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Loeser J, Bauer J, Janßen K, Rockenbach K, Wachter A. A transient in planta editing assay identifies specific binding of the splicing regulator PTB as a prerequisite for cassette exon inclusion. PLANT MOLECULAR BIOLOGY 2024; 114:22. [PMID: 38443687 PMCID: PMC10914923 DOI: 10.1007/s11103-024-01414-3] [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: 09/18/2023] [Accepted: 12/31/2023] [Indexed: 03/07/2024]
Abstract
The dynamic interaction of RNA-binding proteins (RBPs) with their target RNAs contributes to the diversity of ribonucleoprotein (RNP) complexes that are involved in a myriad of biological processes. Identifying the RNP components at high resolution and defining their interactions are key to understanding their regulation and function. Expressing fusions between an RBP of interest and an RNA editing enzyme can result in nucleobase changes in target RNAs, representing a recent addition to experimental approaches for profiling RBP/RNA interactions. Here, we have used the MS2 protein/RNA interaction to test four RNA editing proteins for their suitability to detect target RNAs of RBPs in planta. We have established a transient test system for fast and simple quantification of editing events and identified the hyperactive version of the catalytic domain of an adenosine deaminase (hADARcd) as the most suitable editing enzyme. Examining fusions between homologs of polypyrimidine tract binding proteins (PTBs) from Arabidopsis thaliana and hADARcd allowed determining target RNAs with high sensitivity and specificity. Moreover, almost complete editing of a splicing intermediate provided insight into the order of splicing reactions and PTB dependency of this particular splicing event. Addition of sequences for nuclear localisation of the fusion protein increased the editing efficiency, highlighting this approach's potential to identify RBP targets in a compartment-specific manner. Our studies have established the editing-based analysis of interactions between RBPs and their RNA targets in a fast and straightforward assay, offering a new system to study the intricate composition and functions of plant RNPs in vivo.
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Affiliation(s)
- Jorinde Loeser
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Julia Bauer
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Kim Janßen
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Kevin Rockenbach
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Andreas Wachter
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany.
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2
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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.
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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
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3
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Chehelgerdi M, Chehelgerdi M. The use of RNA-based treatments in the field of cancer immunotherapy. Mol Cancer 2023; 22:106. [PMID: 37420174 PMCID: PMC10401791 DOI: 10.1186/s12943-023-01807-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 06/13/2023] [Indexed: 07/09/2023] Open
Abstract
Over the past several decades, mRNA vaccines have evolved from a theoretical concept to a clinical reality. These vaccines offer several advantages over traditional vaccine techniques, including their high potency, rapid development, low-cost manufacturing, and safe administration. However, until recently, concerns over the instability and inefficient distribution of mRNA in vivo have limited their utility. Fortunately, recent technological advancements have mostly resolved these concerns, resulting in the development of numerous mRNA vaccination platforms for infectious diseases and various types of cancer. These platforms have shown promising outcomes in both animal models and humans. This study highlights the potential of mRNA vaccines as a promising alternative approach to conventional vaccine techniques and cancer treatment. This review article aims to provide a thorough and detailed examination of mRNA vaccines, including their mechanisms of action and potential applications in cancer immunotherapy. Additionally, the article will analyze the current state of mRNA vaccine technology and highlight future directions for the development and implementation of this promising vaccine platform as a mainstream therapeutic option. The review will also discuss potential challenges and limitations of mRNA vaccines, such as their stability and in vivo distribution, and suggest ways to overcome these issues. By providing a comprehensive overview and critical analysis of mRNA vaccines, this review aims to contribute to the advancement of this innovative approach to cancer treatment.
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Affiliation(s)
- Mohammad Chehelgerdi
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran.
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Matin Chehelgerdi
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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4
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Mateos JL, Staiger D. Toward a systems view on RNA-binding proteins and associated RNAs in plants: Guilt by association. THE PLANT CELL 2023; 35:1708-1726. [PMID: 36461946 PMCID: PMC10226577 DOI: 10.1093/plcell/koac345] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/08/2022] [Accepted: 11/17/2022] [Indexed: 05/30/2023]
Abstract
RNA-binding proteins (RBPs) have a broad impact on most biochemical, physiological, and developmental processes in a plant's life. RBPs engage in an on-off relationship with their RNA partners, accompanying virtually every stage in RNA processing and function. While the function of a plethora of RBPs in plant development and stress responses has been described, we are lacking a systems-level understanding of components in RNA-based regulation. Novel techniques have substantially enlarged the compendium of proteins with experimental evidence for binding to RNAs in the cell, the RNA-binding proteome. Furthermore, ribonomics methods have been adapted for use in plants to profile the in vivo binding repertoire of RBPs genome-wide. Here, we discuss how recent technological achievements have provided novel insights into the mode of action of plant RBPs at a genome-wide scale. Furthermore, we touch upon two emerging topics, the connection of RBPs to phase separation in the cell and to extracellular RNAs. Finally, we define open questions to be addressed to move toward an integrated understanding of RBP function.
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Affiliation(s)
- Julieta L Mateos
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET-UBA), Buenos Aires, Argentina
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
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5
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Kufel J, Diachenko N, Golisz A. Alternative splicing as a key player in the fine-tuning of the immunity response in Arabidopsis. MOLECULAR PLANT PATHOLOGY 2022; 23:1226-1238. [PMID: 35567423 PMCID: PMC9276941 DOI: 10.1111/mpp.13228] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 06/01/2023]
Abstract
Plants, like animals, are constantly exposed to abiotic and biotic stresses, which often inhibit plant growth and development, and cause tissue damage, disease, and even plant death. Efficient and timely response to stress requires appropriate co- and posttranscriptional reprogramming of gene expression. Alternative pre-mRNA splicing provides an important layer of this regulation by controlling the level of factors involved in stress response and generating additional protein isoforms with specific features. Recent high-throughput studies have revealed that several defence genes undergo alternative splicing that is often affected by pathogen infection. Despite extensive work, the exact mechanisms underlying these relationships are still unclear, but the contribution of alternative protein isoforms to the defence response and the role of regulatory factors, including components of the splicing machinery, have been established. Modulation of gene expression in response to stress includes alternative splicing, chromatin remodelling, histone modifications, and nucleosome occupancy. How these processes affect plant immunity is mostly unknown, but these facets open new regulatory possibilities. Here we provide an overview of the current state of knowledge and recent findings regarding the growing importance of alternative splicing in plant response to biotic stress.
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Affiliation(s)
- Joanna Kufel
- Institute of Genetics and BiotechnologyFaculty of BiologyUniversity of WarsawWarsawPoland
| | - Nataliia Diachenko
- Institute of Genetics and BiotechnologyFaculty of BiologyUniversity of WarsawWarsawPoland
| | - Anna Golisz
- Institute of Genetics and BiotechnologyFaculty of BiologyUniversity of WarsawWarsawPoland
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6
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Rosenkranz RRE, Ullrich S, Löchli K, Simm S, Fragkostefanakis S. Relevance and Regulation of Alternative Splicing in Plant Heat Stress Response: Current Understanding and Future Directions. FRONTIERS IN PLANT SCIENCE 2022; 13:911277. [PMID: 35812973 PMCID: PMC9260394 DOI: 10.3389/fpls.2022.911277] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/26/2022] [Indexed: 05/26/2023]
Abstract
Alternative splicing (AS) is a major mechanism for gene expression in eukaryotes, increasing proteome diversity but also regulating transcriptome abundance. High temperatures have a strong impact on the splicing profile of many genes and therefore AS is considered as an integral part of heat stress response. While many studies have established a detailed description of the diversity of the RNAome under heat stress in different plant species and stress regimes, little is known on the underlying mechanisms that control this temperature-sensitive process. AS is mainly regulated by the activity of splicing regulators. Changes in the abundance of these proteins through transcription and AS, post-translational modifications and interactions with exonic and intronic cis-elements and core elements of the spliceosomes modulate the outcome of pre-mRNA splicing. As a major part of pre-mRNAs are spliced co-transcriptionally, the chromatin environment along with the RNA polymerase II elongation play a major role in the regulation of pre-mRNA splicing under heat stress conditions. Despite its importance, our understanding on the regulation of heat stress sensitive AS in plants is scarce. In this review, we summarize the current status of knowledge on the regulation of AS in plants under heat stress conditions. We discuss possible implications of different pathways based on results from non-plant systems to provide a perspective for researchers who aim to elucidate the molecular basis of AS under high temperatures.
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Affiliation(s)
| | - Sarah Ullrich
- Molecular Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
| | - Karin Löchli
- Molecular Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
| | - Stefan Simm
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
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7
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RNA-binding proteins and their role in translational regulation in plants. Essays Biochem 2022; 66:87-97. [PMID: 35612383 DOI: 10.1042/ebc20210069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 12/16/2022]
Abstract
Translation is a fundamental process for life that needs to be finely adapted to the energetical, developmental and environmental conditions; however, the molecular mechanisms behind such adaptation are not yet fully understood. By directly recognizing and binding to cis-elements present in their target mRNAs, RBPs govern all post-transcriptional regulatory processes. They orchestrate the balance between mRNA stability, storage, decay, and translation of their client mRNAs, playing a crucial role in the modulation of gene expression. In the last years exciting discoveries have been made regarding the roles of RBPs in fine-tuning translation. In this review, we focus on how these RBPs recognize their targets and modulate their translation, highlighting the complex and diverse molecular mechanisms implicated. Since the repertoire of RBPs keeps growing, future research promises to uncover new fascinating means of translational modulation, and thus, of gene expression.
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8
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The Multifunctional Faces of T-Cell Intracellular Antigen 1 in Health and Disease. Int J Mol Sci 2022; 23:ijms23031400. [PMID: 35163320 PMCID: PMC8836218 DOI: 10.3390/ijms23031400] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/13/2022] [Accepted: 01/22/2022] [Indexed: 02/06/2023] Open
Abstract
T-cell intracellular antigen 1 (TIA1) is an RNA-binding protein that is expressed in many tissues and in the vast majority of species, although it was first discovered as a component of human cytotoxic T lymphocytes. TIA1 has a dual localization in the nucleus and cytoplasm, where it plays an important role as a regulator of gene-expression flux. As a multifunctional master modulator, TIA1 controls biological processes relevant to the physiological functioning of the organism and the development and/or progression of several human pathologies. This review summarizes our current knowledge of the molecular aspects and cellular processes involving TIA1, with relevance for human pathophysiology.
