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Tang Y, Yang X, Huang A, Seong K, Ye M, Li M, Zhao Q, Krasileva K, Gu Y. Proxiome assembly of the plant nuclear pore reveals an essential hub for gene expression regulation. NATURE PLANTS 2024:10.1038/s41477-024-01698-9. [PMID: 38773271 DOI: 10.1038/s41477-024-01698-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/11/2024] [Indexed: 05/23/2024]
Abstract
The nuclear pore complex (NPC) is vital for nucleocytoplasmic communication. Recent evidence emphasizes its extensive association with proteins of diverse functions, suggesting roles beyond cargo transport. Yet, our understanding of NPC's composition and functionality at this extended level remains limited. Here, through proximity-labelling proteomics, we uncover both local and global NPC-associated proteome in Arabidopsis, comprising over 500 unique proteins, predominantly associated with NPC's peripheral extension structures. Compositional analysis of these proteins revealed that the NPC concentrates chromatin remodellers, transcriptional regulators and mRNA processing machineries in the nucleoplasmic region while recruiting translation regulatory machinery on the cytoplasmic side, achieving a remarkable orchestration of the genetic information flow by coupling RNA transcription, maturation, transport and translation regulation. Further biochemical and structural modelling analyses reveal that extensive interactions with nucleoporins, along with phase separation mediated by substantial intrinsically disordered proteins, may drive the formation of the unexpectedly large nuclear pore proteome assembly.
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Affiliation(s)
- Yu Tang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Institute of Advanced Agricultural Sciences, Peking University, Weifang, Shandong, China
| | - Xiangyun Yang
- Institute of Advanced Agricultural Sciences, Peking University, Weifang, Shandong, China
| | - Aobo Huang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Kyungyong Seong
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Mao Ye
- Institute of Advanced Agricultural Sciences, Peking University, Weifang, Shandong, China
| | - Mengting Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Qiao Zhao
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ksenia Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Yangnan Gu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
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2
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Kim YO, Safdar M, Kang H, Kim J. Glycine-Rich RNA-Binding Protein AtGRP7 Functions in Nickel and Lead Tolerance in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2024; 13:187. [PMID: 38256744 PMCID: PMC10818801 DOI: 10.3390/plants13020187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024]
Abstract
Plant glycine-rich RNA-binding proteins (GRPs) play crucial roles in the response to environmental stresses. However, the functions of AtGRP7 in plants under heavy metal stress remain unclear. In the present study, in Arabidopsis, the transcript level of AtGRP7 was markedly increased by Ni but was decreased by Pb. AtGRP7-overexpressing plants improved Ni tolerance, whereas the knockout mutant (grp7) was more susceptible than the wild type to Ni. In addition, grp7 showed greatly enhanced Pb tolerance, whereas overexpression lines showed high Pb sensitivity. Ni accumulation was reduced in overexpression lines but increased in grp7, whereas Pb accumulation in grp7 was lower than that in overexpression lines. Ni induced glutathione synthase genes GS1 and GS2 in overexpression lines, whereas Pb increased metallothionein genes MT4a and MT4b and phytochelatin synthase genes PCS1 and PCS2 in grp7. Furthermore, Ni increased CuSOD1 and GR1 in grp7, whereas Pb significantly induced FeSOD1 and FeSOD2 in overexpression lines. The mRNA stability of GS2 and PCS1 was directly regulated by AtGRP7 under Ni and Pb, respectively. Collectively, these results indicate that AtGRP7 plays a crucial role in Ni and Pb tolerance by reducing Ni and Pb accumulation and the direct or indirect post-transcriptional regulation of genes related to heavy metal chelators and antioxidant enzymes.
