1
|
Wu ZH, He LL, Wang CC, Liang C, Li HY, Zhong DW, Dong ZX, Zhang LJ, Zhang XQ, Ge LF, Chen S. Unveiling unique alternative splicing responses to low temperature in Zoysia japonica through ZjRTD1.0, a high-quality reference transcript dataset. PHYSIOLOGIA PLANTARUM 2024; 176:e14280. [PMID: 38644527 DOI: 10.1111/ppl.14280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/29/2024] [Accepted: 03/09/2024] [Indexed: 04/23/2024]
Abstract
Inadequate reference databases in RNA-seq analysis can hinder data utilization and interpretation. In this study, we have successfully constructed a high-quality reference transcript dataset, ZjRTD1.0, for Zoysia japonica, a widely-used turfgrass with exceptional tolerance to various abiotic stress, including low temperatures and salinity. This dataset comprises 113,089 transcripts from 57,143 genes. BUSCO analysis demonstrates exceptional completeness (92.4%) in ZjRTD1.0, with reduced proportions of fragmented (3.3%) and missing (4.3%) orthologs compared to prior datasets. ZjRTD1.0 enables more precise analyses, including transcript quantification and alternative splicing assessments using public datasets, which identified a substantial number of differentially expressed transcripts (DETs) and differential alternative splicing (DAS) events, leading to several novel findings on Z. japonica's responses to abiotic stresses. First, spliceosome gene expression influenced alternative splicing significantly under abiotic stress, with a greater impact observed during low-temperature stress. Then, a significant positive correlation was found between the number of differentially expressed genes (DEGs) encoding protein kinases and the frequency of DAS events, suggesting the role of protein phosphorylation in regulating alternative splicing. Additionally, our results suggest possible involvement of serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs) in generating inclusion/exclusion isoforms under low-temperature stress. Furthermore, our investigation revealed a significantly enhanced overlap between DEGs and differentially alternatively spliced genes (DASGs) in response to low-temperature stress, suggesting a unique co-regulatory mechanism governing transcription and splicing in the context of low-temperature response. In conclusion, we have proven that ZjRTD1.0 will serve as a reliable and useful resource for future transcriptomic analyses in Z. japonica.
Collapse
Affiliation(s)
- Zhi-Hao Wu
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Liang-Liang He
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Cong-Cong Wang
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Chen Liang
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Han-Ying Li
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Dan-Wen Zhong
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Zhao-Xia Dong
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Li-Juan Zhang
- Shenzhen Tourism College of Jinan University, Shenzhen, Guangdong, China
| | - Xiang-Qian Zhang
- College of Food Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - Liang-Fa Ge
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Shu Chen
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| |
Collapse
|
2
|
Li L, Li J, Liu K, Jiang C, Jin W, Ye J, Qin T, Luo B, Chen Z, Li J, Lv F, Li X, Wang H, Jin J, Deng Q, Wang S, Zhu J, Zou T, Liu H, Li S, Li P, Liang Y. DGW1, encoding an hnRNP-like RNA binding protein, positively regulates grain size and weight by interacting with GW6 mRNA. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:512-526. [PMID: 37862261 PMCID: PMC10826988 DOI: 10.1111/pbi.14202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/13/2023] [Accepted: 10/03/2023] [Indexed: 10/22/2023]
Abstract
Grain size and weight determine rice yield. Although numerous genes and pathways involved in regulating grain size have been identified, our knowledge of post-transcriptional control of grain size remains elusive. In this study, we characterize a rice mutant, decreased grain width and weight 1 (dgw1), which produces small grains. We show that DGW1 encodes a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family protein and preferentially expresses in developing panicles, positively regulating grain size by promoting cell expansion in spikelet hulls. Overexpression of DGW1 increases grain weight and grain numbers, leading to a significant rise in rice grain yield. We further demonstrate that DGW1 functions in grain size regulation by directly binding to the mRNA of Grain Width 6 (GW6), a critical grain size regulator in rice. Overexpression of GW6 restored the grain size phenotype of DGW1-knockout plants. DGW1 interacts with two oligouridylate binding proteins (OsUBP1a and OsUBP1b), which also bind the GW6 mRNA. In addition, the second RRM domain of DGW1 is indispensable for its mediated protein-RNA and protein-protein interactions. In summary, our findings identify a new regulatory module of DGW1-GW6 that regulates rice grain size and weight, providing important insights into the function of hnRNP-like proteins in the regulation of grain size.
