing cycle. Cwf10/Snu114 family members are highly homologous to eukaryotic translation elongation factor EF2, and they contain a conserved N-terminal extension (NTE) to the EF2-like portion, predicted to be an intrinsically unfolded domain. Using S. pombe as a model system, we show that the NTE is not essential, but cells lacking this domain are defective in pre-mRNA splicing. Genetic interactions between cwf10-ΔNTE and other pre-mRNA splicing mutants are consistent with a role for the NTE in spliceosome activation and second-step catalysis. Characterization of Cwf10-NTE by various biophysical techniques shows that in solution the NTE contains regions of both structure and disorder. The first 23 highly conserved amino acids of the NTE are essential for its role in splicing but when overexpressed are not sufficient to restore pre-mRNA splicing to wild-type levels in cwf10-ΔNTE cells. When the entire NTE is overexpressed in the cwf10-ΔNTE background, it can complement the truncated Cwf10 protein in trans, and it immunoprecipitates a complex similar in composition to the late-stage U5.U2/U6 spliceosome. These data show that the structurally flexible NTE is capable of independently incorporating into the spliceosome and improving splicing function, possibly indicating a role for the NTE in stabilizing conformational rearrangements during a splice cycle.
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Affiliation(s)
- S. Brent Livesay
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Scott E. Collier
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Danny A. Bitton
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Jürg Bähler
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Melanie D. Ohi
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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29
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Fontrodona L, Porta-de-la-Riva M, Morán T, Niu W, Díaz M, Aristizábal-Corrales D, Villanueva A, Schwartz S, Reinke V, Cerón J. RSR-2, the Caenorhabditis elegans ortholog of human spliceosomal component SRm300/SRRM2, regulates development by influencing the transcriptional machinery. PLoS Genet 2013; 9:e1003543. [PMID: 23754964 PMCID: PMC3675011 DOI: 10.1371/journal.pgen.1003543] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 04/20/2013] [Indexed: 02/04/2023] Open
Abstract
Protein components of the spliceosome are highly conserved in eukaryotes and can influence several steps of the gene expression process. RSR-2, the Caenorhabditis elegans ortholog of the human spliceosomal protein SRm300/SRRM2, is essential for viability, in contrast to the yeast ortholog Cwc21p. We took advantage of mutants and RNA interference (RNAi) to study rsr-2 functions in C. elegans, and through genetic epistasis analysis found that rsr-2 is within the germline sex determination pathway. Intriguingly, transcriptome analyses of rsr-2(RNAi) animals did not reveal appreciable splicing defects but instead a slight global decrease in transcript levels. We further investigated this effect in transcription and observed that RSR-2 colocalizes with DNA in germline nuclei and coprecipitates with chromatin, displaying a ChIP-Seq profile similar to that obtained for the RNA Polymerase II (RNAPII). Consistent with a novel transcription function we demonstrate that the recruitment of RSR-2 to chromatin is splicing-independent and that RSR-2 interacts with RNAPII and affects RNAPII phosphorylation states. Proteomic analyses identified proteins associated with RSR-2 that are involved in different gene expression steps, including RNA metabolism and transcription with PRP-8 and PRP-19 being the strongest interacting partners. PRP-8 is a core component of the spliceosome and PRP-19 is the core component of the PRP19 complex, which interacts with RNAPII and is necessary for full transcriptional activity. Taken together, our study proposes that RSR-2 is a multifunctional protein whose role in transcription influences C. elegans development.
