1
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Jiang T, Wang L, Tang L, Zeb A, Hou Y. Identification of two short peptide motifs from serine/arginine-rich protein ribonucleic acid recognition motif-1 domain acting as splicing regulators. PeerJ 2023; 11:e16103. [PMID: 37744237 PMCID: PMC10512959 DOI: 10.7717/peerj.16103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023] Open
Abstract
Background Serine/arginine-rich (SR) proteins regulate pre-mRNA splicing. However, structurally similar proteins often behave differently in splicing regulation and the underlying mechanisms are largely unknown. Here, using SMN1/2 minigenes we extensively analyzed four SR proteins, SRSF1/5/6/9. Methods In this study, the effects of these proteins on SMN1/2 exon 7 splicing when tethered at either intron 6 or 7 were evaluated using an MS2-tethering assay. Deletion analysis in four SR proteins and co-overexpression analysis were performed. Results Splicing outcomes varied among all four SR proteins, SRSF1 and SRSF5 function the same at the two sites, acting as repressor and stimulator, respectively; while SRSF6 and SRSF9 promote exon 7 inclusion at only one site. Further, the key domains of each SR proteins were investigated, which identified a potent inhibitory nonapeptide in the C-terminus of SRSF1/9 ribonucleic acid recognition motif-1 (RRM1) and a potent stimulatory heptapeptide at the N-terminus of SRSF5/6 RRM1. Conclusion The insight of the four SR proteins and their domains in affecting SMN gene splicing brings a new perspective on the modes of action of SR proteins; and the functional peptides obtained here offers new ideas for developing splice switching-related therapies.
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Affiliation(s)
- Tao Jiang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
- Department of Rehabilitation, Southwest Hospital, Third Military Medical University Army Medical University, Chongqing, China
| | - Li Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
| | - Liang Tang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
| | - Azhar Zeb
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
| | - Yanjun Hou
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
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2
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Hu W, Li P, Zeng N, Tan S. Exploring the hub mechanisms of ischemic stroke based on protein-protein interaction networks related to ischemic stroke and inflammatory bowel disease. Sci Rep 2023; 13:1741. [PMID: 36720935 PMCID: PMC9887582 DOI: 10.1038/s41598-023-27459-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 01/02/2023] [Indexed: 02/01/2023] Open
Abstract
Ischemic stroke is highly concerning because it often leads to severe long-term neurological disability. Among clinical trials, ischemic stroke and inflammatory bowel disease interactions have been increasingly reported in recent years. Therefore, using bioinformatics approaches to explore novel protein interactions between them is of interest. We performed this exploratory analysis by using bioinformatics tools such as string to analyze gene data downloaded from NHGRI-GWAS data related to ischemic stroke and inflammatory bowel disease. We constructed a prospective protein interaction network for ischemic stroke and inflammatory bowel disease, identifying cytokine and interleukin-related signaling pathways, Spliceosome, Ubiquitin-Proteasome System (UPS), Thrombus, and Anticoagulation pathways as the crucial biological mechanisms of the network. Furthermore, we also used data-independent acquisition mass spectrometry (DIA-MS) to detect differential protein expression in eight samples, which also suggested that immune system, signal transduction, and hemostasis-related pathways are key signaling pathways. These findings may provide a basis for understanding the interaction between these two states and exploring possible molecular and therapeutic studies in the future.
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Affiliation(s)
- Wei Hu
- Department of Neurology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, China.,Department of Rehabilitation, Xiangya Bo'ai Rehabilitation Hospital, Changsha, 410004, China
| | - Ping Li
- Department of Rehabilitation, Xiangya Bo'ai Rehabilitation Hospital, Changsha, 410004, China
| | - Nianju Zeng
- Department of Rehabilitation, Xiangya Bo'ai Rehabilitation Hospital, Changsha, 410004, China.
| | - Sheng Tan
- Department of Neurology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, China.
