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Ackah M, Jin X, Zhang Q, Amoako FK, Wang L, Attaribo T, Zhao M, Yuan F, Herman RA, Qiu C, Lin Q, Yin Z, Zhao W. Long noncoding RNA transcriptome analysis reveals novel lncRNAs in Morus alba 'Yu-711' response to drought stress. THE PLANT GENOME 2024; 17:e20273. [PMID: 36285722 DOI: 10.1002/tpg2.20273] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Drought stress has been a key environmental factor affecting plant growth and development. The plant genome is capable of producing long noncoding RNAs (lncRNAs). To better understand white mulberry (Morus alba L.) drought response mechanism, we conducted a comparative transcriptome study comparing two treatments: drought-stressed (EG) and well-watered (CK) plants. A total of 674 differentially expressed lncRNAs (DElncRNAs) were identified. In addition, 782 differentially expressed messenger RNAs (DEmRNAs) were identified. We conducted Gene Ontology (GO) and KEGG enrichment analyses focusing on the differential lncRNAs cis-target genes. The target genes of the DElncRNAs were most significantly involved in the biosynthesis of secondary metabolites. Gene regulatory networks of the target genes involving DElncRNAs-mRNAs-DEmRNAs and DElncRNA-miRNA-DEmRNA were constructed. In the DElncRNAs-DEmRNAs network, 30 DEmRNAs involved in the biosynthesis of secondary metabolites are collocated with 46 DElncRNAs. The interaction between DElncRNAs and candidate genes was identified using LncTar. In summary, quantitative real-time polymerase chain reaction (qRT-PCR) validated nine candidate genes and seven target lncRNAs including those identified by LncTar. We predicted that the DElncRNAs-DEmRNAs might recruit microRNAs (miRNAs) to interact with gene regulatory networks under the drought stress response in mulberry. The findings will contribute to our understanding of the regulatory functions of lncRNAs under drought stress and will shed new light on the mulberry-drought stress interactions.
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Affiliation(s)
- Michael Ackah
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu Univ. of Science and Technology, Zhenjiang, 212100, China
- School of Food and Biological Engineering, Jiangsu Univ., Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Xin Jin
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu Univ. of Science and Technology, Zhenjiang, 212100, China
| | - Qiaonan Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu Univ. of Science and Technology, Zhenjiang, 212100, China
| | - Frank Kwarteng Amoako
- Institute of Plant Nutrition and Soil Science, Kiel Univ., Hermann-Rodewald-Straße 2, Kiel, 24118, Germany
| | - Lei Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu Univ. of Science and Technology, Zhenjiang, 212100, China
| | - Thomas Attaribo
- School of Agriculture, C. K. Tedam Univ. of Technology and Applied Sciences, Navrongo, UK-0215-5321, Ghana
| | - Mengdi Zhao
- Dep. of Materials Science and Engineering, Suzhou Univ. of Science and Technology, 99 Xuefu Road, Huqiu District, Suzhou, 215004, China
| | - Feng Yuan
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu Univ. of Science and Technology, Zhenjiang, 212100, China
| | - Richard Ansah Herman
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu Univ. of Science and Technology, Zhenjiang, 212100, China
| | - Changyu Qiu
- Sericultural Research Institute, Guangxi Zhuang Autonomous Region, Nanning, 530007, China
| | - Qiang Lin
- Sericultural Research Institute, Guangxi Zhuang Autonomous Region, Nanning, 530007, China
| | - Zhi Yin
- Nanjing Univ. of Finance & Economics, Nanjing, 210023, China
| | - Weiguo Zhao
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu Univ. of Science and Technology, Zhenjiang, 212100, China
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Li S, Zhao Y, Tan S, Li Z. Non-coding RNAs and leaf senescence: Small molecules with important roles. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108399. [PMID: 38277833 DOI: 10.1016/j.plaphy.2024.108399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024]
Abstract
Non-coding RNAs (ncRNAs) are a special class of functional RNA molecules that are not translated into proteins. ncRNAs have emerged as pivotal regulators of diverse developmental processes in plants. Recent investigations have revealed the association of ncRNAs with the regulation of leaf senescence, a complex and tightly regulated developmental process. However, a comprehensive review of the involvement of ncRNAs in the regulation of leaf senescence is still lacking. This manuscript aims to summarize the molecular mechanisms underlying ncRNAs-mediated leaf senescence and the potential applications of ncRNAs to manipulate the onset and progression of leaf senescence. Various classes of ncRNAs, including microRNAs (miRNAs), small interfering RNAs (siRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), are discussed in terms of their regulatory mechanisms in leaf senescence. Furthermore, we explore the interactions between ncRNA and the key regulators of senescence, including transcription factors as well as core components in phytohormone signaling pathways. We also discuss the possible challenges and approaches related to ncRNA-mediated leaf senescence. This review contributes to a further understanding of the intricate regulatory network involving ncRNAs in leaf senescence.