Collapse
Affiliation(s)
- Lingfeng Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Jijin Li
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Keke Liu
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Chenglong Jiang
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Wenhu Jin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Jiangkun Ye
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Tierui Qin
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Binjiu Luo
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Zeyu Chen
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Jinzhao Li
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Fuxiang Lv
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Xiaojun Li
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Haipeng Wang
- Neijiang Academy of Agricultural Science in Sichuan ProvinceNeijiangChina
| | - Jinghua Jin
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Qiming Deng
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Shiquan Wang
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Jun Zhu
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Ting Zou
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Huainian Liu
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Shuangcheng Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Ping Li
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Yueyang Liang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| |
Collapse
|
3
|
Yuan J, Cheng L, Li H, An C, Wang Y, Zhang F. Physiological and protein profiling analysis provides insight into the underlying molecular mechanism of potato tuber development regulated by jasmonic acid in vitro. BMC PLANT BIOLOGY 2022; 22:481. [PMID: 36210448 PMCID: PMC9549635 DOI: 10.1186/s12870-022-03852-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/19/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND Jasmonates (JAs) are one of important phytohormones regulating potato tuber development. It is a complex process and the underlying molecular mechanism regulating tuber development by JAs is still limited. This study attempted to illuminate it through the potential proteomic dynamics information about tuber development in vitro regulated by exogenous JA. RESULTS A combined analysis of physiological and iTRAQ (isobaric tags for relative and absolute quantification)-based proteomic approach was performed in tuber development in vitro under exogenous JA treatments (0, 0.5, 5 and 50 μΜ). Physiological results indicated that low JA concentration (especially 5 μM) promoted tuber development, whereas higher JA concentration (50 μM) showed inhibition effect. A total of 257 differentially expressed proteins (DEPs) were identified by iTRAQ, which provided a comprehensive overview on the functional protein profile changes of tuber development regulated by JA. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that low JA concentration (especially 5 μM) exhibited the promotion effects on tuber development in various cellular processes. Some cell wall polysaccharide synthesis and cytoskeleton formation-related proteins were up-regulated by JA to promote tuber cell expansion. Some primary carbon metabolism-related enzymes were up-regulated by JA to provide sufficient metabolism intermediates and energy for tuber development. And, a large number of protein biosynthesis, degradation and assembly-related were up-regulated by JA to promote tuber protein biosynthesis and maintain strict protein quality control during tuber development. CONCLUSIONS This study is the first to integrate physiological and proteomic data to provide useful information about the JA-signaling response mechanism of potato tuber development in vitro. The results revealed that the levels of a number of proteins involved in various cellular processes were regulated by JA during tuber development. The proposed hypothetical model would explain the interaction of these DEPs that associated with tuber development in vitro regulated by JA.
Collapse
Affiliation(s)
- Jianlong Yuan
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lixiang Cheng
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Huijun Li
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Congcong An
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuping Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Feng Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China.