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3
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Kumari NS, Ashwini K, Gollapalli P, Shetty S, Raghotham A, Shetty P, Shetty J. Gene enrichment analysis and protein–protein interaction network topology delineates S-Phase kinase-associated protein 1 and catenin beta-1 as potential signature genes linked to glioblastoma prognosis. BIOMEDICAL AND BIOTECHNOLOGY RESEARCH JOURNAL (BBRJ) 2023. [DOI: 10.4103/bbrj.bbrj_344_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
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4
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Biology of the mRNA Splicing Machinery and Its Dysregulation in Cancer Providing Therapeutic Opportunities. Int J Mol Sci 2021; 22:ijms22105110. [PMID: 34065983 PMCID: PMC8150589 DOI: 10.3390/ijms22105110] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
Dysregulation of messenger RNA (mRNA) processing—in particular mRNA splicing—is a hallmark of cancer. Compared to normal cells, cancer cells frequently present aberrant mRNA splicing, which promotes cancer progression and treatment resistance. This hallmark provides opportunities for developing new targeted cancer treatments. Splicing of precursor mRNA into mature mRNA is executed by a dynamic complex of proteins and small RNAs called the spliceosome. Spliceosomes are part of the supraspliceosome, a macromolecular structure where all co-transcriptional mRNA processing activities in the cell nucleus are coordinated. Here we review the biology of the mRNA splicing machinery in the context of other mRNA processing activities in the supraspliceosome and present current knowledge of its dysregulation in lung cancer. In addition, we review investigations to discover therapeutic targets in the spliceosome and give an overview of inhibitors and modulators of the mRNA splicing process identified so far. Together, this provides insight into the value of targeting the spliceosome as a possible new treatment for lung cancer.
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5
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Wang X, Li Y, Dai H, Xu C. Crystal structure of the WD40 domain of human PLRG1. Biochem Biophys Res Commun 2020; 534:474-477. [PMID: 33239170 DOI: 10.1016/j.bbrc.2020.11.057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 12/11/2022]
Abstract
PLRG1 is a evolutionarily conserved protein in spliceosome and plays an important role in maintaining the integral part of the splicoeosme and its proper splicing. Here we solved the high resolution crystal structure of the WD40 domain of human PLRG1 by crystallography and compared our crystal structure with the cryo-EM structure of PLRG1 bound with other splicing factors. We found that two loops of the WD40 domain become resolved upon binding to the proteins within the spliceosome. Thus our work characterize the dynamic property of PLRG1 during the spliceosome assembly by presenting its apo structure.
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Affiliation(s)
- Xiaoyang Wang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Yanjun Li
- Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, Ontario, M5G 1L7, Canada
| | - Haiming Dai
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
| | - Chao Xu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.
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6
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Lau LY, Nguyen LT, Reverter A, Moore SS, Lynn A, McBride‐Kelly L, Phillips‐Rose L, Plath M, Macfarlane R, Vasudivan V, Morton L, Ardley R, Ye Y, Fortes MRS. Gene regulation could be attributed to TCF3 and other key transcription factors in the muscle of pubertal heifers. Vet Med Sci 2020; 6:695-710. [PMID: 32432381 PMCID: PMC7738712 DOI: 10.1002/vms3.278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 03/13/2020] [Accepted: 04/09/2020] [Indexed: 01/17/2023] Open
Abstract
Puberty is a whole-body event, driven by the hypothalamic integration of peripheral signals such as leptin or IGF-1. In the process of puberty, reproductive development is simultaneous to growth, including muscle growth. To enhance our understanding of muscle function related to puberty, we performed transcriptome analyses of muscle samples from six pre- and six post-pubertal Brahman heifers (Bos indicus). Our aims were to perform differential expression analyses and co-expression analyses to derive a regulatory gene network associate with puberty. As a result, we identified 431 differentially expressed (DEx) transcripts (genes and non-coding RNAs) when comparing pre- to post-pubertal average gene expression. The DEx transcripts were compared with all expressed transcripts in our samples (over 14,000 transcripts) for functional enrichment analyses. The DEx transcripts were associated with "extracellular region," "inflammatory response" and "hormone activity" (adjusted p < .05). Inflammatory response for muscle regeneration is a necessary aspect of muscle growth, which is accelerated during puberty. The term "hormone activity" may signal genes that respond to progesterone signalling in the muscle, as the presence of this hormone is an important difference between pre- and post-pubertal heifers in our experimental design. The DEx transcript with the highest average expression difference was a mitochondrial gene, ENSBTAG00000043574 that might be another important link between energy metabolism and puberty. In the derived co-expression gene network, we identified six hub genes: CDC5L, MYC, TCF3, RUNX2, ATF2 and CREB1. In the same network, 48 key regulators of DEx transcripts were identified, using a regulatory impact factor metric. The hub gene TCF3 was also a key regulator. The majority of the key regulators (22 genes) are members of the zinc finger family, which has been implicated in bovine puberty in other tissues. In conclusion, we described how puberty may affect muscle gene expression in cattle.
