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Sun Q, Sun Y, Liu X, Li M, Li Q, Xiao J, Xu P, Zhang S, Ding X. Regulation of plant resistance to salt stress by the SnRK1-dependent splicing factor SRRM1L. THE NEW PHYTOLOGIST 2024; 242:2093-2114. [PMID: 38511255 DOI: 10.1111/nph.19699] [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: 11/27/2023] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
Most splicing factors are extensively phosphorylated but their physiological functions in plant salt resistance are still elusive. We found that phosphorylation by SnRK1 kinase is essential for SRRM1L nuclear speckle formation and its splicing factor activity in plant cells. In Arabidopsis, loss-of-function of SRRM1L leads to the occurrence of alternative pre-mRNA splicing events and compromises plant resistance to salt stress. In Arabidopsis srrm1l mutant line, we identified an intron-retention Nuclear factor Y subunit A 10 (NFYA10) mRNA variant by RNA-Seq and found phosphorylation-dependent RNA-binding of SRRM1L is indispensable for its alternative splicing activity. In the wild-type Arabidopsis, salt stress can activate SnRK1 to phosphorylate SRRM1L, triggering enrichment of functional NFYA10.1 variant to enhance plant salt resistance. By contrast, the Arabidopsis srrm1l mutant accumulates nonfunctional NFYA10.3 variant, sensitizing plants to salt stress. In summary, this work deciphered the molecular mechanisms and physiological functions of SnRK1-SRRM1L-NFYA10 module, shedding light on a regulatory pathway to fine-tune plant adaptation to abiotic stress at the post-transcriptional and post-translational levels.
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Affiliation(s)
- Qi Sun
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, China
| | - Yixin Sun
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
| | - Xin Liu
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
| | - Minglong Li
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
| | - Qiang Li
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, China
| | - Jialei Xiao
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, China
| | - Pengfei Xu
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, China
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shuzhen Zhang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, China
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaodong Ding
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, China
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Baba T, Tanimura S, Yamaguchi A, Horikawa K, Yokozeki M, Hachiya S, Iemura SI, Natsume T, Matsuda N, Takeda K. Cleaved PGAM5 dephosphorylates nuclear serine/arginine-rich proteins during mitophagy. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119045. [PMID: 33872670 DOI: 10.1016/j.bbamcr.2021.119045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 04/02/2021] [Accepted: 04/13/2021] [Indexed: 01/23/2023]
Abstract
PGAM5 is a protein phosphatase located in the inner mitochondrial membrane through its transmembrane (TM) domain and is cleaved within the TM domain upon mitochondrial dysfunction. We found previously that cleaved PGAM5 is released from mitochondria, following proteasome-mediated rupture of the outer mitochondrial membrane during mitophagy, a selective form of autophagy specific to mitochondria. Here, we examined the role of cleaved PGAM5 outside mitochondria. Deletion mutants that mimic cleaved PGAM5 existed not only in the cytosol but also in the nucleus, and a fraction of cleaved PGAM5 translocated to the nucleus during mitophagy induced by the uncoupler CCCP. We identified serine/arginine-related nuclear matrix protein of 160 kDa (SRm160)/SRRM1, which contains a highly phosphorylated domain rich in arginine/serine dipeptides, called the RS domain, as a nuclear protein that interacts with PGAM5. PGAM5 dephosphorylated SRm160, and incubation of lysates from WT cells, but not of those from PGAM5-deficient cells, induced dephosphorylation of SRm160 and another RS domain-containing protein SRSF1, one of the most characterized serine/arginine-rich (SR) proteins. Moreover, phosphorylation of these proteins and other SR proteins, which are commonly reactive toward the 1H4 monoclonal antibody that detects phosphorylated SR proteins, decreased during mitophagy, largely because of PGAM5 activity. These results suggest that PGAM5 regulates phosphorylation of these nuclear proteins during mitophagy. Because SRm160 and SR proteins play critical roles in mRNA metabolism, PGAM5 may coordinate cellular responses to mitochondrial stress at least in part through post-transcriptional and pre-translational events.
