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Jia ZC, Das D, Zhang Y, Fernie AR, Liu YG, Chen M, Zhang J. Plant serine/arginine-rich proteins: versatile players in RNA processing. PLANTA 2023; 257:109. [PMID: 37145304 DOI: 10.1007/s00425-023-04132-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 04/05/2023] [Indexed: 05/06/2023]
Abstract
MAIN CONCLUSION Serine/arginine-rich (SR) proteins participate in RNA processing by interacting with precursor mRNAs or other splicing factors to maintain plant growth and stress responses. Alternative splicing is an important mechanism involved in mRNA processing and regulation of gene expression at the posttranscriptional level, which is the main reason for the diversity of genes and proteins. The process of alternative splicing requires the participation of many specific splicing factors. The SR protein family is a splicing factor in eukaryotes. The vast majority of SR proteins' existence is an essential survival factor. Through its RS domain and other unique domains, SR proteins can interact with specific sequences of precursor mRNA or other splicing factors and cooperate to complete the correct selection of splicing sites or promote the formation of spliceosomes. They play essential roles in the composition and alternative splicing of precursor mRNAs, providing pivotal functions to maintain growth and stress responses in animals and plants. Although SR proteins have been identified in plants for three decades, their evolutionary trajectory, molecular function, and regulatory network remain largely unknown compared to their animal counterparts. This article reviews the current understanding of this gene family in eukaryotes and proposes potential key research priorities for future functional studies.
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Affiliation(s)
- Zi-Chang Jia
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Debatosh Das
- College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences and Technology, 52 Agricultural Building, University of Missouri, Columbia, MO, 65201, USA
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Youjun Zhang
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
- Max-Planck-Institut Für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
- Max-Planck-Institut Für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Ying-Gao Liu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
| | - Moxian Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China.
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
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Chen S, Mo Y, Zhang Y, Zhu H, Ling Y. Insights into sweet potato SR proteins: from evolution to species-specific expression and alternative splicing. PLANTA 2022; 256:72. [PMID: 36083517 DOI: 10.1007/s00425-022-03965-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
SR proteins from sweet potato have conserved functional domains and similar gene structures as that of Arabidopsis and rice in general. However, expression patterns and alternative splicing regulations of SR genes from different species have changed under stresses. Novel alternative splicing regulations were found in sweet potato SR genes. Serine/arginine-rich (SR) proteins play important roles in plant development and stress response by regulating the pre-mRNA splicing process. However, SR proteins have not been identified so far from an important crop sweet potato. Through bioinformatics analysis, our study identified 24 SR proteins from sweet potato, with comprehensively analyzing of protein characteristics, gene structure, chromosome localization, and cis-acting elements in promotors. Salt, heat, and mimic drought stresses triggered extensive but different expressional regulations on sweet potato SR genes. Interestingly, heat stress caused the most active disturbances in both gene transcription and pre-mRNA alternative splicing (AS). Tissue and species-specific transcriptional and pre-mRNA AS regulations in response to stresses were found in sweet potato, in comparison with Arabidopsis and rice. Moreover, novel patterns of pre-mRNA alternative splicing were found in SR proteins from sweet potato. Our study provided an insight into similarities and differences of SR proteins in different plant species from gene sequences to gene structures and stress responses, indicating SR proteins may regulate their downstream genes differently between different species and tissues by varied transcriptional and pre-mRNA AS regulations.
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Affiliation(s)
- Shanlan Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yujian Mo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yingjie Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Hongbao Zhu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China.
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Fuchs A, Riegler S, Ayatollahi Z, Cavallari N, Giono LE, Nimeth BA, Mutanwad KV, Schweighofer A, Lucyshyn D, Barta A, Petrillo E, Kalyna M. Targeting alternative splicing by RNAi: from the differential impact on splice variants to triggering artificial pre-mRNA splicing. Nucleic Acids Res 2021; 49:1133-1151. [PMID: 33406240 PMCID: PMC7826280 DOI: 10.1093/nar/gkaa1260] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/08/2020] [Accepted: 12/17/2020] [Indexed: 12/25/2022] Open
Abstract
Alternative splicing generates multiple transcript and protein isoforms from a single gene and controls transcript intracellular localization and stability by coupling to mRNA export and nonsense-mediated mRNA decay (NMD). RNA interference (RNAi) is a potent mechanism to modulate gene expression. However, its interactions with alternative splicing are poorly understood. We used artificial microRNAs (amiRNAs, also termed shRNAmiR) to knockdown all splice variants of selected target genes in Arabidopsis thaliana. We found that splice variants, which vary by their protein-coding capacity, subcellular localization and sensitivity to NMD, are affected differentially by an amiRNA, although all of them contain the target site. Particular transcript isoforms escape amiRNA-mediated degradation due to their nuclear localization. The nuclear and NMD-sensitive isoforms mask RNAi action in alternatively spliced genes. Interestingly, Arabidopsis SPL genes, which undergo alternative splicing and are targets of miR156, are regulated in the same manner. Moreover, similar results were obtained in mammalian cells using siRNAs, indicating cross-kingdom conservation of these interactions among RNAi and splicing isoforms. Furthermore, we report that amiRNA can trigger artificial alternative splicing, thus expanding the RNAi functional repertoire. Our findings unveil novel interactions between different post-transcriptional processes in defining transcript fates and regulating gene expression.
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Affiliation(s)
- Armin Fuchs
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria
| | - Stefan Riegler
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria.,Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
| | - Zahra Ayatollahi
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria
| | - Nicola Cavallari
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria
| | - Luciana E Giono
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
| | - Barbara A Nimeth
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
| | - Krishna V Mutanwad
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
| | | | - Doris Lucyshyn
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
| | - Andrea Barta
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria
| | - Ezequiel Petrillo
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
| | - Maria Kalyna
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
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Harb A, Simpson C, Guo W, Govindan G, Kakani VG, Sunkar R. The Effect of Drought on Transcriptome and Hormonal Profiles in Barley Genotypes With Contrasting Drought Tolerance. FRONTIERS IN PLANT SCIENCE 2020; 11:618491. [PMID: 33424910 PMCID: PMC7786106 DOI: 10.3389/fpls.2020.618491] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 11/27/2020] [Indexed: 05/21/2023]
Abstract
Like many cereal crops, barley is also negatively affected by drought stress. However, due to its simple genome as well as enhanced stress resilient nature compared to rice and wheat, barley has been considered as a model to decipher drought tolerance in cereals. In the present study, transcriptomic and hormonal profiles along with several biochemical features were compared between drought-tolerant (Otis) and drought-sensitive (Baronesse) barley genotypes subjected to drought to identify molecular and biochemical differences between the genotypes. The drought-induced decrease in the leaf relative water content, net photosynthesis, and biomass accumulation was relatively low in Otis compared to Baronesse. The hormonal profiles did not reveal significant differences for majority of the compounds other than the GA20 and the cis-zeatin-o-glucoside (c-ZOG), whose levels were greatly increased in Otis compared to Baronesse under drought. The major differences that emerged from the transcriptome analysis are; (1), the overall number of differentially expressed genes was relatively low in drought-tolerant Otis compared to drought-sensitive Baronesse; (2), a wax biosynthesis gene (CER1), and NAC transcription factors were specifically induced in Otis but not in Baronesse; (3), the degree of upregulation of betaine aldehyde dehydrogenase and a homeobox transcription factor (genes with proven roles in imparting drought tolerance), was greater in Otis compared to Baronesse; (4) the extent of downregulation of gene expression profiles for proteins of the reaction center photosystem II (PSII) (D1 and D2) was low in Otis compared to Baronesse; and, (5), alternative splicing (AS) was also found to differ between the genotypes under drought. Taken together, the overall transcriptional responses were low in drought-tolerant Otis but the genes that could confer drought tolerance were either specifically induced or greatly upregulated in the tolerant genotype and these differences could be important for drought tolerance in barley.
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Affiliation(s)
- Amal Harb
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, United States
- Department of Biological Sciences, Faculty of Science, Yarmouk University, Irbid, Jordan
- *Correspondence: Amal Harb ;
| | - Craig Simpson
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Wenbin Guo
- Informatics and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Ganesan Govindan
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, United States
| | - Vijaya Gopal Kakani
- Department of Plant and Soil Science, Oklahoma State University, Stillwater, OK, United States
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, United States
- Ramanjulu Sunkar
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5
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Genome-Wide Analysis of Serine/Arginine-Rich Protein Family in Wheat and Brachypodium distachyon. PLANTS 2019; 8:plants8070188. [PMID: 31247888 PMCID: PMC6681277 DOI: 10.3390/plants8070188] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/20/2019] [Accepted: 06/22/2019] [Indexed: 12/15/2022]
Abstract
By regulating the pre-mRNA splicing of other genes and themselves, plant serine/arginine-rich (SR) proteins play important roles in development and in response to abiotic stresses. Presently, the functions of most plant SR protein genes remain unclear. Wheat (Triticumaestivum) and Brachypodiumdistachyon are closely related species. In this study, 40 TaSR and 18 BdSR proteins were identified respectively, and they were classified into seven subfamilies: SR, RS, SCL, RSZ, RS2Z, SC35, and SR45. Similar to Arabidopsis and rice SR protein genes, most TaSR and BdSR protein genes are expressed extensively. Surprisingly, real-time polymerase chain reaction (RT-PCR) analyses showed that no alternative splicing event was found in TaSR protein genes, and only six BdSR protein genes are alternatively spliced genes. The detected alternatively spliced BdSR protein genes and transcripts are much fewer than in Arabidopsis, rice, maize, and sorghum. In the promoter regions, 92 development-related, stress-related, and hormone-related cis-elements were detected, indicating their functions in development and in response to environmental stresses. Meanwhile, 19 TaSR and 16 BdSR proteins were predicted to interact with other SR proteins or non-SR proteins, implying that they are involved in other functions in addition to modulating pre-mRNA splicing as essential components of the spliceosome. These results lay a foundation for further analyses of these genes.
