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Wang S, Cai Y, Li T, Wang Y, Bao Z, Wang R, Qin J, Wang Z, Liu Y, Liu Z, Chan WY, Chen X, Lu G, Chen ZJ, Huang T, Liu H. CWF19L2 is Essential for Male Fertility and Spermatogenesis by Regulating Alternative Splicing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403866. [PMID: 38889293 DOI: 10.1002/advs.202403866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/12/2024] [Indexed: 06/20/2024]
Abstract
The progression of spermatogenesis along specific developmental trajectories depends on the coordinated regulation of pre-mRNA alternative splicing (AS) at the post-transcriptional level. However, the fundamental mechanism of AS in spermatogenesis remains to be investigated. Here, it is demonstrated that CWF19L2 plays a pivotal role in spermatogenesis and male fertility. In germline conditional Cwf19l2 knockout mice exhibiting male sterility, impaired spermatogenesis characterized by increased apoptosis and decreased differentiated spermatogonia and spermatocytes is observed. That CWF19L2 interacted with several spliceosome proteins to participate in the proper assembly and stability of the spliceosome is discovered. By integrating RNA-seq and LACE-seq data, it is further confirmed CWF19L2 directly bound and regulated the splicing of genes related to spermatogenesis (Znhit1, Btrc, and Fbxw7) and RNA splicing (Rbfox1, Celf1, and Rbm10). Additionally, CWF19L2 can indirectly amplify its effect on splicing regulation through modulating RBFOX1. Collectively, this research establishes that CWF19L2 orchestrates a splicing factor network to ensure accurate pre-mRNA splicing during the early steps of spermatogenesis.
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Affiliation(s)
- Shiyu Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan, Shandong, 250012, China
| | - Yuling Cai
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan, Shandong, 250012, China
| | - Tongtong Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan, Shandong, 250012, China
| | - Yan Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan, Shandong, 250012, China
| | - Ziyou Bao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan, Shandong, 250012, China
| | - Renxue Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan, Shandong, 250012, China
| | - Junchao Qin
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Ziqi Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan, Shandong, 250012, China
| | - Yining Liu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan, Shandong, 250012, China
| | - Zhaojian Liu
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong, 250012, China
| | - Wai-Yee Chan
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan, Shandong, 250012, China
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Xiangfeng Chen
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, 200000, China
- Department of Reproductive Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200000, China
| | - Gang Lu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Zi-Jiang Chen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan, Shandong, 250012, China
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, 999077, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, 200000, China
- Department of Reproductive Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200000, China
| | - Tao Huang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan, Shandong, 250012, China
| | - Hongbin Liu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan, Shandong, 250012, China
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, 999077, China
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Henke-Schulz L, Minocha R, Maier NH, Sträßer K. The Prp19C/NTC subunit Syf2 and the Prp19C/NTC-associated protein Cwc15 function in TREX occupancy and transcription elongation. RNA (NEW YORK, N.Y.) 2024; 30:854-865. [PMID: 38627018 PMCID: PMC11182008 DOI: 10.1261/rna.079944.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/02/2024] [Indexed: 06/19/2024]
Abstract
The Prp19 complex (Prp19C), also named NineTeen Complex (NTC), is conserved from yeast to human and functions in many different processes such as genome stability, splicing, and transcription elongation. In the latter, Prp19C ensures TREX occupancy at transcribed genes. TREX, in turn, couples transcription to nuclear mRNA export by recruiting the mRNA exporter to transcribed genes and consequently to nascent mRNAs. Here, we assess the function of the nonessential Prp19C subunit Syf2 and the nonessential Prp19C-associated protein Cwc15 in the interaction of Prp19C and TREX with the transcription machinery, Prp19C and TREX occupancy, and transcription elongation. Whereas both proteins are important for Prp19C-TREX interaction, Syf2 is needed for full Prp19C occupancy, and Cwc15 is important for the interaction of Prp19C with RNA polymerase II and TREX occupancy. These partially overlapping functions are corroborated by a genetic interaction between Δcwc15 and Δsyf2 Finally, Cwc15 also interacts genetically with the transcription elongation factor Dst1 and functions in transcription elongation. In summary, we uncover novel roles of the Prp19C component Syf2 and the Prp19C-associated protein Cwc15 in Prp19C's function in transcription elongation.
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Affiliation(s)
- Laura Henke-Schulz
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany
| | - Rashmi Minocha
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany
| | - Nils Holger Maier
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany
| | - Katja Sträßer
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany
- Cardio-Pulmonary Institute (CPI), EXC 2026, 35392 Giessen, Germany
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3
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Phulpagar P, Holla VV, Tomar D, Kamble N, Yadav R, Pal PK, Muthusamy B. Novel CWF19L1 mutations in patients with spinocerebellar ataxia, autosomal recessive 17. J Hum Genet 2023; 68:859-866. [PMID: 37752213 DOI: 10.1038/s10038-023-01195-5] [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: 02/02/2023] [Revised: 08/09/2023] [Accepted: 09/06/2023] [Indexed: 09/28/2023]
Abstract
Spinocerebellar ataxia, autosomal recessive-17 (SCAR17) is a rare hereditary ataxia characterized by ataxic gait, cerebellar signs and occasionally accompanied by intellectual disability and seizures. Pathogenic mutations in the CWF19L1 gene that code for CWF19 like cell cycle control factor 1 cause SCAR17. We report here two unrelated families with the clinical characteristics of global developmental delay, cerebellar ataxia, pyramidal signs, and seizures. Cerebellar atrophy, and T2/FLAIR hypointense transverse pontine stripes were observed in brain imaging. Exome sequencing identified novel homozygous mutations including a splice acceptor site variant c.1375-2 A > G on intron 12 in a male patient and a single nucleotide variant c.452 T > G on exon 5 resulting in a missense variant p.Ile151Ser in the female patient from two unrelated families, respectively. Sanger sequencing confirmed the segregation of these variants in the family members with autosomal recessive inheritance. Transcript analysis of the splice site variant revealed activation of a novel cryptic splice acceptor site on exon 13 resulting in an alternative transcription with a loss of nine nucleotides on exon 13. Translation of this transcript predicted an in-frame deletion of three amino acids p.(459_461del). We also observed a novel exon 13 skipping which results in premature termination of the protein product. Our study expands the phenotype, radiological features, and genotypes known in SCAR17.
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Affiliation(s)
- Prashant Phulpagar
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Vikram V Holla
- Department of Neurology, NIMHANS, Hosur Road, Bangalore, 560029, India
| | - Deepti Tomar
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
| | - Nitish Kamble
- Department of Neurology, NIMHANS, Hosur Road, Bangalore, 560029, India
| | - Ravi Yadav
- Department of Neurology, NIMHANS, Hosur Road, Bangalore, 560029, India
| | - Pramod Kumar Pal
- Department of Neurology, NIMHANS, Hosur Road, Bangalore, 560029, India.
| | - Babylakshmi Muthusamy
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India.
- Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
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Yao X, Wang C, Sun L, Yan L, Chen X, Lv Z, Xie X, Tian S, Liu W, Li L, Zhang H, Liu J. BCAS2 regulates granulosa cell survival by participating in mRNA alternative splicing. J Ovarian Res 2023; 16:104. [PMID: 37248466 DOI: 10.1186/s13048-023-01187-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/14/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND Granulosa cell proliferation and differentiation are essential for follicle development. Breast cancer amplified sequence 2 (BCAS2) is necessary for spermatogenesis, oocyte development, and maintaining the genome integrity of early embryos in mice. However, the function of BCAS2 in granulosa cells is still unknown. RESULTS We show that conditional disruption of Bcas2 in granulosa cells caused follicle development failure; the ratio of the positive cells of the cell proliferation markers PCNA and Ki67 were unchanged in granulosa cells. Specific deletion of Bcas2 caused a decrease in the BrdU-positive cell ratio, cell cycle arrest, DNA damage, and an increase in apoptosis in granulosa cells, and RPA1 was abnormally stained in granulosa cells. RNA-seq results revealed that knockout of Bcas2 results in unusual expression of cellular senescence genes. BCAS2 participated in the PRP19 complex to mediate alternative splicing (AS) of E2f3 and Flt3l mRNA to inhibit the cell cycle. Knockout of Bcas2 resulted in a significant decrease in the ratio of BrdU-positive cells in the human granulosa-like tumour (KGN) cell line. CONCLUSIONS Our results suggest that BCAS2 may influence the proliferation and survival of granulosa cells through regulating pre-mRNA splicing of E2f3 and Flt3l by forming the splicing complex with CDC5L and PRP19.
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Affiliation(s)
- Xiaohong Yao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Chaofan Wang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Longjie Sun
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Lu Yan
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xuexue Chen
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zheng Lv
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaomei Xie
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Shuang Tian
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Wenbo Liu
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Hua Zhang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Jiali Liu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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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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Fu X, Kaur H, Rodgers ML, Montemayor EJ, Butcher SE, Hoskins AA. Identification of transient intermediates during spliceosome activation by single molecule fluorescence microscopy. Proc Natl Acad Sci U S A 2022; 119:e2206815119. [PMID: 36417433 PMCID: PMC9860250 DOI: 10.1073/pnas.2206815119] [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: 04/23/2022] [Accepted: 10/05/2022] [Indexed: 11/24/2022] Open
Abstract
Spliceosome activation is the process of creating the catalytic site for RNA splicing and occurs de novo on each intron following spliceosome assembly. Dozens of factors bind to or are released from the activating spliceosome including the Lsm2-8 heteroheptameric ring that binds the U6 small nuclear RNA 3'-end. Lsm2-8 must be released to permit active site stabilization by the Prp19-containing complex (NineTeen Complex, NTC); however, little is known about the temporal order of events and dynamic interactions that lead up to and follow Lsm2-8 release. We have used colocalization single molecule spectroscopy (CoSMoS) to visualize Lsm2-8 dynamics during activation of Saccharomyces cerevisiae spliceosomes in vitro. Lsm2-8 is recruited as a component of the tri-snRNP and is released after integration of the Prp19-containing complex (NTC). Despite Lsm2-8 and the NTC being mutually exclusive in existing cryo-EM structures of yeast B complex spliceosomes, we identify a transient intermediate containing both ([Formula: see text]) and provide a kinetic framework for its formation and transformation during activation. Prior to [Formula: see text] assembly, the NTC rapidly and reversibly samples the spliceosome suggesting a mechanism for preventing NTC sequestration by defective spliceosomes that fail to properly activate. In complementary ensemble assays, we show that a base-pairing-dependent ternary complex can form between Lsm2-8 and U2 and U6 helix II RNAs. We propose that this interaction may play a role in formation of transient spliceosome intermediates formed during activation.