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Affiliation(s)
- Li Yieng Lau
- School of Chemistry and Molecular BiologyThe University of QueenslandBrisbaneQLDAustralia
| | - Loan T. Nguyen
- Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandBrisbaneQLDAustralia
| | - Antonio Reverter
- CSIRO Agriculture and FoodQueensland Biosciences PrecinctBrisbaneQLDAustralia
| | - Stephen S. Moore
- Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandBrisbaneQLDAustralia
| | - Aaron Lynn
- School of Chemistry and Molecular BiologyThe University of QueenslandBrisbaneQLDAustralia
| | - Liam McBride‐Kelly
- School of Chemistry and Molecular BiologyThe University of QueenslandBrisbaneQLDAustralia
| | - Louis Phillips‐Rose
- School of Chemistry and Molecular BiologyThe University of QueenslandBrisbaneQLDAustralia
| | - Mackenzie Plath
- School of Chemistry and Molecular BiologyThe University of QueenslandBrisbaneQLDAustralia
| | - Rhys Macfarlane
- School of Chemistry and Molecular BiologyThe University of QueenslandBrisbaneQLDAustralia
| | - Vanisha Vasudivan
- School of Chemistry and Molecular BiologyThe University of QueenslandBrisbaneQLDAustralia
| | - Lachlan Morton
- School of Chemistry and Molecular BiologyThe University of QueenslandBrisbaneQLDAustralia
| | - Ryan Ardley
- School of Chemistry and Molecular BiologyThe University of QueenslandBrisbaneQLDAustralia
| | - Yunan Ye
- School of Chemistry and Molecular BiologyThe University of QueenslandBrisbaneQLDAustralia
| | - Marina R. S. Fortes
- School of Chemistry and Molecular BiologyThe University of QueenslandBrisbaneQLDAustralia
- Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandBrisbaneQLDAustralia
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7
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Prp19 Arrests Cell Cycle via Cdc5L in Hepatocellular Carcinoma Cells. Int J Mol Sci 2017; 18:ijms18040778. [PMID: 28387715 PMCID: PMC5412362 DOI: 10.3390/ijms18040778] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/23/2017] [Accepted: 03/31/2017] [Indexed: 12/17/2022] Open
Abstract
Pre-mRNA processing factor 19 (Prp19) is involved in many cellular events including pre-mRNA processing and DNA damage response. Recently, it has been identified as a candidate oncogene in hepatocellular carcinoma (HCC). However, the role of Prp19 in tumor biology is still elusive. Here, we reported that Prp19 arrested cell cycle in HCC cells via regulating G2/M transition. Mechanistic insights revealed that silencing Prp19 inhibited the expression of cell division cycle 5-like (Cdc5L) via repressing the translation of Cdc5L mRNA and facilitating lysosome-mediated degradation of Cdc5L in HCC cells. Furthermore, we found that silencing Prp19 induced cell cycle arrest could be partially resumed by overexpressing Cdc5L. This work implied that Prp19 participated in mitotic progression and thus could be a promising therapeutic target of HCC.
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8
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Expression and Clinical Role of Cdc5L as a Novel Cell Cycle Protein in Hepatocellular Carcinoma. Dig Dis Sci 2016; 61:795-805. [PMID: 26553251 DOI: 10.1007/s10620-015-3937-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 10/22/2015] [Indexed: 12/20/2022]
Abstract
BACKGROUND Cell division cycle 5-like (Cdc5L), as a pre-mRNA splicing factor, is a regulator of mitotic progression. Previous study found that deletion of endogenous Cdc5L decreases the cell viability via dramatic mitotic arrest, while the role of Cdc5L in cancer biology remains under debate. AIMS To investigate the involvement of Cdc5L in the progression of hepatocellular carcinoma (HCC). METHODS In this study, the expression of Cdc5L was evaluated by Western blot in 8 paired fresh HCC tissues and immunohistochemistry on 116 paraffin-embedded slices. We treated HCC cells by nocodazole to analyze the role of Cdc5L in mitotic progress. To determine whether Cdc5L could regulate the proliferation of HCC cells, we increased endogenous Cdc5L and analyzed the proliferation of HCC cells using Western blot, CCK8, flow cytometry assays, and colony formation analyses. Furthermore, Cdc5L-siRNA oligos were used to confirm that Cdc5L plays an essential role in HCC development. RESULTS Cdc5L was highly expressed in HCC and significantly associated with multiple clinicopathological factors, including AJCC stage, tumor size, and Ki-67. Besides, univariate and multivariate survival analyses demonstrated that high Cdc5L expression was an independent prognostic factor for HCC patients' poor survival. Overexpression of Cdc5L favors cell cycle progress of HCC cells, while downregulation of Cdc5L results in cell cycle arrest at G2/M phase and reduced cell proliferation of HCC cells. CONCLUSIONS Our findings suggested that Cdc5L could play an important role in the tumorigenesis of HCC and thus be a potential therapeutical target to prevent HCC progression.