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6
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He P, Wang X, Zhang X, Jiang Y, Tian W, Zhang X, Li Y, Sun Y, Xie J, Ni J, He G, Sang X. Short and narrow flag leaf1, a GATA zinc finger domain-containing protein, regulates flag leaf size in rice (Oryza sativa). BMC PLANT BIOLOGY 2018; 18:273. [PMID: 30413183 PMCID: PMC6230254 DOI: 10.1186/s12870-018-1452-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 09/27/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND The flag leaf of rice (Oryza sativa L.) is an important determinant of plant type characteristics and grain yield. Identification of flag leaf mutants of rice is crucial to elucidate the molecular mechanism of flag-leaf development, and for exploitation of rice germplasm resources. RESULTS In this study, we describe a mutant designated short and narrow flag leaf 1 (snfl1). Histological analysis showed that the length of epidermal cells and number of longitudinal veins were decreased in the flag leaf of the snfl1 mutant. Map-based cloning indicated that a member of the GATA family of transcription factors is a candidate gene for SNFL1. A single-nucleotide transition at the last base in the single intron of snfl1 led to variation in alternative splicing and early termination of translation. Complemented transgenic plants harbouring the candidate SNFL1 gene rescued the snfl1 mutant. Analysis of RT-PCR and the SNFL1 promoter by means of a GUS fusion expression assay showed that abundance of SNFL1 transcripts was higher in the culm, leaf sheath, and root. Expression of the SNFL1-GFP fusion protein in rice protoplasts showed that SNFL1 was localized in nucleus. CONCLUSIONS We conclude that SNFL1 is an important regulator of leaf development, the identification of which might have important implications for future research on GATA transcription factors.
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Affiliation(s)
- Peilong He
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Xiaowen Wang
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Xiaobo Zhang
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Yudong Jiang
- Key Laboratory of Southwest Rice Biology and Genetic Breeding, Institute of Rice and Sorghum, Sichuan Academy of Agricultural Sciences, Deyang, China
| | - Weijiang Tian
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Xiaoqiong Zhang
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Yangyang Li
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Ying Sun
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jia Xie
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jile Ni
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Guanghua He
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, China.
| | - Xianchun Sang
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, China.
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7
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Zhou B, Lin JZ, Peng D, Yang YZ, Guo M, Tang DY, Tan X, Liu XM. Plant architecture and grain yield are regulated by the novel DHHC-type zinc finger protein genes in rice (Oryza sativa L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 254:12-21. [PMID: 27964781 DOI: 10.1016/j.plantsci.2016.08.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 08/08/2016] [Accepted: 08/29/2016] [Indexed: 06/06/2023]
Abstract
In many plants, architecture and grain yield are affected by both the environment and genetics. In rice, the tiller is a vital factor impacting plant architecture and regulated by many genes. In this study, we cloned a novel DHHC-type zinc finger protein gene Os02g0819100 and its alternative splice variant OsDHHC1 from the cDNA of rice (Oryza sativa L.), which regulate plant architecture by altering the tiller in rice. The tillers increased by about 40% when this type of DHHC-type zinc finger protein gene was over-expressed in Zhong Hua 11 (ZH11) rice plants. Moreover, the grain yield of transgenic rice increased approximately by 10% compared with wild-type ZH11. These findings provide an important genetic engineering approach for increasing rice yields.
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Affiliation(s)
- Bo Zhou
- College of Bioscience and Biotechnology of Central South University of Forestry and Technology, Changsha 410018, Hunan, China; Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, 410018 Changsha, China
| | - Jian Zhong Lin
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Changsha 410082, Hunan, China; College of Biology, Hunan University, Changsha 410082, Hunan, China; Bioenergy and Biomaterial Research Center, College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, Hunan, China
| | - Dan Peng
- College of Bioscience and Biotechnology of Central South University of Forestry and Technology, Changsha 410018, Hunan, China; Academy of Seed Industry of Hunan Yahua, Changsha 410013, Hunan, China; Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, 410018 Changsha, China
| | - Yuan Zhu Yang
- Academy of Seed Industry of Hunan Yahua, Changsha 410013, Hunan, China
| | - Ming Guo
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Changsha 410082, Hunan, China; College of Biology, Hunan University, Changsha 410082, Hunan, China; Bioenergy and Biomaterial Research Center, College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, Hunan, China
| | - Dong Ying Tang
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Changsha 410082, Hunan, China; College of Biology, Hunan University, Changsha 410082, Hunan, China; Bioenergy and Biomaterial Research Center, College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, Hunan, China
| | - Xiaofeng Tan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, 410018 Changsha, China
| | - Xuan Ming Liu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Changsha 410082, Hunan, China; College of Biology, Hunan University, Changsha 410082, Hunan, China; Bioenergy and Biomaterial Research Center, College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, Hunan, China.
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Dai Y, Li W, An L. NMD mechanism and the functions of Upf proteins in plant. PLANT CELL REPORTS 2016; 35:5-15. [PMID: 26400685 DOI: 10.1007/s00299-015-1867-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 09/01/2015] [Accepted: 09/05/2015] [Indexed: 05/18/2023]
Abstract
Nonsense-mediated decay (NMD) mechanism, also called mRNA surveillance, is a universal mRNA degradation pathway in eukaryotes. Hundreds of genes can be regulated by NMD whether in single-celled or higher organisms. There have been many studies on NMD and NMD factors (Upf proteins) with regard to their crucial roles in mRNA decay, especially in mammals and yeast. However, research focusing on NMD in plant is still lacking compared to the research that has been dedicated to NMD in mammals and yeast. Even so, recent study has shown that NMD factors in Arabidopsis can provide resistance against biotic and abiotic stresses. This discovery and its associated developments have given plant NMD mechanism a new outlook and since then, more and more research has focused on this area. In this review, we focused mainly on the distinctive NMD micromechanism and functions of Upf proteins in plant with references to the role of mRNA surveillance in mammals and yeast. We also highlighted recent insights into the roles of premature termination codon location, trans-elements and functions of other NMD factors to emphasize the particularity of plant NMD. Furthermore, we also discussed conventional approaches and neoteric methods used in plant NMD researches.
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Affiliation(s)
- Yiming Dai
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China.
| | - Wenli Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China.
| | - Lijia An
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China.
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9
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Petrillo E, Godoy Herz MA, Barta A, Kalyna M, Kornblihtt AR. Let there be light: regulation of gene expression in plants. RNA Biol 2015; 11:1215-20. [PMID: 25590224 PMCID: PMC4615654 DOI: 10.4161/15476286.2014.972852] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Gene expression regulation relies on a variety of molecular mechanisms affecting different steps of a messenger RNA (mRNA) life: transcription, processing, splicing, alternative splicing, transport, translation, storage and decay. Light induces massive reprogramming of gene expression in plants. Differences in alternative splicing patterns in response to environmental stimuli suggest that alternative splicing plays an important role in plant adaptation to changing life conditions. In a recent publication, our laboratories showed that light regulates alternative splicing of a subset of Arabidopsis genes encoding proteins involved in RNA processing by chloroplast retrograde signals. The light effect on alternative splicing is also observed in roots when the communication with the photosynthetic tissues is not interrupted, suggesting that a signaling molecule travels through the plant. These results point at alternative splicing regulation by retrograde signals as an important mechanism for plant adaptation to their environment.
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Key Words
- DBMIB, 2,5-dibromo-3-methyl-6-isopropyl-benzoquinone
- DCMU, 3-(3,4-dichlorophenyl)-1,1-dimethylurea
- PQ, plastoquinone
- PS, photosystem
- Pol II, RNA polymerase II
- RNA
- ROS, reactive oxygen species
- alternative splicing
- chloroplast
- light
- mRNA, messenger RNA
- photoreceptors
- retrograde signaling
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Affiliation(s)
- Ezequiel Petrillo
- a Max F. Perutz Laboratories ; Medical University of Vienna ; Vienna , Austria
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10
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Chen T, Cui P, Xiong L. The RNA-binding protein HOS5 and serine/arginine-rich proteins RS40 and RS41 participate in miRNA biogenesis in Arabidopsis. Nucleic Acids Res 2015; 43:8283-98. [PMID: 26227967 PMCID: PMC4787832 DOI: 10.1093/nar/gkv751] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 07/11/2015] [Indexed: 12/28/2022] Open
Abstract
MicroRNAs are a class of small regulatory RNAs that are generated from primary miRNA (pri-miRNA) transcripts with a stem-loop structure. Accuracy of the processing of pri-miRNA into mature miRNA in plants can be enhanced by SERRATE (SE) and HYPONASTIC LEAVES 1 (HYL1). HYL1 activity is regulated by the FIERY2 (FRY2)/RNA polymerase II C-terminal domain phosphatase-like 1 (CPL1). Here, we discover that HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5) and two serine/arginine-rich splicing factors RS40 and RS41, previously shown to be involved in pre-mRNA splicing, affect the biogenesis of a subset of miRNA. These proteins are required for correct miRNA strand selection and the maintenance of miRNA levels. FRY2 dephosphorylates HOS5 whose phosphorylation status affects its subnuclear localization. HOS5 and the RS proteins bind both intronless and intron-containing pri-miRNAs. Importantly, all of these splicing-related factors directly interact with both HYL1 and SE in nuclear splicing speckles. Our results indicate that these splicing factors are directly involved in the biogenesis of a group of miRNA.