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Affiliation(s)
- Xingyang Fu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Harpreet Kaur
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Margaret L. Rodgers
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Eric J. Montemayor
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Samuel E. Butcher
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Aaron A. Hoskins
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
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7
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Li YH, Chang ZT, Yen MR, Huang YF, Chen TH, Chang JC, Wu MC, Yang YL, Chen YW, Nai YS. Transcriptome of Nosema ceranae and Upregulated Microsporidia Genes during Its Infection of Western Honey Bee ( Apis mellifera). INSECTS 2022; 13:716. [PMID: 36005340 PMCID: PMC9409478 DOI: 10.3390/insects13080716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/29/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Nosema ceranae is one of the fungal parasites of Apis mellifera. It causes physical and behavioral effects in honey bees. However, only a few studies have reported on gene expression profiling during A. mellifera infection. In this study, the transcriptome profile of mature spores at each time point of infection (5, 10, and 20 days post-infection, d.p.i.) were investigated. Based on the transcriptome and expression profile analysis, a total of 878, 952, and 981 differentially expressed genes (DEGs) (fold change ≥ 2 or ≤ -2) were identified in N. ceranae spores (NcSp) at 5 d.p.i., 10 d.p.i., and 20 d.p.i., respectively. Moreover, 70 upregulated genes and 340 downregulated genes among common DEGs (so-called common DEGs) and 166 stage-specific genes at each stage of infection were identified. The Gene Ontology (GO) analysis indicated that the DEGs and corresponding common DEGs are involved in the functions of cytosol (GO:0005829), cytoplasm (GO:0005737), and ATP binding (GO:0005524). Furthermore, the pathway analysis found that the DEGs and common DEGs are involved in metabolism, environmental information processing, and organismal systems. Four upregulated common DEGs with higher fold-change values, highly associated with spore proteins and transcription factors, were selected for validation. In addition, the stage-specific genes are highly involved in the mechanism of pre-mRNA splicing according to GO enrichment analysis; thus, three of them showed high expression at each d.p.i. and were also subjected to validation. The relative gene expression levels showed a similar tendency as the transcriptome predictions at different d.p.i., revealing that the gene expression of N. ceranae during infection may be related to the mechanism of gene transcription, protein synthesis, and structural proteins. Our data suggest that the gene expression profiling of N. ceranae at the transcriptomic level could be a reference for the monitoring of nosemosis at the genetic level.
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Affiliation(s)
- Yi-Hsuan Li
- Department of Entomology, National Chung Hsing University, Taichung City 40227, Taiwan
| | - Zih-Ting Chang
- Department of Biotechnology and Animal Science, National Ilan University, Yi-Lan City 26047, Taiwan
| | - Ming-Ren Yen
- Department of Entomology, National Chung Hsing University, Taichung City 40227, Taiwan
| | - Yu-Feng Huang
- Department of Entomology, National Chung Hsing University, Taichung City 40227, Taiwan
- Department of Computer Science and Engineering, Yuan-Ze University, Tao-Yuan City 32003, Taiwan
| | - Tzu-Han Chen
- Department of Entomology, National Chung Hsing University, Taichung City 40227, Taiwan
| | - Ju-Chun Chang
- Department of Entomology, National Chung Hsing University, Taichung City 40227, Taiwan
| | - Ming-Cheng Wu
- Department of Entomology, National Chung Hsing University, Taichung City 40227, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei City 11529, Taiwan
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711010, Taiwan
| | - Yue-Wen Chen
- Department of Biotechnology and Animal Science, National Ilan University, Yi-Lan City 26047, Taiwan
| | - Yu-Shin Nai
- Department of Entomology, National Chung Hsing University, Taichung City 40227, Taiwan
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8
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Zhan X, Lu Y, Zhang X, Yan C, Shi Y. Mechanism of exon ligation by human spliceosome. Mol Cell 2022; 82:2769-2778.e4. [PMID: 35705093 DOI: 10.1016/j.molcel.2022.05.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/07/2022] [Accepted: 05/18/2022] [Indexed: 11/18/2022]
Abstract
Pre-mRNA splicing involves two sequential reactions: branching and exon ligation. The C complex after branching undergoes remodeling to become the C∗ complex, which executes exon ligation. Here, we report cryo-EM structures of two intermediate human spliceosomal complexes, pre-C∗-I and pre-C∗-II, both at 3.6 Å. In both structures, the 3' splice site is already docked into the active site, the ensuing 3' exon sequences are anchored on PRP8, and the step II factor FAM192A contacts the duplex between U2 snRNA and the branch site. In the transition of pre-C∗-I to pre-C∗-II, the step II factors Cactin, FAM32A, PRKRIP1, and SLU7 are recruited. Notably, the RNA helicase PRP22 is positioned quite differently in the pre-C∗-I, pre-C∗-II, and C∗ complexes, suggesting a role in 3' exon binding and proofreading. Together with information on human C and C∗ complexes, our studies recapitulate a molecular choreography of the C-to-C∗ transition, revealing mechanistic insights into exon ligation.
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Affiliation(s)
- Xiechao Zhan
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.
| | - Yichen Lu
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; College of Life Sciences, Fudan University, Shanghai 200433, China
| | - Xiaofeng Zhang
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Chuangye Yan
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yigong Shi
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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9
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Idrissou M, Maréchal A. The PRP19 Ubiquitin Ligase, Standing at the Cross-Roads of mRNA Processing and Genome Stability. Cancers (Basel) 2022; 14:cancers14040878. [PMID: 35205626 PMCID: PMC8869861 DOI: 10.3390/cancers14040878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/01/2022] [Accepted: 02/04/2022] [Indexed: 12/07/2022] Open
Abstract
mRNA processing factors are increasingly being recognized as important regulators of genome stability. By preventing and resolving RNA:DNA hybrids that form co-transcriptionally, these proteins help avoid replication-transcription conflicts and thus contribute to genome stability through their normal function in RNA maturation. Some of these factors also have direct roles in the activation of the DNA damage response and in DNA repair. One of the most intriguing cases is that of PRP19, an evolutionarily conserved essential E3 ubiquitin ligase that promotes mRNA splicing, but also participates directly in ATR activation, double-strand break resection and mitosis. Here, we review historical and recent work on PRP19 and its associated proteins, highlighting their multifarious cellular functions as central regulators of spliceosome activity, R-loop homeostasis, DNA damage signaling and repair and cell division. Finally, we discuss open questions that are bound to shed further light on the functions of PRP19-containing complexes in both normal and cancer cells.
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Affiliation(s)
- Mouhamed Idrissou
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada;
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H 5N3, Canada
| | - Alexandre Maréchal
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada;
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H 5N3, Canada
- Correspondence:
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10
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Liu X, Pan X, Chen D, Yin C, Peng J, Shi W, Qi L, Wang R, Zhao W, Zhang Z, Yang J, Peng YL. Prp19-associated splicing factor Cwf15 regulates fungal virulence and development in the rice blast fungus. Environ Microbiol 2021; 23:5901-5916. [PMID: 34056823 DOI: 10.1111/1462-2920.15616] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 11/29/2022]
Abstract
The splicing factor Cwf15 is an essential component of the Prp19-associated component of the spliceosome and regulates intron splicing in several model species, including yeasts and human cells. However, the roles of Cwf15 remain unexplored in plant pathogenic fungi. Here, we report that MoCWF15 in the rice blast fungus Magnaporthe oryzae is non-essential to viability and important to fungal virulence, growth and conidiation. MoCwf15 contains a putative nuclear localization signal (NLS) and is localized into the nucleus. The NLS sequence but not the predicted phosphorylation site or two sumoylation sites was essential for the biological functions of MoCwf15. Importantly, MoCwf15 physically interacted with the Prp19-associated splicing factors MoCwf4, MoSsa1 and MoCyp1, and negatively regulated protein accumulations of MoCyp1 and MoCwf4. Furthermore, with the deletion of MoCWF15, aberrant intron splicing occurred in near 400 genes, 20 of which were important to the fungal development and virulence. Taken together, MoCWF15 regulates fungal growth and infection-related development by modulating the intron splicing efficiency of a subset of genes in the rice blast fungus.