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Affiliation(s)
- Laura Fontrodona
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Montserrat Porta-de-la-Riva
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- C. elegans Core Facility, Bellvitge Biomedical Research Institute - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Tomás Morán
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Institute of Molecular Biology of Barcelona, IBMB - CSIC, Parc Científic de Barcelona, Barcelona, Spain
| | - Wei Niu
- Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Mònica Díaz
- Drug Delivery and Targeting, CIBBIM-Nanomedicine, Vall d'Hebron Research Institute, Universidad Autónoma de Barcelona, Barcelona, Spain
- Omnia Molecular, Parc Científic de Barcelona – UB, Barcelona, Spain
| | - David Aristizábal-Corrales
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Drug Delivery and Targeting, CIBBIM-Nanomedicine, Vall d'Hebron Research Institute, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Alberto Villanueva
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- C. elegans Core Facility, Bellvitge Biomedical Research Institute - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Simó Schwartz
- Drug Delivery and Targeting, CIBBIM-Nanomedicine, Vall d'Hebron Research Institute, Universidad Autónoma de Barcelona, Barcelona, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - Valerie Reinke
- Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Julián Cerón
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- C. elegans Core Facility, Bellvitge Biomedical Research Institute - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
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30
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Dreumont N, Séraphin B. Rapid screening of yeast mutants with reporters identifies new splicing phenotypes. FEBS J 2013; 280:2712-26. [PMID: 23560879 DOI: 10.1111/febs.12277] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 04/01/2013] [Accepted: 04/02/2013] [Indexed: 11/29/2022]
Abstract
Nuclear precursor mRNA splicing requires the stepwise assembly of a large complex, the spliceosome. Recent large-scale analyses, including purification of splicing complexes, high-throughput genetic screens and interactomic studies, have linked numerous factors to this dynamic process, including a well-defined core conserved from yeast to human. Intriguingly, despite extensive studies, no splicing defects were reported for some of the corresponding yeast mutants. To resolve this paradox, we screened a collection of viable yeast strains carrying mutations in splicing-related factors with a set of reporters including artificial constructs carrying competing splice sites. Previous analyses have indeed demonstrated that this strategy identifies yeast factors able to regulate alternative splicing and whose properties are conserved in human cells. The method, sensitive to subtle defects, revealed new splicing phenotypes for most analyzed factors such as the Urn1 protein. Interestingly, a mutant of PRP8 specifically lacking an N-terminal proline-rich region stimulated the splicing of a reporter containing competing branchpoint/3' splice site regions. Thus, using appropriate reporters, yeast can be used to quickly delineate the effect of various factors on splicing and identify those with the propensity to regulate alternative splicing events.
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Affiliation(s)
- Natacha Dreumont
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 67404 Illkirch, France
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31
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Discovery of a splicing regulator required for cell cycle progression. PLoS Genet 2013; 9:e1003305. [PMID: 23437009 PMCID: PMC3578776 DOI: 10.1371/journal.pgen.1003305] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 12/19/2012] [Indexed: 01/30/2023] Open
Abstract
In the G1 phase of the cell division cycle, eukaryotic cells prepare many of the resources necessary for a new round of growth including renewal of the transcriptional and protein synthetic capacities and building the machinery for chromosome replication. The function of G1 has an early evolutionary origin and is preserved in single and multicellular organisms, although the regulatory mechanisms conducting G1 specific functions are only understood in a few model eukaryotes. Here we describe a new G1 mutant from an ancient family of apicomplexan protozoans. Toxoplasma gondii temperature-sensitive mutant 12-109C6 conditionally arrests in the G1 phase due to a single point mutation in a novel protein containing a single RNA-recognition-motif (TgRRM1). The resulting tyrosine to asparagine amino acid change in TgRRM1 causes severe temperature instability that generates an effective null phenotype for this protein when the mutant is shifted to the restrictive temperature. Orthologs of TgRRM1 are widely conserved in diverse eukaryote lineages, and the human counterpart (RBM42) can functionally replace the missing Toxoplasma factor. Transcriptome studies demonstrate that gene expression is downregulated in the mutant at the restrictive temperature due to a severe defect in splicing that affects both cell cycle and constitutively expressed mRNAs. The interaction of TgRRM1 with factors of the tri-SNP complex (U4/U6 & U5 snRNPs) indicate this factor may be required to assemble an active spliceosome. Thus, the TgRRM1 family of proteins is an unrecognized and evolutionarily conserved class of splicing regulators. This study demonstrates investigations into diverse unicellular eukaryotes, like the Apicomplexa, have the potential to yield new insights into important mechanisms conserved across modern eukaryotic kingdoms. The study of eukaryotic cell division has overwhelmingly focused on cells from two branches of evolution, fungal and metazoan, with more distant eukaryotes rarely studied. One exception is apicomplexan pathogens where in the last two decades development of genetic models has been rapid. While not a perfect solution to fill the missing evolutionary diversity, Apicomplexans represent one of the oldest eukaryotic lineages possibly pre-dating the divergence of plant and animal kingdoms. A key to uncovering novel and conserved cell cycle mechanisms in these protists was the development of forward genetic approaches that permit unbiased discovery of essential growth factors. The apicomplexan, Toxoplasma has provided the best resource so far with ∼60,000 chemical mutants yielding a collection of 165 temperature-sensitive isolates that arrest in all phases of the parasite cell cycle. Efforts to identify the defective genes in this model are providing insights into the regulatory factors possibly active in the original eukaryote cell cycle, like the mRNA splicing factor discovered in this study.