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9
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Zhao N, Su XM, Liu ZW, Zhou JX, Su YN, Cai XW, Chen L, Wu Z, He XJ. The RNA recognition motif-containing protein UBA2c prevents early flowering by promoting transcription of the flowering repressor FLM in Arabidopsis. THE NEW PHYTOLOGIST 2022; 233:751-765. [PMID: 34724229 DOI: 10.1111/nph.17836] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
FLOWERING LOCUS M (FLM) is a well-known MADS-box transcription factor that is required for preventing early flowering under low temperatures in Arabidopsis thaliana. Alternative splicing of FLM is involved in the regulation of temperature-responsive flowering. However, how the basic transcript level of FLM is regulated is largely unknown. Here, we conducted forward genetic screening and identified a previously uncharacterized flowering repressor gene, UBA2c. Genetic analyses indicated that UBA2c represses flowering at least by promoting FLM transcription. We further demonstrated that UBA2c directly binds to FLM chromatin and facilitates FLM transcription by inhibiting histone H3K27 trimethylation, a histone marker related to transcriptional repression. UBA2c encodes a protein containing two putative RNA recognition motifs (RRMs) and one prion-like domain (PrLD). We found that UBA2c forms speckles in the nucleus and that both the RRMs and PrLD are required not only for forming the nuclear speckles but also for the biological function of UBA2c. These results identify a previously unknown flowering repressor and provide insights into the regulation of flowering time.
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Affiliation(s)
- Nan Zhao
- National Institute of Biological Sciences, Beijing, 102206, China
- Graduate School of Peking Union Medical College, Beijing, 100730, China
| | - Xiao-Min Su
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Zhang-Wei Liu
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Jin-Xing Zhou
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xue-Wei Cai
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Ling Chen
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Zhe Wu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China
- Graduate School of Peking Union Medical College, Beijing, 100730, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China
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10
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Lin J, Zhu Z. Plant responses to high temperature: a view from pre-mRNA alternative splicing. PLANT MOLECULAR BIOLOGY 2021; 105:575-583. [PMID: 33550520 DOI: 10.1007/s11103-021-01117-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/09/2021] [Indexed: 05/14/2023]
Abstract
This review focused on the recent breakthroughs in plant high temperature responses from an alternative splicing angle. With the inevitable global warming, high temperature triggers plants to change their growth and developmental programs for adapting temperature increase. In the past decades, the signaling mechanisms from plant thermo-sensing to downstream transcriptional cascades have been extensively studied. Plenty of elegant review papers have summarized these breakthroughs from signal transduction to cross-talk within plant hormones and environmental cues. Precursor messenger RNA (pre-mRNA) splicing enables plants to produce a series of functional un-related proteins and thus enhances the regulation flexibility. Plants take advantage of this strategy to modulate their proteome diversity under high ambient temperature and elicit developmental plasticity. In this review, we particularly focus on pre-mRNA splicing regulation underlying plant high temperature responses, and will shed new light on the understanding of post-transcriptional regulation on plant growth and development.
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Affiliation(s)
- Jingya Lin
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Ziqiang Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
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11
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Wolff H, Jakoby M, Stephan L, Koebke E, Hülskamp M. Heat Stress-Dependent Association of Membrane Trafficking Proteins With mRNPs Is Selective. FRONTIERS IN PLANT SCIENCE 2021; 12:670499. [PMID: 34249042 PMCID: PMC8264791 DOI: 10.3389/fpls.2021.670499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/27/2021] [Indexed: 05/03/2023]
Abstract
The Arabidopsis AAA ATPase SKD1 is essential for ESCRT-dependent endosomal sorting by mediating the disassembly of the ESCRTIII complex in an ATP-dependent manner. In this study, we show that SKD1 localizes to messenger ribonucleoprotein complexes upon heat stress. Consistent with this, the interactome of SKD1 revealed differential interactions under normal and stress conditions and included membrane transport proteins as well as proteins associated with RNA metabolism. Localization studies with selected interactome proteins revealed that not only RNA associated proteins but also several ESCRTIII and membrane trafficking proteins were recruited to messenger ribonucleoprotein granules after heat stress.
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Affiliation(s)
- Heike Wolff
- Cluster of Excellence on Plant Sciences (CEPLAS), Botanical Institute, Cologne University, Cologne, Germany
| | - Marc Jakoby
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Lisa Stephan
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Eva Koebke
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Martin Hülskamp
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
- *Correspondence: Martin Hülskamp
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12
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Robles-Luna G, Furman N, Barbarich MF, Carlotto N, Attorresi A, García ML, Kobayashi K. Interplay between potato virus X and RNA granules in Nicotiana benthamiana. Virus Res 2020; 276:197823. [PMID: 31765690 DOI: 10.1016/j.virusres.2019.197823] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/16/2019] [Accepted: 11/20/2019] [Indexed: 01/26/2023]
Abstract
Cytoplasmic RNA granules consist of microscopic agglomerates of mRNAs and proteins and occur when the translation is reversibly and temporally halted (stress granules, SGs) or mRNAs are targeted for decapping (processing bodies, PBs). The induction of RNA granules formation by virus infection is a common feature of mammalian cells. However, plant-virus systems still remain poorly characterized. In this work, the SG marker AtUBP1b was expressed in Nicotiana benthamiana plants to decipher how the virus infection of plant cells affects SG dynamics. We found that the hypoxia-induced SG assembly was substantially inhibited in Potato virus X (PVX)-infected cells. Furthermore, we determined that the expression of PVX movement protein TGBp1 by itself, mimics the inhibitory effect of PVX on SG formation under hypoxia. Importantly, overexpression of AtUBP1b showed inhibition of the PVX spreading, whereas the overexpression of the dominant negative AtUBP1brrm enhanced PVX spreding, indicating that AtUBP1b negatively affects PVX infection. Notably, PVX infection did not inhibit the formation of processing bodies (PBs), indicating PVX has distinct effects depending on the type of RNA granule. Our results suggest that SG inhibition could be part of the virus strategy to infect the plant.
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Affiliation(s)
- Gabriel Robles-Luna
- Instituto de Biotecnología y Biología Molecular (IBBM)-CONICET-UNLP, Calle 115 y 49 s/n (1900), Universidad Nacional de la Plata, Facultad de Ciencias Exactas, La Plata, Argentina.
| | - Nicolás Furman
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA, CONICET-UBA), Laboratorio de Agrobiotecnología, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular (FBMC), Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - María Florencia Barbarich
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA, CONICET-UBA), Laboratorio de Agrobiotecnología, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular (FBMC), Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - Nicolás Carlotto
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA, CONICET-UBA), Laboratorio de Agrobiotecnología, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular (FBMC), Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - Alejandra Attorresi
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) -CONICET- Partner Institute of the Max Planck Society, Argentina.
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular (IBBM)-CONICET-UNLP, Calle 115 y 49 s/n (1900), Universidad Nacional de la Plata, Facultad de Ciencias Exactas, La Plata, Argentina.
| | - Ken Kobayashi
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA, CONICET-UBA), Laboratorio de Agrobiotecnología, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular (FBMC), Universidad de Buenos Aires, Buenos Aires, Argentina.
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13
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Yeap WC, Namasivayam P, Ooi TEK, Appleton DR, Kulaveerasingam H, Ho CL. EgRBP42 from oil palm enhances adaptation to stress in Arabidopsis through regulation of nucleocytoplasmic transport of stress-responsive mRNAs. PLANT, CELL & ENVIRONMENT 2019; 42:1657-1673. [PMID: 30549047 DOI: 10.1111/pce.13503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 12/11/2018] [Indexed: 06/09/2023]
Abstract
Abiotic stress reduces plant growth and crop productivity. However, the mechanism underlying posttranscriptional regulations of stress response remains elusive. Herein, we report the posttranscriptional mechanism of nucleocytoplasmic RNA transport of stress-responsive transcripts mediated by EgRBP42, a heterogeneous nuclear ribonucleoprotein-like RNA-binding protein from oil palm, which could be necessary for rapid protein translation to confer abiotic stress tolerance in plants. Transgenic Arabidopsis overexpressing EgRBP42 showed early flowering through alteration of gene expression of flowering regulators and exhibited tolerance towards heat, cold, drought, flood, and salinity stresses with enhanced poststress recovery response by increasing the expression of its target stress-responsive genes. EgRBP42 harbours nucleocytoplasmic shuttling activity mediated by the nuclear localization signal and the M9-like domain of EgRBP42 and interacts directly with regulators in the nucleus, membrane, and the cytoplasm. EgRBP42 regulates the nucleocytoplasmic RNA transport of target stress-responsive transcripts through direct binding to their AG-rich motifs. Additionally, EgRBP42 transcript and protein induction by environmental stimuli are regulated at the transcriptional and posttranscriptional levels. Taken together, the posttranscriptional regulation of RNA transport mediated by EgRBP42 may change the stress-responsive protein profiles under abiotic stress conditions leading to a better adaptation of plants to environmental changes.
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Affiliation(s)
- Wan-Chin Yeap
- Sime Darby Plantation Berhad, Research and Development, Biotechnology and Breeding, Sime Darby Technology Centre Sdn. Bhd., Serdang, Malaysia
| | - Parameswari Namasivayam
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Tony Eng Keong Ooi
- Sime Darby Plantation Berhad, Research and Development, Biotechnology and Breeding, Sime Darby Technology Centre Sdn. Bhd., Serdang, Malaysia
| | - David Ross Appleton
- Sime Darby Plantation Berhad, Research and Development, Biotechnology and Breeding, Sime Darby Technology Centre Sdn. Bhd., Serdang, Malaysia
| | - Harikrishna Kulaveerasingam
- Sime Darby Plantation Berhad, Research and Development, Sime Darby Research Sdn Bhd, R&D Centre-Upstream, Kuala Langat, Malaysia
| | - Chai-Ling Ho
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
- Institute of Plantation Studies, Universiti Putra Malaysia, Serdang, Malaysia
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14
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Tang F, Chu L, Shu W, He X, Wang L, Lu M. Selection and validation of reference genes for quantitative expression analysis of miRNAs and mRNAs in Poplar. PLANT METHODS 2019; 15:35. [PMID: 30996729 PMCID: PMC6451301 DOI: 10.1186/s13007-019-0420-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 04/01/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) is a rapid and sensitive approach to identify miRNA and protein-coding gene expression in plants. However, because of the specially designated reverse transcription and shorter PCR products, very few reference genes have been identified for the quantitative analysis of miRNA expression in plants, and different internal reference genes are needed to normalize the expression of miRNAs and mRNA genes respectively. Therefore, it is particularly important to select the suitable common reference genes for normalization of quantitative PCR of miRNA and mRNA. RESULTS In this study, a modified reverse transcription PCR protocol was adopted for selecting and validating universal internal reference genes of mRNAs and miRNAs. Eight commonly used reference genes, four stably expressed novel genes in Populus tremula, three small noncoding RNAs and three conserved miRNAs were selected as candidate genes, and the stability of their expression was examined across a set of 38 tissue samples from four developmental stages of poplar clone 84K (Populus alba × Populus glandulosa). The expression stability of these candidate genes was evaluated systematically by four algorithms: geNorm, NormFinder, Bestkeeper and DeltaCt. The results showed that Eukaryotic initiation factor 4A III (EIF4A) and U6-2 were suitable for samples of the callus stage; U6-1 and U6-2 were best for the seedling stage; Protein phosphatase 2A-2 (PP2A-2) and U6-1 were best for the plant stage; and Protein phosphatase 2A-2 (PP2A-2) and Oligouridylate binding protein 1B (UBP) were the best reference genes in the adventitious root (AR) regeneration stage. CONCLUSIONS The purpose of this study was to identify the most appropriate reference genes for qRT-PCR of miRNAs and mRNAs in different tissues at several developmental stages in poplar. U6-1, EIF4A and PP2A-2 were the three most appropriate reference genes for qRT-PCR normalization of miRNAs and mRNAs during the plant regeneration process, and PP2A-2 and UBP represent the best reference genes in the AR regeneration stage of poplar. This work will benefit future studies of expression and function analysis of miRNAs and their target genes in poplar.