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9
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Small Molecule Modulators of Pre-mRNA Splicing in Cancer Therapy. Trends Mol Med 2015; 22:28-37. [PMID: 26700537 DOI: 10.1016/j.molmed.2015.11.005] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 11/09/2015] [Accepted: 11/13/2015] [Indexed: 12/24/2022]
Abstract
Pre-mRNA splicing is a fundamental process in mammalian gene expression and alternative RNA splicing plays a considerable role in generating protein diversity. RNA splicing events are also key to the pathology of numerous diseases, particularly cancers. Some tumors are molecularly addicted to specific RNA splicing isoforms making interference with pre-mRNA processing a viable therapeutic strategy. Several RNA splicing modulators have recently been characterized, some showing promise in preclinical studies. While the targets of most splicing modulators are constitutive RNA processing components, possibly leading to undesirable side effects, selectivity for individual splicing events has been observed. Given the high prevalence of splicing defects in cancer, small molecule modulators of RNA processing represent a potentially promising novel therapeutic strategy in cancer treatment. Here, we review their reported effects, mechanisms, and limitations.
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10
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Expression of CDC5L is associated with tumor progression in gliomas. Tumour Biol 2015; 37:4093-103. [PMID: 26490980 DOI: 10.1007/s13277-015-4088-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/13/2015] [Indexed: 10/22/2022] Open
Abstract
Cell division cycle 5-like (CDC5L) protein is a cell cycle regulator of the G2/M transition and has been reported to participate in the catalytic step of pre-messenger RNA (mRNA) splicing and DNA damage repair. Recently, it was also found to act as a candidate oncogene in osteosarcoma and cervical tumors. However, the role of CDC5L expression in tumor biology was still unclear. Here, we analyzed the expression and clinical significance of CDC5L in gliomas. The expression of CDC5L in fresh glioma tissues and paraffin-embedded slices was evaluated by western blot and immunohistochemistry, respectively. We found that CDC5L was highly expressed in glioma tissues. The expression of CDC5L was significantly associated with glioma pathology grade and Ki-67 expression. Univariate and multivariate analyses showed that high CDC5L expression was an independent prognostic factor for glioma patients' survival. To determine whether CDC5L could regulate the proliferation of glioma cells, we transfected glioma cells with interfering RNA target CDC5L, then investigated cell proliferation with cell counting kit (CCK)-8, flow cytometry assays and colony formation analyses. Our results indicated that knockdown of CDC5L would inhibit proliferation of glioma cells. Besides, reduced expression of CDC5L could induce the apoptosis of glioma cells. These findings suggested that CDC5L might play an important role in glioma and thus be a promising therapeutic target of glioma.
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11
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Nancy MM, Nora RM, Rebeca MC. Peptidic tools applied to redirect alternative splicing events. Peptides 2015; 67:1-11. [PMID: 25748022 DOI: 10.1016/j.peptides.2015.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 02/05/2015] [Accepted: 02/26/2015] [Indexed: 01/25/2023]
Abstract
Peptides are versatile and attractive biomolecules that can be applied to modulate genetic mechanisms like alternative splicing. In this process, a single transcript yields different mature RNAs leading to the production of protein isoforms with diverse or even antagonistic functions. During splicing events, errors can be caused either by mutations present in the genome or by defects or imbalances in regulatory protein factors. In any case, defects in alternative splicing have been related to several genetic diseases including muscular dystrophy, Alzheimer's disease and cancer from almost every origin. One of the most effective approaches to redirect alternative splicing events has been to attach cell-penetrating peptides to oligonucleotides that can modulate a single splicing event and restore correct gene expression. Here, we summarize how natural existing and bioengineered peptides have been applied over the last few years to regulate alternative splicing and genetic expression. Under different genetic and cellular backgrounds, peptides have been shown to function as potent vehicles for splice correction, and their therapeutic benefits have reached clinical trials and patenting stages, emphasizing the use of regulatory peptides as an exciting therapeutic tool for the treatment of different genetic diseases.