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Affiliation(s)
- Xinsen Liu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Xiao Pan
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Deng Chen
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Changfa Yin
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Junbo Peng
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Wei Shi
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Linlu Qi
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Ruijin Wang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Wensheng Zhao
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China.,Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Jun Yang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - You-Liang Peng
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
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11
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Wong DK, Stark MS, Rader SD, Fast NM. Characterization of Pre-mRNA Splicing and Spliceosomal Machinery in Porphyridium purpureum and Evolutionary Implications for Red Algae. J Eukaryot Microbiol 2021; 68:e12844. [PMID: 33569840 DOI: 10.1111/jeu.12844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/28/2021] [Accepted: 02/05/2021] [Indexed: 11/29/2022]
Abstract
Pre-mRNA splicing is a highly conserved eukaryotic process, but our understanding of it is limited by a historical focus on well-studied organisms such as humans and yeast. There is considerable diversity in mechanisms and components of pre-mRNA splicing, especially in lineages that have evolved under the pressures of genome reduction. The ancestor of red algae is thought to have undergone genome reduction prior to the lineage's radiation, resulting in overall gene and intron loss in extant groups. Previous studies on the extremophilic red alga Cyanidioschyzon merolae revealed an intron-sparse genome with a highly reduced spliceosome. To determine whether these features applied to other red algae, we investigated multiple aspects of pre-mRNA splicing in the mesophilic red alga Porphyridium purpureum. Through strand-specific RNA-Seq, we observed high levels of intron retention across a large number of its introns, and nearly half of the transcripts for these genes are not spliced at all. We also discovered a relationship between variability of 5' splice site sequences and levels of splicing. To further investigate the connections between intron retention and splicing machinery, we bioinformatically assembled the P. purpureum spliceosome, and biochemically verified the presence of snRNAs. While most other core spliceosomal components are present, our results suggest highly divergent or missing U1 snRNP proteins, despite the presence of an uncharacteristically long U1 snRNA. These unusual aspects highlight the diverse nature of pre-mRNA splicing that can be seen in lesser-studied eukaryotes, raising the importance of investigating fundamental eukaryotic processes outside of model organisms.
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Affiliation(s)
- Donald K Wong
- Department of Botany, University of British Columbia, 3156-6270 University Boulevard, Vancouver, BC, Canada
| | - Martha S Stark
- Department of Chemistry, University of Northern British Columbia, 3333 University Way, Prince George, BC, Canada
| | - Stephen D Rader
- Department of Chemistry, University of Northern British Columbia, 3333 University Way, Prince George, BC, Canada
| | - Naomi M Fast
- Department of Botany, University of British Columbia, 3156-6270 University Boulevard, Vancouver, BC, Canada
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12
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Petasny M, Bentata M, Pawellek A, Baker M, Kay G, Salton M. Splicing to Keep Cycling: The Importance of Pre-mRNA Splicing during the Cell Cycle. Trends Genet 2020; 37:266-278. [PMID: 32950269 DOI: 10.1016/j.tig.2020.08.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/09/2020] [Accepted: 08/18/2020] [Indexed: 12/16/2022]
Abstract
Pre-mRNA splicing is a fundamental process in mammalian gene expression, and alternative splicing plays an extensive role in generating protein diversity. Because the majority of genes undergo pre-mRNA splicing, most cellular processes depend on proper spliceosome function. We focus on the cell cycle and describe its dependence on pre-mRNA splicing and accurate alternative splicing. We outline the key cell-cycle factors and their known alternative splicing isoforms. We discuss different levels of pre-mRNA splicing regulation such as post-translational modifications and changes in the expression of splicing factors. We describe the effect of chromatin dynamics on pre-mRNA splicing during the cell cycle. In addition, we focus on spliceosome component SF3B1, which is mutated in many types of cancer, and describe the link between SF3B1 and its inhibitors and the cell cycle.
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Affiliation(s)
- Mayra Petasny
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Mercedes Bentata
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Andrea Pawellek
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Mai Baker
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Gillian Kay
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Maayan Salton
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.
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13
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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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14
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Hervas R, Rau MJ, Park Y, Zhang W, Murzin AG, Fitzpatrick JAJ, Scheres SHW, Si K. Cryo-EM structure of a neuronal functional amyloid implicated in memory persistence in Drosophila. Science 2020; 367:1230-1234. [PMID: 32165583 DOI: 10.1126/science.aba3526] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/18/2020] [Indexed: 12/14/2022]
Abstract
How long-lived memories withstand molecular turnover is a fundamental question. Aggregates of a prion-like RNA-binding protein, cytoplasmic polyadenylation element-binding (CPEB) protein, is a putative substrate of long-lasting memories. We isolated aggregated Drosophila CPEB, Orb2, from adult heads and determined its activity and atomic structure, at 2.6-angstrom resolution, using cryo-electron microscopy. Orb2 formed ~75-nanometer-long threefold-symmetric amyloid filaments. Filament formation transformed Orb2 from a translation repressor to an activator and "seed" for further translationally active aggregation. The 31-amino acid protofilament core adopted a cross-β unit with a single hydrophilic hairpin stabilized through interdigitated glutamine packing. Unlike the hydrophobic core of pathogenic amyloids, the hydrophilic core of Orb2 filaments suggests how some neuronal amyloids could be a stable yet regulatable substrate of memory.
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Affiliation(s)
- Ruben Hervas
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Michael J Rau
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Younshim Park
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Wenjuan Zhang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Alexey G Murzin
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA.,Departments of Neuroscience and Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Sjors H W Scheres
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kausik Si
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA. .,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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15
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Zhao X, Xiao T, Jin S, Wang J, Wang J, Luo H, Li R, Sun T, Zou J, Li Y. Characterization and immune function of the interferon-β promoter stimulator-1 in the barbel chub, Squaliobarbus curriculus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 104:103571. [PMID: 31837379 DOI: 10.1016/j.dci.2019.103571] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/29/2019] [Accepted: 12/10/2019] [Indexed: 06/10/2023]
Abstract
To elucidate the immunity-protecting role of the interferon-β promoter stimulator-1 (ScIPS-1) in barbel chub Squaliobarbus curriculus, the full-length cDNA of ScIPS-1 was cloned and expression levels in response to stimulation were investigated. In addition, the function of ScIPS-1 and its domains were analyzed. The full-length cDNA of ScIPS-1 is 2524 bp and encodes 601 aa. The N-terminal caspase activation and recruitment domain, central proline-rich domain, C-terminal transmembrane domain, C2HC-zinc finger, and Cwf21 domains were identified. The mRNA level of ScIPS-1 was the highest in the kidney, whereas the highest protein level was observed in the liver. The ScIPS-1 expressions were significantly up-regulated after lipopolysaccharide and poly I:C treatment. The ScIPS-1 protein level was up-regulated at 12 h in the head kidney and was up-regulated at 12 h and then down-regulated from 12 to 48 h in the liver after grass carp reovirus (GCRV) infection. The CiIFN and CiMx transcription levels were significantly enhanced in pEGFP-C1-IPS-1 and pcDNA3.1-ΔCwf21 overexpressing cells after GCRV infection. The results indicate that ScIPS-1 may function in the immune response against pathogens and provide a basis for achieving resistance to diseases in fish breeding.
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Affiliation(s)
- Xin Zhao
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Tiaoyi Xiao
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Shengzhen Jin
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Jing'an Wang
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Junya Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Hong Luo
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Rui Li
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Tong Sun
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Jun Zou
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, 410128, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Yaoguo Li
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, 410128, China.
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16
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Haeberlein S, Angrisano A, Quack T, Lu Z, Kellershohn J, Blohm A, Grevelding CG, Hahnel SR. Identification of a new panel of reference genes to study pairing-dependent gene expression in Schistosoma mansoni. Int J Parasitol 2019; 49:615-624. [PMID: 31136746 DOI: 10.1016/j.ijpara.2019.01.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 01/09/2019] [Accepted: 01/15/2019] [Indexed: 12/18/2022]
Abstract
Facilitated by the Schistosoma mansoni genome project, multiple transcriptomic studies were performed over the last decade to elucidate gene expression patterns among different developmental stages of the complex schistosome life cycle. While these analyses enable the identification of candidate genes with key functions in schistosome biology, a diverse molecular tool set is needed that allows comprehensive functional characterization at the single gene level. This includes the availability of reliable reference genes to confirm changes in the transcription of genes of interest over different biological samples and experimental conditions. In particular, the investigation of one key aspect of schistosome biology, the pairing-dependent gene expression in females and males, requires knowledge on reference genes that are expressed independently of both pairing and of in vitro culture effects. Therefore, the present study focused on the identification of quantitative reverse transcription (qRT)-PCR reference genes suitable for the investigation of pairing-dependent gene expression in the S. mansoni male. The "pipeline" we present here is based on qRT-PCR analyses of high biological replication combined with three different statistical analysis tools, BestKeeper, geNorm, and NormFinder. Our approach resulted in a statistically robust ranking of 15 selected reference genes with respect to their transcription stability between pairing-unexperienced and -experienced males. We further tested the top seven candidate genes for their transcription stability during invitro culture of adult S. mansoni. Of these, the two most suitable reference genes were used to investigate the influence of the pairing contact on the transcription of genes of interest, comprising a tyrosine decarboxylase gene Smtdc1, an ebony ortholog Smebony, and the follistatin ortholog Smfst in S. mansoni males. Performing pairing, separation and re-pairing experiments with adult S. mansoni in vitro, our results indicate for the first time that pairing can act as a molecular on/off-switch of specific genes to strictly control their expression in schistosome males.
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Affiliation(s)
- Simone Haeberlein
- Institute of Parasitology, BFS, Justus-Liebig-University, Giessen, Germany
| | | | - Thomas Quack
- Institute of Parasitology, BFS, Justus-Liebig-University, Giessen, Germany
| | - Zhigang Lu
- Institute of Parasitology, BFS, Justus-Liebig-University, Giessen, Germany; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Josina Kellershohn
- Institute of Parasitology, BFS, Justus-Liebig-University, Giessen, Germany
| | - Ariane Blohm
- Institute of Parasitology, BFS, Justus-Liebig-University, Giessen, Germany
| | | | - Steffen R Hahnel
- Institute of Parasitology, BFS, Justus-Liebig-University, Giessen, Germany.