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Affiliation(s)
- Tao Chen
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Peng Cui
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Liming Xiong
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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11
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Abstract
Alternative pre-messenger RNA splicing in higher plants emerges as an important layer of regulation upon exposure to exogenous and endogenous cues. Accordingly, mutants defective in RNA-binding proteins predicted to function in the splicing process show severe phenotypic alterations. Among those are developmental defects, impaired responses to pathogen threat or abiotic stress factors, and misregulation of the circadian timing system. A suite of splicing factors has been identified in the model plant Arabidopsis thaliana. Here we summarize recent insights on how defects in these splicing factors impair plant performance.
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12
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Du JL, Zhang SW, Huang HW, Cai T, Li L, Chen S, He XJ. The Splicing Factor PRP31 Is Involved in Transcriptional Gene Silencing and Stress Response in Arabidopsis. MOLECULAR PLANT 2015; 8:1053-68. [PMID: 25684655 DOI: 10.1016/j.molp.2015.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Revised: 01/11/2015] [Accepted: 02/05/2015] [Indexed: 05/10/2023]
Abstract
Although DNA methylation is known to play an important role in the silencing of transposable elements (TEs) and introduced transgenes, the mechanisms that generate DNA methylation-independent transcriptional silencing are poorly understood. Previous studies suggest that RNA-directed DNA methylation (RdDM) is required for the silencing of the RD29A-LUC transgene in the Arabidopsis ros1 mutant background with defective DNA demethylase. Loss of function of ARGONAUTE 4 (AGO4) gene, which encodes a core RdDM component, partially released the silencing of RD29A-LUC in the ros1/ago4 double mutant plants. A forward genetic screen was performed to identify the mutants with elevated RD29A-LUC transgene expression in the ros1/ago4 mutant background. We identified a mutation in the homologous gene of PRP31, which encodes a conserved pre-mRNA splicing factor that regulates the formation of the U4/U6.U5 snRNP complex in fungi and animals. We previously demonstrated that the splicing factors ZOP1 and STA1 contribute to transcriptional gene silencing. Here, we reveal that Arabidopsis PRP31 associates with ZOP1, STA1, and several other splicing-related proteins, suggesting that these splicing factors are both physically and functionally connected. We show that Arabidopsis PRP31 participates in transcriptional gene silencing. Moreover, we report that PRP31, STA1, and ZOP1 are required for development and stress response. Under cold stress, PRP31 is not only necessary for pre-mRNA splicing but also for regulation of cold-responsive gene expression. Our results suggest that the splicing machinery has multiple functions including pre-mRNA splicing, gene regulation, transcriptional gene silencing, and stress response.
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Affiliation(s)
- Jin-Lu Du
- College of Life Sciences, Beijing Normal University, Beijing 100875, China; National Institute of Biological Sciences, Beijing 102206, China
| | - Su-Wei Zhang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Huan-Wei Huang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Tao Cai
- National Institute of Biological Sciences, Beijing 102206, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - She Chen
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing 102206, China.
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13
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Alternative splicing in plant immunity. Int J Mol Sci 2014; 15:10424-45. [PMID: 24918296 PMCID: PMC4100160 DOI: 10.3390/ijms150610424] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 05/12/2014] [Accepted: 05/14/2014] [Indexed: 12/01/2022] Open
Abstract
Alternative splicing (AS) occurs widely in plants and can provide the main source of transcriptome and proteome diversity in an organism. AS functions in a range of physiological processes, including plant disease resistance, but its biological roles and functional mechanisms remain poorly understood. Many plant disease resistance (R) genes undergo AS, and several R genes require alternatively spliced transcripts to produce R proteins that can specifically recognize pathogen invasion. In the finely-tuned process of R protein activation, the truncated isoforms generated by AS may participate in plant disease resistance either by suppressing the negative regulation of initiation of immunity, or by directly engaging in effector-triggered signaling. Although emerging research has shown the functional significance of AS in plant biotic stress responses, many aspects of this topic remain to be understood. Several interesting issues surrounding the AS of R genes, especially regarding its functional roles and regulation, will require innovative techniques and additional research to unravel.
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Petrillo E, Godoy Herz MA, Fuchs A, Reifer D, Fuller J, Yanovsky MJ, Simpson C, Brown JWS, Barta A, Kalyna M, Kornblihtt AR. A chloroplast retrograde signal regulates nuclear alternative splicing. Science 2014; 344:427-30. [PMID: 24763593 DOI: 10.1126/science.1250322] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Light is a source of energy and also a regulator of plant physiological adaptations. We show here that light/dark conditions affect alternative splicing of a subset of Arabidopsis genes preferentially encoding proteins involved in RNA processing. The effect requires functional chloroplasts and is also observed in roots when the communication with the photosynthetic tissues is not interrupted, suggesting that a signaling molecule travels through the plant. Using photosynthetic electron transfer inhibitors with different mechanisms of action, we deduce that the reduced pool of plastoquinones initiates a chloroplast retrograde signaling that regulates nuclear alternative splicing and is necessary for proper plant responses to varying light conditions.
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Affiliation(s)
- Ezequiel Petrillo
- Laboratorio de Fisiología y Biología Molecular, Departamento de Fisiología, Biología Molecular y Celular, IFIBYNE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
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15
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Reddy AS, Marquez Y, Kalyna M, Barta A. Complexity of the alternative splicing landscape in plants. THE PLANT CELL 2013; 25:3657-83. [PMID: 24179125 PMCID: PMC3877793 DOI: 10.1105/tpc.113.117523] [Citation(s) in RCA: 516] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Revised: 09/27/2013] [Accepted: 10/08/2013] [Indexed: 05/18/2023]
Abstract
Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) from multiexon genes allows organisms to increase their coding potential and regulate gene expression through multiple mechanisms. Recent transcriptome-wide analysis of AS using RNA sequencing has revealed that AS is highly pervasive in plants. Pre-mRNAs from over 60% of intron-containing genes undergo AS to produce a vast repertoire of mRNA isoforms. The functions of most splice variants are unknown. However, emerging evidence indicates that splice variants increase the functional diversity of proteins. Furthermore, AS is coupled to transcript stability and translation through nonsense-mediated decay and microRNA-mediated gene regulation. Widespread changes in AS in response to developmental cues and stresses suggest a role for regulated splicing in plant development and stress responses. Here, we review recent progress in uncovering the extent and complexity of the AS landscape in plants, its regulation, and the roles of AS in gene regulation. The prevalence of AS in plants has raised many new questions that require additional studies. New tools based on recent technological advances are allowing genome-wide analysis of RNA elements in transcripts and of chromatin modifications that regulate AS. Application of these tools in plants will provide significant new insights into AS regulation and crosstalk between AS and other layers of gene regulation.
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Affiliation(s)
- Anireddy S.N. Reddy
- Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
- Address correspondence to
| | - Yamile Marquez
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
| | - Maria Kalyna
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
| | - Andrea Barta
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
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16
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Liu JZ, Whitham SA. Overexpression of a soybean nuclear localized type-III DnaJ domain-containing HSP40 reveals its roles in cell death and disease resistance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 74:110-21. [PMID: 23289813 DOI: 10.1111/tpj.12108] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Revised: 12/18/2012] [Accepted: 12/20/2012] [Indexed: 05/19/2023]
Abstract
Heat-shock proteins such as HSP70 and HSP90 are important molecular chaperones that play critical roles in biotic and abiotic stress responses; however, the involvement of their co-chaperones in stress biology remains largely uninvestigated. In a screen for candidate genes stimulating cell death in Glycine max (soybean), we transiently overexpressed full-length cDNAs of soybean genes that are highly induced during soybean rust infection in Nicotiana benthamiana leaves. Overexpression of a type-III DnaJ domain-containing HSP40 (GmHSP40.1), a co-chaperone of HSP70, caused hypersensitive response (HR)-like cell death. The HR-like cell death was dependent on MAPKKKα and WIPK, because silencing each of these genes suppressed the HR. Consistent with the presence of a nuclear localization signal (NLS) motif within the GmHSP40.1 coding sequence, GFP-GmHSP40.1 was exclusively present in nuclear bodies or speckles. Nuclear localization of GmHSP40.1 was necessary for its function, because deletion of the NLS or addition of a nuclear export signal abolished its HR-inducing ability. GmHSP40.1 co-localized with HcRed-SE, a protein involved in pri-miRNA processing, which has been shown to be co-localized with SR33-YFP, a protein involved in pre-mRNA splicing, suggesting a possible role for GmHSP40.1 in mRNA splicing or miRNA processing, and a link between these processes and cell death. Silencing GmHSP40.1 enhanced the susceptibility of soybean plants to Soybean mosaic virus, confirming its positive role in pathogen defense. Together, the results demonstrate a critical role of a nuclear-localized DnaJ domain-containing GmHSP40.1 in cell death and disease resistance in soybean.
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Affiliation(s)
- Jian-Zhong Liu
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
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17
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Meier I. mRNA export and sumoylation-Lessons from plants. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:531-7. [PMID: 22306659 DOI: 10.1016/j.bbagrm.2012.01.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 01/15/2012] [Accepted: 01/19/2012] [Indexed: 01/22/2023]
Abstract
SUMO is a small ubiquitin-related protein modifier that is involved in a number of biological processes, including transcription, DNA repair, genome stability, and chromatin organization. Its potential role in mRNA biogenesis is less well investigated. The biogenesis of mRNA is closely coupled to transcription as well as mRNA nuclear export and several of the involved proteins have dual roles and appear in several complexes. Recently, SUMO-proteome analyses have discovered a number of these proteins as putative targets of SUMO regulation. In the model plant Arabidopsis thaliana, several mutants as well as environmental conditions have been identified that show a close correlation between over- and under-sumoylation of nuclear proteins and mRNA export retention. Three new plant SUMO-proteome studies add to the list of potentially sumoylated RNA-related proteins. Here, the emerging connection between SUMO and mRNA export is compared across kingdoms and its potential mechanistic role is discussed. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.