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Affiliation(s)
- Martínez-Montiel Nancy
- Laboratorio de Ecología Molecular Microbiana, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Mexico
| | - Rosas-Murrieta Nora
- Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Mexico
| | - Martínez-Contreras Rebeca
- Laboratorio de Ecología Molecular Microbiana, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Mexico.
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12
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Depletion of pre-mRNA splicing factor Cdc5L inhibits mitotic progression and triggers mitotic catastrophe. Cell Death Dis 2014; 5:e1151. [PMID: 24675469 PMCID: PMC3973201 DOI: 10.1038/cddis.2014.117] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 01/21/2014] [Accepted: 02/11/2014] [Indexed: 01/22/2023]
Abstract
Disturbing mitotic progression via targeted anti-mitotic therapy is an attractive strategy for cancer treatment. Therefore, the exploration and elucidation of molecular targets and pathways in mitosis are critical for the development of anti-mitotic drugs. Here, we show that cell division cycle 5-like (Cdc5L), a pre-mRNA splicing factor, is a regulator of mitotic progression. Depletion of Cdc5L causes dramatic mitotic arrest, chromosome misalignments and sustained activation of spindle assembly checkpoint, eventually leading to mitotic catastrophe. Moreover, these defects result from severe impairment of kinetochore-microtubule attachment and serious DNA damage. Genome-wide gene expression analysis reveals that Cdc5L modulates the expression of a set of genes involved in the mitosis and the DNA damage response. We further found that the pre-mRNA splicing efficiency of these genes were impaired when Cdc5L was knocked down. Interestingly, Cdc5L is highly expressed in cervical tumors and osteosarcoma. Finally, we demonstrate that downregulation of Cdc5L decreases the cell viability of related tumor cells. These results suggest that Cdc5L is a key regulator of mitotic progression and highlight the potential of Cdc5L as a target for cancer therapy.
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13
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Yin J, Zhu JM, Shen XZ. New insights into pre-mRNA processing factor 19: A multi-faceted protein in humans. Biol Cell 2012; 104:695-705. [DOI: 10.1111/boc.201200011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2011] [Accepted: 09/06/2012] [Indexed: 11/27/2022]
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14
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Grillari J, Löscher M, Denegri M, Lee K, Fortschegger K, Eisenhaber F, Ajuh P, Lamond AI, Katinger H, Grillari-Voglauer R. Blom7alpha is a novel heterogeneous nuclear ribonucleoprotein K homology domain protein involved in pre-mRNA splicing that interacts with SNEVPrp19-Pso4. J Biol Chem 2009; 284:29193-204. [PMID: 19641227 PMCID: PMC2781463 DOI: 10.1074/jbc.m109.036632] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Revised: 07/28/2009] [Indexed: 02/05/2023] Open
Abstract
The removal of introns from pre-mRNA is performed by the spliceosome that stepwise assembles on the pre-mRNA before performing two catalytic steps. The spliceosome-associated CDC5L-SNEV(Prp19-Pso4) complex is implicated in activation of the second catalytic step of pre-mRNA splicing, and one of its members, SNEV(Prp19-Pso4), is also implicated in spliceosome assembly. To identify interaction partners of SNEVPrp19-Pso4, we have performed yeast two-hybrid screenings. Among the putative binding partners was a so far uncharacterized protein carrying two heterogeneous nuclear ribonucleoprotein K homology domains that we termed Blom7alpha. Blom7alpha is expressed in all tissues tested, and at least three splice variants exist. After confirming direct and physical interaction of SNEV and Blom7alpha, we investigated if it plays a functional role during pre-mRNA splicing. Indeed, Blom7alpha co-localizes and co-precipitates with splicing factors and pre-mRNA and is present in affinity-purified spliceosomes. More importantly, addition of Blom7alpha to HeLa nuclear extracts increased splicing activity in a dose-dependent manner. Furthermore, we tested if Blom7alpha influences splice site selection using two different minigene constructs. Indeed, both 5'- as well as 3'-site selection was altered upon Blom7alpha overexpression. Thus we suggest that Blom7alpha is a novel splicing factor of the K homology domain family that might be implicated in alternative splicing by helping to position the CDC5L-SNEV(Prp19-Pso4) complex at the splice sites.