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Affiliation(s)
- Taiki Baba
- Department of Cell Regulation, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan
| | - Susumu Tanimura
- Department of Cell Regulation, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan
| | - Ayane Yamaguchi
- Department of Cell Regulation, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan
| | - Koichiro Horikawa
- Department of Cell Regulation, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan
| | - Masashi Yokozeki
- Department of Cell Regulation, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan
| | - Saki Hachiya
- Department of Cell Regulation, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan
| | - Shun-Ichiro Iemura
- Translational Research Center, Fukushima Medical University, Fukushima 960-1295, Japan
| | - Tohru Natsume
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Noriyuki Matsuda
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Kohsuke Takeda
- Department of Cell Regulation, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan.
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Qiu C, Zhang Y, Fan YJ, Pang TL, Su Y, Zhan S, Xu YZ. HITS-CLIP reveals sex-differential RNA binding and alterative splicing regulation of SRm160 in Drosophila. J Mol Cell Biol 2020; 11:170-181. [PMID: 29750417 DOI: 10.1093/jmcb/mjy029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 03/20/2018] [Accepted: 05/07/2018] [Indexed: 12/27/2022] Open
Abstract
Serine/arginine (SR)-rich proteins are critical for the regulation of alternative splicing (AS), which generates multiple mRNA isoforms from one gene and provides protein diversity for cell differentiation and tissue development. Genetic evidence suggests that Drosophila genital-specific overexpression of SR-related nuclear matrix protein of 160 kDa (SRm160), an SR protein with a PWI RNA-binding motif, causes defective development only in male flies and results in abnormal male genital structures and abnormal testis. However, the molecular characterization of SRm160 is limited. Using the high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) method in two sex-specific embryonic cell lines, S2 from the male and Kc from the female, we first identified the genome-wide RNA-binding characteristics of SRm160, which preferred binding to the exonic tri-nucleotide repeats GCA and AAC. We then validated this binding through both in vitro gel-shift assay and in vivo splicing of minigenes and found that SRm160 level affects AS of many transcripts. Furthermore, we identified 492 differential binding sites (DBS) of SRm160 varying between the two sex-specific cell lines. Among these DBS-containing genes, splicing factors were highly enriched, including transformer, a key regulator in the sex determination cascade. Analyses of fly mutants demonstrated that the SRm160 level affects AS isoforms of transformer. These findings shed crucial light on SRm160's RNA-binding specificity and regulation of AS in Drosophila sex determination and development.
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Affiliation(s)
- Chen Qiu
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - Yu Zhang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - Yu-Jie Fan
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Ting-Lin Pang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - Yan Su
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Shuai Zhan
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yong-Zhen Xu
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
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Ustaoglu P, Haussmann IU, Liao H, Torres-Mendez A, Arnold R, Irimia M, Soller M. Srrm234, but not canonical SR and hnRNP proteins, drive inclusion of Dscam exon 9 variable exons. RNA (NEW YORK, N.Y.) 2019; 25:1353-1365. [PMID: 31292260 PMCID: PMC6800468 DOI: 10.1261/rna.071316.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/04/2019] [Indexed: 05/24/2023]
Abstract
Alternative splicing of pre-mRNA is a major mechanism to diversify protein functionality in metazoans from a limited number of genes. The Drosophila melanogaster Down syndrome cell adhesion molecule (Dscam) gene, which is important for neuronal wiring and phagocytosis of bacteria, can generate up to 38,016 isoforms by mutually exclusive alternative splicing in four clusters of variable exons. However, it is not understood how a specific exon is chosen from the many variables and how variable exons are prevented from being spliced together. A main role in the regulation of Dscam alternative splicing has been attributed to RNA binding proteins (RBPs), but how they impact on exon selection is not well understood. Serine-arginine rich (SR) proteins and hnRNP proteins are the two main types of RBPs with major roles in exon definition and splice site selection. Here, we analyzed the role of SR and hnRNP proteins in Dscam exon 9 alternative splicing in mutant Drosophila melanogaster embryos because of their essential function for development. Strikingly, loss or overexpression of canonical SR and hnRNP proteins even when multiple proteins are depleted together, does not affect Dscam alternative exon selection very dramatically. Conversely, noncanonical SR protein Serine-arginine repetitive matrix 2/3/4 (Srrm234) is a main determinant of exon inclusion in the Dscam exon 9 cluster. Since long-range base-pairings are absent in the exon 9 cluster, our data argue for a small complement of regulatory factors as main determinants of exon inclusion in the Dscam exon 9 cluster.