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17
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Gatti da Silva GH, Jurica MS, Chagas da Cunha JP, Oliveira CC, Coltri PP. Human RNF113A participates of pre-mRNA splicing in vitro. J Cell Biochem 2019; 120:8764-8774. [PMID: 30506991 DOI: 10.1002/jcb.28163] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 11/08/2018] [Indexed: 01/24/2023]
Abstract
Pre-messenger RNA (mRNA) splicing is an essential step in the control of eukaryotic gene expression. During splicing, the introns are removed from the gene transcripts as the exons are ligated to create mature mRNA sequences. Splicing is performed by the spliceosome, which is a macromolecular complex composed of five small nuclear RNAs (snRNAs) and more than 100 proteins. Except for the core snRNP proteins, most spliceosome proteins are transiently associated and presumably involved with the regulation of spliceosome activity. In this study, we explored the association and participation of the human protein RNF113A in splicing. The addition of excess recombinant RNF113A to in vitro splicing reactions results in splicing inhibition. In whole-cell lysates, RNF113A co-immunoprecipitated with U2, U4, and U6 snRNAs, which are components of the tri-snRNP, and with proteins PRP19 and BRR2. When HeLa cells were CRISPR-edited to reduce the RNF113A levels, the in vitro splicing efficiency was severely affected. Consistently, the splicing activity was partially restored after the addition of the recombinant GST-RNF113A. On the basis on these results, we propose a model in which RNF113A associates with the spliceosome by interacting with PRP19, promoting essential rearrangements that lead to splicing.
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Affiliation(s)
- Guilherme H Gatti da Silva
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Melissa S Jurica
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California
| | | | - Carla C Oliveira
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Patricia P Coltri
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California.,Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
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18
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Raut S, Yadav K, Verma AK, Tak Y, Waiker P, Sahi C. Co-evolution of spliceosomal disassembly interologs: crowning J-protein component with moonlighting RNA-binding activity. Curr Genet 2018; 65:561-573. [DOI: 10.1007/s00294-018-0906-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/30/2018] [Accepted: 11/14/2018] [Indexed: 11/28/2022]
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19
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Bai R, Wan R, Yan C, Lei J, Shi Y. Structures of the fully assembled Saccharomyces cerevisiae spliceosome before activation. Science 2018; 360:1423-1429. [PMID: 29794219 DOI: 10.1126/science.aau0325] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 05/16/2018] [Indexed: 11/02/2022]
Abstract
The precatalytic spliceosome (B complex) is preceded by the pre-B complex. Here we report the cryo-electron microscopy structures of the Saccharomyces cerevisiae pre-B and B complexes at average resolutions of 3.3 to 4.6 and 3.9 angstroms, respectively. In the pre-B complex, the duplex between the 5' splice site (5'SS) and U1 small nuclear RNA (snRNA) is recognized by Yhc1, Luc7, and the Sm ring. In the B complex, U1 small nuclear ribonucleoprotein is dissociated, the 5'-exon-5'SS sequences are translocated near U6 snRNA, and three B-specific proteins may orient the precursor messenger RNA. In both complexes, U6 snRNA is anchored to loop I of U5 snRNA, and the duplex between the branch point sequence and U2 snRNA is recognized by the SF3b complex. Structural analysis reveals the mechanism of assembly and activation for the yeast spliceosome.
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Affiliation(s)
- Rui Bai
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Schools of Life Sciences and Medicine, Tsinghua University, Beijing 100084, China
| | - Ruixue Wan
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Schools of Life Sciences and Medicine, Tsinghua University, Beijing 100084, China
| | - Chuangye Yan
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Schools of Life Sciences and Medicine, Tsinghua University, Beijing 100084, China
| | - Jianlin Lei
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Schools of Life Sciences and Medicine, Tsinghua University, Beijing 100084, China.,Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yigong Shi
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Schools of Life Sciences and Medicine, Tsinghua University, Beijing 100084, China. .,Institute of Biology, Westlake Institute for Advanced Study, Westlake University, 18 Shilongshan Road, Xihu District, Hangzhou 310064, Zhejiang Province, China
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20
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Su YL, Chen HC, Tsai RT, Lin PC, Cheng SC. Cwc23 is a component of the NTR complex and functions to stabilize Ntr1 and facilitate disassembly of spliceosome intermediates. Nucleic Acids Res 2018; 46:3764-3773. [PMID: 29390077 PMCID: PMC6044358 DOI: 10.1093/nar/gky052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/17/2018] [Accepted: 01/19/2018] [Indexed: 01/22/2023] Open
Abstract
Cwc23 is a member of the J protein family, and has been shown to interact with Ntr1, a scaffold protein that interacts with Ntr2 and Prp43 to form the NTR complex that mediates spliceosome disassembly. We show that Cwc23 is also an intrinsic component of the NTR complex, and that it interacts with the carboxyl terminus of Ntr1. Metabolic depletion of Cwc23 concurrently depleted Ntr1 and Ntr2, suggesting a role for Cwc23 in stabilizing these two proteins. Ntr1, Ntr2 and Cwc23 are stoichiometrically balanced, and form a stable heterotrimer. Depletion of Cwc23 from splicing extracts using antibodies resulted in depletion of all three proteins and accumulation of intron-lariat in the splicing reaction. Cwc23 is not required for disassembly of intron-lariat spliceosome (ILS), but facilitates disassembly of spliceosome intermediates after the actions of Prp2 and Prp16 by stabilizing the association of Ntr1 with the spliceosome. Cwc23 has a more limited effect on the association of Ntr1 with the ILS. Our data suggest that Cwc23 is important for maintaining the levels of Ntr1 and Ntr2, and that it also plays a regulatory role in targeting spliceosome intermediates for disassembly.
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Affiliation(s)
- Yu-Lun Su
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
| | - Hsin-Chou Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
| | - Rong-Tzong Tsai
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
| | - Pei-Chun Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
| | - Soo-Chen Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
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21
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Zhang X, Yan C, Zhan X, Li L, Lei J, Shi Y. Structure of the human activated spliceosome in three conformational states. Cell Res 2018; 28:307-322. [PMID: 29360106 PMCID: PMC5835773 DOI: 10.1038/cr.2018.14] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/02/2018] [Accepted: 01/08/2018] [Indexed: 12/13/2022] Open
Abstract
During each cycle of pre-mRNA splicing, the pre-catalytic spliceosome (B complex) is converted into the activated spliceosome (Bact complex), which has a well-formed active site but cannot proceed to the branching reaction. Here, we present the cryo-EM structure of the human Bact complex in three distinct conformational states. The EM map allows atomic modeling of nearly all protein components of the U2 small nuclear ribonucleoprotein (snRNP), including three of the SF3a complex and seven of the SF3b complex. The structure of the human Bact complex contains 52 proteins, U2, U5, and U6 small nuclear RNA (snRNA), and a pre-mRNA. Three distinct conformations have been captured, representing the early, mature, and late states of the human Bact complex. These complexes differ in the orientation of the Switch loop of Prp8, the splicing factors RNF113A and NY-CO-10, and most components of the NineTeen complex (NTC) and the NTC-related complex. Analysis of these three complexes and comparison with the B and C complexes reveal an ordered flux of components in the B-to-Bact and the Bact-to-B* transitions, which ultimately prime the active site for the branching reaction.
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Affiliation(s)
- Xiaofeng Zhang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Chuangye Yan
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiechao Zhan
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Lijia Li
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jianlin Lei
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yigong Shi
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Shilongshan Road No. 18, Hangzhou, Zhejiang 310064, China
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22
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Abstract
The synthesis, processing and function of coding and non-coding RNA molecules and their interacting proteins has been the focus of a great deal of research that has boosted our understanding of key molecular pathways that underlie higher order events such as cell cycle control, development, innate immune response and the occurrence of genetic diseases. In this study, we have found that formamide preferentially weakens RNA related processes in vivo. Using a non-essential Schizosaccharomyces pombe gene deletion collection, we identify deleted loci that make cells sensitive to formamide. Sensitive deletions are significantly enriched in genes involved in RNA metabolism. Accordingly, we find that previously known temperature-sensitive splicing mutants become lethal in the presence of the drug under permissive temperature. Furthermore, in a wild type background, splicing efficiency is decreased and R-loop formation is increased in the presence of formamide. In addition, we have also isolated 35 formamide-sensitive mutants, many of which display remarkable morphology and cell cycle defects potentially unveiling new players in the regulation of these processes. We conclude that formamide preferentially targets RNA related processes in vivo, probably by relaxing RNA secondary structures and/or RNA-protein interactions, and can be used as an effective tool to characterize these processes.
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23
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Hálová M, Gahura O, Převorovský M, Cit Z, Novotný M, Valentová A, Abrhámová K, Půta F, Folk P. Nineteen complex-related factor Prp45 is required for the early stages of cotranscriptional spliceosome assembly. RNA (NEW YORK, N.Y.) 2017; 23:1512-1524. [PMID: 28701519 PMCID: PMC5602110 DOI: 10.1261/rna.061986.117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 06/21/2017] [Indexed: 05/22/2023]
Abstract
Splicing in S. cerevisiae has been shown to proceed cotranscriptionally, but the nature of the coupling remains a subject of debate. Here, we examine the effect of nineteen complex-related splicing factor Prp45 (a homolog of SNW1/SKIP) on cotranscriptional splicing. RNA-sequencing and RT-qPCR showed elevated pre-mRNA levels but only limited reduction of spliced mRNAs in cells expressing C-terminally truncated Prp45, Prp45(1-169). Assays with a series of reporters containing the AMA1 intron with regulatable splicing confirmed decreased splicing efficiency and showed the leakage of unspliced RNAs in prp45(1-169) cells. We also measured pre-mRNA accumulation of the meiotic MER2 gene, which depends on the expression of Mer1 factor for splicing. prp45(1-169) cells accumulated approximately threefold higher levels of MER2 pre-mRNA than WT cells only when splicing was induced. To monitor cotranscriptional splicing, we determined the presence of early spliceosome assembly factors and snRNP complexes along the ECM33 and ACT1 genes. We found that prp45(1-169) hampered the cotranscriptional recruitment of U2 and, to a larger extent, U5 and NTC, while the U1 profile was unaffected. The recruitment of Prp45(1-169) was impaired similarly to U5 snRNP and NTC. Our results imply that Prp45 is required for timely formation of complex A, prior to stable physical association of U5/NTC with the emerging pre-mRNA substrate. We suggest that Prp45 facilitates conformational rearrangements and/or contacts that couple U1 snRNP-recognition to downstream assembly events.