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Affiliation(s)
- Johannes Grillari
- Institute of Applied Microbiology, University of Natural Resources and Applied Life Sciences, Vienna A-1190, Austria.
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15
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Aukema KG, Chohan KK, Plourde GL, Reimer KB, Rader SD. Small molecule inhibitors of yeast pre-mRNA splicing. ACS Chem Biol 2009; 4:759-68. [PMID: 19634919 DOI: 10.1021/cb900090z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The spliceosome catalyzes pre-messenger RNA (pre-mRNA) splicing, an essential process in eukaryotic gene expression in which non-protein-coding sequences are removed from pre-mRNA. The spliceosome is a large, molecular complex composed of five small nuclear RNAs (snRNAs) and over 100 proteins. Large-scale rearrangements of the snRNAs and their associated proteins, including changes in base-pairing partners, are required to properly identify the intron-containing pre-mRNA, position it within the spliceosome, and complete the cleavage and ligation reactions of splicing. Despite detailed knowledge of the composition of the spliceosome at various stages of assembly, the critical signals and conformational changes that drive the dynamic rearrangements required for pre-mRNA splicing remain largely unknown. Just as ribosome-binding antibiotics facilitated mechanistic studies of the ribosome, study of the catalytic mechanisms of the spliceosome could be enhanced by the availability of small molecule inhibitors that block spliceosome assembly and splicing at defined stages. We sought to identify inhibitors of Saccharomyces cerevisiae splicing by screening for small molecules that block yeast splicing in vitro. We identified 10 small molecule inhibitors of yeast splicing, including four antibiotics, one kinase inhibitor, and five oxaspiro compounds. We also report that a subset of the oxaspiro derivatives permitted assembly of spliceosomal complexes onto pre-mRNA but blocked splicing prior to the first cleavage reaction.
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Affiliation(s)
- Kelly G. Aukema
- Department of Chemistry, University of Northern British Columbia, 3333 University Way, Prince George BC V2N 4Z9, Canada
| | - Kamalprit K. Chohan
- Department of Chemistry, University of Northern British Columbia, 3333 University Way, Prince George BC V2N 4Z9, Canada
| | - Guy L. Plourde
- Department of Chemistry, University of Northern British Columbia, 3333 University Way, Prince George BC V2N 4Z9, Canada
| | - Kerry B. Reimer
- Department of Chemistry, University of Northern British Columbia, 3333 University Way, Prince George BC V2N 4Z9, Canada
| | - Stephen D. Rader
- Department of Chemistry, University of Northern British Columbia, 3333 University Way, Prince George BC V2N 4Z9, Canada
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16
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Monaghan J, Xu F, Gao M, Zhao Q, Palma K, Long C, Chen S, Zhang Y, Li X. Two Prp19-like U-box proteins in the MOS4-associated complex play redundant roles in plant innate immunity. PLoS Pathog 2009; 5:e1000526. [PMID: 19629177 PMCID: PMC2709443 DOI: 10.1371/journal.ppat.1000526] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Accepted: 06/30/2009] [Indexed: 01/01/2023] Open
Abstract
Plant Resistance (R) proteins play an integral role in defense against pathogen infection. A unique gain-of-function mutation in the R gene SNC1, snc1, results in constitutive activation of plant immune pathways and enhanced resistance against pathogen infection. We previously found that mutations in MOS4 suppress the autoimmune phenotypes of snc1, and that MOS4 is part of a nuclear complex called the MOS4-Associated Complex (MAC) along with the transcription factor AtCDC5 and the WD-40 protein PRL1. Here we report the immuno-affinity purification of the MAC using HA-tagged MOS4 followed by protein sequence analysis by mass spectrometry. A total of 24 MAC proteins were identified, 19 of which have predicted roles in RNA processing based on their homology to proteins in the Prp19-Complex, an evolutionarily conserved spliceosome-associated complex containing homologs of MOS4, AtCDC5, and PRL1. Among these were two highly similar U-box proteins with homology to the yeast and human E3 ubiquitin ligase Prp19, which we named MAC3A and MAC3B. MAC3B was recently shown to exhibit E3 ligase activity in vitro. Through reverse genetics analysis we show that MAC3A and MAC3B are functionally redundant and are required for basal and R protein-mediated resistance in Arabidopsis. Like mos4-1 and Atcdc5-1, mac3a mac3b suppresses snc1-mediated autoimmunity. MAC3 localizes to the nucleus and interacts with AtCDC5 in planta. Our results suggest that MAC3A and MAC3B are members of the MAC that function redundantly in the regulation of plant innate immunity.