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Affiliation(s)
- Fang Tang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 China
| | - Liwei Chu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| | - Wenbo Shu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xuejiao He
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| | - Lijuan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 China
| | - Mengzhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 China
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15
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Tian L, Chou HL, Zhang L, Hwang SK, Starkenburg SR, Doroshenk KA, Kumamaru T, Okita TW. RNA-Binding Protein RBP-P Is Required for Glutelin and Prolamine mRNA Localization in Rice Endosperm Cells. THE PLANT CELL 2018; 30:2529-2552. [PMID: 30190374 PMCID: PMC6241268 DOI: 10.1105/tpc.18.00321] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 08/08/2018] [Accepted: 08/31/2018] [Indexed: 05/18/2023]
Abstract
In developing rice (Oryza sativa) endosperm, mRNAs of the major storage proteins, glutelin and prolamine, are transported and anchored to distinct subdomains of the cortical endoplasmic reticulum. RNA binding protein RBP-P binds to both glutelin and prolamine mRNAs, suggesting a role in some aspect of their RNA metabolism. Here, we show that rice lines expressing mutant RBP-P mislocalize both glutelin and prolamine mRNAs. Different mutant RBP-P proteins exhibited varying degrees of reduced RNA binding and/or protein-protein interaction properties, which may account for the mislocalization of storage protein RNAs. In addition, partial loss of RBP-P function conferred a broad phenotypic variation ranging from dwarfism, chlorophyll deficiency, and sterility to late flowering and low spikelet fertility. Transcriptome analysis highlighted the essential role of RBP-P in regulating storage protein genes and several essential biological processes during grain development. Overall, our data demonstrate the significant roles of RBP-P in glutelin and prolamine mRNA localization and in the regulation of genes important for plant growth and development through its RNA binding activity and cooperative regulation with interacting proteins.
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Affiliation(s)
- Li Tian
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
| | - Hong-Li Chou
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Laining Zhang
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
| | - Seon-Kap Hwang
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
| | | | - Kelly A Doroshenk
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
| | | | - Thomas W Okita
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
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16
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Wang G, Jiang H, Del Toro de León G, Martinez G, Köhler C. Sequestration of a Transposon-Derived siRNA by a Target Mimic Imprinted Gene Induces Postzygotic Reproductive Isolation in Arabidopsis. Dev Cell 2018; 46:696-705.e4. [PMID: 30122632 DOI: 10.1016/j.devcel.2018.07.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/08/2018] [Accepted: 07/18/2018] [Indexed: 12/20/2022]
Abstract
Genomic imprinting is an epigenetic phenomenon occurring in mammals and flowering plants, causing genes to be expressed depending on their parent of origin. In plants, genomic imprinting is mainly confined to the endosperm, a nutritive tissue supporting embryo growth, similar to the placenta in mammals. Here, we show that the paternally expressed imprinted gene PEG2 transcript sequesters the transposable element (TE)-derived small interfering RNA (siRNA) siRNA854 in the endosperm. siRNA854 is present in the vegetative cell of pollen and transferred to the central cell of the female gametophyte after fertilization, where it is captured by PEG2. Depletion of siRNA854 as a consequence of increased PEG2 transcript levels establishes a reproductive barrier and prevents successful hybridizations between plants differing in chromosome number (ploidy). Thus, the balance of a male gamete accumulating TE-derived siRNA and a paternally expressed imprinted gene regulate triploid seed viability, revealing a transgenerational speciation mechanism.
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Affiliation(s)
- Guifeng Wang
- Department of Plant Biology, Swedish University of Agricultural Sciences, Linnean Center for Plant Biology, Uppsala 75007, Sweden; Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Hua Jiang
- Department of Plant Biology, Swedish University of Agricultural Sciences, Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Gerardo Del Toro de León
- Department of Plant Biology, Swedish University of Agricultural Sciences, Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - German Martinez
- Department of Plant Biology, Swedish University of Agricultural Sciences, Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Swedish University of Agricultural Sciences, Linnean Center for Plant Biology, Uppsala 75007, Sweden.
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17
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Govender N, Senan S, Mohamed-Hussein ZA, Wickneswari R. A gene co-expression network model identifies yield-related vicinity networks in Jatropha curcas shoot system. Sci Rep 2018; 8:9211. [PMID: 29907786 PMCID: PMC6003958 DOI: 10.1038/s41598-018-27493-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 06/04/2018] [Indexed: 11/18/2022] Open
Abstract
The plant shoot system consists of reproductive organs such as inflorescences, buds and fruits, and the vegetative leaves and stems. In this study, the reproductive part of the Jatropha curcas shoot system, which includes the aerial shoots, shoots bearing the inflorescence and inflorescence were investigated in regard to gene-to-gene interactions underpinning yield-related biological processes. An RNA-seq based sequencing of shoot tissues performed on an Illumina HiSeq. 2500 platform generated 18 transcriptomes. Using the reference genome-based mapping approach, a total of 64 361 genes was identified in all samples and the data was annotated against the non-redundant database by the BLAST2GO Pro. Suite. After removing the outlier genes and samples, a total of 12 734 genes across 17 samples were subjected to gene co-expression network construction using petal, an R library. A gene co-expression network model built with scale-free and small-world properties extracted four vicinity networks (VNs) with putative involvement in yield-related biological processes as follow; heat stress tolerance, floral and shoot meristem differentiation, biosynthesis of chlorophyll molecules and laticifers, cell wall metabolism and epigenetic regulations. Our VNs revealed putative key players that could be adapted in breeding strategies for J. curcas shoot system improvements.
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Affiliation(s)
- Nisha Govender
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
- Center for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
| | - Siju Senan
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Zeti-Azura Mohamed-Hussein
- Center for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Ratnam Wickneswari
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
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18
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Köster T, Marondedze C, Meyer K, Staiger D. RNA-Binding Proteins Revisited - The Emerging Arabidopsis mRNA Interactome. TRENDS IN PLANT SCIENCE 2017; 22:512-526. [PMID: 28412036 DOI: 10.1016/j.tplants.2017.03.009] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/10/2017] [Accepted: 03/09/2017] [Indexed: 06/07/2023]
Abstract
RNA-protein interaction is an important checkpoint to tune gene expression at the RNA level. Global identification of proteins binding in vivo to mRNA has been possible through interactome capture - where proteins are fixed to target RNAs by UV crosslinking and purified through affinity capture of polyadenylated RNA. In Arabidopsis over 500 RNA-binding proteins (RBPs) enriched in UV-crosslinked samples have been identified. As in mammals and yeast, the mRNA interactomes came with a few surprises. For example, a plethora of the proteins caught on RNA had not previously been linked to RNA-mediated processes, for example proteins of intermediary metabolism. Thus, the studies provide unprecedented insights into the composition of the mRNA interactome, highlighting the complexity of RNA-mediated processes.
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Affiliation(s)
- Tino Köster
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Claudius Marondedze
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Cambridge, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Katja Meyer
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Dorothee Staiger
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany.
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19
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Koguchi M, Yamasaki K, Hirano T, Sato MH. Vascular plant one-zinc-finger protein 2 is localized both to the nucleus and stress granules under heat stress in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2017; 12:e1295907. [PMID: 28277968 PMCID: PMC5399895 DOI: 10.1080/15592324.2017.1295907] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
VASCULAR PLANT ONE-ZINC FINGER (VOZ)1/and VOZ2 have an ability to bind to the specific cis-element in the AVP1 promoter of Arabidopsis, which function on the PhyB-dependent flowering and possibly in various stress responses as potential transcription factors, although nuclear localization of VOZ proteins is still unclear. In this study, we found that VOZ2 is dispersed throughout the cytoplasm under normal growth conditions, whereas VOZ2 is transferred not only to the nucleus but also to the cytoplasmic foci under heat stress conditions. The VOZ2 foci predominantly co-localized with a marker of stress granules (SGs), which were cytoplasmic granular structures for mRNA storage and decay under abiotic stress conditions. We also demonstrated that GFP-VOZ2 with a nuclear localization signal was rapidly degraded via the ubiquitin/proteasome pathway under the heat stress conditions. Also, stress-related expression of DREB2A in the voz1voz2 mutant was significantly upregulated by heat stress as compared with that in the wild-type Arabidopsis. Our results suggest that VOZ2 is localized to SGs and nucleus under heat stress conditions, and functions as a transcriptional repressor of DREB2A in Arabidopsis.