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Affiliation(s)
- Shichun Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yaning Zhao
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shuya Tan
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Zhonghai Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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Zhang Y, Huang D, Miao Y. Epigenetic control of plant senescence and cell death and its application in crop improvement. FRONTIERS IN PLANT SCIENCE 2023; 14:1258487. [PMID: 37965008 PMCID: PMC10642554 DOI: 10.3389/fpls.2023.1258487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023]
Abstract
Plant senescence is the last stage of plant development and a type of programmed cell death, occurring at a predictable time and cell. It involves the functional conversion from nutrient assimilation to nutrient remobilization, which substantially impacts plant architecture and plant biomass, crop quality, and horticultural ornamental traits. In past two decades, DNA damage was believed to be a main reason for cell senescence. Increasing evidence suggests that the alteration of epigenetic information is a contributing factor to cell senescence in organisms. In this review, we summarize the current research progresses of epigenetic and epitranscriptional mechanism involved in cell senescence of plant, at the regulatory level of DNA methylation, histone methylation and acetylation, chromatin remodeling, non-coding RNAs and RNA methylation. Furthermore, we discuss their molecular genetic manipulation and potential application in agriculture for crop improvement. Finally we point out the prospects of future research topics.
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Affiliation(s)
- Yu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dongmei Huang
- Department of Biochemistry and Molecular Biology, Xiamen Medical College, Xiamen, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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Unel NM, Baloglu MC, Altunoglu YÇ. Comprehensive investigation of cucumber heat shock proteins under abiotic stress conditions: A multi-omics survey. J Biotechnol 2023; 374:49-69. [PMID: 37517677 DOI: 10.1016/j.jbiotec.2023.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 08/01/2023]
Abstract
Heat-shock proteins (Hsps) are a family of proteins essential in preserving the vitality and functionality of proteins under stress conditions. Cucumber (Cucumis sativus) is a widely grown plant with high nutritional value and is used as a model organism in many studies. This study employed a genomics, transcriptomics, and metabolomics approach to investigate cucumbers' Hsps against abiotic stress conditions. Bioinformatics methods were used to identify six Hsp families in the cucumber genome and to characterize family members. Transcriptomics data from the Sequence Read Archive (SRA) database was also conducted to select CsHsp genes for further study. Real-time PCR was used to evaluate gene expression levels under different stress conditions, revealing that CssHsp-08 was a vital gene for resistance to stress conditions; including drought, salinity, cold, heat stresses, and ABA application. Gas Chromatography-Mass Spectrometry (GC-MS) analysis of plant extracts revealed that amino acids accumulate in leaves under high temperatures and roots under drought, while sucrose accumulates in both tissues under applied most stress factors. The study provides valuable insights into the structure, organization, evolution, and expression profiles of the Hsp family and contributes to a better understanding of plant stress mechanisms. These findings have important implications for developing crops that can withstand environmental stress conditions better.
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Affiliation(s)
- Necdet Mehmet Unel
- Research and Application Center, Kastamonu University, Kastamonu, Turkey; Plantomics Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
| | - Mehmet Cengiz Baloglu
- Plantomics Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey; Sabancı University Nanotechnology Research and Application Center (SUNUM), Sabancı University, Turkey.
| | - Yasemin Çelik Altunoglu
- Plantomics Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
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Hu Y, Ji J, Cheng H, Luo R, Zhang J, Li W, Wang X, Zhang J, Yao Y. The miR408a-BBP-LAC3/CSD1 module regulates anthocyanin biosynthesis mediated by crosstalk between copper homeostasis and ROS homeostasis during light induction in Malus plants. J Adv Res 2023; 51:27-44. [PMID: 36371057 PMCID: PMC10491975 DOI: 10.1016/j.jare.2022.11.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/19/2022] [Accepted: 11/06/2022] [Indexed: 11/11/2022] Open
Abstract
INTRODUCTION The expression of miR408 is affected by copper (Cu) conditions and positively regulates anthocyanin biosynthesis in Arabidopsis. However, the underlying mechanisms by which miR408 regulates anthocyanin biosynthesis mediated by Cu homeostasis and reactive oxygen species (ROS) homeostasis remain unclear in Malus plants. OBJECTIVES Our study aims to elucidate how miR408a and its target, basic blue protein (BBP) regulate Cu homeostasis and ROS homeostasis, and anthocyanin biosynthesis in Malus plants. METHODS The roles of miR408a and its target BBP in regulating anthocyanin biosynthesis, Cu homeostasis, and ROS homeostasis were mainly identified in Malus plants. RESULTS We found that the BBP protein interacted with the copper-binding proteins LAC3 (laccase) and CSD1 (Cu/Zn SOD superoxide dismutase), indicating a potential crosstalk between Cu homeostasis and ROS homeostasis might be mediated by miR408 to regulate the anthocyanin accumulation. Further studies showed that overexpressing miR408a or suppressing BBP transiently significantly increased the expression of genes related to Cu binding and Cu transport, leading to anthocyanin accumulation under light induction in apple fruit and Malus plantlets. Consistently, opposite results were obtained when repressing miR408a or overexpressing BBP. Moreover, light induction significantly increased the expression of miR408a, CSD1, and LAC3, but significantly reduced the BBP expression, resulting in increased Cu content and anthocyanin accumulation. Furthermore, excessive Cu significantly increased the anthocyanin accumulation, accompanied by reduced expression of miR408a and Cu transport genes, and upregulated expression of Cu binding proteins including BBP, LAC3, and CSD1 to maintain the Cu homeostasis and ROS homeostasis in Malus plantlets. CONCLUSION Our findings provide new insights into the mechanism by which the miR408a-BBP-LAC3/CSD1 module perceives light and Cu signals regulating Cu and ROS homeostasis, ultimately affecting anthocyanin biosynthesis in Malus plants.