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Affiliation(s)
- Jacqueline Monaghan
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Fang Xu
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- National Institute of Biological Sciences (NIBS), Beijing, People's Republic of China
| | - Minghui Gao
- National Institute of Biological Sciences (NIBS), Beijing, People's Republic of China
| | - Qingguo Zhao
- National Institute of Biological Sciences (NIBS), Beijing, People's Republic of China
| | - Kristoffer Palma
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chengzu Long
- National Institute of Biological Sciences (NIBS), Beijing, People's Republic of China
| | - She Chen
- National Institute of Biological Sciences (NIBS), Beijing, People's Republic of China
| | - Yuelin Zhang
- National Institute of Biological Sciences (NIBS), Beijing, People's Republic of China
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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PLRG1 is an essential regulator of cell proliferation and apoptosis during vertebrate development and tissue homeostasis. Mol Cell Biol 2009; 29:3173-85. [PMID: 19307306 DOI: 10.1128/mcb.01807-08] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PLRG1, an evolutionarily conserved component of the spliceosome, forms a complex with Pso4/SNEV/Prp19 and the cell division and cycle 5 homolog (CDC5L) that is involved in both pre-mRNA splicing and DNA repair. Here, we show that the inactivation of PLRG1 in mice results in embryonic lethality at 1.5 days postfertilization. Studies of heart- and neuron-specific PLRG1 knockout mice further reveal an essential role of PLRG1 in adult tissue homeostasis and the suppression of apoptosis. PLRG1-deficient mouse embryonic fibroblasts (MEFs) fail to progress through S phase upon serum stimulation and exhibit increased rates of apoptosis. PLRG1 deficiency causes enhanced p53 phosphorylation and stabilization in the presence of increased gamma-H2AX immunoreactivity as an indicator of an activated DNA damage response. p53 downregulation rescues lethality in both PLRG1-deficient MEFs and zebrafish in vivo, showing that apoptosis resulting from PLRG1 deficiency is p53 dependent. Moreover, the deletion of PLRG1 results in the relocation of its interaction partner CDC5L from the nucleus to the cytoplasm without general alterations in pre-mRNA splicing. Taken together, the results of this study identify PLRG1 as a critical nuclear regulator of p53-dependent cell cycle progression and apoptosis during both embryonic development and adult tissue homeostasis.
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18
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Mourot M, Dufort I, Gravel C, Algriany O, Dieleman S, Sirard MA. The influence of follicle size, FSH-enriched maturation medium, and early cleavage on bovine oocyte maternal mRNA levels. Mol Reprod Dev 2006; 73:1367-79. [PMID: 16894554 DOI: 10.1002/mrd.20585] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Transcription is arrested in the bovine oocyte within the first few hours of in vitro maturation, thus the stored maternal mRNAs accumulated in the oocyte are essential to sustain development until the Maternal-Zygotic Transition. In vivo matured oocytes have superior blastocyst formation rates than in vitro matured oocytes, suggesting that the mRNA content of these oocytes is of higher quality. To determine which transcripts may be associated with developmental competence, a Suppressive Subtractive Hybridization was performed between oocytes collected by ovariectomy at 6 hr post-LH surge and oocytes from slaughterhouse collected after 6 hr of maturation, resulting in a library enriched in these functionally important mRNAs. The clones were spotted onto a cDNA microarray and transcripts potentially associated with developmental competence were hybridized onto these slides. Hybridizations were performed with transcripts up-regulated in oocytes cultured for 6 hr in the presence or absence of rFSH in vitro, and secondly with transcripts up regulated in early-cleaving embryos versus those at the one-cell stage at 36 hr postfertilization. From these hybridizations, 13 candidates were selected. Their functional association with embryonic competence was validated by measuring their relative transcript levels by quantitative real-time PCR in eight different conditions: oocytes cultured with or without rFSH, early--versus late-cleaving embryos, and oocytes from different follicle sizes (1-3, 3-5, 5-8, and >8 mm of diameter). The gene candidates CCNB2, PTTG1, H2A, CKS1, PSMB2, SKIIP, CDC5L, RGS16, and PRDX1 showed a significant quantitative association with competence compared to BMP15, GDF9, CCNB1, and STK6.