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Affiliation(s)
- Martina Hálová
- Department of Cell Biology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | - Ondřej Gahura
- Department of Cell Biology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | - Martin Převorovský
- Department of Cell Biology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | - Zdeněk Cit
- Department of Cell Biology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | - Marian Novotný
- Department of Cell Biology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | - Anna Valentová
- Department of Cell Biology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | - Kateřina Abrhámová
- Department of Cell Biology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | - František Půta
- Department of Cell Biology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | - Petr Folk
- Department of Cell Biology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
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24
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Vilhais-Neto GC, Fournier M, Plassat JL, Sardiu ME, Saraf A, Garnier JM, Maruhashi M, Florens L, Washburn MP, Pourquié O. The WHHERE coactivator complex is required for retinoic acid-dependent regulation of embryonic symmetry. Nat Commun 2017; 8:728. [PMID: 28959017 PMCID: PMC5620087 DOI: 10.1038/s41467-017-00593-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 07/11/2017] [Indexed: 12/23/2022] Open
Abstract
Bilateral symmetry is a striking feature of the vertebrate body plan organization. Vertebral precursors, called somites, provide one of the best illustrations of embryonic symmetry. Maintenance of somitogenesis symmetry requires retinoic acid (RA) and its coactivator Rere/Atrophin2. Here, using a proteomic approach we identify a protein complex, containing Wdr5, Hdac1, Hdac2 and Rere (named WHHERE), which regulates RA signaling and controls embryonic symmetry. We demonstrate that Wdr5, Hdac1, and Hdac2 are required for RA signaling in vitro and in vivo. Mouse mutants for Wdr5 and Hdac1 exhibit asymmetrical somite formation characteristic of RA-deficiency. We also identify the Rere-binding histone methyltransferase Ehmt2/G9a, as a RA coactivator controlling somite symmetry. Upon RA treatment, WHHERE and Ehmt2 become enriched at RA target genes to promote RNA polymerase II recruitment. Our work identifies a protein complex linking key epigenetic regulators acting in the molecular control of embryonic bilateral symmetry.Retinoic acid (RA) regulates the maintenance of somitogenesis symmetry. Here, the authors use a proteomic approach to identify a protein complex of Wdr5, Hdac1, Hdac2 that act together with RA and coactivator Rere/Atrophin2 and a histone methyltransferase Ehmt2 to regulate embryonic symmetry.
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Affiliation(s)
- Gonçalo C Vilhais-Neto
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch, F-67400, France.,Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Marjorie Fournier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch, F-67400, France
| | - Jean-Luc Plassat
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch, F-67400, France
| | - Mihaela E Sardiu
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Anita Saraf
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Jean-Marie Garnier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch, F-67400, France
| | - Mitsuji Maruhashi
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch, F-67400, France.,Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA.,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Olivier Pourquié
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch, F-67400, France. .,Stowers Institute for Medical Research, Kansas City, MO, 64110, USA. .,Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA. .,Howard Hughes Medical Institute, Kansas City, MO, 64110, USA. .,Department of Genetics, Harvard Medical School and Department of Pathology, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA, 02115, USA.
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25
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Nissen KE, Homer CM, Ryan CJ, Shales M, Krogan NJ, Patrick KL, Guthrie C. The histone variant H2A.Z promotes splicing of weak introns. Genes Dev 2017; 31:688-701. [PMID: 28446597 PMCID: PMC5411709 DOI: 10.1101/gad.295287.116] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/22/2017] [Indexed: 12/12/2022]
Abstract
In this study, Nissen et al. investigated the function of the highly conserved histone variant H2A.Z in pre-mRNA splicing using the intron-rich model yeast S. pombe. The findings suggest that H2A.Z occupancy promotes cotranscriptional splicing of suboptimal introns that may otherwise be discarded via proofreading ATPases. Multiple lines of evidence implicate chromatin in the regulation of premessenger RNA (pre-mRNA) splicing. However, the influence of chromatin factors on cotranscriptional splice site usage remains unclear. Here we investigated the function of the highly conserved histone variant H2A.Z in pre-mRNA splicing using the intron-rich model yeast Schizosaccharomyces pombe. Using epistatic miniarray profiles (EMAPs) to survey the genetic interaction landscape of the Swr1 nucleosome remodeling complex, which deposits H2A.Z, we uncovered evidence for functional interactions with components of the spliceosome. In support of these genetic connections, splicing-specific microarrays show that H2A.Z and the Swr1 ATPase are required during temperature stress for the efficient splicing of a subset of introns. Notably, affected introns are enriched for H2A.Z occupancy and more likely to contain nonconsensus splice sites. To test the significance of the latter correlation, we mutated the splice sites in an affected intron to consensus and found that this suppressed the requirement for H2A.Z in splicing of that intron. These data suggest that H2A.Z occupancy promotes cotranscriptional splicing of suboptimal introns that may otherwise be discarded via proofreading ATPases. Consistent with this model, we show that overexpression of splicing ATPase Prp16 suppresses both the growth and splicing defects seen in the absence of H2A.Z.
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Affiliation(s)
- Kelly E Nissen
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco 94158, California, USA
| | - Christina M Homer
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco 94158, California, USA
| | - Colm J Ryan
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
| | - Michael Shales
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco 94158, California, USA.,California Institute for Quantitative Biosciences (QB3), San Francisco 94158, California, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco 94158, California, USA.,California Institute for Quantitative Biosciences (QB3), San Francisco 94158, California, USA.,J. David Gladstone Institutes, San Francisco 94158, California, USA
| | - Kristin L Patrick
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco 94158, California, USA.,Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, Texas 77807, USA
| | - Christine Guthrie
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco 94158, California, USA
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26
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Pfannenstiel BT, Zhao X, Wortman J, Wiemann P, Throckmorton K, Spraker JE, Soukup AA, Luo X, Lindner DL, Lim FY, Knox BP, Haas B, Fischer GJ, Choera T, Butchko RAE, Bok JW, Affeldt KJ, Keller NP, Palmer JM. Revitalization of a Forward Genetic Screen Identifies Three New Regulators of Fungal Secondary Metabolism in the Genus Aspergillus. mBio 2017; 8:e01246-17. [PMID: 28874473 PMCID: PMC5587912 DOI: 10.1128/mbio.01246-17] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 08/08/2017] [Indexed: 11/24/2022] Open
Abstract
The study of aflatoxin in Aspergillus spp. has garnered the attention of many researchers due to aflatoxin's carcinogenic properties and frequency as a food and feed contaminant. Significant progress has been made by utilizing the model organism Aspergillus nidulans to characterize the regulation of sterigmatocystin (ST), the penultimate precursor of aflatoxin. A previous forward genetic screen identified 23 A. nidulans mutants involved in regulating ST production. Six mutants were characterized from this screen using classical mapping (five mutations in mcsA) and complementation with a cosmid library (one mutation in laeA). The remaining mutants were backcrossed and sequenced using Illumina and Ion Torrent sequencing platforms. All but one mutant contained one or more sequence variants in predicted open reading frames. Deletion of these genes resulted in identification of mutant alleles responsible for the loss of ST production in 12 of the 17 remaining mutants. Eight of these mutations were in genes already known to affect ST synthesis (laeA, mcsA, fluG, and stcA), while the remaining four mutations (in laeB, sntB, and hamI) were in previously uncharacterized genes not known to be involved in ST production. Deletion of laeB, sntB, and hamI in A. flavus results in loss of aflatoxin production, confirming that these regulators are conserved in the aflatoxigenic aspergilli. This report highlights the multifaceted regulatory mechanisms governing secondary metabolism in Aspergillus Additionally, these data contribute to the increasing number of studies showing that forward genetic screens of fungi coupled with whole-genome resequencing is a robust and cost-effective technique.IMPORTANCE In a postgenomic world, reverse genetic approaches have displaced their forward genetic counterparts. The techniques used in forward genetics to identify loci of interest were typically very cumbersome and time-consuming, relying on Mendelian traits in model organisms. The current work was pursued not only to identify alleles involved in regulation of secondary metabolism but also to demonstrate a return to forward genetics to track phenotypes and to discover genetic pathways that could not be predicted through a reverse genetics approach. While identification of mutant alleles from whole-genome sequencing has been done before, here we illustrate the possibility of coupling this strategy with a genetic screen to identify multiple alleles of interest. Sequencing of classically derived mutants revealed several uncharacterized genes, which represent novel pathways to regulate and control the biosynthesis of sterigmatocystin and of aflatoxin, a societally and medically important mycotoxin.