| |
Collapse
|
4
|
Chacon DS, Santos MDM, Bonilauri B, Vilasboa J, da Costa CT, da Silva IB, Torres TDM, de Araújo TF, Roque ADA, Pilon AC, Selegatto DM, Freire RT, Reginaldo FPS, Voigt EL, Zuanazzi JAS, Scortecci KC, Cavalheiro AJ, Lopes NP, Ferreira LDS, dos Santos LV, Fontes W, de Sousa MV, Carvalho PC, Fett-Neto AG, Giordani RB. Non-target molecular network and putative genes of flavonoid biosynthesis in Erythrina velutina Willd., a Brazilian semiarid native woody plant. FRONTIERS IN PLANT SCIENCE 2022; 13:947558. [PMID: 36161018 PMCID: PMC9493460 DOI: 10.3389/fpls.2022.947558] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/26/2022] [Indexed: 06/16/2023]
Abstract
Erythrina velutina is a Brazilian native tree of the Caatinga (a unique semiarid biome). It is widely used in traditional medicine showing anti-inflammatory and central nervous system modulating activities. The species is a rich source of specialized metabolites, mostly alkaloids and flavonoids. To date, genomic information, biosynthesis, and regulation of flavonoids remain unknown in this woody plant. As part of a larger ongoing research goal to better understand specialized metabolism in plants inhabiting the harsh conditions of the Caatinga, the present study focused on this important class of bioactive phenolics. Leaves and seeds of plants growing in their natural habitat had their metabolic and proteomic profiles analyzed and integrated with transcriptome data. As a result, 96 metabolites (including 43 flavonoids) were annotated. Transcripts of the flavonoid pathway totaled 27, of which EvCHI, EvCHR, EvCHS, EvCYP75A and EvCYP75B1 were identified as putative main targets for modulating the accumulation of these metabolites. The highest correspondence of mRNA vs. protein was observed in the differentially expressed transcripts. In addition, 394 candidate transcripts encoding for transcription factors distributed among the bHLH, ERF, and MYB families were annotated. Based on interaction network analyses, several putative genes of the flavonoid pathway and transcription factors were related, particularly TFs of the MYB family. Expression patterns of transcripts involved in flavonoid biosynthesis and those involved in responses to biotic and abiotic stresses were discussed in detail. Overall, these findings provide a base for the understanding of molecular and metabolic responses in this medicinally important species. Moreover, the identification of key regulatory targets for future studies aiming at bioactive metabolite production will be facilitated.
Collapse
Affiliation(s)
- Daisy Sotero Chacon
- Department of Pharmacy, Federal University of Rio Grande do Norte (UFRN), Natal, RN, Brazil
| | | | - Bernardo Bonilauri
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, United States
| | - Johnatan Vilasboa
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Cibele Tesser da Costa
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | - Taffarel de Melo Torres
- Bioinformatics, Biostatistics and Computer Biology Nucleus, Rural Federal University of the Semiarid, Mossoró, RN, Brazil
| | | | - Alan de Araújo Roque
- Institute for Sustainable Development and Environment, Dunas Park Herbarium, Natal, RN, Brazil
| | - Alan Cesar Pilon
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (FCFRP-USP), Ribeirão Preto, SP, Brazil
| | - Denise Medeiros Selegatto
- Zimmermann Group, European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Rafael Teixeira Freire
- Signal and Information Processing for Sensing Systems, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Eduardo Luiz Voigt
- Department of Cell Biology and Genetics, Center for Biosciences, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | | | - Kátia Castanho Scortecci
- Department of Cell Biology and Genetics, Center for Biosciences, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | | | - Norberto Peporine Lopes
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (FCFRP-USP), Ribeirão Preto, SP, Brazil
| | | | - Leandro Vieira dos Santos
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Wagner Fontes
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasilia, DF, Brazil
| | - Marcelo Valle de Sousa
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasilia, DF, Brazil
| | - Paulo Costa Carvalho
- Computational and Structural Proteomics Laboratory, Carlos Chagas Institute, Fiocruz, PR, Brazil
| | - Arthur Germano Fett-Neto
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Raquel Brandt Giordani
- Department of Pharmacy, Federal University of Rio Grande do Norte (UFRN), Natal, RN, Brazil
| |
Collapse
|
5
|
Liu T, Zhang X, Zhang H, Cheng Z, Liu J, Zhou C, Luo S, Luo W, Li S, Xing X, Chang Y, Shi C, Ren Y, Zhu S, Lei C, Guo X, Wang J, Zhao Z, Wang H, Zhai H, Lin Q, Wan J. Dwarf and High Tillering1 represses rice tillering through mediating the splicing of D14 pre-mRNA. THE PLANT CELL 2022; 34:3301-3318. [PMID: 35670739 PMCID: PMC9421477 DOI: 10.1093/plcell/koac169] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 05/11/2022] [Indexed: 06/09/2023]
Abstract
Strigolactones (SLs) constitute a class of plant hormones that regulate many aspects of plant development, including repressing tillering in rice (Oryza sativa). However, how SL pathways are regulated is still poorly understood. Here, we describe a rice mutant dwarf and high tillering1 (dht1), which exhibits pleiotropic phenotypes (such as dwarfism and increased tiller numbers) similar to those of mutants defective in SL signaling. We show that DHT1 encodes a monocotyledon-specific hnRNP-like protein that acts as a previously unrecognized intron splicing factor for many precursor mRNAs (pre-mRNAs), including for the SL receptor gene D14. We find that the dht1 (DHT1I232F) mutant protein is impaired in its stability and RNA binding activity, causing defective splicing of D14 pre-mRNA and reduced D14 expression, and consequently leading to the SL signaling-defective phenotypes. Overall, our findings deepen our understanding of the functional diversification of hnRNP-like proteins and establish a connection between posttranscriptional splicing and SL signaling in the regulation of plant development.