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Affiliation(s)
- Iris Meier
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
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18
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Reddy ASN, Shad Ali G. Plant serine/arginine-rich proteins: roles in precursor messenger RNA splicing, plant development, and stress responses. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:875-89. [PMID: 21766458 DOI: 10.1002/wrna.98] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Global analyses of splicing of precursor messenger RNAs (pre-mRNAs) have revealed that alternative splicing (AS) is highly pervasive in plants. Despite the widespread occurrence of AS in plants, the mechanisms that control splicing and the roles of splice variants generated from a gene are poorly understood. Studies on plant serine/arginine-rich (SR) proteins, a family of highly conserved proteins, suggest their role in both constitutive splicing and AS of pre-mRNAs. SR proteins have a characteristic domain structure consisting of one or two RNA recognition motifs at the N-terminus and a C-terminal RS domain rich in arginine/serine dipeptides. Plants have many more SR proteins compared to animals including several plant-specific subfamilies. Pre-mRNAs of plant SR proteins are extensively alternatively spliced to increase the transcript complexity by about six-fold. Some of this AS is controlled in a tissue- and development-specific manner. Furthermore, AS of SR pre-mRNAs is altered by various stresses, raising the possibility of rapid reprogramming of the whole transcriptome by external signals through regulation of the splicing of these master regulators of splicing. Most SR splice variants contain a premature termination codon and are degraded by up-frameshift 3 (UPF3)-mediated nonsense-mediated decay (NMD), suggesting a link between NMD and regulation of expression of the functional transcripts of SR proteins. Limited functional studies with plant SRs suggest key roles in growth and development and plant responses to the environment. Here, we discuss the current status of research on plant SRs and some promising approaches to address many unanswered questions about plant SRs.
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Affiliation(s)
- Anireddy S N Reddy
- Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA.
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Xu S, Zhang Z, Jing B, Gannon P, Ding J, Xu F, Li X, Zhang Y. Transportin-SR is required for proper splicing of resistance genes and plant immunity. PLoS Genet 2011; 7:e1002159. [PMID: 21738492 PMCID: PMC3128105 DOI: 10.1371/journal.pgen.1002159] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 05/14/2011] [Indexed: 01/18/2023] Open
Abstract
Transportin-SR (TRN-SR) is a member of the importin-β super-family that functions as the nuclear import receptor for serine-arginine rich (SR) proteins, which play diverse roles in RNA metabolism. Here we report the identification and cloning of mos14 (modifier of snc1-1, 14), a mutation that suppresses the immune responses conditioned by the auto-activated Resistance (R) protein snc1 (suppressor of npr1-1, constitutive 1). MOS14 encodes a nuclear protein with high similarity to previously characterized TRN-SR proteins in animals. Yeast two-hybrid assays showed that MOS14 interacts with AtRAN1 via its N-terminus and SR proteins via its C-terminus. In mos14-1, localization of several SR proteins to the nucleus was impaired, confirming that MOS14 functions as a TRN-SR. The mos14-1 mutation results in altered splicing patterns of SNC1 and another R gene RPS4 and compromised resistance mediated by snc1 and RPS4, suggesting that nuclear import of SR proteins by MOS14 is required for proper splicing of these two R genes and is important for their functions in plant immunity. Plant immune receptors encoded by Resistance (R) genes play essential roles in defense against pathogens. Multiple R genes are alternatively spliced. How plants regulate the splicing of these R genes is unclear. In this study, we identified MOS14 as an important regulator of two R genes, SNC1 and RPS4. Further analysis showed that MOS14 functions as the nuclear import receptor for serine-arginine rich (SR) proteins, which play diverse roles in RNA metabolism. Loss of the function of MOS14 results in altered splicing patterns of SNC1 and RPS4 and compromised resistance mediated by snc1 and RPS4, suggesting that nuclear import of SR proteins by MOS14 is required for proper splicing of these two R genes and is important for their functions in plant immunity.
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Affiliation(s)
- Shaohua Xu
- Graduate Program in Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Institute of Biological Sciences, Beijing, China
| | - Zhibin Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Beibei Jing
- National Institute of Biological Sciences, Beijing, China
| | - Patrick Gannon
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Jinmei Ding
- National Institute of Biological Sciences, Beijing, China
| | - Fang Xu
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Yuelin Zhang
- National Institute of Biological Sciences, Beijing, China
- * E-mail:
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20
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Duque P. A role for SR proteins in plant stress responses. PLANT SIGNALING & BEHAVIOR 2011; 6:49-54. [PMID: 21258207 PMCID: PMC3122005 DOI: 10.4161/psb.6.1.14063] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2010] [Accepted: 10/31/2010] [Indexed: 05/19/2023]
Abstract
Members of the SR (serine/arginine-rich) protein gene family are key players in the regulation of alternative splicing, an important means of generating proteome diversity and regulating gene expression. In plants, marked changes in alternative splicing are induced by a wide variety of abiotic stresses, suggesting a role for this highly versatile gene regulation mechanism in the response to environmental cues. In support of this notion, the expression of plant SR proteins is stress-regulated at multiple levels, with environmental signals controlling their own alternative splicing patterns, phosphorylation status and subcellular distribution. Most importantly, functional links between these RNA-binding proteins and plant stress tolerance are beginning to emerge, including a role in the regulation of abscisic acid (ABA) signaling. Future identification of the physiological mRNA targets of plant SR proteins holds much promise for the elucidation of the molecular mechanisms underlying their role in the response to abiotic stress.
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Affiliation(s)
- Paula Duque
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.
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21
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Barta A, Kalyna M, Reddy ASN. Implementing a rational and consistent nomenclature for serine/arginine-rich protein splicing factors (SR proteins) in plants. THE PLANT CELL 2010; 22:2926-9. [PMID: 20884799 PMCID: PMC2965536 DOI: 10.1105/tpc.110.078352] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Revised: 09/15/2010] [Accepted: 09/16/2010] [Indexed: 05/20/2023]
Abstract
Growing interest in alternative splicing in plants and the extensive sequencing of new plant genomes necessitate more precise definition and classification of genes coding for splicing factors. SR proteins are a family of RNA binding proteins, which function as essential factors for constitutive and alternative splicing. We propose a unified nomenclature for plant SR proteins, taking into account the newly revised nomenclature of the mammalian SR proteins and a number of plant-specific properties of the plant proteins. We identify six subfamilies of SR proteins in Arabidopsis thaliana and rice (Oryza sativa), three of which are plant specific. The proposed subdivision of plant SR proteins into different subfamilies will allow grouping of paralogous proteins and simple assignment of newly discovered SR orthologs from other plant species and will promote functional comparisons in diverse plant species.
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Affiliation(s)
- Andrea Barta
- Max F. Perutz Laboratories, Medical University of Viena, A-1030 Viena, Austria.
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RamachandraRao SP, Zhu Y, Ravasi T, McGowan TA, Toh I, Dunn SR, Okada S, Shaw MA, Sharma K. Pirfenidone is renoprotective in diabetic kidney disease. J Am Soc Nephrol 2009; 20:1765-75. [PMID: 19578007 DOI: 10.1681/asn.2008090931] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Although several interventions slow the progression of diabetic nephropathy, current therapies do not halt progression completely. Recent preclinical studies suggested that pirfenidone (PFD) prevents fibrosis in various diseases, but the mechanisms underlying its antifibrotic action are incompletely understood. Here, we evaluated the role of PFD in regulation of the extracellular matrix. In mouse mesangial cells, PFD decreased TGF-beta promoter activity, reduced TGF-beta protein secretion, and inhibited TGF-beta-induced Smad2-phosphorylation, 3TP-lux promoter activity, and generation of reactive oxygen species. To explore the therapeutic potential of PFD, we administered PFD to 17-wk-old db/db mice for 4 wk. PFD treatment significantly reduced mesangial matrix expansion and expression of renal matrix genes but did not affect albuminuria. Using liquid chromatography with subsequent electrospray ionization tandem mass spectrometry, we identified 21 proteins unique to PFD-treated diabetic kidneys. Analysis of gene ontology and protein-protein interactions of these proteins suggested that PFD may regulate RNA processing. Immunoblotting demonstrated that PFD promotes dosage-dependent dephosphorylation of eukaryotic initiation factor, potentially inhibiting translation of mRNA. In conclusion, PFD is renoprotective in diabetic kidney disease and may exert its antifibrotic effects, in part, via inhibiting RNA processing.
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Affiliation(s)
- Satish P RamachandraRao
- Center for Renal Translational Medicine, Division of Nephrology and Hypertension, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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Abstract
The spliceosome is a large nuclear structure consisting of dynamically interacting RNAs and proteins. This chapter briefly reviews some of the known components and their interactions. Large-scale proteomics and gene expression studies may be required to unravel the many intricate mechanisms involved in splice site recognition and selection.