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Affiliation(s)
- Yeon-Ok Kim
- Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea;
| | - Mahpara Safdar
- Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea;
- Department of Convergence Biosystems Engineering, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
- Department of Rural and Biosystems Engineering, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jangho Kim
- Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea;
- Department of Convergence Biosystems Engineering, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
- Department of Rural and Biosystems Engineering, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
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3
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Pradhan UK, Meher PK, Naha S, Pal S, Gupta S, Gupta A, Parsad R. RBPLight: a computational tool for discovery of plant-specific RNA-binding proteins using light gradient boosting machine and ensemble of evolutionary features. Brief Funct Genomics 2023; 22:401-410. [PMID: 37158175 DOI: 10.1093/bfgp/elad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/12/2023] [Accepted: 04/21/2023] [Indexed: 05/10/2023] Open
Abstract
RNA-binding proteins (RBPs) are essential for post-transcriptional gene regulation in eukaryotes, including splicing control, mRNA transport and decay. Thus, accurate identification of RBPs is important to understand gene expression and regulation of cell state. In order to detect RBPs, a number of computational models have been developed. These methods made use of datasets from several eukaryotic species, specifically from mice and humans. Although some models have been tested on Arabidopsis, these techniques fall short of correctly identifying RBPs for other plant species. Therefore, the development of a powerful computational model for identifying plant-specific RBPs is needed. In this study, we presented a novel computational model for locating RBPs in plants. Five deep learning models and ten shallow learning algorithms were utilized for prediction with 20 sequence-derived and 20 evolutionary feature sets. The highest repeated five-fold cross-validation accuracy, 91.24% AU-ROC and 91.91% AU-PRC, was achieved by light gradient boosting machine. While evaluated using an independent dataset, the developed approach achieved 94.00% AU-ROC and 94.50% AU-PRC. The proposed model achieved significantly higher accuracy for predicting plant-specific RBPs as compared to the currently available state-of-art RBP prediction models. Despite the fact that certain models have already been trained and assessed on the model organism Arabidopsis, this is the first comprehensive computer model for the discovery of plant-specific RBPs. The web server RBPLight was also developed, which is publicly accessible at https://iasri-sg.icar.gov.in/rbplight/, for the convenience of researchers to identify RBPs in plants.
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Affiliation(s)
- Upendra K Pradhan
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Prabina K Meher
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Sanchita Naha
- Division of Computer Applications, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Soumen Pal
- Division of Computer Applications, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Sagar Gupta
- CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur (HP) 176061, India
| | - Ajit Gupta
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Rajender Parsad
- ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
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4
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Cheng K, Zhang C, Lu Y, Li J, Tang H, Ma L, Zhu H. The Glycine-Rich RNA-Binding Protein Is a Vital Post-Transcriptional Regulator in Crops. PLANTS (BASEL, SWITZERLAND) 2023; 12:3504. [PMID: 37836244 PMCID: PMC10575402 DOI: 10.3390/plants12193504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Abstract
Glycine-rich RNA binding proteins (GR-RBPs), a branch of RNA binding proteins (RBPs), play integral roles in regulating various aspects of RNA metabolism regulation, such as RNA processing, transport, localization, translation, and stability, and ultimately regulate gene expression and cell fate. However, our current understanding of GR-RBPs has predominantly been centered on Arabidopsis thaliana, a model plant for investigating plant growth and development. Nonetheless, an increasing body of literature has emerged in recent years, shedding light on the presence and functions of GRPs in diverse crop species. In this review, we not only delineate the distinctive structural domains of plant GR-RBPs but also elucidate several contemporary mechanisms of GR-RBPs in the post-transcriptional regulation of RNA. These mechanisms encompass intricate processes, including RNA alternative splicing, polyadenylation, miRNA biogenesis, phase separation, and RNA translation. Furthermore, we offer an exhaustive synthesis of the diverse roles that GR-RBPs fulfill within crop plants. Our overarching objective is to provide researchers and practitioners in the field of agricultural genetics with valuable insights that may inform and guide the application of plant genetic engineering for enhanced crop development and sustainable agriculture.
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Affiliation(s)
- Ke Cheng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Chunjiao Zhang
- Supervision, Inspection & Testing Center of Agricultural Products Quality, Ministry of Agriculture and Rural Affairs, Beijing 100083, China;
| | - Yao Lu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Jinyan Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Hui Tang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Liqun Ma
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Hongliang Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
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5
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Zhang Y, Xu Y, Skaggs TH, Ferreira JFS, Chen X, Sandhu D. Plant phase extraction: A method for enhanced discovery of the RNA-binding proteome and its dynamics in plants. THE PLANT CELL 2023; 35:2750-2772. [PMID: 37144845 PMCID: PMC10396368 DOI: 10.1093/plcell/koad124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 05/06/2023]
Abstract
RNA-binding proteins (RBPs) play critical roles in posttranscriptional gene regulation. Current methods of systematically profiling RBPs in plants have been predominantly limited to proteins interacting with polyadenylated (poly(A)) RNAs. We developed a method called plant phase extraction (PPE), which yielded a highly comprehensive RNA-binding proteome (RBPome), uncovering 2,517 RBPs from Arabidopsis (Arabidopsis thaliana) leaf and root samples with a highly diverse array of RNA-binding domains. We identified traditional RBPs that participate in various aspects of RNA metabolism and a plethora of nonclassical proteins moonlighting as RBPs. We uncovered constitutive and tissue-specific RBPs essential for normal development and, more importantly, revealed RBPs crucial for salinity stress responses from a RBP-RNA dynamics perspective. Remarkably, 40% of the RBPs are non-poly(A) RBPs that were not previously annotated as RBPs, signifying the advantage of PPE in unbiasedly retrieving RBPs. We propose that intrinsically disordered regions contribute to their nonclassical binding and provide evidence that enzymatic domains from metabolic enzymes have additional roles in RNA binding. Taken together, our findings demonstrate that PPE is an impactful approach for identifying RBPs from complex plant tissues and pave the way for investigating RBP functions under different physiological and stress conditions at the posttranscriptional level.