Collapse
Affiliation(s)
| | | | | | | | - Jun Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chunlei Zhou
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Sheng Luo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Weifeng Luo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuai Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xinxin Xing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanqi Chang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cuilan Shi
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yulong Ren
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shanshan Zhu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cailin Lei
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuping Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jie Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhichao Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiyang Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huqu Zhai
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qibing Lin
- Author for correspondence: (J.W.), (Q.L.)
| | | |
Collapse
|
6
|
Butt H, Bazin J, Alshareef S, Eid A, Benhamed M, Reddy ASN, Crespi M, Mahfouz MM. Overlapping roles of spliceosomal components SF3B1 and PHF5A in rice splicing regulation. Commun Biol 2021; 4:529. [PMID: 33953336 PMCID: PMC8100303 DOI: 10.1038/s42003-021-02051-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/26/2021] [Indexed: 01/02/2023] Open
Abstract
The SF3B complex, a multiprotein component of the U2 snRNP of the spliceosome, plays a crucial role in recognizing branch point sequence and facilitates spliceosome assembly and activation. Several chemicals that bind SF3B1 and PHF5A subunits of the SF3B complex inhibit splicing. We recently generated a splicing inhibitor-resistant SF3B1 mutant named SF3B1GEX1ARESISTANT 4 (SGR4) using CRISPR-mediated directed evolution, whereas splicing inhibitor-resistant mutant of PHF5A (Overexpression-PHF5A GEX1A Resistance, OGR) was generated by expressing an engineered version PHF5A-Y36C. Global analysis of splicing in wild type and these two mutants revealed the role of SF3B1 and PHF5A in splicing regulation. This analysis uncovered a set of genes whose intron retention is regulated by both proteins. Further analysis of these retained introns revealed that they are shorter, have a higher GC content, and contain shorter and weaker polypyrimidine tracts. Furthermore, splicing inhibition increased seedlings sensitivity to salt stress, consistent with emerging roles of splicing regulation in stress responses. In summary, we uncovered the functions of two members of the plant branch point recognition complex. The novel strategies described here should be broadly applicable in elucidating functions of splicing regulators, especially in studying the functions of redundant paralogs in plants. Butt et al. used CRISPR-mediated directed evolution to generate rice mutants for the spliceosome components SF3B1 and PHF5A. They demonstrate that these mutants have different levels of sensitivity to salt treatments and suggest that the strategies they employed can be used in the future to study functions of redundant paralogs in plants.