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Affiliation(s)
- Yujing Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Jiayi Ji
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China; Beijing Forestry University, China
| | - Hao Cheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Rongli Luo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Wenjing Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Xingsui Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China.
| | - Yuncong Yao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China.
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Tripathi AM, Singh R, Verma AK, Singh A, Mishra P, Dwivedi V, Narayan S, Gandhivel VHS, Shirke PA, Shivaprasad PV, Roy S. Indian Himalayan natural Arabidopsis thaliana accessions with abolished miR158 levels exhibit robust miR173-initiated trans-acting cascade silencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:855-874. [PMID: 36883862 DOI: 10.1111/tpj.16175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/13/2023] [Accepted: 03/03/2023] [Indexed: 05/27/2023]
Abstract
Small RNAs (sRNAs) such as microRNAs (miRNAs) and small interfering RNAs (siRNAs) are short 20-24-nucleotide non-coding RNAs. They are key regulators of gene expression in plants and other organisms. Several 22-nucleotide miRNAs trigger biogenesis cascades of trans-acting secondary siRNAs, which are involved in various developmental and stress responses. Here we show that Himalayan Arabidopsis thaliana accessions having natural mutations in the miR158 locus exhibit robust cascade silencing of the pentatricopeptide repeat (PPR)-like locus. Furthermore, we show that these cascade sRNAs trigger tertiary silencing of a gene involved in transpiration and stomatal opening. The natural deletions or insertions in MIR158 led to improper processing of miR158 precursors, thereby blocking synthesis of mature miR158. Reduced miR158 levels led to increased levels of its target, a pseudo-PPR gene that is targeted by tasiRNAs generated by the miR173 cascade in other accessions. Using sRNA datasets derived from Indian Himalayan accessions, as well as overexpression and knockout lines of miR158, we show that absence of miR158 led to buildup of pseudo-PPR-derived tertiary sRNAs. These tertiary sRNAs mediated robust silencing of a gene involved in stomatal closure in Himalayan accessions lacking miR158 expression. We functionally validated the tertiary phasiRNA that targets NHX2, which encodes a Na+ -K+ /H+ antiporter protein, thereby regulating transpiration and stomatal conductance. Overall, we report the role of the miRNA-TAS-siRNA-pseudogene-tertiary phasiRNA-NHX2 pathway in plant adaptation.
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Affiliation(s)
- Abhinandan Mani Tripathi
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rajneesh Singh
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ashwani Kumar Verma
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Akanksha Singh
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Parneeta Mishra
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Varun Dwivedi
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Shiv Narayan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Plant Physiology Laboratory, CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Vivek Hari Sundar Gandhivel
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Pramod Arvind Shirke
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Plant Physiology Laboratory, CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Padubidri V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Sribash Roy
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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Sasi JM, VijayaKumar C, Kukreja B, Budhwar R, Shukla RN, Agarwal M, Katiyar-Agarwal S. Integrated transcriptomics and miRNAomics provide insights into the complex multi-tiered regulatory networks associated with coleoptile senescence in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:985402. [PMID: 36311124 PMCID: PMC9597502 DOI: 10.3389/fpls.2022.985402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Coleoptile is the small conical, short-lived, sheath-like organ that safeguards the first leaf and shoot apex in cereals. It is also the first leaf-like organ to senesce that provides nutrition to the developing shoot and is, therefore, believed to play a crucial role in seedling establishment in rice and other grasses. Though histochemical studies have helped in understanding the pattern of cell death in senescing rice coleoptiles, genome-wide expression changes during coleoptile senescence have not yet been explored. With an aim to investigate the gene regulation underlying the coleoptile senescence (CS), we performed a combinatorial whole genome expression analysis by sequencing transcriptome and miRNAome of senescing coleoptiles. Transcriptome analysis revealed extensive reprogramming of 3439 genes belonging to several categories, the most prominent of which encoded for transporters, transcription factors (TFs), signaling components, cell wall organization enzymes, redox homeostasis, stress response and hormone metabolism. Small RNA sequencing identified 41 known and 21 novel miRNAs that were differentially expressed during CS. Comparison of gene expression and miRNA profiles generated for CS with publicly available leaf senescence (LS) datasets revealed that the two aging programs are remarkably distinct at molecular level in rice. Integration of expression data of transcriptome and miRNAome identified high confidence 140 miRNA-mRNA pairs forming 42 modules, thereby demonstrating multi-tiered regulation of CS. The present study has generated a comprehensive resource of the molecular networks that enrich our understanding of the fundamental pathways regulating coleoptile senescence in rice.