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Affiliation(s)
- Yong Zhang
- U.S. Salinity Lab (USDA-ARS), Riverside, CA 92507, USA
- Department of Environmental Sciences, University of California, Riverside, CA 92521, USA
| | - Ye Xu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Todd H Skaggs
- U.S. Salinity Lab (USDA-ARS), Riverside, CA 92507, USA
| | | | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
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6
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Wegener M, Dietz KJ. The mutual interaction of glycolytic enzymes and RNA in post-transcriptional regulation. RNA (NEW YORK, N.Y.) 2022; 28:1446-1468. [PMID: 35973722 PMCID: PMC9745834 DOI: 10.1261/rna.079210.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
About three decades ago, researchers suggested that metabolic enzymes participate in cellular processes that are unrelated to their catalytic activity, and the term "moonlighting functions" was proposed. Recently developed advanced technologies in the field of RNA interactome capture now unveil the unexpected RNA binding activity of many metabolic enzymes, as exemplified here for the enzymes of glycolysis. Although for most of these proteins a precise binding mechanism, binding conditions, and physiological relevance of the binding events still await in-depth clarification, several well explored examples demonstrate that metabolic enzymes hold crucial functions in post-transcriptional regulation of protein synthesis. This widely conserved RNA-binding function of glycolytic enzymes plays major roles in controlling cell activities. The best explored examples are glyceraldehyde 3-phosphate dehydrogenase, enolase, phosphoglycerate kinase, and pyruvate kinase. This review summarizes current knowledge about the RNA-binding activity of the ten core enzymes of glycolysis in plant, yeast, and animal cells, its regulation and physiological relevance. Apparently, a tight bidirectional regulation connects core metabolism and RNA biology, forcing us to rethink long established functional singularities.
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Affiliation(s)
- Melanie Wegener
- Biochemistry and Physiology of Plants, Bielefeld University, 33615 Bielefeld, Germany
| | - Karl-Josef Dietz
- Biochemistry and Physiology of Plants, Bielefeld University, 33615 Bielefeld, Germany
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7
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Yang L, Yang L, Zhao C, Liu J, Tong C, Zhang Y, Cheng X, Jiang H, Shen J, Xie M, Liu S. Differential alternative splicing genes and isoform co-expression networks of Brassica napus under multiple abiotic stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:1009998. [PMID: 36311064 PMCID: PMC9608124 DOI: 10.3389/fpls.2022.1009998] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Alternative splicing (AS) is an important regulatory process that affects plant development and stress responses by greatly increasing the complexity of transcriptome and proteome. To understand how the AS landscape of B. napus changes in response to abiotic stresses, we investigated 26 RNA-seq libraries, including control and treatments with cold, dehydration, salt, and abscisic acid (ABA) at two different time points, to perform comparative alternative splicing analysis. Apparently, AS events increased under all stresses except dehydration for 1 h, and intron retention was the most common AS mode. In addition, a total of 357 differential alternative splicing (DAS) genes were identified under four abiotic stresses, among which 81 DAS genes existed in at least two stresses, and 276 DAS genes were presented under only one stress. A weighted gene co-expression network analysis (WGCNA) based on the splicing isoforms, rather than the genes, pinpointed out 23 co-expression modules associated with different abiotic stresses. Among them, a number of significant hub genes were also found to be DAS genes, which encode key isoforms involved in responses to single stress or multiple stresses, including RNA-binding proteins, transcription factors, and other important genes, such as RBP45C, LHY, MYB59, SCL30A, RS40, MAJ23.10, and DWF4. The splicing isoforms of candidate genes identified in this study could be a valuable resource for improving tolerance of B. napus against multiple abiotic stresses.