Collapse
Affiliation(s)
- Haroon Butt
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah, University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jeremie Bazin
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Sahar Alshareef
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah, University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ayman Eid
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah, University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Moussa Benhamed
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Anireddy S N Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Martin Crespi
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah, University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| |
Collapse
|
7
|
Nimeth BA, Riegler S, Kalyna M. Alternative Splicing and DNA Damage Response in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:91. [PMID: 32140165 PMCID: PMC7042379 DOI: 10.3389/fpls.2020.00091] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/21/2020] [Indexed: 05/06/2023]
Abstract
Plants are exposed to a variety of abiotic and biotic stresses that may result in DNA damage. Endogenous processes - such as DNA replication, DNA recombination, respiration, or photosynthesis - are also a threat to DNA integrity. It is therefore essential to understand the strategies plants have developed for DNA damage detection, signaling, and repair. Alternative splicing (AS) is a key post-transcriptional process with a role in regulation of gene expression. Recent studies demonstrate that the majority of intron-containing genes in plants are alternatively spliced, highlighting the importance of AS in plant development and stress response. Not only does AS ensure a versatile proteome and influence the abundance and availability of proteins greatly, it has also emerged as an important player in the DNA damage response (DDR) in animals. Despite extensive studies of DDR carried out in plants, its regulation at the level of AS has not been comprehensively addressed. Here, we provide some insights into the interplay between AS and DDR in plants.
Collapse
|
8
|
Nakaminami K, Seki M. RNA Regulation in Plant Cold Stress Response. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1081:23-44. [PMID: 30288702 DOI: 10.1007/978-981-13-1244-1_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In addition to plants, all organisms react to environmental stimuli via the perception of signals and subsequently respond through alterations of gene expression. However, genes/mRNAs are usually not the functional unit themselves, and instead, resultant protein products with individual functions result in various acquired phenotypes. In order to fully characterize the adaptive responses of plants to environmental stimuli, it is essential to determine the level of proteins, in addition to the regulation of mRNA expression. This regulatory step, which is referred to as "mRNA posttranscriptional regulation," occurs subsequent to mRNA transcription and prior to translation. Although these RNA regulatory mechanisms have been well-studied in many organisms, including plants, it is not fully understood how plants respond to environmental stimuli, such as cold stress, via these RNA regulations.A recent study described several RNA regulatory factors in relation to environmental stress responses, including plant cold stress tolerance. In this chapter, the functions of RNA regulatory factors and comprehensive analyses related to the RNA regulations involved in cold stress response are summarized, such as mRNA maturation, including capping, splicing, polyadenylation of mRNA, and the quality control system of mRNA; mRNA degradation, including the decapping step; and mRNA stabilization. In addition, the putative roles of messenger ribonucleoprotein (mRNP) granules, such as processing bodies (PBs) and stress granules (SGs), which are cytoplasmic particles, are described in relation to RNA regulations under stress conditions. These RNA regulatory systems are important for adjusting or fine-tuning and determining the final levels of mRNAs and proteins in order to adapt or respond to environmental stresses. Collectively, these new areas of study revealed that plants possess precise novel regulatory mechanisms which specifically function in the response to cold stress.
Collapse
Affiliation(s)
- Kentaro Nakaminami
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan.
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- Plant Epigenome Regulation Laboratory, Cluster for Pioneering Research, RIKEN, Wako, Saitama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology (JST), Kawaguchi, Saitama, Japan
| |
Collapse
|
9
|
Van Ruyskensvelde V, Van Breusegem F, Van Der Kelen K. Post-transcriptional regulation of the oxidative stress response in plants. Free Radic Biol Med 2018; 122:181-192. [PMID: 29496616 DOI: 10.1016/j.freeradbiomed.2018.02.032] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/22/2018] [Accepted: 02/23/2018] [Indexed: 12/30/2022]
Abstract
Due to their sessile lifestyle, plants can be exposed to several kinds of stresses that will increase the production of reactive oxygen species (ROS), such as hydrogen peroxide, singlet oxygen, and hydroxyl radicals, in the plant cells and activate several signaling pathways that cause alterations in the cellular metabolism. Nevertheless, when ROS production outreaches a certain level, oxidative damage to nucleic acids, lipids, metabolites, and proteins will occur, finally leading to cell death. Until now, the most comprehensive and detailed readout of oxidative stress responses is undoubtedly obtained at the transcriptome level. However, transcript levels often do not correlate with the corresponding protein levels. Indeed, together with transcriptional regulations, post-transcriptional, translational, and/or post-translational regulations will shape the active proteome. Here, we review the current knowledge on the post-transcriptional gene regulation during the oxidative stress responses in planta.