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32
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Abstract
In eukaryotic cells, introns are spliced from pre-mRNAs by the spliceosome. Both the composition and the structure of the spliceosome are highly dynamic, and eight DExD/H RNA helicases play essential roles in controlling conformational rearrangements. There is evidence that the various helicases are functionally and physically connected with each other and with many other factors in the spliceosome. Understanding the dynamics of those interactions is essential to comprehend the mechanism and regulation of normal as well as of pathological splicing. This review focuses on recent advances in the characterization of the splicing helicases and their interactions, and highlights the deep integration of splicing helicases in global mRNP biogenesis pathways.
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Affiliation(s)
- Olivier Cordin
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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33
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Abstract
RNA splicing is one of the fundamental processes in gene expression in eukaryotes. Splicing of pre-mRNA is catalysed by a large ribonucleoprotein complex called the spliceosome, which consists of five small nuclear RNAs and numerous protein factors. The spliceosome is a highly dynamic structure, assembled by sequential binding and release of the small nuclear RNAs and protein factors. DExD/H-box RNA helicases are required to mediate structural changes in the spliceosome at various steps in the assembly pathway and have also been implicated in the fidelity control of the splicing reaction. Other proteins also play key roles in mediating the progression of the spliceosome pathway. In this review, we discuss the functional roles of the protein factors involved in the spliceosome pathway primarily from studies in the yeast system.
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34
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Yin J, Zhu JM, Shen XZ. New insights into pre-mRNA processing factor 19: A multi-faceted protein in humans. Biol Cell 2012; 104:695-705. [DOI: 10.1111/boc.201200011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2011] [Accepted: 09/06/2012] [Indexed: 11/27/2022]
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35
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Sorrells S, Carbonneau S, Harrington E, Chen AT, Hast B, Milash B, Pyati U, Major MB, Zhou Y, Zon LI, Stewart RA, Look AT, Jette C. Ccdc94 protects cells from ionizing radiation by inhibiting the expression of p53. PLoS Genet 2012; 8:e1002922. [PMID: 22952453 PMCID: PMC3431329 DOI: 10.1371/journal.pgen.1002922] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 07/13/2012] [Indexed: 01/07/2023] Open
Abstract
DNA double-strand breaks (DSBs) represent one of the most deleterious forms of DNA damage to a cell. In cancer therapy, induction of cell death by DNA DSBs by ionizing radiation (IR) and certain chemotherapies is thought to mediate the successful elimination of cancer cells. However, cancer cells often evolve to evade the cytotoxicity induced by DNA DSBs, thereby forming the basis for treatment resistance. As such, a better understanding of the DSB DNA damage response (DSB–DDR) pathway will facilitate the design of more effective strategies to overcome chemo- and radioresistance. To identify novel mechanisms that protect cells from the cytotoxic effects of DNA DSBs, we performed a forward genetic screen in zebrafish for recessive mutations that enhance the IR–induced apoptotic response. Here, we describe radiosensitizing mutation 7 (rs7), which causes a severe sensitivity of zebrafish embryonic neurons to IR–induced apoptosis and is required for the proper development of the central nervous system. The rs7 mutation disrupts the coding sequence of ccdc94, a highly conserved gene that has no previous links to the DSB–DDR pathway. We demonstrate that Ccdc94 is a functional member of the Prp19 complex and that genetic knockdown of core members of this complex causes increased sensitivity to IR–induced apoptosis. We further show that Ccdc94 and the Prp19 complex protect cells from IR–induced apoptosis by repressing the expression of p53 mRNA. In summary, we have identified a new gene regulating a dosage-sensitive response to DNA DSBs during embryonic development. Future studies in human cancer cells will determine whether pharmacological inactivation of CCDC94 reduces