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Affiliation(s)
- Lingli Yang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Li Yang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Chuanji Zhao
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jie Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuanyuan Zhang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaohui Cheng
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Huifang Jiang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Meili Xie
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shengyi Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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8
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Ramakrishnan M, Rajan KS, Mullasseri S, Palakkal S, Kalpana K, Sharma A, Zhou M, Vinod KK, Ramasamy S, Wei Q. The plant epitranscriptome: revisiting pseudouridine and 2'-O-methyl RNA modifications. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1241-1256. [PMID: 35445501 PMCID: PMC9241379 DOI: 10.1111/pbi.13829] [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: 02/11/2022] [Revised: 04/11/2022] [Accepted: 04/18/2022] [Indexed: 06/01/2023]
Abstract
There is growing evidence that post-transcriptional RNA modifications are highly dynamic and can be used to improve crop production. Although more than 172 unique types of RNA modifications have been identified throughout the kingdom of life, we are yet to leverage upon the understanding to optimize RNA modifications in crops to improve productivity. The contributions of internal mRNA modifications such as N6-methyladenosine (m6 A) and 5-methylcytosine (m5 C) methylations to embryonic development, root development, leaf morphogenesis, flowering, fruit ripening and stress response are sufficiently known, but the roles of the two most abundant RNA modifications, pseudouridine (Ψ) and 2'-O-methylation (Nm), in the cell remain unclear due to insufficient advances in high-throughput technologies in plant development. Therefore, in this review, we discuss the latest methods and insights gained in mapping internal Ψ and Nm and their unique properties in plants and other organisms. In addition, we discuss the limitations that remain in high-throughput technologies for qualitative and quantitative mapping of these RNA modifications and highlight future challenges in regulating the plant epitranscriptome.
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Affiliation(s)
- Muthusamy Ramakrishnan
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingJiangsuChina
- Bamboo Research InstituteNanjing Forestry UniversityNanjingJiangsuChina
| | - K. Shanmugha Rajan
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology InstituteBar‐Ilan University52900Ramat‐GanIsrael
- Department of Chemical and Structural BiologyWeizmann Institute7610001RehovotIsrael
| | - Sileesh Mullasseri
- School of Ocean Science and TechnologyKerala University of Fisheries and Ocean StudiesCochinIndia
| | - Sarin Palakkal
- The Institute for Drug ResearchSchool of PharmacyThe Hebrew University of JerusalemJerusalemIsrael
| | - Krishnan Kalpana
- Department of Plant PathologyAgricultural College and Research InstituteTamilnadu Agricultural University625 104MaduraiTamil NaduIndia
| | - Anket Sharma
- State Key Laboratory of Subtropical SilvicultureZhejiang A&F UniversityHangzhouZhejiangChina
| | - Mingbing Zhou
- State Key Laboratory of Subtropical SilvicultureZhejiang A&F UniversityHangzhouZhejiangChina
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High‐Efficiency UtilizationZhejiang A&F UniversityHangzhouZhejiangChina
| | | | - Subbiah Ramasamy
- Cardiac Metabolic Disease LaboratoryDepartment of BiochemistrySchool of Biological SciencesMadurai Kamaraj UniversityMaduraiTamil NaduIndia
| | - Qiang Wei
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingJiangsuChina
- Bamboo Research InstituteNanjing Forestry UniversityNanjingJiangsuChina
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9
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Cuerda-Gil D, Hung YH, Panda K, Slotkin RK. A plant tethering system for the functional study of protein-RNA interactions in vivo. PLANT METHODS 2022; 18:75. [PMID: 35658900 PMCID: PMC9166424 DOI: 10.1186/s13007-022-00907-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
The sorting of RNA transcripts dictates their ultimate post-transcriptional fates, such as translation, decay or degradation by RNA interference (RNAi). This sorting of RNAs into distinct fates is mediated by their interaction with RNA-binding proteins. While hundreds of RNA binding proteins have been identified, which act to sort RNAs into different pathways is largely unknown. Particularly in plants, this is due to the lack of reliable protein-RNA artificial tethering tools necessary to determine the mechanism of protein action on an RNA in vivo. Here we generated a protein-RNA tethering system which functions on an endogenous Arabidopsis RNA that is tracked by the quantitative flowering time phenotype. Unlike other protein-RNA tethering systems that have been attempted in plants, our system circumvents the inadvertent triggering of RNAi. We successfully in vivo tethered a protein epitope, deadenylase protein and translation factor to the target RNA, which function to tag, decay and boost protein production, respectively. We demonstrated that our tethering system (1) is sufficient to engineer the downstream fate of an RNA, (2) enables the determination of any protein's function upon recruitment to an RNA, and (3) can be used to discover new interactions with RNA-binding proteins.
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Affiliation(s)
- Diego Cuerda-Gil
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Yu-Hung Hung
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Kaushik Panda
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA.