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Affiliation(s)
| | - Cheeni VijayaKumar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | | | - Roli Budhwar
- Bionivid Technology Pvt. Limited, Bengaluru, Karnataka, India
| | | | - Manu Agarwal
- Department of Botany, University of Delhi, Delhi, India
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Noureddine Y, Mejias J, da Rocha M, Thomine S, Quentin M, Abad P, Favery B, Jaubert-Possamai S. Copper microRNAs modulate the formation of giant feeding cells induced by the root knot nematode Meloidogyne incognita in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2022; 236:283-295. [PMID: 35801827 DOI: 10.1111/nph.18362] [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: 11/17/2021] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Root-knot nematodes (RKNs) are root endoparasites that induce the dedifferentiation of a few root cells and the reprogramming of their gene expression to generate giant hypermetabolic feeding cells. We identified two microRNA families, miR408 and miR398, as upregulated in Arabidopsis thaliana and Solanum lycopersicum roots infected by RKNs. In plants, the expression of these two conserved microRNA families is known to be activated by the SPL7 transcription factor in response to copper starvation. By combining functional approaches, we deciphered the network involving these microRNAs, their regulator and their targets. MIR408 expression was located within nematode-induced feeding cells like its regulator SPL7 and was regulated by copper. Moreover, infection assays with mir408 and spl7 knockout mutants or lines expressing targets rendered resistant to cleavage by miR398 demonstrated the essential role of the SPL7/MIR408/MIR398 module in the formation of giant feeding cells. Our findings reveal how perturbation of plant copper homeostasis, via the SPL7/MIR408/MIR398 module, modulates the development of nematode-induced feeding cells.
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Affiliation(s)
- Yara Noureddine
- INRAE, Université Côte d'Azur, CNRS, ISA, Sophia Antipolis, F-06903, France
| | - Joffrey Mejias
- INRAE, Université Côte d'Azur, CNRS, ISA, Sophia Antipolis, F-06903, France
| | - Martine da Rocha
- INRAE, Université Côte d'Azur, CNRS, ISA, Sophia Antipolis, F-06903, France
| | - Sébastien Thomine
- Institute for Integrative Biology of the Cell (I2BC), UMR9198 CNRS/CEA/Univ. Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Michaël Quentin
- INRAE, Université Côte d'Azur, CNRS, ISA, Sophia Antipolis, F-06903, France
| | - Pierre Abad
- INRAE, Université Côte d'Azur, CNRS, ISA, Sophia Antipolis, F-06903, France
| | - Bruno Favery
- INRAE, Université Côte d'Azur, CNRS, ISA, Sophia Antipolis, F-06903, France
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Zhang Y, Li Y, Zhang Y, Zhang Z, Zhang D, Wang X, Lai B, Huang D, Gu L, Xie Y, Miao Y. Genome-wide H3K9 acetylation level increases with age-dependent senescence of flag leaf in rice. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4696-4715. [PMID: 35429161 DOI: 10.1093/jxb/erac155] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Flag leaf senescence is an important biological process that drives the remobilization of nutrients to the growing organs of rice. Leaf senescence is controlled by genetic information via gene expression and histone modification, but the precise mechanism is as yet unclear. Here, we analysed genome-wide acetylated lysine residue 9 of histone H3 (H3K9ac) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq), and examined its association with transcriptomes by RNA-seq during flag leaf aging in rice (Oryza sativa). We found that genome-wide H3K9 acetylation levels increased with age-dependent senescence in rice flag leaf, and there was a positive correlation between the density and breadth of H3K9ac with gene expression and transcript elongation. During flag leaf aging, we observed 1249 up-regulated differentially expressed genes (DEGs) and 996 down-regulated DEGs, showing a strong relationship between temporal changes in gene expression and gain/loss of H3K9ac. We produced a landscape of H3K9 acetylation-modified gene expression targets that include known senescence-associated genes, metabolism-related genes, as well as miRNA biosynthesis-related genes. Our findings reveal a complex regulatory network of metabolism- and senescence-related pathways mediated by H3K9ac, and elucidate patterns of H3K9ac-mediated regulation of gene expression during flag leaf aging in rice.