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Affiliation(s)
| | - Xixi Zhao
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jennifer Wortman
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Philipp Wiemann
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kurt Throckmorton
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Joseph E Spraker
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alexandra A Soukup
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Xingyu Luo
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel L Lindner
- Center for Forest Mycology Research, Northern Research Station, U.S. Forest Service, Madison, Wisconsin, USA
| | - Fang Yun Lim
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Benjamin P Knox
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Brian Haas
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gregory J Fischer
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Tsokyi Choera
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Robert A E Butchko
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, USA
| | - Jin-Woo Bok
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Katharyn J Affeldt
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jonathan M Palmer
- Center for Forest Mycology Research, Northern Research Station, U.S. Forest Service, Madison, Wisconsin, USA
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Microbial cyclophilins: specialized functions in virulence and beyond. World J Microbiol Biotechnol 2017; 33:164. [PMID: 28791545 DOI: 10.1007/s11274-017-2330-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/05/2017] [Indexed: 01/18/2023]
Abstract
Cyclophilins belong to the superfamily of peptidyl-prolyl cis/trans isomerases (PPIases, EC: 5.2.1.8), the enzymes that catalyze the cis/trans isomerization of peptidyl-prolyl peptide bonds in unfolded and partially folded polypeptide chains and native state proteins. Cyclophilins have been extensively studied, since they are involved in multiple cellular processes related to human pathologies, such as neurodegenerative disorders, infectious diseases, and cancer. However, the presence of cyclophilins in all domains of life indicates a broader biological importance. In this mini-review, we summarize current advances in the study of microbial cyclophilins. Apart from their anticipated role in protein folding and chaperoning, cyclophilins are involved in several other biological processes, such as cellular signal transduction, adaptation to stress, control of pathogens virulence, and modulation of host immune response. Since many existing family members do not have well-defined functions and novel ones are being characterized, the requirement for further studies on their biological role and molecular mechanism of action is apparent.
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Role of Cwc24 in the First Catalytic Step of Splicing and Fidelity of 5' Splice Site Selection. Mol Cell Biol 2017; 37:MCB.00580-16. [PMID: 27994011 DOI: 10.1128/mcb.00580-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 12/11/2016] [Indexed: 12/17/2022] Open
Abstract
Cwc24 is an essential splicing factor but only transiently associates with the spliceosome, with an unknown function. The protein contains a RING finger and a zinc finger domain in the carboxyl terminus. The human ortholog of Cwc24, RNF113A, has been associated with the disorder trichothiodystrophy. Here, we show that the zinc finger domain is essential for Cwc24 function, while the RING finger domain is dispensable. Cwc24 binds to the spliceosome after the Prp19-associated complex and is released upon Prp2 action. Cwc24 is not required for Prp2-mediated remodeling of the spliceosome, but the spliceosome becomes inactive if remodeling occurs before the addition of Cwc24. Cwc24 binds directly to pre-mRNA at the 5' splice site, spanning the splice junction. In the absence of Cwc24, U5 and U6 modes of interaction with the 5' splice site are altered, and splicing is very inefficient, with aberrant cleavage at the 5' splice site. Our data suggest roles for Cwc24 in orchestrating organization of the spliceosome into an active configuration prior to Prp2-mediated spliceosome remodeling and in promoting specific interaction of U5 and U6 with the 5' splice site for fidelity of 5' splice site selection.
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Workflow for Genome-Wide Determination of Pre-mRNA Splicing Efficiency from Yeast RNA-seq Data. BIOMED RESEARCH INTERNATIONAL 2016; 2016:4783841. [PMID: 28050562 PMCID: PMC5168555 DOI: 10.1155/2016/4783841] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/02/2016] [Indexed: 11/17/2022]
Abstract
Pre-mRNA splicing represents an important regulatory layer of eukaryotic gene expression. In the simple budding yeast Saccharomyces cerevisiae, about one-third of all mRNA molecules undergo splicing, and splicing efficiency is tightly regulated, for example, during meiotic differentiation. S. cerevisiae features a streamlined, evolutionarily highly conserved splicing machinery and serves as a favourite model for studies of various aspects of splicing. RNA-seq represents a robust, versatile, and affordable technique for transcriptome interrogation, which can also be used to study splicing efficiency. However, convenient bioinformatics tools for the analysis of splicing efficiency from yeast RNA-seq data are lacking. We present a complete workflow for the calculation of genome-wide splicing efficiency in S. cerevisiae using strand-specific RNA-seq data. Our pipeline takes sequencing reads in the FASTQ format and provides splicing efficiency values for the 5′ and 3′ splice junctions of each intron. The pipeline is based on up-to-date open-source software tools and requires very limited input from the user. We provide all relevant scripts in a ready-to-use form. We demonstrate the functionality of the workflow using RNA-seq datasets from three spliceosome mutants. The workflow should prove useful for studies of yeast splicing mutants or of regulated splicing, for example, under specific growth conditions.
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Yan C, Wan R, Bai R, Huang G, Shi Y. Structure of a yeast activated spliceosome at 3.5 Å resolution. Science 2016; 353:904-11. [PMID: 27445306 DOI: 10.1126/science.aag0291] [Citation(s) in RCA: 200] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/13/2016] [Indexed: 12/18/2022]
Abstract
Pre-messenger RNA (pre-mRNA) splicing is carried out by the spliceosome, which undergoes an intricate assembly and activation process. Here, we report an atomic structure of an activated spliceosome (known as the B(act) complex) from Saccharomyces cerevisiae, determined by cryo-electron microscopy at an average resolution of 3.52 angstroms. The final refined model contains U2 and U5 small nuclear ribonucleoprotein particles (snRNPs), U6 small nuclear RNA (snRNA), nineteen complex (NTC), NTC-related (NTR) protein, and a 71-nucleotide pre-mRNA molecule, which amount to 13,505 amino acids from 38 proteins and a combined molecular mass of about 1.6 megadaltons. The 5' exon is anchored by loop I of U5 snRNA, whereas the 5' splice site (5'SS) and the branch-point sequence (BPS) of the intron are specifically recognized by U6 and U2 snRNA, respectively. Except for coordination of the catalytic metal ions, the RNA elements at the catalytic cavity of Prp8 are mostly primed for catalysis. The catalytic latency is maintained by the SF3b complex, which encircles the BPS, and the splicing factors Cwc24 and Prp11, which shield the 5' exon-5'SS junction. This structure, together with those determined earlier, outlines a molecular framework for the pre-mRNA splicing reaction.
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Affiliation(s)
- Chuangye Yan
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ruixue Wan
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Rui Bai
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Gaoxingyu Huang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yigong Shi
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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Yadav S, Sonkar A, Ahamad N, Ahmed S. Mutant allele of rna14 in fission yeast affects pre-mRNA splicing. J Genet 2016; 95:389-97. [PMID: 27350684 DOI: 10.1007/s12041-016-0652-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Spliceosome and 3'-end processing complexes are necessary for the precursor mRNA (pre-mRNA) maturation. Spliceosome complex removes noncoding introns, while 3'-end processing involves in cleavage and addition of poly(A) tails to the nascent transcript. Rna14 protein in budding yeast has been implicated in cleavage and polyadenylation of mRNA in the nucleus but their role in the pre-mRNA splicing has not been studied. Here, we report the isolation of a mutant allele of rna14 in fission yeast, Schizosaccharomyces pombe that exhibits reduction in protein level of Chk1 at the nonpermissive temperature, primarily due to the defects in posttranscriptional processing. Reverse transcriptase-polymerase chain reaction analysis reveals defective splicing of the chk1(+) transcript at the nonpermissive temperature. Apart from chk1(+), the splicing of some other genes were also found to be defective at the nonpermissive temperature suggesting that Rna14 might be involved in pre-mRNA splicing. Subsequently, genetic interaction of Rna14 with prp1 and physical interactions with Prp28 suggest that the Rna14 might be part of a larger protein complex responsible for the pre-mRNA maturation.
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Affiliation(s)
- Sudhanshu Yadav
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226 031,
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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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Gao X, Jin Q, Jiang C, Li Y, Li C, Liu H, Kang Z, Xu JR. FgPrp4 Kinase Is Important for Spliceosome B-Complex Activation and Splicing Efficiency in Fusarium graminearum. PLoS Genet 2016; 12:e1005973. [PMID: 27058959 PMCID: PMC4825928 DOI: 10.1371/journal.pgen.1005973] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/11/2016] [Indexed: 12/23/2022] Open
Abstract
PRP4 encodes the only kinase among the spliceosome components. Although it is an essential gene in the fission yeast and other eukaryotic organisms, the Fgprp4 mutant was viable in the wheat scab fungus Fusarium graminearum. Deletion of FgPRP4 did not block intron splicing but affected intron splicing efficiency in over 60% of the F. graminearum genes. The Fgprp4 mutant had severe growth defects and produced spontaneous suppressors that were recovered in growth rate. Suppressor mutations were identified in the PRP6, PRP31, BRR2, and PRP8 orthologs in nine suppressor strains by sequencing analysis with candidate tri-snRNP component genes. The Q86K mutation in FgMSL1 was identified by whole genome sequencing in suppressor mutant S3. Whereas two of the suppressor mutations in FgBrr2 and FgPrp8 were similar to those characterized in their orthologs in yeasts, suppressor mutations in Prp6 and Prp31 orthologs or FgMSL1 have not been reported. Interestingly, four and two suppressor mutations identified in FgPrp6 and FgPrp31, respectively, all are near the conserved Prp4-phosphorylation sites, suggesting that these mutations may have similar effects with phosphorylation by Prp4 kinase. In FgPrp31, the non-sense mutation at R464 resulted in the truncation of the C-terminal 130 aa region that contains all the conserved Prp4-phosphorylation sites. Deletion analysis showed that the N-terminal 310-aa rich in SR residues plays a critical role in the localization and functions of FgPrp4. We also conducted phosphoproteomics analysis with FgPrp4 and identified S289 as the phosphorylation site that is essential for its functions. These results indicated that FgPrp4 is critical for splicing efficiency but not essential for intron splicing, and FgPrp4 may regulate pre-mRNA splicing by phosphorylation of other components of the tri-snRNP although itself may be activated by phosphorylation at S289.