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10
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Ribonomics Approaches to Identify RBPome in Plants and Other Eukaryotes: Current Progress and Future Prospects. Int J Mol Sci 2022; 23:ijms23115923. [PMID: 35682602 PMCID: PMC9180120 DOI: 10.3390/ijms23115923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/16/2022] [Accepted: 05/20/2022] [Indexed: 02/01/2023] Open
Abstract
RNA-binding proteins (RBPs) form complex interactions with RNA to regulate the cell’s activities including cell development and disease resistance. RNA-binding proteome (RBPome) aims to profile and characterize the RNAs and proteins that interact with each other to carry out biological functions. Generally, RNA-centric and protein-centric ribonomic approaches have been successfully developed to profile RBPome in different organisms including plants and animals. Further, more and more novel methods that were firstly devised and applied in mammalians have shown great potential to unravel RBPome in plants such as RNA-interactome capture (RIC) and orthogonal organic phase separation (OOPS). Despise the development of various robust and state-of-the-art ribonomics techniques, genome-wide RBP identifications and characterizations in plants are relatively fewer than those in other eukaryotes, indicating that ribonomics techniques have great opportunities in unraveling and characterizing the RNA–protein interactions in plant species. Here, we review all the available approaches for analyzing RBPs in living organisms. Additionally, we summarize the transcriptome-wide approaches to characterize both the coding and non-coding RBPs in plants and the promising use of RBPome for booming agriculture.
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11
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(De)Activation (Ir)Reversibly or Degradation: Dynamics of Post-Translational Protein Modifications in Plants. Life (Basel) 2022; 12:life12020324. [PMID: 35207610 PMCID: PMC8874572 DOI: 10.3390/life12020324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 11/22/2022] Open
Abstract
The increasing dynamic functions of post-translational modifications (PTMs) within protein molecules present outstanding challenges for plant biology even at this present day. Protein PTMs are among the first and fastest plant responses to changes in the environment, indicating that the mechanisms and dynamics of PTMs are an essential area of plant biology. Besides being key players in signaling, PTMs play vital roles in gene expression, gene, and protein localization, protein stability and interactions, as well as enzyme kinetics. In this review, we take a broader but concise approach to capture the current state of events in the field of plant PTMs. We discuss protein modifications including citrullination, glycosylation, phosphorylation, oxidation and disulfide bridges, N-terminal, SUMOylation, and ubiquitination. Further, we outline the complexity of studying PTMs in relation to compartmentalization and function. We conclude by challenging the proteomics community to engage in holistic approaches towards identification and characterizing multiple PTMs on the same protein, their interaction, and mechanism of regulation to bring a deeper understanding of protein function and regulation in plants.
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12
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Yan Y, Gan J, Tao Y, Okita TW, Tian L. RNA-Binding Proteins: The Key Modulator in Stress Granule Formation and Abiotic Stress Response. FRONTIERS IN PLANT SCIENCE 2022; 13:882596. [PMID: 35783947 PMCID: PMC9240754 DOI: 10.3389/fpls.2022.882596] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/04/2022] [Indexed: 05/08/2023]
Abstract
To cope with abiotic environmental stress, plants rapidly change their gene expression transcriptionally and post-transcriptionally, the latter by translational suppression of selected proteins and the assembly of cytoplasmic stress granules (SGs) that sequester mRNA transcripts. RNA-binding proteins (RBPs) are the major players in these post-transcriptional processes, which control RNA processing in the nucleus, their export from the nucleus, and overall RNA metabolism in the cytoplasm. Because of their diverse modular domain structures, various RBP types dynamically co-assemble with their targeted RNAs and interacting proteins to form SGs, a process that finely regulates stress-responsive gene expression. This review summarizes recent findings on the involvement of RBPs in adapting plants to various abiotic stresses via modulation of specific gene expression events and SG formation. The relationship of these processes with the stress hormone abscisic acid (ABA) is discussed.
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Affiliation(s)
- Yanyan Yan
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable (Ministry of Agriculture and Rural Affairs), Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Jianghuang Gan
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable (Ministry of Agriculture and Rural Affairs), Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Yilin Tao
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable (Ministry of Agriculture and Rural Affairs), Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Thomas W. Okita
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
- *Correspondence: Thomas W. Okita,
| | - Li Tian
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable (Ministry of Agriculture and Rural Affairs), Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
- Li Tian,
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13
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Huang D, Kosentka PZ, Liu W. Synthetic biology approaches in regulation of targeted gene expression. CURRENT OPINION IN PLANT BIOLOGY 2021; 63:102036. [PMID: 33930839 DOI: 10.1016/j.pbi.2021.102036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 05/15/2023]
Abstract
Synthetic biology approaches are highly sought-after to facilitate the regulation of targeted gene expression in plants for functional genomics research and crop trait improvement. To date, synthetic regulation of gene expression predominantly focuses at the transcription level via engineering of synthetic promoters and transcription factors, while pioneering examples have started to emerge for synthetic regulation of gene expression at the levels of mRNA stability, translation, and protein degradation. This review discusses recent advances in plant synthetic biology for the regulation of gene expression at multiple levels, and highlights their future directions.