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Affiliation(s)
- Yu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanyun Li
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuanyuan Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zeyu Zhang
- Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Deyu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaonan Wang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Binfan Lai
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dandan Huang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yakun Xie
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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10
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The Evolution and Functional Roles of miR408 and Its Targets in Plants. Int J Mol Sci 2022; 23:ijms23010530. [PMID: 35008962 PMCID: PMC8745667 DOI: 10.3390/ijms23010530] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/21/2021] [Accepted: 12/29/2021] [Indexed: 12/20/2022] Open
Abstract
MicroRNA408 (miR408) is an ancient and highly conserved miRNA, which is involved in the regulation of plant growth, development and stress response. However, previous research results on the evolution and functional roles of miR408 and its targets are relatively scattered, and there is a lack of a systematic comparison and comprehensive summary of the detailed evolutionary pathways and regulatory mechanisms of miR408 and its targets in plants. Here, we analyzed the evolutionary pathway of miR408 in plants, and summarized the functions of miR408 and its targets in regulating plant growth and development and plant responses to various abiotic and biotic stresses. The evolutionary analysis shows that miR408 is an ancient and highly conserved microRNA, which is widely distributed in different plants. miR408 regulates the growth and development of different plants by down-regulating its targets, encoding blue copper (Cu) proteins, and by transporting Cu to plastocyanin (PC), which affects photosynthesis and ultimately promotes grain yield. In addition, miR408 improves tolerance to stress by down-regulating target genes and enhancing cellular antioxidants, thereby increasing the antioxidant capacity of plants. This review expands and promotes an in-depth understanding of the evolutionary and regulatory roles of miR408 and its targets in plants.
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11
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Ren Y, Li M, Wang W, Lan W, Schenke D, Cai D, Miao Y. MicroRNA840 (MIR840) accelerates leaf senescence by targeting the overlapping 3'UTRs of PPR and WHIRLY3 in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:126-143. [PMID: 34724261 DOI: 10.1111/tpj.15559] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 10/13/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
MicroRNAs negatively regulate gene expression by promoting target mRNA cleavage and/or impairing its translation, thereby playing a crucial role in plant development and environmental stress responses. In Arabidopsis, the MIR840 gene is located within the overlapping 3'UTR of the PPR and WHIRLY3 (WHY3) genes, both being predicted targets of miR840* and miR840, the short maturation products of MIR840. Gain- and loss-of-function of MIR840 in Arabidopsis resulted in opposite senescence phenotypes. The highest expression levels of the MIR840 precursor transcript pre-miR840 were observed at senescence initiation, and pre-miR840 expression is significantly correlated with a reduction in PPR, but not WHY3, transcript levels. Although a reduction of transcript level of PPR, but not WHY3 transcript levels were not significantly affected by MIR840 overexpression, its protein levels were strongly reduced. Mutating the cleavage sites or replacing the target sequences abolishes the miR840*/miR840-mediated degradation of PPR transcripts and accumulation of WHY3 protein. In support for this, concurrent knockdown of both PPR and WHY3 in wild-type plants resulted in a senescence phenotype resembling that of the MIR840-overexpressing plant. This indicates that both PRR and WHY3 are targets in the MIR840-mediated senescence pathway. Moreover, single knockout mutants of PPR and WHY3 show a convergent upregulated subset of senescence-associated genes, which are also found among those induced by MIR840 overexpression. Our data provide evidence for a regulatory role of MIR840 in plant senescence.
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Affiliation(s)
- Yujun Ren
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mengsi Li
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wanzhen Wang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei Lan
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dirk Schenke
- Department of Molecular Phytopathology, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Daguang Cai
- Department of Molecular Phytopathology, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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Guo Y, Ren G, Zhang K, Li Z, Miao Y, Guo H. Leaf senescence: progression, regulation, and application. MOLECULAR HORTICULTURE 2021; 1:5. [PMID: 37789484 PMCID: PMC10509828 DOI: 10.1186/s43897-021-00006-9] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/11/2021] [Indexed: 05/24/2023]
Abstract
Leaf senescence, the last stage of leaf development, is a type of postmitotic senescence and is characterized by the functional transition from nutrient assimilation to nutrient remobilization which is essential for plants' fitness. The initiation and progression of leaf senescence are regulated by a variety of internal and external factors such as age, phytohormones, and environmental stresses. Significant breakthroughs in dissecting the molecular mechanisms underpinning leaf senescence have benefited from the identification of senescence-altered mutants through forward genetic screening and functional assessment of hundreds of senescence-associated genes (SAGs) via reverse genetic research in model plant Arabidopsis thaliana as well as in crop plants. Leaf senescence involves highly complex genetic programs that are tightly tuned by multiple layers of regulation, including chromatin and transcription regulation, post-transcriptional, translational and post-translational regulation. Due to the significant impact of leaf senescence on photosynthesis, nutrient remobilization, stress responses, and productivity, much effort has been made in devising strategies based on known senescence regulatory mechanisms to manipulate the initiation and progression of leaf senescence, aiming for higher yield, better quality, or improved horticultural performance in crop plants. This review aims to provide an overview of leaf senescence and discuss recent advances in multi-dimensional regulation of leaf senescence from genetic and molecular network perspectives. We also put forward the key issues that need to be addressed, including the nature of leaf age, functional stay-green trait, coordination between different regulatory pathways, source-sink relationship and nutrient remobilization, as well as translational researches on leaf senescence.