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Affiliation(s)
- Marina Mourot
- Département des Sciences Animales, Centre de Recherche en Biologie de la Reproduction, Université Laval, Sainte Foy, Québec, Canada
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Grillari J, Ajuh P, Stadler G, Löscher M, Voglauer R, Ernst W, Chusainow J, Eisenhaber F, Pokar M, Fortschegger K, Grey M, Lamond AI, Katinger H. SNEV is an evolutionarily conserved splicing factor whose oligomerization is necessary for spliceosome assembly. Nucleic Acids Res 2005; 33:6868-83. [PMID: 16332694 PMCID: PMC1310963 DOI: 10.1093/nar/gki986] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Revised: 11/11/2005] [Accepted: 11/11/2005] [Indexed: 11/25/2022] Open
Abstract
We have isolated the human protein SNEV as downregulated in replicatively senescent cells. Sequence homology to the yeast splicing factor Prp19 suggested that SNEV might be the orthologue of Prp19 and therefore might also be involved in pre-mRNA splicing. We have used various approaches including gene complementation studies in yeast using a temperature sensitive mutant with a pleiotropic phenotype and SNEV immunodepletion from human HeLa nuclear extracts to determine its function. A human-yeast chimera was indeed capable of restoring the wild-type phenotype of the yeast mutant strain. In addition, immunodepletion of SNEV from human nuclear extracts resulted in a decrease of in vitro pre-mRNA splicing efficiency. Furthermore, as part of our analysis of protein-protein interactions within the CDC5L complex, we found that SNEV interacts with itself. The self-interaction domain was mapped to amino acids 56-74 in the protein's sequence and synthetic peptides derived from this region inhibit in vitro splicing by surprisingly interfering with spliceosome formation and stability. These results indicate that SNEV is the human orthologue of yeast PRP19, functions in splicing and that homo-oligomerization of SNEV in HeLa nuclear extract is essential for spliceosome assembly and that it might also be important for spliceosome stability.
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Affiliation(s)
- Johannes Grillari
- Institute of Applied Microbiology, University of Natural Resources and Applied Life Sciences Vienna, Austria Muthgasse 18, A-1190 Vienna.
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Zhang N, Kaur R, Lu X, Shen X, Li L, Legerski RJ. The Pso4 mRNA splicing and DNA repair complex interacts with WRN for processing of DNA interstrand cross-links. J Biol Chem 2005; 280:40559-67. [PMID: 16223718 DOI: 10.1074/jbc.m508453200] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA interstrand cross-links (ICLs) are perhaps the most formidable lesion encountered by the cellular DNA repair machinery, and the elucidation of the process by which they are removed in eukaryotic cells has proved a daunting task. In particular, the early stages of adduct recognition and uncoupling of the cross-link have remained elusive principally because genetic studies have not been highly revealing. We have developed a biochemical assay in which processing of a DNA substrate containing a site-specific psoralen ICL can be monitored in vitro. Using this assay we have shown previously that the mismatch repair factor MutSbeta, the nucleotide excision repair heterodimer Ercc1-Xpf, and the replication proteins RPA and PCNA are involved in an early stage of psoralen ICL processing. Here, we report the identification of two additional factors required in the ICL repair process, a previously characterized pre-mRNA splicing complex composed of Pso4/Prp19, Cdc5L, Plrg1, and Spf27 (Pso4 complex), and WRN the protein deficient in Werner syndrome. Analysis of the WRN protein indicates that its DNA helicase function, but not its exonuclease activity, is required for ICL processing in vitro. In addition, we show that WRN and the Pso4 complex interact through a direct physical association between WRN and Cdc5L. A putative model for uncoupling of ICLs in mammalian cells is presented.
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Affiliation(s)
- Nianxiang Zhang
- Department of Molecular Genetics, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA
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