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Affiliation(s)
- Xuli Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Qiaojun Jin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Cong Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
- Dept. of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
| | - Yang Li
- Dept. of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
| | - Chaohui Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Jin-Rong Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
- Dept. of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
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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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35
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The effect of the cwf14 gene of fission yeast on cell wall integrity is associated with rho1. J Microbiol 2016; 54:98-105. [DOI: 10.1007/s12275-016-5569-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/14/2016] [Accepted: 01/21/2016] [Indexed: 11/30/2022]
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36
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de Almeida RA, O'Keefe RT. The NineTeen Complex (NTC) and NTC-associated proteins as targets for spliceosomal ATPase action during pre-mRNA splicing. RNA Biol 2015; 12:109-14. [PMID: 25654271 PMCID: PMC4615276 DOI: 10.1080/15476286.2015.1008926] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Pre-mRNA splicing is an essential step in gene expression that removes intron sequences efficiently and accurately to produce a mature mRNA for translation. It is the large and dynamic RNA-protein complex called the spliceosome that catalyzes intron removal. To carry out splicing the spliceosome not only needs to assemble correctly with the pre-mRNA but the spliceosome requires extensive remodelling of its RNA and protein components to execute the 2 steps of intron removal. Spliceosome remodelling is achieved through the action of ATPases that target both RNA and proteins to produce spliceosome conformations competent for each step of spliceosome activation, catalysis and disassembly. An increasing amount of research has pointed to the spliceosome associated NineTeen Complex (NTC) of proteins as targets for the action of a number of the spliceosomal ATPases during spliceosome remodelling. In this point-of-view article we present the latest findings on the changes in the NTC that occur following ATPase action that are required for spliceosome activation, catalysis and disassembly. We proposed that the NTC is one of the main targets of ATPase action during spliceosome remodelling required for pre-mRNA splicing.
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37
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Klus P, Ponti RD, Livi CM, Tartaglia GG. Protein aggregation, structural disorder and RNA-binding ability: a new approach for physico-chemical and gene ontology classification of multiple datasets. BMC Genomics 2015; 16:1071. [PMID: 26673865 PMCID: PMC4681139 DOI: 10.1186/s12864-015-2280-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 12/08/2015] [Indexed: 01/27/2023] Open
Abstract
Background Comparison between multiple protein datasets requires the choice of an appropriate reference system and a number of variables to describe their differences. Here we introduce an innovative approach to discriminate multiple protein datasets (multiCM) and to measure enrichments in gene ontology terms (cleverGO) using semantic similarities. Results We illustrate the powerfulness of our approach by investigating the links between RNA-binding ability and other protein features, such as structural disorder and aggregation, in S. cerevisiae, C. elegans, M. musculus and H. sapiens. Our results are in striking agreement with available experimental evidence and unravel features that are key to understand the mechanisms regulating cellular homeostasis. Conclusions In an intuitive way, multiCM and cleverGO provide accurate classifications of physico-chemical features and annotations of biological processes, molecular functions and cellular components, which is extremely useful for the discovery and characterization of new trends in protein datasets. The multiCM and cleverGO can be freely accessed on the Web at http://www.tartaglialab.com/cs_multi/submission and http://www.tartaglialab.com/GO_analyser/universal. Each of the pages contains links to the corresponding documentation and tutorial. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2280-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Petr Klus
- Gene Function and Evolution, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Riccardo Delli Ponti
- Gene Function and Evolution, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Carmen Maria Livi
- Gene Function and Evolution, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Gian Gaetano Tartaglia
- Gene Function and Evolution, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), 23 Passeig Lluís Companys, 08010, Barcelona, Spain.
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38
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Pires MM, Cantor M, Guimarães PR, de Aguiar MAM, Dos Reis SF, Coltri PP. The network organization of protein interactions in the spliceosome is reproduced by the simple rules of food-web models. Sci Rep 2015; 5:14865. [PMID: 26443080 PMCID: PMC4595644 DOI: 10.1038/srep14865] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 09/09/2015] [Indexed: 12/02/2022] Open
Abstract
The network structure of biological systems provides information on the underlying processes shaping their organization and dynamics. Here we examined the structure of the network depicting protein interactions within the spliceosome, the macromolecular complex responsible for splicing in eukaryotic cells. We show the interactions of less connected spliceosome proteins are nested subsets of the connections of the highly connected proteins. At the same time, the network has a modular structure with groups of proteins sharing similar interaction patterns. We then investigated the role of affinity and specificity in shaping the spliceosome network by adapting a probabilistic model originally designed to reproduce food webs. This food-web model was as successful in reproducing the structure of protein interactions as it is in reproducing interactions among species. The good performance of the model suggests affinity and specificity, partially determined by protein size and the timing of association to the complex, may be determining network structure. Moreover, because network models allow building ensembles of realistic networks while encompassing uncertainty they can be useful to examine the dynamics and vulnerability of intracelullar processes. Unraveling the mechanisms organizing the spliceosome interactions is important to characterize the role of individual proteins on splicing catalysis and regulation.
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Affiliation(s)
- Mathias M Pires
- Departamento de Ecologia, Instituto de Biociências, 05508-090, Universidade de São Paulo, São Paulo, Brazil
| | - Maurício Cantor
- Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4J1, Canada
| | - Paulo R Guimarães
- Departamento de Ecologia, Instituto de Biociências, 05508-090, Universidade de São Paulo, São Paulo, Brazil
| | - Marcus A M de Aguiar
- Departamento de Física da Matéria Condensada, Instituto de Física 'Gleb Wataghin', 13083-859, Universidade Estadual de Campinas, Campinas, Brazil
| | - Sérgio F Dos Reis
- Departamento de Biologia Animal, Instituto de Biologia, 13083-970, Universidade Estadual de Campinas, Campinas, Brazil
| | - Patricia P Coltri
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, 05508-000, Universidade de São Paulo, São Paulo, Brazil
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Cwf16p Associating with the Nineteen Complex Ensures Ordered Exon Joining in Constitutive Pre-mRNA Splicing in Fission Yeast. PLoS One 2015; 10:e0136336. [PMID: 26302002 PMCID: PMC4547733 DOI: 10.1371/journal.pone.0136336] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/01/2015] [Indexed: 12/13/2022] Open
Abstract
Exons are ligated in an ordered manner without the skipping of exons in the constitutive splicing of pre-mRNAs with multiple introns. To identify factors ensuring ordered exon joining in constitutive pre-mRNA splicing, we previously screened for exon skipping mutants in Schizosaccharomyces pombe using a reporter plasmid, and characterized three exon skipping mutants named ods1 (ordered splicing 1), ods2, and ods3, the responsible genes of which encode Prp2/U2AF59, U2AF23, and SF1, respectively. They form an SF1-U2AF59-U2AF23 complex involved in recognition of the branch and 3' splice sites in pre-mRNA. In the present study, we identified a fourth ods mutant, ods4, which was isolated in an exon-skipping screen. The ods4+ gene encodes Cwf16p, which interacts with the NineTeen Complex (NTC), a complex thought to be involved in the first catalytic step of the splicing reaction. We isolated two multi-copy suppressors for the ods4-1 mutation, Srp2p, an SR protein essential for pre-mRNA splicing, and Tif213p, a translation initiation factor, in S. pombe. The overexpression of Srp2p suppressed the exon-skipping phenotype of all ods mutants, whereas Tif213p suppressed only ods4-1, which has a mutation in the translational start codon of the cwf16 gene. We also showed that the decrease in the transcriptional elongation rate induced by drug treatment suppressed exon skipping in ods4-1. We propose that Cwf16p/NTC participates in the early recognition of the branch and 3' splice sites and cooperates with the SF1-U2AF59-U2AF23 complex to maintain ordered exon joining.
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40
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Yan C, Hang J, Wan R, Huang M, Wong CCL, Shi Y. Structure of a yeast spliceosome at 3.6-angstrom resolution. Science 2015; 349:1182-91. [DOI: 10.1126/science.aac7629] [Citation(s) in RCA: 278] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/10/2015] [Indexed: 12/20/2022]
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41
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Petersen HO, Höger SK, Looso M, Lengfeld T, Kuhn A, Warnken U, Nishimiya-Fujisawa C, Schnölzer M, Krüger M, Özbek S, Simakov O, Holstein TW. A Comprehensive Transcriptomic and Proteomic Analysis of Hydra Head Regeneration. Mol Biol Evol 2015; 32:1928-47. [PMID: 25841488 PMCID: PMC4833066 DOI: 10.1093/molbev/msv079] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The cnidarian freshwater polyp Hydra sp. exhibits an unparalleled regeneration capacity in the animal kingdom. Using an integrative transcriptomic and stable isotope labeling by amino acids in cell culture proteomic/phosphoproteomic approach, we studied stem cell-based regeneration in Hydra polyps. As major contributors to head regeneration, we identified diverse signaling pathways adopted for the regeneration response as well as enriched novel genes. Our global analysis reveals two distinct molecular cascades: an early injury response and a subsequent, signaling driven patterning of the regenerating tissue. A key factor of the initial injury response is a general stabilization of proteins and a net upregulation of transcripts, which is followed by a subsequent activation cascade of signaling molecules including Wnts and transforming growth factor (TGF) beta-related factors. We observed moderate overlap between the factors contributing to proteomic and transcriptomic responses suggesting a decoupled regulation between the transcriptional and translational levels. Our data also indicate that interstitial stem cells and their derivatives (e.g., neurons) have no major role in Hydra head regeneration. Remarkably, we found an enrichment of evolutionarily more recent genes in the early regeneration response, whereas conserved genes are more enriched in the late phase. In addition, genes specific to the early injury response were enriched in transposon insertions. Genetic dynamicity and taxon-specific factors might therefore play a hitherto underestimated role in Hydra regeneration.