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Affiliation(s)
- Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101 Shandong China
| | - Guodong Ren
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Kewei Zhang
- Institute of Plant Genetics and Developmental Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004 Zhejiang China
| | - Zhonghai Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083 China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Hongwei Guo
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, 518055 Guangdong China
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Ma C, Chen Q, Wang S, Lers A. Downregulation of GeBP-like α factor by MiR827 suggests their involvement in senescence and phosphate homeostasis. BMC Biol 2021; 19:90. [PMID: 33941183 PMCID: PMC8091714 DOI: 10.1186/s12915-021-01015-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 03/29/2021] [Indexed: 01/15/2023] Open
Abstract
Background Leaf senescence is a genetically controlled degenerative process intimately linked to phosphate homeostasis during plant development and responses to environmental conditions. Senescence is accelerated by phosphate deficiency, with recycling and mobilization of phosphate from senescing leaves serving as a major phosphate source for sink tissues. Previously, miR827 was shown to play a significant role in regulating phosphate homeostasis, and induction of its expression was also observed during Arabidopsis leaf senescence. However, whether shared mechanisms underlie potentially common regulatory roles of miR827 in both processes is not understood. Here, we dissect the regulatory machinery downstream of miR827. Results Overexpression or inhibited expression of miR827 led to an acceleration or delay in the progress of senescence, respectively. The transcriptional regulator GLABRA1 enhancer-binding protein (GeBP)-like (GPLα) gene was identified as a possible target of miR827. GPLα expression was elevated in miR827-suppressed lines and reduced in miR827-overexpressing lines. Furthermore, heterologous co-expression of pre-miR827 in tobacco leaves reduced GPLα transcript levels, but this effect was eliminated when pre-miR827 recognition sites in GPLα were mutated. GPLα expression is induced during senescence and its inhibition or overexpression resulted in senescence acceleration and inhibition, accordingly. Furthermore, GPLα expression was induced by phosphate deficiency, and overexpression of GPLα led to reduced expression of phosphate transporter 1 genes, lower leaf phosphate content, and related root morphology. The encoded GPLα protein was localized to the nucleus. Conclusions We suggest that MiR827 and the transcription factor GPLα may be functionally involved in senescence and phosphate homeostasis, revealing a potential new role for miR827 and the function of the previously unstudied GPLα. The close interactions between senescence and phosphate homeostasis are further emphasized by the functional involvement of the two regulatory components, miR827 and GPLα, in both processes and the interactions between them.
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Affiliation(s)
- Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Department of Postharvest Science, Agricultural Research Organization, Volcani Center, HaMaccabim Road 68, 7505101, Rishon LeZion, Israel
| | - Qiuju Chen
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Amnon Lers
- Department of Postharvest Science, Agricultural Research Organization, Volcani Center, HaMaccabim Road 68, 7505101, Rishon LeZion, Israel.
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Ó’Maoiléidigh DS, van Driel AD, Singh A, Sang Q, Le Bec N, Vincent C, de Olalla EBG, Vayssières A, Romera Branchat M, Severing E, Martinez Gallegos R, Coupland G. Systematic analyses of the MIR172 family members of Arabidopsis define their distinct roles in regulation of APETALA2 during floral transition. PLoS Biol 2021; 19:e3001043. [PMID: 33529186 PMCID: PMC7853530 DOI: 10.1371/journal.pbio.3001043] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/29/2020] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs (miRNAs) play important roles in regulating flowering and reproduction of angiosperms. Mature miRNAs are encoded by multiple MIRNA genes that can differ in their spatiotemporal activities and their contributions to gene regulatory networks, but the functions of individual MIRNA genes are poorly defined. We functionally analyzed the activity of all 5 Arabidopsis thaliana MIR172 genes, which encode miR172 and promote the floral transition by inhibiting the accumulation of APETALA2 (AP2) and APETALA2-LIKE (AP2-LIKE) transcription factors (TFs). Through genome editing and detailed confocal microscopy, we show that the activity of miR172 at the shoot apex is encoded by 3 MIR172 genes, is critical for floral transition of the shoot meristem under noninductive photoperiods, and reduces accumulation of AP2 and TARGET OF EAT2 (TOE2), an AP2-LIKE TF, at the shoot meristem. Utilizing the genetic resources generated here, we show that the promotion of flowering by miR172 is enhanced by the MADS-domain TF FRUITFULL, which may facilitate long-term silencing of AP2-LIKE transcription, and that their activities are partially coordinated by the TF SQUAMOSA PROMOTER-BINDING-LIKE PROTEIN 15. Thus, we present a genetic framework for the depletion of AP2 and AP2-LIKE TFs at the shoot apex during floral transition and demonstrate that this plays a central role in floral induction.