Collapse
Affiliation(s)
- Valerie Van Ruyskensvelde
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium.
| | - Katrien Van Der Kelen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| |
Collapse
|
10
|
Guzicka M, Pawlowski TA, Staszak A, Rozkowski R, Chmura DJ. Molecular and structural changes in vegetative buds of Norway spruce during dormancy in natural weather conditions. TREE PHYSIOLOGY 2018; 38:721-734. [PMID: 29300984 DOI: 10.1093/treephys/tpx156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 11/20/2017] [Indexed: 05/08/2023]
Abstract
The dormancy and the growth of trees in temperate climates are synchronized with seasons. Preparation for dormancy and its proper progression are key for survival and development in the next season. Using a unique approach that combined microscopy and proteomic methods, we investigated changes in Norway spruce (Picea abies (L.) H. Karst.) embryonic shoots during four distinct stages of dormancy in natural weather conditions. We identified 13 proteins that varied among dormancy stages, and were linked to regulation of protein level; functioning of chloroplasts and other plastids; DNA and RNA regulation; and oxidative stress. We also found a group of five proteins, related to cold hardiness, that did not differ in expression among stages of dormancy, but had the highest abundancy level. Ultrastructure of organelles is tightly linked to their metabolic activity, and hence may indicate dormancy status. The observed ultrastructure during endodormancy was stable, whereas during ecodormancy, the structural changes were dynamic and related mainly to nucleus, plastids and mitochondria. At the ultrastructural level, the lack of starch and the presence of callose in plasmodesmata in all regions of embryonic shoot were indicators of full endodormancy. At the initiation of ecodormancy, we noted an increase in metabolic activity of organelles, tissue-specific starch hyperaccumulation and degradation. However, in proteomic analysis, we did not find variation in expression of proteins related to starch degradation or to symplastic isolation of cells. The combination of ultrastructural and proteomic methods gave a more complete picture of vegetative bud dormancy than either of them applied separately. We found some changes at the structural level, but not their analogues in the proteome. Our study suggests a very important role of plastids' organization and metabolism, and their protection in the course of dormancy and during the shift from endo- to ecodormancy and the acquisition of growth competence.
Collapse
Affiliation(s)
- Marzenna Guzicka
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Tomasz A Pawlowski
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Aleksandra Staszak
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Roman Rozkowski
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Daniel J Chmura
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| |
Collapse
|
11
|
Laloum T, Martín G, Duque P. Alternative Splicing Control of Abiotic Stress Responses. TRENDS IN PLANT SCIENCE 2018; 23:140-150. [PMID: 29074233 DOI: 10.1016/j.tplants.2017.09.019] [Citation(s) in RCA: 281] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 09/25/2017] [Accepted: 09/26/2017] [Indexed: 05/20/2023]
Abstract
Alternative splicing, which generates multiple transcripts from the same gene, is an important modulator of gene expression that can increase proteome diversity and regulate mRNA levels. In plants, this post-transcriptional mechanism is markedly induced in response to environmental stress, and recent studies have identified alternative splicing events that allow rapid adjustment of the abundance and function of key stress-response components. In agreement, plant mutants defective in splicing factors are severely impaired in their response to abiotic stress. Notably, mounting evidence indicates that alternative splicing regulates stress responses largely by targeting the abscisic acid (ABA) pathway. We review here current understanding of post-transcriptional control of plant stress tolerance via alternative splicing and discuss research challenges for the near future.