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Affiliation(s)
- Misaki Koguchi
- Laboratory of Cellular Dynamics, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo-nakaragi-cho, Sakyo-ku, Kyoto, Japan
| | - Kanako Yamasaki
- Laboratory of Cellular Dynamics, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo-nakaragi-cho, Sakyo-ku, Kyoto, Japan
| | - Tomoko Hirano
- Laboratory of Cellular Dynamics, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo-nakaragi-cho, Sakyo-ku, Kyoto, Japan
| | - Masa H. Sato
- Laboratory of Cellular Dynamics, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo-nakaragi-cho, Sakyo-ku, Kyoto, Japan
- CONTACT Masa H. Sato Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo-nakaragi-cho, Sakyo-ku, Kyoto 606-8522, Japan
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20
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Nguyen CC, Nakaminami K, Matsui A, Watanabe S, Kanno Y, Seo M, Seki M. Overexpression of oligouridylate binding protein 1b results in ABA hypersensitivity. PLANT SIGNALING & BEHAVIOR 2017; 12:e1282591. [PMID: 28112571 PMCID: PMC5351729 DOI: 10.1080/15592324.2017.1282591] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Oligouridylate binding protein 1b (UBP1b), a marker protein of plant stress granules (SGs), plays a role in heat stress tolerance in plants. A previous microarray analysis revealed that the expression of several ABA signaling-related genes is higher in UBP1b-overexpressing Arabidopsis plants (UBP1b-ox) subjected to both non-stressed and heat stress conditions. Root elongation and seed germination assays demonstrated that UBP1b-ox exhibited hypersensitivity to ABA. RT-qPCR analysis confirmed that mitogen-activated protein kinase (MAPK) cascade genes, such as MPK3, MKK4, and MKK9 were upregulated in UBP1b-ox plants. ABA receptor genes, including PYL5 and PYL6, were also upregulated in UBP1b-ox plants. mRNA of WRKY33 - a downstream gene of MPK3 and an upstream gene of ethylene biosynthesis, exhibited high levels of accumulation, although the level of endogenous ABA was not significantly different between UBP1b-ox and control plants. In addition, RNA decay analysis revealed that WRKY33 was more stable in UBP1b-ox plants, indicating that the mRNA of WRKY33 was protected within UBP1b SGs. Collectively, these data demonstrate that UBP1b plays an important role in plant response to ABA.
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Affiliation(s)
- Cam Chau Nguyen
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Kentaro Nakaminami
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, Japan
| | - Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, Japan
| | - Shunsuke Watanabe
- Dormancy and Adaptation Research Unit, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, Japan
| | - Yuri Kanno
- Dormancy and Adaptation Research Unit, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, Japan
| | - Mitsunori Seo
- Dormancy and Adaptation Research Unit, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
- CREST, JST, Honcho, Kawaguchi, Saitama, Japan
- CONTACT Motoaki Seki Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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21
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Zhang Z, Boonen K, Ferrari P, Schoofs L, Janssens E, van Noort V, Rolland F, Geuten K. UV crosslinked mRNA-binding proteins captured from leaf mesophyll protoplasts. PLANT METHODS 2016; 12:42. [PMID: 27822292 PMCID: PMC5093948 DOI: 10.1186/s13007-016-0142-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 10/11/2016] [Indexed: 05/29/2023]
Abstract
BACKGROUND The complexity of RNA regulation is one of the current frontiers in animal and plant molecular biology research. RNA-binding proteins (RBPs) are characteristically involved in post-transcriptional gene regulation through interaction with RNA. Recently, the mRNA-bound proteome of mammalian cell lines has been successfully cataloged using a new method called interactome capture. This method relies on UV crosslinking of proteins to RNA, purifying the mRNA using complementary oligo-dT beads and identifying the crosslinked proteins using mass spectrometry. We describe here an optimized system of mRNA interactome capture for Arabidopsis thaliana leaf mesophyll protoplasts, a cell type often used in functional cellular assays. RESULTS We established the conditions for optimal protein yield, namely the amount of starting tissue, the duration of UV irradiation and the effect of UV intensity. We demonstrated high efficiency mRNA-protein pull-down by oligo-d(T)25 bead capture. Proteins annotated to have RNA-binding capacity were overrepresented in the obtained medium scale mRNA-bound proteome, indicating the specificity of the method and providing in vivo UV crosslinking experimental evidence for several candidate RBPs from leaf mesophyll protoplasts. CONCLUSIONS The described method, applied to plant cells, allows identifying proteins as having the capacity to bind mRNA directly. The method can now be scaled and applied to other plant cell types and species to contribute to the comprehensive description of the RBP proteome of plants.
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Affiliation(s)
- Zhicheng Zhang
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Louvain, Belgium
| | - Kurt Boonen
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Louvain, Belgium
| | - Piero Ferrari
- Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200d, 3001 Louvain, Belgium
| | - Liliane Schoofs
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Louvain, Belgium
| | - Ewald Janssens
- Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200d, 3001 Louvain, Belgium
| | - Vera van Noort
- Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 22, 3001 Louvain, Belgium
| | - Filip Rolland
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Louvain, Belgium
| | - Koen Geuten
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Louvain, Belgium
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22
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Lokdarshi A, Conner WC, McClintock C, Li T, Roberts DM. Arabidopsis CML38, a Calcium Sensor That Localizes to Ribonucleoprotein Complexes under Hypoxia Stress. PLANT PHYSIOLOGY 2016; 170:1046-59. [PMID: 26634999 PMCID: PMC4734562 DOI: 10.1104/pp.15.01407] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/30/2015] [Indexed: 05/18/2023]
Abstract
During waterlogging and the associated oxygen deprivation stress, plants respond by the induction of adaptive programs, including the redirected expression of gene networks toward the synthesis of core hypoxia-response proteins. Among these core response proteins in Arabidopsis (Arabidopsis thaliana) is the calcium sensor CML38, a protein related to regulator of gene silencing calmodulin-like proteins (rgsCaMs). CML38 transcripts are up-regulated more than 300-fold in roots within 6 h of hypoxia treatment. Transfer DNA insertional mutants of CML38 show an enhanced sensitivity to hypoxia stress, with lowered survival and more severe inhibition of root and shoot growth. By using yellow fluorescent protein (YFP) translational fusions, CML38 protein was found to be localized to cytosolic granule structures similar in morphology to hypoxia-induced stress granules. Immunoprecipitation of CML38 from the roots of hypoxia-challenged transgenic plants harboring CML38pro::CML38:YFP followed by liquid chromatography-tandem mass spectrometry analysis revealed the presence of protein targets associated with messenger RNA ribonucleoprotein (mRNP) complexes including stress granules, which are known to accumulate as messenger RNA storage and triage centers during hypoxia. This finding is further supported by the colocalization of CML38 with the mRNP stress granule marker RNA Binding Protein 47 (RBP47) upon cotransfection of Nicotiana benthamiana leaves. Ruthenium Red treatment results in the loss of CML38 signal in cytosolic granules, suggesting that calcium is necessary for stress granule association. These results confirm that CML38 is a core hypoxia response calcium sensor protein and suggest that it serves as a potential calcium signaling target within stress granules and other mRNPs that accumulate during flooding stress responses.
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Affiliation(s)
- Ansul Lokdarshi
- Department of Biochemistry and Cellular and Molecular Biology (A.L., W.C.C., C.M., D.M.R.) and Program in Genome Science and Technology (T.L., D.M.R.), University of Tennessee, Knoxville, Tennessee 37996
| | - W Craig Conner
- Department of Biochemistry and Cellular and Molecular Biology (A.L., W.C.C., C.M., D.M.R.) and Program in Genome Science and Technology (T.L., D.M.R.), University of Tennessee, Knoxville, Tennessee 37996
| | - Carlee McClintock
- Department of Biochemistry and Cellular and Molecular Biology (A.L., W.C.C., C.M., D.M.R.) and Program in Genome Science and Technology (T.L., D.M.R.), University of Tennessee, Knoxville, Tennessee 37996
| | - Tian Li
- Department of Biochemistry and Cellular and Molecular Biology (A.L., W.C.C., C.M., D.M.R.) and Program in Genome Science and Technology (T.L., D.M.R.), University of Tennessee, Knoxville, Tennessee 37996
| | - Daniel M Roberts
- Department of Biochemistry and Cellular and Molecular Biology (A.L., W.C.C., C.M., D.M.R.) and Program in Genome Science and Technology (T.L., D.M.R.), University of Tennessee, Knoxville, Tennessee 37996
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23
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Nguyen CC, Nakaminami K, Matsui A, Kobayashi S, Kurihara Y, Toyooka K, Tanaka M, Seki M. Oligouridylate Binding Protein 1b Plays an Integral Role in Plant Heat Stress Tolerance. FRONTIERS IN PLANT SCIENCE 2016; 7:853. [PMID: 27379136 PMCID: PMC4911357 DOI: 10.3389/fpls.2016.00853] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/31/2016] [Indexed: 05/03/2023]
Abstract
Stress granules (SGs), which are formed in the plant cytoplasm under stress conditions, are transient dynamic sites (particles) for mRNA storage. SGs are actively involved in protecting mRNAs from degradation. Oligouridylate binding protein 1b (UBP1b) is a component of SGs. The formation of microscopically visible cytoplasmic foci, referred to as UBP1b SG, was induced by heat treatment in UBP1b-overexpressing Arabidopsis plants (UBP1b-ox). A detailed understanding of the function of UBP1b, however, is still not clear. UBP1b-ox plants displayed increased heat tolerance, relative to control plants, while ubp1b mutants were more sensitive to heat stress than control plants. Microarray analysis identified 117 genes whose expression was heat-inducible and higher in the UBP1b-ox plants. RNA decay analysis was performed using cordycepin, a transcriptional inhibitor. In order to determine if those genes serve as targets of UBP1b, the rate of RNA degradation of a DnaJ heat shock protein and a stress-associated protein (AtSAP3) in UBP1b-ox plants was slower than in control plants; indicating that the mRNAs of these genes were protected within the UBP1b SG granule. Collectively, these data demonstrate that UBP1b plays an integral role in heat stress tolerance in plants.
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Affiliation(s)
- Cam Chau Nguyen
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- Kihara Institute for Biological Research, Yokohama City UniversityYokohama, Japan
| | - Kentaro Nakaminami
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Shuhei Kobayashi
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- Kihara Institute for Biological Research, Yokohama City UniversityYokohama, Japan
| | - Yukio Kurihara
- Synthetic Genomics Research Group, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Kiminori Toyooka
- Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- Kihara Institute for Biological Research, Yokohama City UniversityYokohama, Japan
- Core Research for Evolutional Science and Technology, Japan Science and TechnologyKawaguchi, Japan
- *Correspondence: Motoaki Seki
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24
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Nanjo Y, Jang HY, Kim HS, Hiraga S, Woo SH, Komatsu S. Analyses of flooding tolerance of soybean varieties at emergence and varietal differences in their proteomes. PHYTOCHEMISTRY 2014; 106:25-36. [PMID: 25053003 DOI: 10.1016/j.phytochem.2014.06.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 06/05/2014] [Accepted: 06/06/2014] [Indexed: 06/03/2023]
Abstract
Flooding of fields due to heavy and/or continuous rainfall influences soybean production. To identify soybean varieties with flooding tolerance at the seedling emergence stage, 128 soybean varieties were evaluated using a flooding tolerance index, which is based on plant survival rates, the lack of apparent damage and lateral root development, and post-flooding radicle elongation rate. The soybean varieties were ranked according to their flooding tolerance index, and it was found that the tolerance levels of soybean varieties exhibit a continuum of differences between varieties. Subsequently, tolerant, moderately tolerant and sensitive varieties were selected and subjected to comparative proteomic analysis to clarify the tolerance mechanism. Proteomic analysis of the radicles, combined with correlation analysis, showed that the ratios of RNA binding/processing related proteins and flooding stress indicator proteins were significantly correlated with flooding tolerance index. The RNA binding/processing related proteins were positively correlated in untreated soybeans, whereas flooding stress indicator proteins were negatively correlated in flooded soybeans. These results suggest that flooding tolerance is regulated by mechanisms through multiple factors and is associated with abundance levels of the identified proteins.