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Affiliation(s)
- Diarmuid S. Ó’Maoiléidigh
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, United Kingdom
| | - Annabel D. van Driel
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Anamika Singh
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Qing Sang
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Nolwenn Le Bec
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Coral Vincent
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Alice Vayssières
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Maida Romera Branchat
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Edouard Severing
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Rafael Martinez Gallegos
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - George Coupland
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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15
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Li F, Zhou Y, Yin H, Ai S. Recent advances on signal amplification strategies in photoelectrochemical sensing of microRNAs. Biosens Bioelectron 2020; 166:112476. [DOI: 10.1016/j.bios.2020.112476] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 01/23/2023]
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16
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Zhang Y, Yin S, Tu Y, Mei H, Yang Y. A novel microRNA, SlymiR208, promotes leaf senescence via regulating cytokinin biosynthesis in tomato. PHYSIOLOGIA PLANTARUM 2020; 169:143-155. [PMID: 31985059 DOI: 10.1111/ppl.13068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 01/13/2020] [Accepted: 01/20/2020] [Indexed: 06/10/2023]
Abstract
Leaf senescence is a highly-programmed developmental process during the plant life cycle. Cytokinin (CK) has been widely acknowledged as a negative regulator to delay leaf senescence. MiRNAs play key roles in a variety of developmental and physiological processes through negatively regulating their target gene expression. However, to date, the roles of microRNAs (miRNAs) in CK biosynthesis remain unclear, and the knowledge on miRNA regulation of leaf senescence is still very limited. Isopentenyltransferases (IPTs) catalyze the initial and rate-limiting step of CK biosynthesis in higher plants. Our previous work uncovered that silencing of SlIPT4 expression in tomato resulted in premature leaf senescence. Here, we identified a novel tomato miRNA, SlymiR208, which regulates the expression of SlIPT2 and SlIPT4 at the post-transcriptional level. SlymiR208 expression is ubiquitous in tomato and exhibits an opposite transition to its target transcripts in aged leaf. SlymiR208 overexpression in tomato sharply reduced the transcript levels of SlIPT2 and SlIPT4, and the concentrations of endogenous CKs in leaves. The early leaf senescence caused by SlymiR208 overexpression was consistent with the phenotype of SlIPT4-silenced lines. The data demonstrated that SlymiR208 is a positive regulator in leaf senescence through negatively regulating CK biosynthesis via targeting SlIPT2 and SlIPT4 in tomato. This study indicated that post-transcriptional regulation via miRNA is a control point of CK biosynthesis and added a new layer to the understanding of the regulation of CK biosynthesis in tomato and a new factual proof to support that miRNAs are involved in leaf senescence.
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Affiliation(s)
- Yong Zhang
- Bioengineering College, Chongqing University, Chongqing, 400044, China
| | - Shuangqin Yin
- Bioengineering College, Chongqing University, Chongqing, 400044, China
| | - Yun Tu
- Bioengineering College, Chongqing University, Chongqing, 400044, China
| | - Hu Mei
- Bioengineering College, Chongqing University, Chongqing, 400044, China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing, 400044, China
| | - Yingwu Yang
- Bioengineering College, Chongqing University, Chongqing, 400044, China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing, 400044, China
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Thody J, Moulton V, Mohorianu I. PAREameters: a tool for computational inference of plant miRNA-mRNA targeting rules using small RNA and degradome sequencing data. Nucleic Acids Res 2020; 48:2258-2270. [PMID: 31943065 PMCID: PMC7049721 DOI: 10.1093/nar/gkz1234] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/17/2019] [Accepted: 12/24/2019] [Indexed: 01/19/2023] Open
Abstract
MicroRNAs (miRNAs) are short, non-coding RNAs that modulate the translation-rate of messenger RNAs (mRNAs) by directing the RNA-induced silencing complex to sequence-specific targets. In plants, this typically results in cleavage and subsequent degradation of the mRNA. Degradome sequencing is a high-throughput technique developed to capture cleaved mRNA fragments and thus can be used to support miRNA target prediction. The current criteria used for miRNA target prediction were inferred on a limited number of experimentally validated A. thaliana interactions and were adapted to fit these specific interactions; thus, these fixed criteria may not be optimal across all datasets (organisms, tissues or treatments). We present a new tool, PAREameters, for inferring targeting criteria from small RNA and degradome sequencing datasets. We evaluate its performance using a more extensive set of experimentally validated interactions in multiple A. thaliana datasets. We also perform comprehensive analyses to highlight and quantify the differences between subsets of miRNA-mRNA interactions in model and non-model organisms. Our results show increased sensitivity in A. thaliana when using the PAREameters inferred criteria and that using data-driven criteria enables the identification of additional interactions that further our understanding of the RNA silencing pathway in both model and non-model organisms.