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Abstract
U12-dependent (U12) introns have persisted in the genomes of plants since the ancestral divergence between plants and metazoans. These introns, which are rare, are found in a range of genes that include essential functions in DNA replication and RNA metabolism and are implicated in regulating the expression of their host genes. U12 introns are removed from pre-mRNAs by a U12 intron-specific spliceosome. Although this spliceosome shares many properties with the more abundant U2-dependent (U2) intron spliceosome, four of the five small nuclear RNAs (snRNAs) required for splicing are different and specific for the unique splicing of U12 introns. Evidence in plants so far indicates that splicing signals of plant U12 introns and their splicing machinery are similar to U12 intron splicing in other eukaryotes. In addition to the high conservation of splicing signals, plant U12 introns also retain unique characteristic features of plant U2 introns, such as UA-richness, which suggests a requirement for plant-specific components for both the U2 and U12 splicing reaction. This chapter compares U12 and U2 splicing and reviews what is known about plant U12 introns and their possible role in gene expression.
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Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes. BMC Genomics 2008; 9:159. [PMID: 18402682 PMCID: PMC2375911 DOI: 10.1186/1471-2164-9-159] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Accepted: 04/10/2008] [Indexed: 11/10/2022] Open
Abstract
Background Several recent studies indicate that alternative splicing in Arabidopsis and other plants is a common mechanism for post-transcriptional modulation of gene expression. However, few analyses have been done so far to elucidate the functional relevance of alternative splicing in higher plants. Representing a frequent and universal subtle alternative splicing event among eukaryotes, alternative splicing at NAGNAG acceptors contributes to transcriptome diversity and therefore, proteome plasticity. Alternatively spliced NAGNAG acceptors are overrepresented in genes coding for proteins with RNA-recognition motifs (RRMs). As SR proteins, a family of RRM-containing important splicing factors, are known to be extensively alternatively spliced in Arabidopsis, we analyzed alternative splicing at NAGNAG acceptors in SR and SR-related genes. Results In a comprehensive analysis of the Arabidopsis thaliana genome, we identified 6,772 introns that exhibit a NAGNAG acceptor motif. Alternative splicing at these acceptors was assessed using available EST data, complemented by a sequence-based prediction method. Of the 36 identified introns within 30 SR and SR-related protein-coding genes that have a NAGNAG acceptor, we selected 15 candidates for an experimental analysis of alternative splicing under several conditions. We provide experimental evidence for 8 of these candidates being alternatively spliced. Quantifying the ratio of NAGNAG-derived splice variants under several conditions, we found organ-specific splicing ratios in adult plants and changes in seedlings of different ages. Splicing ratio changes were observed in response to heat shock and most strikingly, cold shock. Interestingly, the patterns of differential splicing ratios are similar for all analyzed genes. Conclusion NAGNAG acceptors frequently occur in the Arabidopsis genome and are particularly prevalent in SR and SR-related protein-coding genes. A lack of extensive EST coverage can be compensated by using the proposed sequence-based method to predict alternative splicing at these acceptors. Our findings indicate that the differential effects on NAGNAG alternative splicing in SR and SR-related genes are organ- and condition-specific rather than gene-specific.
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Abstract
SR proteins are a family of splicing factors important for splice site recognition and spliceosome assembly. Their ability to bind to RNA and to interact with proteins as well identifies them as important players in splice site choice and alternative splicing. Plants possess twice as many SR proteins as animals, and some of the subfamilies are plant specific. Arabidopsis SR proteins are involved in different aspects of plant growth and development as well as in responses to environmental cues. The plant-specific subfamilies have been shown to be regulated by alternative splicing events, which are highly conserved in evolution. The tight regulation of splicing factors by alternative splicing might allow coordinated responses of their target genes.
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Tanabe N, Yoshimura K, Kimura A, Yabuta Y, Shigeoka S. Differential expression of alternatively spliced mRNAs of Arabidopsis SR protein homologs, atSR30 and atSR45a, in response to environmental stress. PLANT & CELL PHYSIOLOGY 2007; 48:1036-49. [PMID: 17556373 DOI: 10.1093/pcp/pcm069] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Serine/arginine-rich (SR) proteins are associated with either the regulation or the execution of both constitutive splicing and the selection of alternative splice sites in animals and plants. We demonstrated the molecular characterization of a homolog of SR protein, atSR45a, in Arabidopsis plants. Six types of mRNA variants (atSR45a-1a-e and atSR45a-2) were generated by the alternative selection of transcriptional initiation sites and the alternative splicing of introns in atSR45a pre-mRNA. The atSR45a-1a and -2 proteins, presumed mature forms, were located in the nucleus and interacted with U1-70K, suggesting that these proteins function as a splicing factor in Arabidopsis. The levels of the transcripts atSR45a and atSR30, SF2/ASF-like SR proteins, were increased by various types of stress, such as high-light irradiation and salinity. Furthermore, the splicing patterns of atSR45a and atSR30 pre-mRNA themselves were altered under these stressful conditions. In particular, the expression of atSR45a-1a, atSR45a-2, atSR30 mRNA1 and atSR30 mRNA3 was greatly increased by high-light irradiation. These results indicate that the regulation of transcription and alternative splicing of atSR45a and atSR30 is responsive to various stressful conditions.
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Affiliation(s)
- Noriaki Tanabe
- Advanced Bioscience, Graduate School, Kinki University, 3327-204 Nakamachi, Nara, 631-8505 Japan
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Pertea M, Mount SM, Salzberg SL. A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana. BMC Bioinformatics 2007; 8:159. [PMID: 17517127 PMCID: PMC1892810 DOI: 10.1186/1471-2105-8-159] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Accepted: 05/21/2007] [Indexed: 02/05/2023] Open
Abstract
Background Algorithmic approaches to splice site prediction have relied mainly on the consensus patterns found at the boundaries between protein coding and non-coding regions. However exonic splicing enhancers have been shown to enhance the utilization of nearby splice sites. Results We have developed a new computational technique to identify significantly conserved motifs involved in splice site regulation. First, 84 putative exonic splicing enhancer hexamers are identified in Arabidopsis thaliana. Then a Gibbs sampling program called ELPH was used to locate conserved motifs represented by these hexamers in exonic regions near splice sites in confirmed genes. Oligomers containing 35 of these motifs have been shown experimentally to induce significant inclusion of A. thaliana exons. Second, integration of our regulatory motifs into two different splice site recognition programs significantly improved the ability of the software to correctly predict splice sites in a large database of confirmed genes. We have released GeneSplicerESE, the improved splice site recognition code, as open source software. Conclusion Our results show that the use of the ESE motifs consistently improves splice site prediction accuracy.
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Affiliation(s)
- Mihaela Pertea
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA.
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Palusa SG, Ali GS, Reddy ASN. Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich proteins: regulation by hormones and stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 49:1091-107. [PMID: 17319848 DOI: 10.1111/j.1365-313x.2006.03020.x] [Citation(s) in RCA: 283] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Precursor mRNAs with introns can undergo alternative splicing (AS) to produce structurally and functionally different proteins from the same gene. Here, we show that the pre-mRNAs of Arabidopsis genes that encode serine/arginine-rich (SR) proteins, a conserved family of splicing regulators in eukaryotes, are extensively alternatively spliced. Remarkably about 95 transcripts are produced from only 15 genes, thereby increasing the complexity of the SR gene family transcriptome by six-fold. The AS of some SR genes is controlled in a developmental and tissue-specific manner. Interestingly, among the various hormones and abiotic stresses tested, temperature stress (cold and heat) dramatically altered the AS of pre-mRNAs of several SR genes, whereas hormones altered the splicing of only three SR genes. These results indicate that abiotic stresses regulate the AS of the pre-mRNAs of SR genes to produce different isoforms of SR proteins that are likely to have altered function(s) in pre-mRNA splicing. Sequence analysis of splice variants revealed that predicted proteins from a majority of these variants either lack one or more modular domains or contain truncated domains. Because of the modular nature of the various domains in SR proteins, the proteins produced from splice variants are likely to have distinct functions. Together our results indicate that Arabidopsis SR genes generate surprisingly large transcriptome complexity, which is altered by stresses and hormones.
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Reddy ASN. Alternative splicing of pre-messenger RNAs in plants in the genomic era. ANNUAL REVIEW OF PLANT BIOLOGY 2007; 58:267-94. [PMID: 17222076 DOI: 10.1146/annurev.arplant.58.032806.103754] [Citation(s) in RCA: 361] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Primary transcripts (precursor-mRNAs) with introns can undergo alternative splicing to produce multiple transcripts from a single gene by differential use of splice sites, thereby increasing the transcriptome and proteome complexity within and between cells and tissues. Alternative splicing in plants is largely an unexplored area of gene expression, as this phenomenon used to be considered rare. However, recent genome-wide computational analyses have revealed that alternative splicing in flowering plants is far more prevalent than previously thought. Interestingly, pre-mRNAs of many spliceosomal proteins, especially serine/arginine-rich (SR) proteins, are extensively alternatively spliced. Furthermore, stresses have a dramatic effect on alternative splicing of pre-mRNAs including those that encode many spliceosomal proteins. Although the mechanisms that regulate alternative splicing in plants are largely unknown, several reports strongly suggest a key role for SR proteins in spliceosome assembly and regulated splicing. Recent studies suggest that alternative splicing in plants is an important posttranscriptional regulatory mechanism in modulating gene expression and eventually plant form and function.
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Affiliation(s)
- Anireddy S N Reddy
- Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, CO 80523, USA.