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Affiliation(s)
- Debao Huang
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Pawel Z Kosentka
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA.
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14
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Plant RNA Binding Proteins as Critical Modulators in Drought, High Salinity, Heat, and Cold Stress Responses: An Updated Overview. Int J Mol Sci 2021; 22:ijms22136731. [PMID: 34201749 PMCID: PMC8269355 DOI: 10.3390/ijms22136731] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023] Open
Abstract
Plant abiotic stress responses are tightly regulated by different players at multiple levels. At transcriptional or post-transcriptional levels, several RNA binding proteins (RBPs) regulate stress response genes through RNA metabolism. They are increasingly recognized as critical modulators of a myriad of biological processes, including stress responses. Plant RBPs are heterogeneous with one or more conservative RNA motifs that constitute canonical/novel RNA binding domains (RBDs), which can bind to target RNAs to determine their regulation as per the plant requirements at given environmental conditions. Given its biological significance and possible consideration as a potential tool in genetic manipulation programs to improve key agronomic traits amidst frequent episodes of climate anomalies, studies concerning the identification and functional characterization of RBP candidate genes are steadily mounting. This paper presents a comprehensive overview of canonical and novel RBPs and their functions in major abiotic stresses including drought, heat, salt, and cold stress conditions. To some extent, we also briefly describe the basic motif structure of RBPs that would be useful in forthcoming studies. Additionally, we also collected RBP genes that were modulated by stress, but that lacked functional characterization, providing an impetus to conduct further research.
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15
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Kim J, Lee H, Lee HG, Seo PJ. Get closer and make hotspots: liquid-liquid phase separation in plants. EMBO Rep 2021; 22:e51656. [PMID: 33913240 DOI: 10.15252/embr.202051656] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/14/2021] [Accepted: 03/30/2021] [Indexed: 12/18/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) facilitates the formation of membraneless compartments in a cell and allows the spatiotemporal organization of biochemical reactions by concentrating macromolecules locally. In plants, LLPS defines cellular reaction hotspots, and stimulus-responsive LLPS is tightly linked to a variety of cellular and biological functions triggered by exposure to various internal and external stimuli, such as stress responses, hormone signaling, and temperature sensing. Here, we provide an overview of the current understanding of physicochemical forces and molecular factors that drive LLPS in plant cells. We illustrate how the biochemical features of cellular condensates contribute to their biological functions. Additionally, we highlight major challenges for the comprehensive understanding of biological LLPS, especially in view of the dynamic and robust organization of biochemical reactions underlying plastic responses to environmental fluctuations in plants.
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Affiliation(s)
- Jiwoo Kim
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Hongwoo Lee
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Hong Gil Lee
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
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16
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Yang J, Cao Y, Ma L. Co-Transcriptional RNA Processing in Plants: Exploring from the Perspective of Polyadenylation. Int J Mol Sci 2021; 22:ijms22073300. [PMID: 33804866 PMCID: PMC8037041 DOI: 10.3390/ijms22073300] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/09/2021] [Accepted: 03/19/2021] [Indexed: 12/13/2022] Open
Abstract
Most protein-coding genes in eukaryotes possess at least two poly(A) sites, and alternative polyadenylation is considered a contributing factor to transcriptomic and proteomic diversity. Following transcription, a nascent RNA usually undergoes capping, splicing, cleavage, and polyadenylation, resulting in a mature messenger RNA (mRNA); however, increasing evidence suggests that transcription and RNA processing are coupled. Plants, which must produce rapid responses to environmental changes because of their limited mobility, exhibit such coupling. In this review, we summarize recent advances in our understanding of the coupling of transcription with RNA processing in plants, and we describe the possible spatial environment and important proteins involved. Moreover, we describe how liquid–liquid phase separation, mediated by the C-terminal domain of RNA polymerase II and RNA processing factors with intrinsically disordered regions, enables efficient co-transcriptional mRNA processing in plants.