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Affiliation(s)
- Pinar Ustaoglu
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Irmgard U Haussmann
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
- Department of Life Science, School of Health Sciences, Birmingham City University, Birmingham B5 3TN, United Kingdom
| | - Hongzhi Liao
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Antonio Torres-Mendez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Roland Arnold
- Institute of Cancer and Genomics Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
- ICREA, Barcelona 08010, Spain
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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Nagy O, Nuez I, Savisaar R, Peluffo AE, Yassin A, Lang M, Stern DL, Matute DR, David JR, Courtier-Orgogozo V. Correlated Evolution of Two Copulatory Organs via a Single cis-Regulatory Nucleotide Change. Curr Biol 2018; 28:3450-3457.e13. [PMID: 30344115 DOI: 10.1016/j.cub.2018.08.047] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 07/12/2018] [Accepted: 08/21/2018] [Indexed: 01/25/2023]
Abstract
Diverse traits often covary between species [1-3]. The possibility that a single mutation could contribute to the evolution of several characters between species [3] is rarely investigated as relatively few cases are dissected at the nucleotide level. Drosophila santomea has evolved additional sex comb sensory teeth on its legs and has lost two sensory bristles on its genitalia. We present evidence that a single nucleotide substitution in an enhancer of the scute gene contributes to both changes. The mutation alters a binding site for the Hox protein Abdominal-B in the developing genitalia, leading to bristle loss, and for another factor in the developing leg, leading to bristle gain. Our study suggests that morphological evolution between species can occur through a single nucleotide change affecting several sexually dimorphic traits. VIDEO ABSTRACT.
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Affiliation(s)
- Olga Nagy
- Institut Jacques Monod, CNRS UMR7592, Université Paris-Diderot, 75013 Paris, France
| | - Isabelle Nuez
- Institut Jacques Monod, CNRS UMR7592, Université Paris-Diderot, 75013 Paris, France
| | - Rosina Savisaar
- Institut Jacques Monod, CNRS UMR7592, Université Paris-Diderot, 75013 Paris, France
| | - Alexandre E Peluffo
- Institut Jacques Monod, CNRS UMR7592, Université Paris-Diderot, 75013 Paris, France
| | - Amir Yassin
- Institut Systématique Évolution Biodiversité (ISYEB), Centre National de Recherche Scientifique, MNHN, Sorbonne Université, EPHE, 57 rue Cuvier, CP 50, 75005 Paris, France
| | - Michael Lang
- Institut Jacques Monod, CNRS UMR7592, Université Paris-Diderot, 75013 Paris, France
| | - David L Stern
- Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, NC, USA
| | - Jean R David
- Institut Systématique Évolution Biodiversité (ISYEB), Centre National de Recherche Scientifique, MNHN, Sorbonne Université, EPHE, 57 rue Cuvier, CP 50, 75005 Paris, France; Laboratoire Evolution, Génomes, Comportement, Biodiversité (EGCE), CNRS, IRD, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
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6
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Gu H, Song IB, Han HJ, Lee NY, Cha JY, Son YK, Kwon J. Antioxidant Activity of Royal Jelly Hydrolysates Obtained by Enzymatic Treatment. Korean J Food Sci Anim Resour 2018; 38:135-142. [PMID: 29725231 PMCID: PMC5932976 DOI: 10.5851/kosfa.2018.38.1.135] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/11/2018] [Accepted: 01/11/2018] [Indexed: 12/02/2022] Open
Abstract