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Tillemans V, Leponce I, Rausin G, Dispa L, Motte P. Insights into nuclear organization in plants as revealed by the dynamic distribution of Arabidopsis SR splicing factors. THE PLANT CELL 2006; 18:3218-34. [PMID: 17114353 PMCID: PMC1693954 DOI: 10.1105/tpc.106.044529] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Serine/arginine-rich (SR) proteins are splicing regulators that share a modular structure consisting of one or two N-terminal RNA recognition motif domains and a C-terminal RS-rich domain. We investigated the dynamic localization of the Arabidopsis thaliana SR protein RSZp22, which, as we showed previously, distributes in predominant speckle-like structures and in the nucleolus. To determine the role of RSZp22 diverse domains in its nucleolar distribution, we investigated the subnuclear localization of domain-deleted mutant proteins. Our results suggest that the nucleolar localization of RSZp22 does not depend on a single targeting signal but likely involves different domains/motifs. Photobleaching experiments demonstrated the unrestricted dynamics of RSZp22 between nuclear compartments. Selective inhibitor experiments of ongoing cellular phosphorylation influenced the rates of exchange of RSZp22 between the different nuclear territories, indicating that SR protein mobility is dependent on the phosphorylation state of the cell. Furthermore, based on a leptomycin B- and fluorescence loss in photobleaching-based sensitive assay, we suggest that RSZp22 is a nucleocytoplasmic shuttling protein. Finally, with electron microscopy, we confirmed that RSp31, a plant-specific SR protein, is dynamically distributed in nucleolar cap-like structures upon phosphorylation inhibition. Our findings emphasize the high mobility of Arabidopsis SR splicing factors and provide insights into the dynamic relationships between the different nuclear compartments.
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Affiliation(s)
- Vinciane Tillemans
- Laboratory of Plant Cell and Molecular Biology, Department of Life Sciences, Institute of Botany, University of Liège, B-4000 Liège, Belgium
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Kalyna M, Lopato S, Voronin V, Barta A. Evolutionary conservation and regulation of particular alternative splicing events in plant SR proteins. Nucleic Acids Res 2006; 34:4395-405. [PMID: 16936312 PMCID: PMC1636356 DOI: 10.1093/nar/gkl570] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing is an important mechanism for fine tuning of gene expression at the post-transcriptional level. SR proteins govern splice site selection and spliceosome assembly. The Arabidopsis genome encodes 19 SR proteins, several of which have no orthologues in metazoan. Three of the plant specific subfamilies are characterized by the presence of a relatively long alternatively spliced intron located in their first RNA recognition motif, which potentially results in an extremely truncated protein. In atRSZ33, a member of the RS2Z subfamily, this alternative splicing event was shown to be autoregulated. Here we show that atRSp31, a member of the RS subfamily, does not autoregulate alternative splicing of its similarily positioned intron. Interestingly, this alternative splicing event is regulated by atRSZ33. We demonstrate that the positions of these long introns and their capability for alternative splicing are conserved from green algae to flowering plants. Moreover, in particular alternative splicing events the splicing signals are embedded into highly conserved sequences. In different taxa, these conserved sequences occur in at least one gene within a subfamily. The evolutionary preservation of alternative splice forms together with highly conserved intron features argues for additional functions hidden in the genes of these plant-specific SR proteins.
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Affiliation(s)
- Maria Kalyna
- Correspondence may also be addressed to Maria Kalyna. Tel: +43 1 4277 61642; Fax: +43 1 4277 9616;
| | | | | | - Andrea Barta
- To whom correspondence should be addressed. Tel: +43 1 4277 61640; Fax: +43 1 4277 9616;
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Wang BB, Brendel V. Molecular characterization and phylogeny of U2AF35 homologs in plants. PLANT PHYSIOLOGY 2006; 140:624-36. [PMID: 16407443 PMCID: PMC1361329 DOI: 10.1104/pp.105.073858] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
U2AF (U2 small nuclear ribonucleoprotein auxiliary factor) is an essential splicing factor with critical roles in recognition of the 3'-splice site. In animals, the U2AF small subunit (U2AF35) can bind to the 3'-AG intron border and promote U2 small nuclear RNP binding to the branch-point sequences of introns through interaction with the U2AF large subunit. Two copies of U2AF35-encoding genes were identified in Arabidopsis (Arabidopsis thaliana; atU2AF35a and atU2AF35b). Both are expressed in all tissues inspected, with atU2AF35a expressed at a higher level than atU2AF35b in most tissues. Differences in the expression patterns of atU2AF35a and atU2AF35b in roots were revealed by a promoter::beta-glucuronidase assay, with atU2AF35b expressed strongly in whole young roots and root tips and atU2AF35a limited to root vascular regions. Altered expression levels of atU2AF35a or atU2AF35b cause pleiotropic phenotypes (including flowering time, leaf morphology, and flower and silique shape). Novel slicing isoforms were generated from FCA pre-mRNA by splicing of noncanonical introns in plants with altered expression levels of atU2AF35. U2AF35 homologs were also identified from maize (Zea mays) and other plants with large-scale expressed sequence tag projects. A C-terminal motif (named SERE) is highly conserved in all seed plant protein homologs, suggesting it may have an important function specific to higher plants.
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Affiliation(s)
- Bing-Bing Wang
- Department of Genetics, Development and Cell Biology , Iowa State University, Ames, Iowa 50010, USA
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Isshiki M, Tsumoto A, Shimamoto K. The serine/arginine-rich protein family in rice plays important roles in constitutive and alternative splicing of pre-mRNA. THE PLANT CELL 2006; 18:146-58. [PMID: 16339852 PMCID: PMC1323490 DOI: 10.1105/tpc.105.037069] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Ser/Arg-rich (SR) proteins play important roles in the constitutive and alternative splicing of pre-mRNA. We isolated 20 rice (Oryza sativa) genes encoding SR proteins, of which six contain plant-specific characteristics. To determine whether SR proteins modulate splicing efficiency and alternative splicing of pre-mRNA in rice, we used transient assays in rice protoplasts by cotransformation of SR protein genes with the rice Waxy(b) (Wx(b))-beta-glucuronidase fusion gene. The results showed that plant-specific RSp29 and RSZp23, an SR protein homologous to human 9G8, enhanced splicing and altered the alternative 5' splice sites of Wx(b) intron 1. The resulting splicing pattern was unique to each SR protein; RSp29 stimulated splicing at the distal site, and RSZp23 enhanced splicing at the proximal site. Results of domain-swapping experiments between plant-specific RSp29 and SCL26, which is a homolog of human SC35, showed the importance of RNA recognition motif 1 and the Arg/Ser-rich (RS) domain for the enhancement of splicing efficiencies. Overexpression of plant-specific RSZ36 and SRp33b, a homolog of human ASF/SF2, in transgenic rice changed the alternative splicing patterns of their own pre-mRNAs and those of other SR proteins. These results show that SR proteins play important roles in constitutive and alternative splicing of rice pre-mRNA.
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Affiliation(s)
- Masayuki Isshiki
- Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, Ikoma, Japan
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35
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Kalyna M, Barta A. A plethora of plant serine/arginine-rich proteins: redundancy or evolution of novel gene functions? Biochem Soc Trans 2005; 32:561-4. [PMID: 15270675 PMCID: PMC5362061 DOI: 10.1042/bst0320561] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Precursor-mRNA (pre-mRNA) processing is an important step in gene expression and its regulation leads to the expansion of the gene product repertoire. SR (serine-arginine)-rich proteins are key players in intron recognition and spliceosome assembly and significantly contribute to the alternative splicing process. Due to several duplication events, at least 19 SR proteins are present in the Arabidopsis genome, which is almost twice as many as in humans. They fall into seven different subfamilies, three of them homologous with metazoan splicing factors, whereas the other four seem to be specific for plants. The current results show that most of the duplicated genes have different spatiotemporal expression patterns indicating functional diversification. Interestingly, most of the SR protein genes are alternatively spliced and in some cases this process was shown to be under developmental and/or environmental control. This might greatly influence gene expression of target genes as also exemplified by ectopic expression studies of particular SR proteins.
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Affiliation(s)
| | - Andrea Barta
- To whom correspondence should be addressed: Dr. Andrea Barta, Max F. Perutz Laboratories, University Departments at the Vienna Biocenter, Department of Biochemistry, Medical University of Vienna, Dr. Bohrgasse 9/3, A-1030 Vienna, Austria, Tel. +43-1-427761640, Fax. +43-1-42779616,
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Gupta S, Wang BB, Stryker GA, Zanetti ME, Lal SK. Two novel arginine/serine (SR) proteins in maize are differentially spliced and utilize non-canonical splice sites. ACTA ACUST UNITED AC 2005; 1728:105-14. [PMID: 15780972 DOI: 10.1016/j.bbaexp.2005.01.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2004] [Revised: 12/28/2004] [Accepted: 01/04/2005] [Indexed: 11/20/2022]
Abstract
The serine-arginine (SR)-rich splicing proteins are highly conserved RNA binding nuclear phosphor-proteins that play important roles in both regular and alternative splicing. Here we describe two novel putative SR genes from maize, designated zmRSp31A and zmRSp31B. Both genes contain characteristic RNA binding motifs RNP-1 and RNP-2, a serine/arginine-rich (RS) domain and share significant sequence similarity to the Arabidopsis atRSp31 family of SR proteins. Both zmRSp31A and zmRSp31B produce multiple transcripts by alternative splicing, of which majority of the alternatively spliced transcripts utilize non-canonical splice sites. zmRSp31A and zmRSp31B produce at least six and four transcripts, respectively, of which only one corresponds to the wild type proteins for each gene. All the alternatively spliced transcripts of both the genes, with one exception, are predicted to encode small truncated proteins containing only the RNP-2 domain of their first RNA recognition motif and completely lack the carboxyl terminal RS domain. We provide evidence that some of the alternatively spliced transcripts of both genes are associated with polysomes and interact with the translational machinery.