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17
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Khalifa KA, Ibrahim SD, El-Garhy HAS, Moustafa MMM, Maalouf F, Alsamman AM, Hamwieh A, El Allali A. Developing a new genic SSR primer database in faba bean (Vicia faba L.). J Appl Genet 2021; 62:373-387. [PMID: 33755893 DOI: 10.1007/s13353-021-00626-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/20/2021] [Accepted: 02/26/2021] [Indexed: 11/24/2022]
Abstract
The goal of this research was to develop a new genetic database of simple sequence repetition (SSR) primers for faba and classify them according to their target genes and respective biological processes. Approximately 75,605 and 148,196 previously published genomic and transcriptomic faba sequences, respectively, have been used to detect possible SSRs. The numbers of identified SSRs from each dataset were 25,502 and 12,319, respectively. The distribution of different repeat classes indicated that trinucleotides represent the largest number of repeat counts, followed by dinucleotides. The extracted genic SSR sequences were used to design 1091 polymerase chain reaction (PCR) primers, of which only 238 (21.8%) primers target genomic sequences and the other 853 PCR primers targeted transcriptomic sequences. The annotation of gene-targeted SSRs showed that approximately 897 genes were targeted by our SSR primers. Approximately 1890 gene ontology (GO) identification codes have been obtained. The GO keywords were distributed among distinct molecular cell features. The highest redundancies involved 554 technical words, 196 domains, and 160 molecular feature phrases. These GO codes belonged to the general level of GO and included molecular function, cellular component, and biological process (544, 670, and 676 GOs, respectively). Twenty-seven SSR PCR primers were synthesized to 12 Egyptian faba bean genotypes. Approximately 11 SSR provided one to two PCR bands, whereas other SSRs provided only one sharp band with polymorphic band size. There were 13 polymorphic primers. The polymorphism information content was 0.3, which implied moderate informativeness.
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Affiliation(s)
- Kareem A Khalifa
- Agricultural Genetic Engineering Research Institute, PO Box 12619, Giza, Egypt
| | - Shafik D Ibrahim
- Agricultural Genetic Engineering Research Institute, PO Box 12619, Giza, Egypt
| | - Hoda A S El-Garhy
- Department of Genetics and Genetic Engineering, Faculty of Agricultural, Benha University, Benha, Egypt
| | - Mahmoud M M Moustafa
- Department of Genetics and Genetic Engineering, Faculty of Agricultural, Benha University, Benha, Egypt
| | - Fouad Maalouf
- International Center for Agricultural Research in the Dry Areas (ICARDA) , Terbol, Lebanon
| | - Alsamman M Alsamman
- Agricultural Genetic Engineering Research Institute, PO Box 12619, Giza, Egypt
| | - Aladdin Hamwieh
- International Center for Agricultural Research in the Dry Areas (ICARDA), PO Box 2416, Cairo, Egypt
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco.
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18
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Burjoski V, Reddy ASN. The Landscape of RNA-Protein Interactions in Plants: Approaches and Current Status. Int J Mol Sci 2021; 22:2845. [PMID: 33799602 PMCID: PMC7999938 DOI: 10.3390/ijms22062845] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/25/2021] [Accepted: 03/10/2021] [Indexed: 12/28/2022] Open
Abstract
RNAs transmit information from DNA to encode proteins that perform all cellular processes and regulate gene expression in multiple ways. From the time of synthesis to degradation, RNA molecules are associated with proteins called RNA-binding proteins (RBPs). The RBPs play diverse roles in many aspects of gene expression including pre-mRNA processing and post-transcriptional and translational regulation. In the last decade, the application of modern techniques to identify RNA-protein interactions with individual proteins, RNAs, and the whole transcriptome has led to the discovery of a hidden landscape of these interactions in plants. Global approaches such as RNA interactome capture (RIC) to identify proteins that bind protein-coding transcripts have led to the identification of close to 2000 putative RBPs in plants. Interestingly, many of these were found to be metabolic enzymes with no known canonical RNA-binding domains. Here, we review the methods used to analyze RNA-protein interactions in plants thus far and highlight the understanding of plant RNA-protein interactions these techniques have provided us. We also review some recent protein-centric, RNA-centric, and global approaches developed with non-plant systems and discuss their potential application to plants. We also provide an overview of results from classical studies of RNA-protein interaction in plants and discuss the significance of the increasingly evident ubiquity of RNA-protein interactions for the study of gene regulation and RNA biology in plants.