the threshold of the cancer cell apoptotic response. Radiation therapy and most chemotherapies elicit cancer cell death through the induction of excessive DNA damage. However, cancer cells can harbor genetic defects that confer resistance to these therapies. To identify cellular components whose targeted therapeutic inactivation could potentially enhance the sensitivity of treatment-resistant cancer cells to DNA–damaging therapies, we have chosen an unbiased genetic approach in live whole zebrafish embryos to identify genes that normally protect cells from the lethal effects of DNA damage. This approach has yielded the discovery of a novel radioprotective gene called ccdc94. Upon inactivation of ccdc94, cells become more sensitive to radiation-induced cell death. Our further analysis revealed that the Ccdc94 protein functions in the Prp19 complex, which is known to regulate gene expression and repair of damaged DNA. We found that this complex normally represses radiation-induced cell death by inhibiting the expression of the p53 gene, a critical mediator of DNA damage–induced cell death. Future experiments that inactivate Ccdc94 and Prp19 complex proteins in human cancer cells will determine if inactivation of this complex represents a novel therapeutic strategy that could increase p53 expression to enhance sensitivity to DNA damaging therapies in chemo- and radio-resistant cancer cells.
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Affiliation(s)
- Shelly Sorrells
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America
| | - Seth Carbonneau
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Erik Harrington
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America
| | - Aye T. Chen
- Department of Hematology/Oncology, Children's Hospital, Boston, Massachusetts, United States of America
| | - Bridgid Hast
- Department of Cell and Developmental Biology, Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, United States of America
| | - Brett Milash
- Bioinformatics Shared Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America
| | - Ujwal Pyati
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael B. Major
- Department of Cell and Developmental Biology, Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, United States of America
| | - Yi Zhou
- Department of Hematology/Oncology, Children's Hospital, Boston, Massachusetts, United States of America
| | - Leonard I. Zon
- Department of Hematology/Oncology, Children's Hospital, Boston, Massachusetts, United States of America
| | - Rodney A. Stewart
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America
| | - A. Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (ATL); (CJ)
| | - Cicely Jette
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail: (ATL); (CJ)
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36
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Tang Z, Luca M, Taggart-Murphy L, Portillio J, Chang C, Guven A, Lin RJ, Murray J, Carr A. Interacting factors and cellular localization of SR protein-specific kinase Dsk1. Exp Cell Res 2012; 318:2071-84. [PMID: 22683458 DOI: 10.1016/j.yexcr.2012.05.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 05/06/2012] [Accepted: 05/23/2012] [Indexed: 01/10/2023]
Abstract
Schizosaccharomyces pombe Dsk1 is an SR protein-specific kinase (SRPK), whose homologs have been identified in every eukaryotic organism examined. Although discovered as a mitotic regulator with protein kinase activity toward SR splicing factors, it remains largely unknown about what and how Dsk1 contributes to cell cycle and pre-mRNA splicing. In this study, we investigated the Dsk1 function by determining interacting factors and cellular localization of the kinase. Consistent with its reported functions, we found that pre-mRNA processing and cell cycle factors are prominent among the proteins co-purified with Dsk1. The identification of these factors led us to find Rsd1 as a novel Dsk1 substrate, as well as the involvement of Dsk1 in cellular distribution of poly(A)(+) RNA. In agreement with its role in nuclear events, we also found that Dsk1 is mainly localized in the nucleus during G(2) phase and at mitosis. Furthermore, we revealed the oscillation of Dsk1 protein in a cell cycle-dependent manner. This paper marks the first comprehensive analysis of in vivo Dsk1-associated proteins in fission yeast. Our results reflect the conserved role of SRPK family in eukaryotic organisms, and provide information about how Dsk1 functions in pre-mRNA processing and cell-division cycle.