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Affiliation(s)
- Smriti Gupta
- Department of Biological Sciences, Oakland University, Rochester, MI 48309-4401, USA
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Tillemans V, Dispa L, Remacle C, Collinge M, Motte P. Functional distribution and dynamics of Arabidopsis SR splicing factors in living plant cells. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 41:567-82. [PMID: 15686520 DOI: 10.1111/j.1365-313x.2004.02321.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Serine/arginine-rich (SR) proteins constitute an important class of splicing regulators in higher eukaryotes that share a modular structure consisting of one or two N-terminal RNA recognition motif (RRM) domains and a C-terminal RS-rich domain. Herein, we have investigated the in vivo functional distribution of Arabidopsis SR factors. Agrobacterium-mediated transient transformation revealed nuclear speckled distribution and the overall colocalization of fluorescent protein (FP)-tagged SR factors in both tobacco and Arabidopsis cells. Their overall colocalization in larger nucleoplasmic domains was further observed after transcriptional and phosphorylation/dephosphorylation inhibition, indicating a close functional association between SR factors, independent of their phosphorylation state. Furthermore, we demonstrated in vivo the conserved role of the RS and RRM domains in the efficient targeting of Arabidopsis SR proteins to nuclear speckles by using a series of structural domain-deleted mutants of atRSp31 and atRSZp22. We suggest additional roles of RS domain such as the shuttling of atRSZp22 between nucleoplasm and nucleolus through its phosphorylation level. The coexpression of deletion mutants with wild-type SR proteins revealed potential complex associations between them. Fluorescence recovery after photobleaching demonstrated similar dynamic properties of SR factors in both tobacco transiently expressing cells and Arabidopsis transgenics. Cell cycle phase-dependent organization of FP-tagged SR proteins was observed in living tobacco BY-2 cells. We showed that atRSp31 is degraded at metaphase by fluorescence quantification. SR proteins also localized within small foci at anaphase. These results demonstrate interesting related features as well as potentially important differences between plant and animal SR proteins.
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Affiliation(s)
- Vinciane Tillemans
- Laboratory of Plant Cell and Molecular Biology, University of Liège, B-4000 Liège, Belgium
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38
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The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing. Genome Biol 2004; 5:R102. [PMID: 15575968 PMCID: PMC545797 DOI: 10.1186/gb-2004-5-12-r102] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2004] [Revised: 09/06/2004] [Accepted: 10/20/2004] [Indexed: 12/02/2022] Open
Abstract
The database of Arabidopsis splicing related genes includes classification of genes encoding snRNAs and other splicing related proteins, together with information on gene structure, alternative splicing, gene duplications and phylogenetic relationships. A total of 74 small nuclear RNA (snRNA) genes and 395 genes encoding splicing-related proteins were identified in the Arabidopsis genome by sequence comparison and motif searches, including the previously elusive U4atac snRNA gene. Most of the genes have not been studied experimentally. Classification of these genes and detailed information on gene structure, alternative splicing, gene duplications and phylogenetic relationships are made accessible as a comprehensive database of Arabidopsis Splicing Related Genes (ASRG) on our website.
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Lorković ZJ, Hilscher J, Barta A. Use of fluorescent protein tags to study nuclear organization of the spliceosomal machinery in transiently transformed living plant cells. Mol Biol Cell 2004; 15:3233-43. [PMID: 15133128 PMCID: PMC452579 DOI: 10.1091/mbc.e04-01-0055] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2004] [Accepted: 04/29/2004] [Indexed: 01/24/2023] Open
Abstract
Although early studies suggested that little compartmentalization exists within the nucleus, more recent studies on metazoan systems have identified a still increasing number of specific subnuclear compartments. Some of these compartments are dynamic structures; indeed, protein and RNA-protein components can cycle between different domains. This is particularly evident for RNA processing components. In plants, lack of tools has hampered studies on nuclear compartmentalization and dynamics of RNA processing components. Here, we show that transient expression of fluorescent protein fusions of U1 and U2 small nuclear ribonucleoprotein particle (snRNP)-specific proteins U1-70K, U2B", and U2A ', nucleolar proteins Nop10 and PRH75, and serine-arginine-rich proteins in plant protoplasts results in their correct localization. Furthermore, snRNP-specific proteins also were correctly assembled into mature snRNPs. This system allowed a systematic analysis of the cellular localization of Arabidopsis serine-arginine-rich proteins, which, like their animal counterparts, localize to speckles but not to nucleoli and Cajal bodies. Finally, markers for three different nuclear compartments, namely, nucleoli, Cajal bodies, and speckles, have been established and were shown to be applicable for colocalization studies in living plant protoplasts. Thus, transient expression of proteins tagged with four different fluorescent proteins is a suitable system for studying the nuclear organization of spliceosomal proteins in living plant cells and should therefore allow studies of their dynamics as well.
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MESH Headings
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Cell Nucleolus/immunology
- Cell Nucleolus/metabolism
- Cell Nucleolus/ultrastructure
- Cell Nucleus Structures/chemistry
- Chloroplasts/metabolism
- Coiled Bodies/metabolism
- Luminescent Proteins/analysis
- Luminescent Proteins/genetics
- Microscopy, Fluorescence
- Nuclear Proteins/analysis
- Nuclear Proteins/metabolism
- Phosphoproteins/analysis
- Phosphoproteins/metabolism
- Plant Proteins/analysis
- Protoplasts/metabolism
- RNA-Binding Proteins
- Ribonucleoprotein, U1 Small Nuclear/analysis
- Ribonucleoprotein, U1 Small Nuclear/genetics
- Ribonucleoprotein, U1 Small Nuclear/metabolism
- Ribonucleoprotein, U2 Small Nuclear/analysis
- Ribonucleoprotein, U2 Small Nuclear/genetics
- Ribonucleoprotein, U2 Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/analysis
- Ribonucleoproteins, Small Nuclear/metabolism
- Serine-Arginine Splicing Factors
- Spliceosomes/metabolism
- Nicotiana/genetics
- Nicotiana/metabolism
- Transformation, Genetic
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Affiliation(s)
- Zdravko J Lorković
- Max F. Perutz Laboratories, University Departments at the Vienna Biocenter, Institute of Medical Biochemistry, 1030 Vienna, Austria.
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40
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Lewandowska D, Simpson CG, Clark GP, Jennings NS, Barciszewska-Pacak M, Lin CF, Makalowski W, Brown JWS, Jarmolowski A. Determinants of plant U12-dependent intron splicing efficiency. THE PLANT CELL 2004; 16:1340-52. [PMID: 15100401 PMCID: PMC423220 DOI: 10.1105/tpc.020743] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2004] [Accepted: 02/25/2004] [Indexed: 05/18/2023]
Abstract
Factors affecting splicing of plant U12-dependent introns have been examined by extensive mutational analyses in an in vivo tobacco (Nicotiana tabacum) protoplast system using introns from three different Arabidopsis thaliana genes: CBP20, GSH2, and LD. The results provide evidence that splicing efficiency of plant U12 introns depends on a combination of factors, including UA content, exon bridging interactions between the U12 intron and flanking U2-dependent introns, and exon splicing enhancer sequences (ESEs). Unexpectedly, all three plant U12 introns required an adenosine at the upstream purine position in the branchpoint consensus UCCUURAUY. The exon upstream of the LD U12 intron is a major determinant of its higher level of splicing efficiency and potentially contains two ESE regions. These results suggest that in plants, U12 introns represent a level at which expression of their host genes can be regulated.
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Affiliation(s)
- Dominika Lewandowska
- Department of Gene Expression, Adam Mickiewicz University, Poznan 60-371, Poland
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41
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Fang Y, Hearn S, Spector DL. Tissue-specific expression and dynamic organization of SR splicing factors in Arabidopsis. Mol Biol Cell 2004; 15:2664-73. [PMID: 15034145 PMCID: PMC420091 DOI: 10.1091/mbc.e04-02-0100] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The organization of the pre-mRNA splicing machinery has been extensively studied in mammalian and yeast cells and far less is known in living plant cells and different cell types of an intact organism. Here, we report on the expression, organization, and dynamics of pre-mRNA splicing factors (SR33, SR1/atSRp34, and atSRp30) under control of their endogenous promoters in Arabidopsis. Distinct tissue-specific expression patterns were observed, and differences in the distribution of these proteins within nuclei of different cell types were identified. These factors localized in a cell type-dependent speckled pattern as well as being diffusely distributed throughout the nucleoplasm. Electron microscopic analysis has revealed that these speckles correspond to interchromatin granule clusters. Time-lapse microscopy revealed that speckles move within a constrained nuclear space, and their organization is altered during the cell cycle. Fluorescence recovery after photobleaching analysis revealed a rapid exchange rate of splicing factors in nuclear speckles. The dynamic organization of plant speckles is closely related to the transcriptional activity of the cells. The organization and dynamic behavior of speckles in Arabidopsis cell nuclei provides significant insight into understanding the functional compartmentalization of the nucleus and its relationship to chromatin organization within various cell types of a single organism.
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Affiliation(s)
- Yuda Fang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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42
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Kalyna M, Lopato S, Barta A. Ectopic expression of atRSZ33 reveals its function in splicing and causes pleiotropic changes in development. Mol Biol Cell 2003; 14:3565-77. [PMID: 12972547 PMCID: PMC196550 DOI: 10.1091/mbc.e03-02-0109] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Splicing provides an additional level in the regulation of gene expression and contributes to proteome diversity. Herein, we report the functional characterization of a recently described plant-specific protein, atRSZ33, which has characteristic features of a serine/arginine-rich protein and the ability to interact with other splicing factors, implying that this protein might be involved in constitutive and/or alternative splicing. Overexpression of atRSZ33 leads to alteration of splicing patterns of atSRp30 and atSRp34/SR1, indicating that atRSZ33 is indeed a splicing factor. Moreover, atRSZ33 is a regulator of its own expression, as splicing of its pre-mRNA is changed in transgenic plants. Investigations by promoter-beta-glucuronidase (GUS) fusion and in situ hybridization revealed that atRSZ33 is expressed during embryogenesis and early stages of seedling formation, as well as in flower and root development. Ectopic expression of atRSZ33 caused pleiotropic changes in plant development resulting in increased cell expansion and changed polarization of cell elongation and division. In addition, changes in activity of an auxin-responsive promoter suggest that auxin signaling is disturbed in these transgenic plants.