Recently, research on the processing of raw functional materials with the aim of improving various physiological activities has been conducted. In this study, we investigated the antioxidant activity of royal jelly (RJ) hydrolysates obtained from three commercial proteases. Enzyme-treated royal jelly (ERJ), in which the RJ hydrolysates were converted into easy-to-absorb shorter chain monomers through the removal of two known allergen proteins, showed no difference in the content of (E)-10-hydroxydec-2-enoicacid (10-HDA) or the freshness parameter and showed a significant increase in total free amino acid content. The antioxidant activity of ERJ was determined by 1,1-diphenyl-2-picrylhydrazyl (DPPH) and chemical assays. The ERJ showed about 80% DPPH-radical scavenging activity at same concentration of ascorbic acid. The antioxidant effect of ERJ was confirmed to be due to reduction of intracellular reactive oxidative species (ROS) and nitric oxide (NO) production in LPS-treated macrophages. Moreover, ERJ significantly increased the activity of the antioxidant enzyme superoxide dismutase (SOD) and the level of the antioxidant glutathione (GSH) in a dose-dependent manner. Interestingly, these antioxidant activities of ERJ were stronger than those of non-treated RJ. These findings indicate that ERJ has high potential as an antioxidant agent for use in human and animal diets.
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Affiliation(s)
- Hyejung Gu
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Chonbuk National University, Iksan 54596, Korea
| | - In-Bong Song
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Chonbuk National University, Iksan 54596, Korea
| | - Hye-Ju Han
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Chonbuk National University, Iksan 54596, Korea
| | - Na-Young Lee
- R&D Team, Food & Supplement Health Claims, Vitech, Jeonju 54810, Korea
| | - Ji-Yun Cha
- R&D Team, Food & Supplement Health Claims, Vitech, Jeonju 54810, Korea
| | - Yeon-Kyong Son
- R&D Team, Food & Supplement Health Claims, Vitech, Jeonju 54810, Korea
| | - Jungkee Kwon
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Chonbuk National University, Iksan 54596, Korea
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Rhythmic Behavior Is Controlled by the SRm160 Splicing Factor in Drosophila melanogaster. Genetics 2017; 207:593-607. [PMID: 28801530 DOI: 10.1534/genetics.117.300139] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 08/02/2017] [Indexed: 02/06/2023] Open
Abstract
Circadian clocks organize the metabolism, physiology, and behavior of organisms throughout the day-night cycle by controlling daily rhythms in gene expression at the transcriptional and post-transcriptional levels. While many transcription factors underlying circadian oscillations are known, the splicing factors that modulate these rhythms remain largely unexplored. A genome-wide assessment of the alterations of gene expression in a null mutant of the alternative splicing regulator SR-related matrix protein of 160 kDa (SRm160) revealed the extent to which alternative splicing impacts on behavior-related genes. We show that SRm160 affects gene expression in pacemaker neurons of the Drosophila brain to ensure proper oscillations of the molecular clock. A reduced level of SRm160 in adult pacemaker neurons impairs circadian rhythms in locomotor behavior, and this phenotype is caused, at least in part, by a marked reduction in period (per) levels. Moreover, rhythmic accumulation of the neuropeptide PIGMENT DISPERSING FACTOR in the dorsal projections of these neurons is abolished after SRm160 depletion. The lack of rhythmicity in SRm160-downregulated flies is reversed by a fully spliced per construct, but not by an extra copy of the endogenous locus, showing that SRm160 positively regulates per levels in a splicing-dependent manner. Our findings highlight the significant effect of alternative splicing on the nervous system and particularly on brain function in an in vivo model.
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Zhao Y, Cocco C, Domenichini S, Samson ML, Rabinow L. The IMD innate immunity pathway of Drosophila influences somatic sex determination via regulation of the Doa locus. Dev Biol 2015; 407:224-31. [DOI: 10.1016/j.ydbio.2015.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/24/2015] [Accepted: 09/24/2015] [Indexed: 11/30/2022]
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