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Affiliation(s)
- Zhaohua Tang
- W.M. Keck Science Center, The Claremont Colleges, Claremont, CA 91711, USA.
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37
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Cheng S, Zhang M, Li W, Wang Y, Liu Y, He Q. Proteomic analysis of porcine alveolar macrophages infected with porcine circovirus type 2. J Proteomics 2012; 75:3258-69. [DOI: 10.1016/j.jprot.2012.03.039] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 03/06/2012] [Accepted: 03/23/2012] [Indexed: 01/20/2023]
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38
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Korneta I, Magnus M, Bujnicki JM. Structural bioinformatics of the human spliceosomal proteome. Nucleic Acids Res 2012; 40:7046-65. [PMID: 22573172 PMCID: PMC3424538 DOI: 10.1093/nar/gks347] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
In this work, we describe the results of a comprehensive structural bioinformatics analysis of the spliceosomal proteome. We used fold recognition analysis to complement prior data on the ordered domains of 252 human splicing proteins. Examples of newly identified domains include a PWI domain in the U5 snRNP protein 200K (hBrr2, residues 258-338), while examples of previously known domains with a newly determined fold include the DUF1115 domain of the U4/U6 di-snRNP protein 90K (hPrp3, residues 540-683). We also established a non-redundant set of experimental models of spliceosomal proteins, as well as constructed in silico models for regions without an experimental structure. The combined set of structural models is available for download. Altogether, over 90% of the ordered regions of the spliceosomal proteome can be represented structurally with a high degree of confidence. We analyzed the reduced spliceosomal proteome of the intron-poor organism Giardia lamblia, and as a result, we proposed a candidate set of ordered structural regions necessary for a functional spliceosome. The results of this work will aid experimental and structural analyses of the spliceosomal proteins and complexes, and can serve as a starting point for multiscale modeling of the structure of the entire spliceosome.
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Affiliation(s)
- Iga Korneta
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw PL-02-109, Poland
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39
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Hegele A, Kamburov A, Grossmann A, Sourlis C, Wowro S, Weimann M, Will CL, Pena V, Lührmann R, Stelzl U. Dynamic protein-protein interaction wiring of the human spliceosome. Mol Cell 2012; 45:567-80. [PMID: 22365833 DOI: 10.1016/j.molcel.2011.12.034] [Citation(s) in RCA: 285] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 11/01/2011] [Accepted: 12/12/2011] [Indexed: 12/12/2022]
Abstract
More than 200 proteins copurify with spliceosomes, the compositionally dynamic RNPs catalyzing pre-mRNA splicing. To better understand protein - protein interactions governing splicing, we systematically investigated interactions between human spliceosomal proteins. A comprehensive Y2H interaction matrix screen generated a protein interaction map comprising 632 interactions between 196 proteins. Among these, 242 interactions were found between spliceosomal core proteins and largely validated by coimmunoprecipitation. To reveal dynamic changes in protein interactions, we integrated spliceosomal complex purification information with our interaction data and performed link clustering. These data, together with interaction competition experiments, suggest that during step 1 of splicing, hPRP8 interactions with SF3b proteins are replaced by hSLU7, positioning this second step factor close to the active site, and that the DEAH-box helicases hPRP2 and hPRP16 cooperate through ordered interactions with GPKOW. Our data provide extensive information about the spliceosomal protein interaction network and its dynamics.