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Affiliation(s)
- Maria Kalyna
- Max F. Perutz Laboratories, University Departments at the Vienna Biocenter, Institut für Med. Biochemie, University of Vienna, A-1030 Vienna, Austria
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43
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Sanford JR, Longman D, Cáceres JF. Multiple roles of the SR protein family in splicing regulation. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2003; 31:33-58. [PMID: 12494762 DOI: 10.1007/978-3-662-09728-1_2] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- J R Sanford
- MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, Scotland, UK
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44
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Lorković ZJ, Barta A. Genome analysis: RNA recognition motif (RRM) and K homology (KH) domain RNA-binding proteins from the flowering plant Arabidopsis thaliana. Nucleic Acids Res 2002; 30:623-35. [PMID: 11809873 PMCID: PMC100298 DOI: 10.1093/nar/30.3.623] [Citation(s) in RCA: 294] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2001] [Revised: 10/18/2001] [Accepted: 11/27/2001] [Indexed: 11/13/2022] Open
Abstract
Regulation of gene expression at the post-transcriptional level is mainly achieved by proteins containing well-defined sequence motifs involved in RNA binding. The most widely spread motifs are the RNA recognition motif (RRM) and the K homology (KH) domain. In this article, we survey the complete Arabidopsis thaliana genome for proteins containing RRM and KH RNA-binding domains. The Arabidopsis genome encodes 196 RRM-containing proteins, a more complex set than found in Caenorhabditis elegans and Drosophila melanogaster. In addition, the Arabidopsis genome contains 26 KH domain proteins. Most of the Arabidopsis RRM-containing proteins can be classified into structural and/or functional groups, based on similarity with either known metazoan or Arabidopsis proteins. Approximately 50% of Arabidopsis RRM-containing proteins do not have obvious homologues in metazoa, and for most of those that are predicted to be orthologues of metazoan proteins, no experimental data exist to confirm this. Additionally, the function of most Arabidopsis RRM proteins and of all KH proteins is unknown. Based on the data presented here, it is evident that among all eukaryotes, only those RNA-binding proteins that are involved in the most essential processes of post-transcriptional gene regulation are preserved in structure and, most probably, in function. However, the higher complexity of RNA-binding proteins in Arabidopsis, as evident in groups of SR splicing factors and poly(A)-binding proteins, may account for the observed differences in mRNA maturation between plants and metazoa. This survey provides a first systematic analysis of plant RNA-binding proteins, which may serve as a basis for functional characterisation of this important protein group in plants.
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Affiliation(s)
- Zdravko J Lorković
- Institute of Medical Biochemistry, Vienna University, Dr. Bohrgasse 9/3, 1030 Vienna, Austria.
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45
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Affiliation(s)
- B R Graveley
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington 06030, USA.
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46
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Isshiki M, Nakajima M, Satoh H, Shimamoto K. dull: rice mutants with tissue-specific effects on the splicing of the waxy pre-mRNA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2000; 23:451-460. [PMID: 10972871 DOI: 10.1046/j.1365-313x.2000.00803.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In the endosperm of japonica rice, du-1 and du-2 mutations cause the reduction of amylose contents. It was previously shown that the Wx(b) allele of rice, which is predominantly distributed in japonica rice, has a mutation in the 5' splice site of intron 1 resulting in the creation of two weak 5' splice sites within exon 1. In du-1 and du-2 mutants, spliced Wx(b) transcripts were highly reduced, whereas the processing of transcripts derived from three other genes highly expressed in endosperm was not apparently influenced. Results of competitive RT-PCR analysis indicate that transcripts spliced at the two newly created 5' splice sites were equally affected in these two mutants. Genetic and molecular analyses of the effects of du-1 and du-2 on Wx(a) pre-mRNA with normal splice sites indicate that these two mutations do not affect the processing of Wx(a) pre-mRNA after splicing, suggesting that du-1 and du-2 are mutations of genes required for the efficient splicing of mutated Wx(b) pre-mRNA. Furthermore, du-1 and du-2 showed differential effects in endosperm and pollen. Although both mutations caused similar effects on the splicing of Wx(a) transcripts in endosperm, du-1 caused higher reduction of Wx(b) mRNA in pollen than in endosperm, while du-2 had a lesser effect in pollen than in endosperm. Based on these results, we propose that the du-1 and du-2 loci of rice encode tissue-specifically regulated splicing factors that are involved in alternative splicing of pre-mRNA in rice.
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Affiliation(s)
- M Isshiki
- Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0101, Japan
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Longman D, Johnstone IL, Cáceres JF. Functional characterization of SR and SR-related genes in Caenorhabditis elegans. EMBO J 2000; 19:1625-37. [PMID: 10747030 PMCID: PMC310231 DOI: 10.1093/emboj/19.7.1625] [Citation(s) in RCA: 126] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The SR proteins constitute a family of nuclear phosphoproteins, which are required for constitutive splicing and also influence alternative splicing regulation. Initially, it was suggested that SR proteins were functionally redundant in constitutive splicing. However, differences have been observed in alternative splicing regulation, suggesting unique functions for individual SR proteins. Homology searches of the Caenorhabditis elegans genome identified seven genes encoding putative orthologues of the human factors SF2/ASF, SRp20, SC35, SRp40, SRp75 and p54, and also several SR-related genes. To address the issue of functional redundancy, we used dsRNA interference (RNAi) to inhibit specific SR protein function during C.elegans development. RNAi with CeSF2/ASF caused late embryonic lethality, suggesting that this gene has an essential function during C.elegans development. RNAi with other SR genes resulted in no obvious phenotype, which is indicative of gene redundancy. Simultaneous interference of two or more SR proteins in certain combinations caused lethality or other developmental defects. RNAi with CeSRPK, an SR protein kinase, resulted in early embryonic lethality, suggesting an essential role for SR protein phosphorylation during development.
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Affiliation(s)
- D Longman
- MRC Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU
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Lorković ZJ, Wieczorek Kirk DA, Lambermon MH, Filipowicz W. Pre-mRNA splicing in higher plants. TRENDS IN PLANT SCIENCE 2000; 5:160-7. [PMID: 10740297 DOI: 10.1016/s1360-1385(00)01595-8] [Citation(s) in RCA: 203] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Most plant mRNAs are synthesized as precursors containing one or more intervening sequences (introns) that are removed during the process of splicing. The basic mechanism of spliceosome assembly and intron excision is similar in all eukaryotes. However, the recognition of introns in plants has some unique features, which distinguishes it from the reactions in vertebrates and yeast. Recent progress has occurred in characterizing the splicing signals in plant pre-mRNAs, in identifying the mutants affected in splicing and in discovering new examples of alternatively spliced mRNAs. In combination with information provided by the Arabidopsis genome-sequencing project, these studies are contributing to a better understanding of the splicing process and its role in the regulation of gene expression in plants.
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Affiliation(s)
- Z J Lorković
- Friedrich Miescher Institute, Basel, Switzerland
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Lazar G, Goodman HM. The Arabidopsis splicing factor SR1 is regulated by alternative splicing. PLANT MOLECULAR BIOLOGY 2000; 42:571-581. [PMID: 10809003 DOI: 10.1023/a:1006394207479] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The serine-arginine (SR)-rich splicing factors play essential roles in general splicing and regulate alternative splice site utilization in a concentration-dependent manner. SR1 is a plant homologue of the human general/alternative splicing factor SF2/ASF. We report here that alternative splicing regulates SR1 itself. Of the five detected SR1 transcripts only one encodes the full-length protein, while the other four are different variants of the essential arginine-serine-rich domain. The data suggest that SR1 pre-mRNA could be committed to two alternate splicing pathways. One, dependent on the alternative utilization of competing 3' splice sites in intron 9, generates SR1, SR1B and SR1C. The other, regulated by suppression of intron 9 5' splice site utilization, generates SR1D and SR1E. The splicing pattern and molecular structure of SR1D indicates an evolutionary conservation of splicing-based regulation between plants and vertebrates and suggests that the various isoforms perform important functions. Results from transient gene expression assays indicate that alternative splicing is not an autoregulatory mechanism used to control the transcript level of the full-length protein. The ratio of SR1/SR1B transcripts, which are generated by alternative 3' splice site utilization in intron 9, is under temperature control. The temperature-dependent increase in SR1B/SR1 ratio suggests a role of SR1B in the adaptation to high-temperature environments. In addition, based on the regulated co-expression of SR1 transcripts, it is possible that some SR1 functions could be determined by the combinatorial action of the various isoforms.
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Affiliation(s)
- G Lazar
- Department of Genetics, Harvard Medical School, Massachusetts General Hospital, Boston 02114, USA
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Abstract
Ethylene signal transduction pathway regulates various aspects of plant physiology and development. Studies of mutants defective in the ethylene response, has led to the elaboration of key genes involved in the perception of ethylene. Among them are putative ethylene receptors, Raf-like kinases, nuclear-targeted proteins and transcription factors. The gene products share common motifs found in other signaling-cascade pathways in organisms ranging from bacteria to mammals. Recent biochemical studies provide insight into the function and regulation of the components of the ethylene cascade and make ethylene perception a paradigm for signal transduction in multicellular organisms.
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