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Affiliation(s)
- Yohei Nanjo
- NARO Institute of Crop Science, Tsukuba 305-8518, Japan.
| | - Hee-Young Jang
- Chungbuk National University, Cheong-ju 361-763, Republic of Korea
| | - Hong-Sig Kim
- Chungbuk National University, Cheong-ju 361-763, Republic of Korea
| | - Susumu Hiraga
- NARO Institute of Crop Science, Tsukuba 305-8518, Japan
| | - Sun-Hee Woo
- Chungbuk National University, Cheong-ju 361-763, Republic of Korea
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25
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Yeap WC, Namasivayam P, Ho CL. HnRNP-like proteins as post-transcriptional regulators. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 227:90-100. [PMID: 25219311 DOI: 10.1016/j.plantsci.2014.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 07/17/2014] [Accepted: 07/18/2014] [Indexed: 05/23/2023]
Abstract
Plant cells contain a diverse repertoire of RNA-binding proteins (RBPs) that coordinate a network of post-transcriptional regulation. RBPs govern diverse developmental processes by modulating the gene expression of specific transcripts. Recent gene annotation and RNA sequencing clearly showed that heterogeneous nuclear ribonucleoprotein (hnRNP)-like proteins which form a family of RBPs, are also expressed in higher plants and serve specific plant functions. In addition to their involvement in post-transcriptional regulation from mRNA capping to translation, they are also involved in telomere regulation, gene silencing and regulation in chloroplast. Here, we review the involvement of plant hnRNP-like proteins in post-transcription regulation of RNA processes and their functional roles in control of plant developmental processes especially plant-specific functions including flowering, chloroplastic-specific mRNA regulation, long-distance phloem transportation and plant responses to environmental stresses.
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Affiliation(s)
- Wan-Chin Yeap
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Sime Darby Technology Centre Sdn. Bhd., 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Parameswari Namasivayam
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Chai-Ling Ho
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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26
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Doroshenk KA, Tian L, Crofts AJ, Kumamaru T, Okita TW. Characterization of RNA binding protein RBP-P reveals a possible role in rice glutelin gene expression and RNA localization. PLANT MOLECULAR BIOLOGY 2014; 85:381-394. [PMID: 24682961 DOI: 10.1007/s11103-014-0191-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 03/22/2014] [Indexed: 06/03/2023]
Abstract
RNA binding proteins (RBPs) play an important role in mRNA metabolism including synthesis, maturation, transport, localization, and stability. In developing rice seeds, RNAs that code for the major storage proteins are transported to specific domains of the cortical endoplasmic reticulum (ER) by a regulated mechanism requiring RNA cis-localization elements, or zipcodes. Putative trans-acting RBPs that recognize prolamine RNA zipcodes required for restricted localization to protein body-ER have previously been identified. Here, we describe the identification of RBP-P using a Northwestern blot approach as an RBP that recognizes and binds to glutelin zipcode RNA, which is required for proper RNA localization to cisternal-ER. RBP-P protein expression coincides with that of glutelin during seed maturation and is localized to both the nucleus and cytosol. RNA-immunoprecipitation and subsequent RT-PCR analysis further demonstrated that RBP-P interacts with glutelin RNAs. In vitro RNA-protein UV-crosslinking assays showed that recombinant RBP-P binds strongly to glutelin mRNA, and in particular, 3' UTR and zipcode RNA. RBP-P also exhibited strong binding activity to a glutelin intron sequence, suggesting that RBP-P might participate in mRNA splicing. Overall, these results support a multifunctional role for RBP-P in glutelin mRNA metabolism, perhaps in nuclear pre-mRNA splicing and cytosolic localization to the cisternal-ER.
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Affiliation(s)
- Kelly A Doroshenk
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, USA
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27
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Nozawa A, Miwa K, Kobayashi M, Fujiwara T. Isolation ofArabidopsis thalianacDNAs That Confer Yeast Boric Acid Tolerance. Biosci Biotechnol Biochem 2014; 70:1724-30. [PMID: 16861809 DOI: 10.1271/bbb.60065] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
An Arabidopsis thaliana cDNA library was introduced into a Saccharomyces cerevisiae mutant that lacks ScBOR1 (YNL275W), a boron (B) efflux transporter. Five cDNAs were identified that confer tolerance to high boric acid. The nucleotide sequence analysis identified the clones as a polyadenylate-binding protein, AtPAB2; a ribosomal small subunit protein, AtRPS20B; an RNA-binding protein, AtRBP47c'; and two Myb transcription factors, AtMYB13 and AtMYB68. The expression of these five genes also conferred boric acid tolerance on wild-type yeast. Two yeast genes, ScRPS20 and ScHRB1, that are similar to the isolated clones, were necessary for this boric acid tolerance. The possible roles of these A. thaliana and S. cerevisiae genes in boric acid tolerance are discussed.
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Affiliation(s)
- Akira Nozawa
- Precursory Research for Embryonic Science and Technology, Kawaguchi, Saitama 332-0012, Japan
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28
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Mehrotra R, Bhalothia P, Bansal P, Basantani MK, Bharti V, Mehrotra S. Abscisic acid and abiotic stress tolerance - different tiers of regulation. JOURNAL OF PLANT PHYSIOLOGY 2014; 171:486-96. [PMID: 24655384 DOI: 10.1016/j.jplph.2013.12.007] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 12/12/2013] [Accepted: 12/13/2013] [Indexed: 05/21/2023]
Abstract
Abiotic stresses affect plant growth, metabolism and sustainability in a significant way and hinder plant productivity. Plants combat these stresses in myriad ways. The analysis of the mechanisms underlying abiotic stress tolerance has led to the identification of a highly complex, yet tightly regulated signal transduction pathway consisting of phosphatases, kinases, transcription factors and other regulatory elements. It is becoming increasingly clear that also epigenetic processes cooperate in a concerted manner with ABA-mediated gene expression in combating stress conditions. Dynamic stress-induced mechanisms, involving changes in the apoplastic pool of ABA, are transmitted by a chain of phosphatases and kinases, resulting in the expression of stress inducible genes. Processes involving DNA methylation and chromatin modification as well as post transcriptional, post translational and epigenetic control mechanisms, forming multiple tiers of regulation, regulate this gene expression. With recent advances in transgenic technology, it has now become possible to engineer plants expressing stress-inducible genes under the control of an inducible promoter, enhancing their ability to withstand adverse conditions. This review briefly discusses the synthesis of ABA, components of the ABA signal transduction pathway and the plants' responses at the genetic and epigenetic levels. It further focuses on the role of RNAs in regulating stress responses and various approaches to develop stress-tolerant transgenic plants.
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Affiliation(s)
- Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Sciences, Pilani, Rajasthan 333031, India; G(o) Unit, Okinawa Institute of Science and Technology, 1919-1, Onnason, Okinawa, Japan
| | - Purva Bhalothia
- Department of Biological Sciences, Birla Institute of Technology & Sciences, Pilani, Rajasthan 333031, India
| | - Prashali Bansal
- Department of Biological Sciences, Birla Institute of Technology & Sciences, Pilani, Rajasthan 333031, India; Cancer Science Institute, National University of Singapore, Singapore, Singapore
| | - Mahesh Kumar Basantani
- Division of Endocrinology, University of Pittsburgh, 200 Lothrop Street, BST E1140, Pittsburgh, PA 15261, USA
| | - Vandana Bharti
- Department of Biotechnology, St. Columba's College, Vinoba Bhave University, Hazaribagh, India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Sciences, Pilani, Rajasthan 333031, India.
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29
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Selective mRNA sequestration by OLIGOURIDYLATE-BINDING PROTEIN 1 contributes to translational control during hypoxia in Arabidopsis. Proc Natl Acad Sci U S A 2014; 111:2373-8. [PMID: 24469793 DOI: 10.1073/pnas.1314851111] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Low oxygen stress dynamically regulates the translation of cellular mRNAs as a means of energy conservation in seedlings of Arabidopsis thaliana. Most of the highly hypoxia-induced mRNAs are recruited to polysomes and actively translated, whereas other cellular mRNAs become translationally inactive and are either targeted for stabilization or degradation. Here we identify the involvement of OLIGOURIDYLATE BINDING PROTEIN 1 (UBP1), a triple RNA Recognition Motif protein, in dynamic and reversible aggregation of translationally repressed mRNAs during hypoxia. Mutation or down-regulation of UBP1C interferes with seedling establishment and reduces survival of low oxygen stress. By use of messenger ribonucleoprotein (mRNP) immunopurification, we show that UBP1C constitutively binds a subpopulation of mRNAs characterized by uracil-rich 3'-untranslated regions under normoxic conditions. During hypoxia, UBP1C association with non-uracil-rich mRNAs is enhanced concomitant with its aggregation into microscopically visible cytoplasmic foci, referred to as UBP1 stress granules (SGs). This UBP1C-mRNA association occurs as global levels of protein synthesis decline. Upon reoxygenation, rapid UBP1 SG disaggregation coincides with the return of the stabilized mRNAs to polysomes. The mRNAs that are highly induced and translated during hypoxia largely circumvent UBP1C sequestration. Thus, UBP1 is established as a component of dynamically assembled cytoplasmic mRNPs that sequester mRNAs that are poorly translated during a transient low energy stress.