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Affiliation(s)
- Hendrik O Petersen
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Stefanie K Höger
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Mario Looso
- Max Planck Institute (MPI) for Heart and Lung Research, Bad Nauheim, Germany
| | - Tobias Lengfeld
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Anne Kuhn
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Uwe Warnken
- Functional Proteome Analysis Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Chiemi Nishimiya-Fujisawa
- Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, Myodaiji, Okazaki, Japan
| | - Martina Schnölzer
- Functional Proteome Analysis Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcus Krüger
- Max Planck Institute (MPI) for Heart and Lung Research, Bad Nauheim, Germany CECAD, University of Cologne, Germany
| | - Suat Özbek
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Oleg Simakov
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany Molecular Genetics Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Thomas W Holstein
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
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42
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van Maldegem F, Maslen S, Johnson CM, Chandra A, Ganesh K, Skehel M, Rada C. CTNNBL1 facilitates the association of CWC15 with CDC5L and is required to maintain the abundance of the Prp19 spliceosomal complex. Nucleic Acids Res 2015; 43:7058-69. [PMID: 26130721 PMCID: PMC4538830 DOI: 10.1093/nar/gkv643] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 06/09/2015] [Indexed: 12/16/2022] Open
Abstract
In order to catalyse the splicing of messenger RNA, multiple proteins and RNA components associate and dissociate in a dynamic highly choreographed process. The Prp19 complex is a conserved essential part of the splicing machinery thought to facilitate the conformational changes the spliceosome undergoes during catalysis. Dynamic protein interactions often involve highly disordered regions that are difficult to study by structural methods. Using amine crosslinking and hydrogen-deuterium exchange coupled to mass spectrometry, we describe the architecture of the Prp19 sub-complex that contains CTNNBL1. Deficiency in CTNNBL1 leads to delayed initiation of cell division and embryonic lethality. Here we show that in vitro CTNNBL1 enhances the association of CWC15 and CDC5L, both core Prp19 complex proteins and identify an overlap in the region of CDC5L that binds either CTNNBL1 or CWC15 suggesting the two proteins might exchange places in the complex. Furthermore, in vivo, CTNNBL1 is required to maintain normal levels of the Prp19 complex and to facilitate the interaction of CWC15 with CDC5L. Our results identify a chaperone function for CTNNBL1 within the essential Prp19 complex, a function required to maintain the integrity of the complex and to support efficient splicing.
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Affiliation(s)
| | - Sarah Maslen
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | | | - Anita Chandra
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Karuna Ganesh
- Department of Medicine and Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Cristina Rada
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
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43
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Chou MH, Hsieh YC, Huang CW, Chen PH, Chan SP, Tsao YP, Lee HH, Wu JT, Chen SL. BCAS2 Regulates Delta-Notch Signaling Activity through Delta Pre-mRNA Splicing in Drosophila Wing Development. PLoS One 2015; 10:e0130706. [PMID: 26091239 PMCID: PMC4475048 DOI: 10.1371/journal.pone.0130706] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 05/23/2015] [Indexed: 11/19/2022] Open
Abstract
Previously, we showed that BCAS2 is essential for Drosophila viability and functions in pre-mRNA splicing. In this study, we provide strong evidence that BCAS2 regulates the activity of Delta-Notch signaling via Delta pre-mRNA splicing. Depletion of dBCAS2 reduces Delta mRNA expression and leads to accumulation of Delta pre-mRNA, resulting in diminished transcriptions of Delta-Notch signaling target genes, such as cut and E(spl)m8. Furthermore, ectopic expression of human BCAS2 (hBCAS2) and Drosophila BCAS2 (dBCAS2) in a dBCAS2-deprived fly can rescue dBCAS2 depletion-induced wing damage to the normal phenotypes. These rescued phenotypes are correlated with the restoration of Delta pre-mRNA splicing, which affects Delta-Notch signaling activity. Additionally, overexpression of Delta can rescue the wing deformation by deprivation of dBCAS2; and the depletion of dBCAS2 can restore the aberrant eye associated with Delta-overexpressing retinas; providing supporting evidence for the regulation of Delta-Notch signaling by dBCAS2. Taken together, dBCAS2 participates in Delta pre-mRNA splicing that affects the regulation of Delta-Notch signaling in Drosophila wing development.
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Affiliation(s)
- Meng-Hsuan Chou
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - Yi-Chen Hsieh
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - Chu-Wei Huang
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - Po-Han Chen
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - Shih-Peng Chan
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - Yeou-Ping Tsao
- Department of Ophthalmology, Mackay Memorial Hospital, Taipei, 104, Taiwan
| | - Hsiu-Hsiang Lee
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - June-Tai Wu
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
- Department of Medical Research, National Taiwan University Hospital, Taipei, 100, Taiwan
- * E-mail: (SLC); (JTW)
| | - Show-Li Chen
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
- * E-mail: (SLC); (JTW)
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44
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Martinho RG, Guilgur LG, Prudêncio P. How gene expression in fast-proliferating cells keeps pace. Bioessays 2015; 37:514-24. [PMID: 25823409 DOI: 10.1002/bies.201400195] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The development of living organisms requires a precise coordination of all basic cellular processes, in space and time. Early embryogenesis of most species with externally deposited eggs starts with a series of extremely fast cleavage cycles. These divisions have a strong influence on gene expression as mitosis represses transcription and pre-mRNA processing. In this review, we will describe the distinct adaptations for efficient gene expression and discuss the emerging role of the multifunctional NineTeen Complex (NTC) in gene expression and genomic stability during fast proliferation.
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Affiliation(s)
- Rui G Martinho
- Departamento de Ciências Biomédicas e Medicina, Regenerative Medicine Program, Universidade do Algarve, Campus de Gambelas, Faro, Portugal; Center for Biomedical Research, Universidade do Algarve, Campus de Gambelas, Faro, Portugal; Instituto Gulbenkian de Ciência, Oeiras, Portugal
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45
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van Roon AMM, Yang JC, Mathieu D, Bermel W, Nagai K, Neuhaus D. ¹¹³Cd NMR experiments reveal an unusual metal cluster in the solution structure of the yeast splicing protein Bud31p. Angew Chem Int Ed Engl 2015; 54:4861-4. [PMID: 25703931 PMCID: PMC4471582 DOI: 10.1002/anie.201412210] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Indexed: 11/09/2022]
Abstract
Establishing the binding topology of structural zinc ions in proteins is an essential part of their structure determination by NMR spectroscopy. Using (113)Cd NMR experiments with (113)Cd-substituted samples is a useful approach but has previously been limited mainly to very small protein domains. Here we used (113)Cd NMR spectroscopy during structure determination of Bud31p, a 157-residue yeast protein containing an unusual Zn3Cys9 cluster, demonstrating that recent hardware developments make this approach feasible for significantly larger systems.
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46
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van Roon AMM, Yang JC, Mathieu D, Bermel W, Nagai K, Neuhaus D. 113Cd NMR Experiments Reveal an Unusual Metal Cluster in the Solution Structure of the Yeast Splicing Protein Bud31p. ACTA ACUST UNITED AC 2015; 127:4943-4946. [PMID: 27478262 PMCID: PMC4954022 DOI: 10.1002/ange.201412210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Indexed: 01/29/2023]
Abstract
Establishing the binding topology of structural zinc ions in proteins is an essential part of their structure determination by NMR spectroscopy. Using 113Cd NMR experiments with 113Cd‐substituted samples is a useful approach but has previously been limited mainly to very small protein domains. Here we used 113Cd NMR spectroscopy during structure determination of Bud31p, a 157‐residue yeast protein containing an unusual Zn3Cys9 cluster, demonstrating that recent hardware developments make this approach feasible for significantly larger systems.
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Affiliation(s)
| | - Ji-Chun Yang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH (UK)
| | - Daniel Mathieu
- Bruker BioSpin GmbH, Silberstreifen, 76287 Rheinstetten (Germany)
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen, 76287 Rheinstetten (Germany)
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH (UK)
| | - David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH (UK)
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47
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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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48
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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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49
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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
![]()
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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50
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Chen HC, Chang KJ, Su YL, Huang YH, Cheng SC. Structural requirement of Ntc77 for spliceosome activation and first catalytic step. Nucleic Acids Res 2014; 42:12261-71. [PMID: 25294830 PMCID: PMC4231770 DOI: 10.1093/nar/gku914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The Prp19-associated complex is required for spliceosome activation by stabilizing the binding of U5 and U6 on the spliceosome after the release of U4. The complex comprises at least eight proteins, among which Ntc90 and Ntc77 contain multiple tetratricopeptide repeat (TPR) elements. We have previously shown that Ntc90 is not involved in spliceosome activation, but is required for the recruitment of essential first-step factor Yju2 to the spliceosome. We demonstrate here that Ntc77 has dual functions in both spliceosome activation and the first catalytic step in recruiting Yju2. We have identified an amino-terminal region of Ntc77, which encompasses the N-terminal domain and the first three TPR motifs, dispensable for spliceosome activation but required for stable interaction of Yju2 with the spliceosome. Deletion of this region had no severe effect on the integrity of the NTC, binding of NTC to the spliceosome or spliceosome activation, but impaired splicing and exhibited a dominant-negative growth phenotype. Our data reveal functional roles of Ntc77 in both spliceosome activation and the first catalytic step, and distinct structural domains of Ntc77 required for these two steps.
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Affiliation(s)
- Hsin-Chou Chen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, Republic of China Institute of Microbiology and Immunology, National Yang-Ming University, Shih-Pai, Taipei, Taiwan 112, Republic of China
| | - Kae-Jiun Chang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, Republic of China
| | - Yu-Lun Su
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, Republic of China
| | - Yu-Hsin Huang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, Republic of China
| | - Soo-Chen Cheng
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, Republic of China
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