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Affiliation(s)
| | - Anireddy S. N. Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA;
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Mishra A, Khanal R, Kabir WU, Hoque T. AIRBP: Accurate identification of RNA-binding proteins using machine learning techniques. Artif Intell Med 2021; 113:102034. [PMID: 33685590 DOI: 10.1016/j.artmed.2021.102034] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 01/19/2021] [Accepted: 02/09/2021] [Indexed: 12/25/2022]
Abstract
Identification of RNA-binding proteins (RBPs) that bind to ribonucleic acid molecules is an important problem in Computational Biology and Bioinformatics. It becomes indispensable to identify RBPs as they play crucial roles in post-transcriptional control of RNAs and RNA metabolism as well as have diverse roles in various biological processes such as splicing, mRNA stabilization, mRNA localization, and translation, RNA synthesis, folding-unfolding, modification, processing, and degradation. The existing experimental techniques for identifying RBPs are time-consuming and expensive. Therefore, identifying RBPs directly from the sequence using computational methods can be useful to annotate RBPs and assist the experimental design efficiently. In this work, we present a method called AIRBP, which is designed using an advanced machine learning technique, called stacking, to effectively predict RBPs by utilizing features extracted from evolutionary information, physiochemical properties, and disordered properties. Moreover, our method, AIRBP, use the majority vote from RBPPred, DeepRBPPred, and the stacking model for the prediction for RBPs. The results show that AIRBP attains Accuracy (ACC), Balanced Accuracy (BACC), F1-score, and Mathews Correlation Coefficient (MCC) of 95.84 %, 94.71 %, 0.928, and 0.899, respectively, based on the training dataset, using 10-fold cross-validation (CV). Further evaluation of AIRBP on independent test set reveals that it achieves ACC, BACC, F1-score, and MCC of 94.36 %, 94.28 %, 0.897, and 0.860, for Human test set; 91.25 %, 93.00 %, 0.896, and 0.835 for S. cerevisiae test set; and 90.60 %, 90.41 %, 0.934, and 0.775 for A. thaliana test set, respectively. These results indicate that the AIRBP outperforms the existing Deep- and TriPepSVM methods. Therefore, the proposed better-performing AIRBP can be useful for accurate identification and annotation of RBPs directly from the sequence and help gain valuable insight to treat critical diseases. Availability: Code-data is available here: http://cs.uno.edu/∼tamjid/Software/AIRBP/code_data.zip.
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Affiliation(s)
- Avdesh Mishra
- Department of Electrical Engineering and Computer Science, Texas A&M University-Kingsville, Kingsville, TX, USA
| | - Reecha Khanal
- Department of Computer Science, University of New Orleans, New Orleans, LA, USA
| | - Wasi Ul Kabir
- Department of Computer Science, University of New Orleans, New Orleans, LA, USA
| | - Tamjidul Hoque
- Department of Computer Science, University of New Orleans, New Orleans, LA, USA.
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Muleya V, Marondedze C. Functional Roles of RNA-Binding Proteins in Plant Signaling. Life (Basel) 2020; 10:life10110288. [PMID: 33217949 PMCID: PMC7698727 DOI: 10.3390/life10110288] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 12/17/2022] Open
Abstract
RNA-binding proteins (RBPs) are typical proteins that bind RNA through single or multiple RNA-binding domains (RBDs). These proteins have a functional role in determining the fate or function of the bound RNAs. A few hundred RBPs were known through in silico prediction based on computational assignment informed by structural similarity and the presence of classical RBDs. However, RBPs lacking such conventional RBDs were omitted. Owing to the recent mRNA interactome capture technology based on UV-crosslinking and fixing proteins to their mRNA targets followed by affinity capture purification and identification of RBPs by tandem mass spectrometry, several hundreds of RBPs have recently been discovered. These proteome-wide studies have colossally increased the number of proteins implicated in RNA binding and unearthed hundreds of novel RBPs lacking classical RBDs, such as proteins involved in intermediary metabolism. These discoveries provide wide insights into the post-transcriptional gene regulation players and their role in plant signaling, such as environmental stress conditions. In this review, novel discoveries of RBPs are explored, particularly on the evolving knowledge of their role in stress responses. The molecular functions of these RBPs, particularly focusing on those that do not have classical RBDs, are also elucidated at the systems level.
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Affiliation(s)
- Victor Muleya
- Department of Biochemistry, Faculty of Medicine, Midlands State University, Main Campus, Senga Road, Gweru P Bag 9055, Zimbabwe;
| | - Claudius Marondedze
- Department of Biochemistry, Faculty of Medicine, Midlands State University, Main Campus, Senga Road, Gweru P Bag 9055, Zimbabwe;
- Rijk Zwaan, 2678 ZG De Lier, The Netherlands
- Correspondence: or or
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