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30
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Akua T, Shaul O. The Arabidopsis thaliana MHX gene includes an intronic element that boosts translation when localized in a 5' UTR intron. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:4255-70. [PMID: 24006416 PMCID: PMC3808313 DOI: 10.1093/jxb/ert235] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The mechanisms that underlie the ability of some introns to increase gene expression, a phenomenon called intron-mediated enhancement (IME), are not fully understood. It is also not known why introns localized in the 5'-untranslated region (5' UTR) are considerably longer than downstream eukaryotic introns. It was hypothesized that this extra length results from the presence of some functional intronic elements. However, deletion analyses studies carried out thus far were unable to identify specific intronic regions necessary for IME. Using deletion analysis and a gain-of-function approach, an internal element that considerably increases translational efficiency, without affecting splicing, was identified in the 5' UTR intron of the Arabidopsis thaliana MHX gene. Moreover, the ability of this element to enhance translation was diminished by a minor downstream shift in the position of introns containing it from the 5' UTR into the coding sequence. These data suggest that some of the extra length of 5' UTR introns results from the presence of elements that enhance translation, and, moreover, from the ability of 5' UTR introns to provide preferable platforms for such elements over downstream introns. The impact of the identified intronic element on translational efficiency was augmented upon removal of neighbouring intronic elements. Interference between different intronic elements had not been reported thus far. This interference may support the bioinformatics-based idea that some of the extra sequence of 5' UTR introns is also necessary for separating different functional intronic elements.
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Affiliation(s)
- Tsofit Akua
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Orit Shaul
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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31
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Staiger D, Brown JWS. Alternative splicing at the intersection of biological timing, development, and stress responses. THE PLANT CELL 2013. [PMID: 24179132 DOI: 10.1105/tcp.113.117523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
High-throughput sequencing for transcript profiling in plants has revealed that alternative splicing (AS) affects a much higher proportion of the transcriptome than was previously assumed. AS is involved in most plant processes and is particularly prevalent in plants exposed to environmental stress. The identification of mutations in predicted splicing factors and spliceosomal proteins that affect cell fate, the circadian clock, plant defense, and tolerance/sensitivity to abiotic stress all point to a fundamental role of splicing/AS in plant growth, development, and responses to external cues. Splicing factors affect the AS of multiple downstream target genes, thereby transferring signals to alter gene expression via splicing factor/AS networks. The last two to three years have seen an ever-increasing number of examples of functional AS. At a time when the identification of AS in individual genes and at a global level is exploding, this review aims to bring together such examples to illustrate the extent and importance of AS, which are not always obvious from individual publications. It also aims to ensure that plant scientists are aware that AS is likely to occur in the genes that they study and that dynamic changes in AS and its consequences need to be considered routinely.
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Affiliation(s)
- Dorothee Staiger
- Molecular Cell Physiology, Bielefeld University, D33615 Bielefeld, Germany
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32
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Reddy AS, Marquez Y, Kalyna M, Barta A. Complexity of the alternative splicing landscape in plants. THE PLANT CELL 2013; 25:3657-83. [PMID: 24179125 PMCID: PMC3877793 DOI: 10.1105/tpc.113.117523] [Citation(s) in RCA: 516] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Revised: 09/27/2013] [Accepted: 10/08/2013] [Indexed: 05/18/2023]
Abstract
Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) from multiexon genes allows organisms to increase their coding potential and regulate gene expression through multiple mechanisms. Recent transcriptome-wide analysis of AS using RNA sequencing has revealed that AS is highly pervasive in plants. Pre-mRNAs from over 60% of intron-containing genes undergo AS to produce a vast repertoire of mRNA isoforms. The functions of most splice variants are unknown. However, emerging evidence indicates that splice variants increase the functional diversity of proteins. Furthermore, AS is coupled to transcript stability and translation through nonsense-mediated decay and microRNA-mediated gene regulation. Widespread changes in AS in response to developmental cues and stresses suggest a role for regulated splicing in plant development and stress responses. Here, we review recent progress in uncovering the extent and complexity of the AS landscape in plants, its regulation, and the roles of AS in gene regulation. The prevalence of AS in plants has raised many new questions that require additional studies. New tools based on recent technological advances are allowing genome-wide analysis of RNA elements in transcripts and of chromatin modifications that regulate AS. Application of these tools in plants will provide significant new insights into AS regulation and crosstalk between AS and other layers of gene regulation.
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Affiliation(s)
- Anireddy S.N. Reddy
- Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
- Address correspondence to
| | - Yamile Marquez
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
| | - Maria Kalyna
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
| | - Andrea Barta
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
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33
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Staiger D, Brown JW. Alternative splicing at the intersection of biological timing, development, and stress responses. THE PLANT CELL 2013; 25:3640-56. [PMID: 24179132 PMCID: PMC3877812 DOI: 10.1105/tpc.113.113803] [Citation(s) in RCA: 425] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 05/15/2013] [Accepted: 10/08/2013] [Indexed: 05/18/2023]
Abstract
High-throughput sequencing for transcript profiling in plants has revealed that alternative splicing (AS) affects a much higher proportion of the transcriptome than was previously assumed. AS is involved in most plant processes and is particularly prevalent in plants exposed to environmental stress. The identification of mutations in predicted splicing factors and spliceosomal proteins that affect cell fate, the circadian clock, plant defense, and tolerance/sensitivity to abiotic stress all point to a fundamental role of splicing/AS in plant growth, development, and responses to external cues. Splicing factors affect the AS of multiple downstream target genes, thereby transferring signals to alter gene expression via splicing factor/AS networks. The last two to three years have seen an ever-increasing number of examples of functional AS. At a time when the identification of AS in individual genes and at a global level is exploding, this review aims to bring together such examples to illustrate the extent and importance of AS, which are not always obvious from individual publications. It also aims to ensure that plant scientists are aware that AS is likely to occur in the genes that they study and that dynamic changes in AS and its consequences need to be considered routinely.
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Affiliation(s)
- Dorothee Staiger
- Molecular Cell Physiology, Bielefeld University, D33615 Bielefeld, Germany
- Institute for Genome Research and Systems Biology, CeBiTec, D33615 Bielefeld, Germany
| | - John W.S. Brown
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie DD2 5DA, Scotland, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie DD2 5DA, Scotland, United Kingdom
- Address correspondence to
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34
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Streitner C, Köster T, Simpson CG, Shaw P, Danisman S, Brown JWS, Staiger D. An hnRNP-like RNA-binding protein affects alternative splicing by in vivo interaction with transcripts in Arabidopsis thaliana. Nucleic Acids Res 2012; 40:11240-55. [PMID: 23042250 PMCID: PMC3526319 DOI: 10.1093/nar/gks873] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Alternative splicing (AS) of pre-mRNAs is an important regulatory mechanism shaping the transcriptome. In plants, only few RNA-binding proteins are known to affect AS. Here, we show that the glycine-rich RNA-binding protein AtGRP7 influences AS in Arabidopsis thaliana. Using a high-resolution RT–PCR-based AS panel, we found significant changes in the ratios of AS isoforms for 59 of 288 analyzed AS events upon ectopic AtGRP7 expression. In particular, AtGRP7 affected the choice of alternative 5′ splice sites preferentially. About half of the events are also influenced by the paralog AtGRP8, indicating that AtGRP7 and AtGRP8 share a network of downstream targets. For 10 events, the AS patterns were altered in opposite directions in plants with elevated AtGRP7 level or lacking AtGRP7. Importantly, RNA immunoprecipitation from plant extracts showed that several transcripts are bound by AtGRP7 in vivo and indeed represent direct targets. Furthermore, the effect of AtGRP7 on these AS events was abrogated by mutation of a single arginine that is required for its RNA-binding activity. This indicates that AtGRP7 impacts AS of these transcripts via direct interaction. As several of the AS events are also controlled by other splicing regulators, our data begin to provide insights into an AS network in Arabidopsis.
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35
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Yeap WC, Ooi TEK, Namasivayam P, Kulaveerasingam H, Ho CL. EgRBP42 encoding an hnRNP-like RNA-binding protein from Elaeis guineensis Jacq. is responsive to abiotic stresses. PLANT CELL REPORTS 2012; 31:1829-1843. [PMID: 22699852 DOI: 10.1007/s00299-012-1297-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 05/31/2012] [Indexed: 06/01/2023]
Abstract
RNA-binding proteins (RBPs) have been implicated as regulatory proteins involved in the post-transcriptional processes of gene expression in plants under various stress conditions. In this study, we report the cloning and characterization of a gene, designated as EgRBP42, encoding a member of the plant heterogeneous nuclear ribonucleoprotein (hnRNP)-like RBP family from oil palm (Elaeis guineensis Jacq.). EgRBP42 consists of two N-terminal RNA recognition motifs and a glycine-rich domain at the C-terminus. The upstream region of EgRBP42 has multiple light-responsive, stress-responsive regulatory elements and regulatory elements associated with flower development. Real-time RT-PCR analysis of EgRBP42 showed that EgRBP42 was expressed in oil palm tissues tested, including leaf, shoot apical meristem, root, female inflorescence, male inflorescence and mesocarp with the lowest transcript level in the roots. EgRBP42 protein interacted with transcripts associated with transcription, translation and stress responses using pull-down assay and electrophoretic mobility shift assay. The accumulation of EgRBP42 and its interacting transcripts were induced by abiotic stresses, including salinity, drought, submergence, cold and heat stresses in leaf discs. Collectively, the data suggested that EgRBP42 is a RBP, which responds to various abiotic stresses and could be advantageous for oil palm under stress conditions. Key message EgRBP42 may be involved in the post-transcriptional regulation of stress-related genes important for plant stress response and adaptation.
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Affiliation(s)
- Wan-Chin Yeap
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia,
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36
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Reddy ASN, Rogers MF, Richardson DN, Hamilton M, Ben-Hur A. Deciphering the plant splicing code: experimental and computational approaches for predicting alternative splicing and splicing regulatory elements. FRONTIERS IN PLANT SCIENCE 2012; 3:18. [PMID: 22645572 PMCID: PMC3355732 DOI: 10.3389/fpls.2012.00018] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2011] [Accepted: 01/18/2012] [Indexed: 05/20/2023]
Abstract
Extensive alternative splicing (AS) of precursor mRNAs (pre-mRNAs) in multicellular eukaryotes increases the protein-coding capacity of a genome and allows novel ways to regulate gene expression. In flowering plants, up to 48% of intron-containing genes exhibit AS. However, the full extent of AS in plants is not yet known, as only a few high-throughput RNA-Seq studies have been performed. As the cost of obtaining RNA-Seq reads continues to fall, it is anticipated that huge amounts of plant sequence data will accumulate and help in obtaining a more complete picture of AS in plants. Although it is not an onerous task to obtain hundreds of millions of reads using high-throughput sequencing technologies, computational tools to accurately predict and visualize AS are still being developed and refined. This review will discuss the tools to predict and visualize transcriptome-wide AS in plants using short-reads and highlight their limitations. Comparative studies of AS events between plants and animals have revealed that there are major differences in the most prevalent types of AS events, suggesting that plants and animals differ in the way they recognize exons and introns. Extensive studies have been performed in animals to identify cis-elements involved in regulating AS, especially in exon skipping. However, few such studies have been carried out in plants. Here, we review the current state of research on splicing regulatory elements (SREs) and briefly discuss emerging experimental and computational tools to identify cis-elements involved in regulation of AS in plants. The availability of curated alternative splice forms in plants makes it possible to use computational tools to predict SREs involved in AS regulation, which can then be verified experimentally. Such studies will permit identification of plant-specific features involved in AS regulation and contribute to deciphering the splicing code in plants.