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Affiliation(s)
- Anna Hegele
- Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics, 14195 Berlin, Germany
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40
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Structure of the mRNA splicing complex component Cwc2: insights into RNA recognition. Biochem J 2012; 441:591-7. [PMID: 21957909 DOI: 10.1042/bj20111385] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Prp19-associated complex [NTC (nineteen complex)] plays a crucial role in intron removal during premature mRNA splicing in eukaryotes. Only one component of the NTC, Cwc2, is capable of binding RNA. In the present study we report the 1.9 Å (1 Å=0.1 nm) X-ray structure of the Cwc2 core domain, which is both necessary and sufficient for RNA binding. The Cwc2 core domain contains two sub-domains, a CCCH-type ZnF (zinc finger) and a RRM (RNA recognition motif). Unexpectedly, the ZnF domain and the RRM form a single folding unit, glued together by extensive hydrophobic interactions and hydrogen bonds. Structure-guided mutational analysis revealed that the intervening loop [known as the RB loop (RNA-binding loop)] between ZnF and RRM plays an essential role in RNA binding. In addition, a number of highly conserved positively charged residues on the β-strands of RRM make an important contribution to RNA binding. Intriguingly, these residues and a portion of the RB loop constitute an extended basic surface strip that encircles Cwc2 halfway. The present study serves as a framework for understanding the regulatory function of the NTC in RNA splicing.
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Koncz C, deJong F, Villacorta N, Szakonyi D, Koncz Z. The spliceosome-activating complex: molecular mechanisms underlying the function of a pleiotropic regulator. FRONTIERS IN PLANT SCIENCE 2012; 3:9. [PMID: 22639636 PMCID: PMC3355604 DOI: 10.3389/fpls.2012.00009] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 01/09/2012] [Indexed: 05/18/2023]
Abstract
Correct interpretation of the coding capacity of RNA polymerase II transcribed eukaryotic genes is determined by the recognition and removal of intronic sequences of pre-mRNAs by the spliceosome. Our current knowledge on dynamic assembly and subunit interactions of the spliceosome mostly derived from the characterization of yeast, Drosophila, and human spliceosomal complexes formed on model pre-mRNA templates in cell extracts. In addition to sequential structural rearrangements catalyzed by ATP-dependent DExH/D-box RNA helicases, catalytic activation of the spliceosome is critically dependent on its association with the NineTeen Complex (NTC) named after its core E3 ubiquitin ligase subunit PRP19. NTC, isolated recently from Arabidopsis, occurs in a complex with the essential RNA helicase and GTPase subunits of the U5 small nuclear RNA particle that are required for both transesterification reactions of splicing. A compilation of mass spectrometry data available on the composition of NTC and spliceosome complexes purified from different organisms indicates that about half of their conserved homologs are encoded by duplicated genes in Arabidopsis. Thus, while mutations of single genes encoding essential spliceosome and NTC components lead to cell death in other organisms, differential regulation of some of their functionally redundant Arabidopsis homologs permits the isolation of partial loss of function mutations. Non-lethal pleiotropic defects of these mutations provide a unique means for studying the roles of NTC in co-transcriptional assembly of the spliceosome and its crosstalk with DNA repair and cell death signaling pathways.
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Affiliation(s)
- Csaba Koncz
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding ResearchCologne, Germany
- Institute of Plant Biology, Biological Research Center of Hungarian Academy of SciencesSzeged, Hungary
- *Correspondence: Csaba Koncz, Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-59829 Cologne, Germany. e-mail:
| | - Femke deJong
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Nicolas Villacorta
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Dóra Szakonyi
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Zsuzsa Koncz
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding ResearchCologne, Germany
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Horowitz DS. The mechanism of the second step of pre-mRNA splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:331-50. [PMID: 22012849 DOI: 10.1002/wrna.112] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The molecular mechanisms of the second step of pre-mRNA splicing in yeast and higher eukaryotes are reviewed. The important elements in the pre-mRNA, the participating proteins, and the proposed secondary structures and roles of the snRNAs are described. The sequence of events in the second step is presented, focusing on the actions of the proteins in setting up and facilitating the second reaction. Mechanisms for avoiding errors in splicing are discussed.
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Affiliation(s)
- David S Horowitz
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
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