Collapse
Affiliation(s)
- Tom Laloum
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Guiomar Martín
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Paula Duque
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal.
| |
Collapse
|
12
|
Wang G, Wang G, Wang J, Du Y, Yao D, Shuai B, Han L, Tang Y, Song R. Comprehensive proteomic analysis of developing protein bodies in maize (Zea mays) endosperm provides novel insights into its biogenesis. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:6323-6335. [PMID: 27789589 PMCID: PMC5181578 DOI: 10.1093/jxb/erw396] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Prolamins, the major cereal seed storage proteins, are sequestered and accumulated in the lumen of the endoplasmic reticulum (ER), and are directly assembled into protein bodies (PBs). The content and composition of prolamins are the key determinants for protein quality and texture-related traits of the grain. Concomitantly, the PB-inducing fusion system provides an efficient target to produce therapeutic and industrial products in plants. However, the proteome of the native PB and the detailed mechanisms underlying its formation still need to be determined. We developed a method to isolate highly purified and intact PBs from developing maize endosperm and conducted proteomic analysis of intact PBs of zein, a class of prolamine protein found in maize. We thus identified 1756 proteins, which fall into five major categories: metabolic pathways, response to stimulus, transport, development, and growth, as well as regulation. By comparing the proteomes of crude and enriched extractions of PBs, we found substantial evidence for the following conclusions: (i) ribosomes, ER membranes, and the cytoskeleton are tightly associated with zein PBs, which form the peripheral border; (ii) zein RNAs are probably transported and localized to the PB-ER subdomain; and (iii) ER chaperones are essential for zein folding, quality control, and assembly into PBs. We futher confirmed that OPAQUE1 (O1) cannot directly interact with FLOURY1 (FL1) in yeast, suggesting that the interaction between myosins XI and DUF593-containing proteins is isoform-specific. This study provides a proteomic roadmap for dissecting zein PB biogenesis and reveals an unexpected diversity and complexity of proteins in PBs.
Collapse
Affiliation(s)
- Guifeng Wang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, P.R. China, and
- Coordinated Crop Biology Research Center, Beijing 100193, P.R. China
| | - Gang Wang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, P.R. China, and
- Coordinated Crop Biology Research Center, Beijing 100193, P.R. China
| | - Jiajia Wang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, P.R. China, and
| | - Yulong Du
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, P.R. China, and
| | - Dongsheng Yao
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, P.R. China, and
| | - Bilian Shuai
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, P.R. China, and
| | - Liang Han
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, P.R. China, and
| | - Yuanping Tang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, P.R. China, and
| | - Rentao Song
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, P.R. China, and
- Coordinated Crop Biology Research Center, Beijing 100193, P.R. China
| |
Collapse
|
13
|
Wang Z, Zhao X, Wang B, Liu E, Chen N, Zhang W, Liu H. Overexpression of an Arabidopsis heterogeneous nuclear ribonucleoprotein gene, AtRNP1, affects plant growth and reduces plant tolerance to drought and salt stresses. Biochem Biophys Res Commun 2016; 472:353-9. [PMID: 26923071 DOI: 10.1016/j.bbrc.2016.02.081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 02/19/2016] [Indexed: 10/22/2022]
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) participate in diverse regulations of plant growth and environmental stress responses. In this work, an Arabidopsis hnRNP of unknown function, AtRNP1, was investigated. We found that AtRNP1 gene is highly expressed in rosette and cauline leaves, and slightly induced under drought, salt, osmotic and ABA stresses. AtRNP1 protein is localized to both the nucleus and cytoplasm. We performed homologous overexpression of AtRNP1 and found that the transgenic plants showed shortened root length and plant height, and accelerated flowering. In addition, the transgenic plants also showed reduced tolerance to drought, salt, osmotic and ABA stresses. Further studies revealed that under both normal and stress conditions, the proline contents in the transgenic plants are markedly decreased, associated with reduced expression levels of a proline synthase gene and several stress-responsive genes. These results suggested that the overexpression of AtRNP1 negatively affects plant growth and abiotic stress tolerance.
Collapse
Affiliation(s)
- Zhenyu Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030, China.
| | - Xiuyang Zhao
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030, China.
| | - Bing Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030, China.
| | - Erlong Liu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030, China.
| | - Ni Chen
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030, China.
| | - Wei Zhang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Heng Liu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030, China.
| |
Collapse
|