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Affiliation(s)
- Anireddy S. N. Reddy
- Program in Molecular Plant Biology, Department of Biology, Colorado State UniversityFort Collins, CO, USA
| | - Mark F. Rogers
- Department of Computer Science, Colorado State UniversityFort Collins, CO, USA
| | - Dale N. Richardson
- Centro de Investigação em Biodiversidade e Recursos Genéticos, University of PortoVairão, Portugal
| | - Michael Hamilton
- Department of Computer Science, Colorado State UniversityFort Collins, CO, USA
| | - Asa Ben-Hur
- Department of Computer Science, Colorado State UniversityFort Collins, CO, USA
- Program in Molecular Plant Biology, Colorado State UniversityFort Collins, CO, USA
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37
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Reddy ASN, Day IS, Göhring J, Barta A. Localization and dynamics of nuclear speckles in plants. PLANT PHYSIOLOGY 2012; 158:67-77. [PMID: 22045923 PMCID: PMC3252098 DOI: 10.1104/pp.111.186700] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 10/31/2011] [Indexed: 05/17/2023]
Affiliation(s)
- Anireddy S N Reddy
- Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA.
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38
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Wachter A, Rühl C, Stauffer E. The Role of Polypyrimidine Tract-Binding Proteins and Other hnRNP Proteins in Plant Splicing Regulation. FRONTIERS IN PLANT SCIENCE 2012; 3:81. [PMID: 22639666 PMCID: PMC3355609 DOI: 10.3389/fpls.2012.00081] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 04/11/2012] [Indexed: 05/18/2023]
Abstract
Alternative precursor mRNA splicing is a widespread phenomenon in multicellular eukaryotes and represents a major means for functional expansion of the transcriptome. While several recent studies have revealed an important link between splicing regulation and fundamental biological processes in plants, many important aspects, such as the underlying splicing regulatory mechanisms, are so far not well understood. Splicing decisions are in general based on a splicing code that is determined by the dynamic interplay of splicing-controlling factors and cis-regulatory elements. Several members of the group of heterogeneous nuclear ribonucleoprotein (hnRNP) proteins are well known regulators of splicing in animals and the comparatively few reports on some of their plant homologs revealed similar functions. This also applies to polypyrimidine tract-binding proteins, a thoroughly investigated class of hnRNP proteins with splicing regulatory functions in both animals and plants. Further examples from plants are auto- and cross-regulatory splicing circuits of glycine-rich RNA binding proteins and splicing enhancement by oligouridylate binding proteins. Besides their role in defining splice site choice, hnRNP proteins are also involved in multiple other steps of nucleic acid metabolism, highlighting the functional versatility of this group of proteins in higher eukaryotes.
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Affiliation(s)
- Andreas Wachter
- Center for Plant Molecular Biology, University of TübingenTübingen, Germany
- *Correspondence: Andreas Wachter, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany. e-mail:
| | - Christina Rühl
- Center for Plant Molecular Biology, University of TübingenTübingen, Germany
| | - Eva Stauffer
- Center for Plant Molecular Biology, University of TübingenTübingen, Germany
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Hunt AG. RNA regulatory elements and polyadenylation in plants. FRONTIERS IN PLANT SCIENCE 2011; 2:109. [PMID: 22629268 PMCID: PMC3355548 DOI: 10.3389/fpls.2011.00109] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 12/17/2011] [Indexed: 05/20/2023]
Abstract
Alternative poly(A) site choice (also known as alternative polyadenylation, or APA) has the potential to affect gene expression in qualitative and quantitative ways. APA may affect as many as 82% of all expressed genes in a plant. The consequences of APA include the generation of transcripts with differing 3'-UTRs (and thus differing regulatory potential) and of transcripts with differing protein-coding potential. Genome-wide studies of possible APA suggest a linkage with pre-mRNA splicing, and indicate a coincidence of and perhaps cooperation between RNA regulatory elements that affect splicing efficiency and the recognition of novel intronic poly(A) sites. These studies also raise the possibility of the existence of a novel class of polyadenylation-related cis elements that are distinct from the well-characterized plant polyadenylation signal. Many potential APA events, however, have not been associated with identifiable cis elements. The present state of the field reveals a broad scope of APA, and also numerous opportunities for research into mechanisms that govern both choice and regulation of poly(A) sites in plants.
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Affiliation(s)
- Arthur G. Hunt
- Department of Plant and Soil Sciences, University of KentuckyLexington, KY, USA
- *Correspondence: Arthur G. Hunt, Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, USA. e-mail:
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Costenaro-da-Silva D, Passaia G, Henriques JAP, Margis R, Pasquali G, Revers LF. Identification and expression analysis of genes associated with the early berry development in the seedless grapevine (Vitis vinifera L.) cultivar Sultanine. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2010; 179:510-9. [PMID: 21802609 DOI: 10.1016/j.plantsci.2010.07.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 07/23/2010] [Accepted: 07/27/2010] [Indexed: 05/13/2023]
Abstract
Sultanine grapevine (Vitis vinifera L.) is one of the most important commercial seedless table-grape varieties and the main source of seedlessness for breeding programs around the world. Despite its commercial relevance, little is known about the genetic control of seedlessness in grapes, remaining unknown the molecular identity of genes responsible for such phenotype. Actually, studies concerning berry development in seedless grapes are scarce at the molecular level. We therefore developed a representational difference analysis (RDA) modified method named Bulk Representational Analysis of Transcripts (BRAT) in the attempt to identify genes specifically associated with each of the main developmental stages of Sultanine grapevine berries. A total of 2400 transcript-derived fragments (TDFs) were identified and cloned by RDA according to three specific developmental berry stages. After sequencing and in silico analysis, 1554 (64.75%) TDFs were validated according to our sequence quality cut-off. The assembly of these expressed sequence tags (ESTs) yielded 504 singletons and 77 clusters, with an overall EST redundancy of approximately 67%. Amongst all stage-specific cDNAs, nine candidate genes were selected and, along with two reference genes, submitted to a deeper analysis of their temporal expression profiles by reverse transcription-quantitative PCR. Seven out of nine genes proved to be in agreement with the stage-specific expression that allowed their isolation by RDA.
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Affiliation(s)
- Danielle Costenaro-da-Silva
- Programa de Pós-graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, P.O. Box 15.005, CEP 91.501-970 Porto Alegre, RS, Brazil
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41
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Zhou C, Yin Y, Dam P, Xu Y. Identification of novel proteins involved in plant cell-wall synthesis based on protein-protein interaction data. J Proteome Res 2010; 9:5025-37. [PMID: 20687615 DOI: 10.1021/pr100249c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The plant cell wall is mainly composed of polysaccharides, representing the richest source of biomass for future biofuel production. Currently, the majority of the cell-wall synthesis-related (CWSR) proteins are unknown even for model plant Arabidopsis thaliana. We report a computational framework for predicting CWSR proteins based on protein-protein interaction (PPI) data and known CWSR proteins. We predict a protein to be a CWSR protein if it interacts with known CWSR proteins (seeds) with high statistical significance. Using this technique, we predicted 100 candidate CWSR proteins in Arabidopsis thaliana, 8 of which were experimentally confirmed by previous reports. Forty-two candidates have either independent supporting evidence or strong functional relevance to cell-wall synthesis and, hence, are considered as the most reliable predictions. For 33 of the predicted CWSR proteins, we have predicted their detailed functional roles in CWS, based on analyses of their domain architectures, phylogeny, and current functional annotation in conjunction with a literature search. We present the constructed PPIs covering all the known and predicted CWSR proteins at http://csbl.bmb.uga.edu/∼zhouchan/CellWallProtein/. The 42 most reliable candidates provide useful targets to experimentalists for further investigation, and the PPI data constructed in this work provides new information for cell-wall research.
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Affiliation(s)
- Chan Zhou
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, USA
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42
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Zhou L, Liu Y, Liu Z, Kong D, Duan M, Luo L. Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:4157-68. [PMID: 20729483 DOI: 10.1093/jxb/erq237] [Citation(s) in RCA: 353] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In addition to regulating growth and development, the most important function of microRNAs (miRNAs) in plants is the regulation of a variety of cellular processes underlying plant adaptation to environmental stresses. To gain a deep understanding of the mechanism of drought tolerance in rice, genome-wide profiling and analysis of miRNAs was carried out in drought-challenged rice across a wide range of developmental stages, from tillering to inflorescence formation, using a microarray platform. Among the 30 miRNAs identified as significantly down- or up-regulated under the drought stress, 11 down-regulated miRNAs (miR170, miR172, miR397, miR408, miR529, miR896, miR1030, miR1035, miR1050, miR1088, and miR1126) and eight up-regulated miRNAs (miR395, miR474, miR845, miR851, miR854, miR901, miR903, and miR1125) were revealed for the first time to be induced by drought stress in plants, and nine (miR156, miR168, miR170, miR171, miR172, miR319, miR396, miR397, and miR408) showed opposite expression to that observed in drought-stressed Arabidopsis. The most conserved down-regulated miRNAs were ath-miR170, the miR171 family, and ath-miR396, and the most conserved up-regulated miRNAs were ptc-miR474 and ath-miR854a. The identification of differentially expressed novel plant miRNAs and their target genes, and the analysis of cis-elements provides molecular evidence for the possible involvement of miRNAs in the process of drought response and/or tolerance in rice.
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Affiliation(s)
- Liguo Zhou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science, Huazhong Agricultural University, Wuhan 430070, China
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Gal-Mark N, Schwartz S, Ram O, Eyras E, Ast G. The pivotal roles of TIA proteins in 5' splice-site selection of alu exons and across evolution. PLoS Genet 2009; 5:e1000717. [PMID: 19911040 PMCID: PMC2766253 DOI: 10.1371/journal.pgen.1000717] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Accepted: 10/13/2009] [Indexed: 01/04/2023] Open
Abstract
More than 5% of alternatively spliced internal exons in the human genome are derived from Alu elements in a process termed exonization. Alus are comprised of two homologous arms separated by an internal polypyrimidine tract (PPT). In most exonizations, splice sites are selected from within the same arm. We hypothesized that the internal PPT may prevent selection of a splice site further downstream. Here, we demonstrate that this PPT enhanced the selection of an upstream 5′ splice site (5′ss), even in the presence of a stronger 5′ss downstream. Deletion of this PPT shifted selection to the stronger downstream 5′ss. This enhancing effect depended on the strength of the downstream 5′ss, on the efficiency of base-pairing to U1 snRNA, and on the length of the PPT. This effect of the PPT was mediated by the binding of TIA proteins and was dependent on the distance between the PPT and the upstream 5′ss. A wide-scale evolutionary analysis of introns across 22 eukaryotes revealed an enrichment in PPTs within ∼20 nt downstream of the 5′ss. For most metazoans, the strength of the 5′ss inversely correlated with the presence of a downstream PPT, indicative of the functional role of the PPT. Finally, we found that the proteins that mediate this effect, TIA and U1C, and in particular their functional domains, are highly conserved across evolution. Overall, these findings expand our understanding of the role of TIA1/TIAR proteins in enhancing recognition of exons, in general, and Alu exons, in particular. Human genes are composed of functional regions, termed exons, separated by non-functional regions, termed introns. Intronic sequences may gradually accumulate mutations and subsequently become recognized by the splicing machinery as exons, a process termed exonization. Alu elements are prone to undergo exonization: more than 5% of alternatively spliced internal exons in the human genome originate from Alu elements. A typical Alu element is ∼300 nucleotides long, consisting of two arms separated by a polypyrimdine tract (PPT). Interestingly, in most cases, exonization occurs almost exclusively within either the right arm or the left, not both. Here we found that the PPT between the two arms serves as a binding site for TIA proteins and prevents the exon selection process from expanding into downstream regions. To obtain a wider overview of TIA function, we performed a cross-evolutionary analysis within 22 eukaryotes of this protein and of U1C, a protein known to interact with it, and found that functional regions of both these proteins were highly conserved. These findings highlight the pivotal role of TIA proteins in 5′ splice-site selection of Alu exons and exon recognition in general.
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Affiliation(s)
- Nurit Gal-Mark
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Schraga Schwartz
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Oren Ram
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Eduardo Eyras
- Computational Genomics, Universitat Pompeu Fabra, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
- * E-mail: (EE); (GA)
| | - Gil Ast
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
- * E-mail: (EE); (GA)
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Bailey-Serres J, Sorenson R, Juntawong P. Getting the message across: cytoplasmic ribonucleoprotein complexes. TRENDS IN PLANT SCIENCE 2009; 14:443-53. [PMID: 19616989 DOI: 10.1016/j.tplants.2009.05.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Revised: 05/29/2009] [Accepted: 05/29/2009] [Indexed: 05/20/2023]
Abstract
mRNA-ribonucleoprotein (mRNP) complexes mediate post-transcriptional control mechanisms in the cell nucleus and cytoplasm. Transcriptional control is paramount to gene expression but is followed by regulated nuclear pre-mRNA maturation and quality control processes that culminate in the export of a functional transcript to the cytoplasm. Once in the cytosol, mRNPs determine the activity of individual mRNAs through regulation of localization, translation, sequestration and turnover. Here, we review how quantitative assessment of mRNAs in distinct cytoplasmic mRNPs, such as polyribosomes (polysomes), has provided new perspectives on post-transcriptional regulation from the global to gene-specific level. In addition, we explore recent genetic and biochemical studies of cytoplasmic mRNPs that have begun to expose RNA-binding proteins in an integrated network that fine-tunes gene expression.
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Affiliation(s)
- J Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521-0124, USA
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Post-transcriptional regulation of gene expression in plants during abiotic stress. Int J Mol Sci 2009; 10:3168-3185. [PMID: 19742130 PMCID: PMC2738917 DOI: 10.3390/ijms10073168] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Revised: 07/04/2009] [Accepted: 07/09/2009] [Indexed: 12/22/2022] Open
Abstract
Land plants are anchored in one place for most of their life cycle and therefore must constantly adapt their growth and metabolism to abiotic stresses such as light intensity, temperature and the availability of water and essential minerals. Thus, plants’ subsistence depends on their ability to regulate rapidly gene expression in order to adapt their physiology to their environment. Recent studies indicate that post-transcriptional regulations of gene expression play an important role in how plants respond to abiotic stresses. We will review the different mechanisms of post-transcriptional regulation of nuclear genes expression including messenger RNA (mRNA) processing, stability, localization and protein translation, and discuss their relative importance for plant adaptation to abiotic stress.
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Lorković ZJ. Role of plant RNA-binding proteins in development, stress response and genome organization. TRENDS IN PLANT SCIENCE 2009; 14:229-36. [PMID: 19285908 DOI: 10.1016/j.tplants.2009.01.007] [Citation(s) in RCA: 215] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Revised: 12/18/2008] [Accepted: 01/08/2009] [Indexed: 05/20/2023]
Abstract
RNA-binding proteins (RBPs) in eukaryotes have crucial roles in all aspects of post-transcriptional gene regulation. They are important governors of diverse developmental processes by modulating expression of specific transcripts. The Arabidopsis (Arabidopsis thaliana) genome encodes for more than 200 different RBPs, most of which are plant specific and are therefore likely to perform plant-specific functions. Indeed, recent identification and analysis of plant RBPs clearly showed that, in addition to the important role in diverse developmental processes, they are also involved in adaptation of plants to various environmental conditions. Clearly, they act by regulating pre-mRNA splicing, polyadenylation, RNA stability and RNA export, as well as by influencing chromatin modification.
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Affiliation(s)
- Zdravko J Lorković
- Max F. Perutz Laboratories, Department of Medical Biochemistry, Medical University of Vienna, Dr. Bohrgasse 9/3, A-1030 Vienna, Austria.
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Lorković ZJ, Barta A. Role of Cajal bodies and nucleolus in the maturation of the U1 snRNP in Arabidopsis. PLoS One 2008; 3:e3989. [PMID: 19098980 PMCID: PMC2600615 DOI: 10.1371/journal.pone.0003989] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Accepted: 11/21/2008] [Indexed: 01/31/2023] Open
Abstract
Background The biogenesis of spliceosomal snRNPs takes place in both the cytoplasm where Sm core proteins are added and snRNAs are modified at the 5′ and 3′ termini and in the nucleus where snRNP-specific proteins associate. U1 snRNP consists of U1 snRNA, seven Sm proteins and three snRNP-specific proteins, U1-70K, U1A, and U1C. It has been shown previously that after import to the nucleus U2 and U4/U6 snRNP-specific proteins first appear in Cajal bodies (CB) and then in splicing speckles. In addition, in cells grown under normal conditions U2, U4, U5, and U6 snRNAs/snRNPs are abundant in CBs. Therefore, it has been proposed that the final assembly of these spliceosomal snRNPs takes place in this nuclear compartment. In contrast, U1 snRNA in both animal and plant cells has rarely been found in this nuclear compartment. Methodology/Principal Findings Here, we analysed the subnuclear distribution of Arabidopsis U1 snRNP-specific proteins fused to GFP or mRFP in transiently transformed Arabidopsis protoplasts. Irrespective of the tag used, U1-70K was exclusively found in the nucleus, whereas U1A and U1C were equally distributed between the nucleus and the cytoplasm. In the nucleus all three proteins localised to CBs and nucleoli although to different extent. Interestingly, we also found that the appearance of the three proteins in nuclear speckles differ significantly. U1-70K was mostly found in speckles whereas U1A and U1C in ∼90% of cells showed diffuse nucleoplasmic in combination with CBs and nucleolar localisation. Conclusions/Significance Our data indicate that CBs and nucleolus are involved in the maturation of U1 snRNP. Differences in nuclear accumulation and distribution between U1-70K and U1A and U1C proteins may indicate that either U1-70K or U1A and U1C associate with, or is/are involved, in other nuclear processes apart from pre-mRNA splicing.
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Affiliation(s)
- Zdravko J Lorković
- Department of Medical Biochemistry, Max F Perutz Laboratories, Medical University of Vienna, Vienna, Austria.
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Weber C, Nover L, Fauth M. Plant stress granules and mRNA processing bodies are distinct from heat stress granules. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 56:517-30. [PMID: 18643965 DOI: 10.1111/j.1365-313x.2008.03623.x] [Citation(s) in RCA: 179] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Similar to the situation in mammalian cells and yeast, messenger ribonucleo protein (mRNP) homeostasis in plant cells depends on rapid transitions between three functional states, i.e. translated mRNPs in polysomes, stored mRNPs and mRNPs under degradation. Studies in mammalian cells showed that whenever the dynamic exchange of the components between these states is disrupted, stalled mRNPs accumulate in cytoplasmic aggregates, such as stress granules (SGs) or processing bodies (PBs). We identified PBs and SGs in plant cells by detection of DCP1, DCP2 and XRN4, as marker proteins for the 5'-->3' mRNA degradation pathway, and eIF4E, as well as the RNA binding proteins RBP47 and UBP1, as marker proteins for stored mRNPs in SGs. Cycloheximide-inhibited translation, stress treatments and mutants defective in mRNP homeostasis were used to study the dynamic transitions of mRNPs between SGs and PBs. SGs and PBs can be clearly discriminated from the previously described heat stress granules (HSGs), which evidently do not contain mRNPs. Thus, the role of HSGs as putative mRNP storage sites must be revised.
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Affiliation(s)
- Christian Weber
- Department of Molecular Cell Biology, Johann Wolfgang Goethe-University Frankfurt, Max von Laue Strasse 9, 60438 Frankfurt, Germany
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Abstract
The spliceosome is a large nuclear structure consisting of dynamically interacting RNAs and proteins. This chapter briefly reviews some of the known components and their interactions. Large-scale proteomics and gene expression studies may be required to unravel the many intricate mechanisms involved in splice site recognition and selection.
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Abstract
U12-dependent (U12) introns have persisted in the genomes of plants since the ancestral divergence between plants and metazoans. These introns, which are rare, are found in a range of genes that include essential functions in DNA replication and RNA metabolism and are implicated in regulating the expression of their host genes. U12 introns are removed from pre-mRNAs by a U12 intron-specific spliceosome. Although this spliceosome shares many properties with the more abundant U2-dependent (U2) intron spliceosome, four of the five small nuclear RNAs (snRNAs) required for splicing are different and specific for the unique splicing of U12 introns. Evidence in plants so far indicates that splicing signals of plant U12 introns and their splicing machinery are similar to U12 intron splicing in other eukaryotes. In addition to the high conservation of splicing signals, plant U12 introns also retain unique characteristic features of plant U2 introns, such as UA-richness, which suggests a requirement for plant-specific components for both the U2 and U12 splicing reaction. This chapter compares U12 and U2 splicing and reviews what is known about plant U12 introns and their possible role in gene expression.
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