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Affiliation(s)
- Joshua Thody
- School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Irina Mohorianu
- School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0XY, UK
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18
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Zheng C, Ye M, Sang M, Wu R. A Regulatory Network for miR156-SPL Module in Arabidopsis thaliana. Int J Mol Sci 2019; 20:ijms20246166. [PMID: 31817723 PMCID: PMC6940959 DOI: 10.3390/ijms20246166] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
Vegetative phase changes in plants describes the transition between juvenile and adult phases of vegetative growth before flowering. It is one of the most fundamental mechanisms for plants to sense developmental signals, presenting a complex process involving many still-unknown determinants. Several studies in annual and perennial plants have identified the conservative roles of miR156 and its targets, SBP/SPL genes, in guiding the switch of plant growth from juvenile to adult phases. Here, we review recent progress in understanding the regulation of miR156 expression and how miR156-SPLs mediated plant age affect other processes in Arabidopsis. Powerful high-throughput sequencing techniques have provided rich data to systematically study the regulatory mechanisms of miR156 regulation network. From this data, we draw an expanded miR156-regulated network that links plant developmental transition and other fundamental biological processes, gaining novel and broad insight into the molecular mechanisms of plant-age-related processes in Arabidopsis.
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Affiliation(s)
- Chenfei Zheng
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (C.Z.); (M.Y.); (M.S.)
| | - Meixia Ye
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (C.Z.); (M.Y.); (M.S.)
| | - Mengmeng Sang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (C.Z.); (M.Y.); (M.S.)
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (C.Z.); (M.Y.); (M.S.)
- Center for Statistical Genetics, Pennsylvania State University, Hershey, PA 17033, USA
- Correspondence: ; Tel.: +86-10-6322-6264
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He J, Jiang Z, Gao L, You C, Ma X, Wang X, Xu X, Mo B, Chen X, Liu L. Genome-Wide Transcript and Small RNA Profiling Reveals Transcriptomic Responses to Heat Stress. PLANT PHYSIOLOGY 2019; 181:609-629. [PMID: 31395615 PMCID: PMC6776850 DOI: 10.1104/pp.19.00403] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/27/2019] [Indexed: 05/17/2023]
Abstract
Because of climate change, crops will experience increasing heat stress. However, the ways in which heat stress affects crop growth and yield at the molecular level remain poorly understood. We generated spatiotemporal mRNA and small RNA transcriptome data, spanning seven tissues at three time points, to investigate the effects of heat stress on vegetative and reproductive development in maize (Zea mays). Among the small RNAs significantly induced by heat stress was a plastid-derived 19-nucleotide small RNA, which is possibly the residual footprint of a pentatricopeptide repeat protein. This suggests that heat stress induces the turnover of certain plastid transcripts. Consistently, genes responsible for photosynthesis in chloroplasts were repressed after heat stress. Analysis also revealed that the abundance of 24-nucletide small interfering RNAs from transposable elements was conspicuously reduced by heat stress in tassels and roots; nearby genes showed a similar expression trend. Finally, specific microRNA and passenger microRNA species were identified, which in other plant species have not before been reported as responsive to heat stress. This study generated an atlas of genome-wide transcriptomic responses to heat stress, revealing several key regulators as potential targets for thermotolerance improvement in maize.
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Affiliation(s)
- Juan He
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Zengming Jiang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Lei Gao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Chenjiang You
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Xuan Ma
- College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin 300387, China
| | - Xufeng Wang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Xiaofeng Xu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
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20
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Liu T, Tang J, Chen L, Zeng J, Wen J, Yi B, Ma C, Tu J, Fu T, Shen J. Differential expression of miRNAs and their targets in wax-deficient rapeseed. Sci Rep 2019; 9:12201. [PMID: 31434948 PMCID: PMC6704058 DOI: 10.1038/s41598-019-48439-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 08/02/2019] [Indexed: 11/25/2022] Open
Abstract
The cuticle of a plant, composed of cutin and wax, is the outermost hydrophobic layer covering the epidermis of all its aerial organs, protecting it from many abiotic and biotic stresses. The biosynthesis and regulation pathways of wax components have been well studied, whereas there are fewer reports on the small RNA-involved post-transcriptional regulation of wax biosynthesis in plants, particularly in Brassica napus. Previously, we conducted a study on a glossy mutant of rapeseed, and we assumed that there was a dominant repressor to inhibit the expression of wax-related genes. To verify this hypothesis and investigate the function of small RNAs in wax biosynthesis in B. napus, we constructed four small RNA libraries from the stem epidermis of wax-deficient mutant and wild-type plants for sequencing. Subsequently, 43,840,451 clean reads were generated and 24 nt sequences represented the dominant percentage. In total, 300 unique known miRNAs were identified and eight of them showed differential expression. In addition, the expression levels of six novel miRNAs were altered. Surprisingly, we found that four up-regulated miRNAs in the wax-deficient plants, bna-miR408b-5p, bna-miR165b-5p, bna-miR160a-3p, and bna-miR398-5p, were all complementary strands of their corresponding mature strands. Stem-loop qRT-PCR verified that the expression of bna-miR165a-5p was increased in the mutant stems, while its putative target, BnaA06g40560D (CYP96A2), was down-regulated. In addition, the expression of bna-miR827a was detected to be down-regulated in glossy mutant. 5' RACE experimental data showed that bna-miR827a cleaves three NITROGEN LIMITATION ADAPTATION (NLA) genes (BnaC08g45940D, BnaA10g01450D and BnaC05g01480D). The down-regulation of bna-miR827a resulted in decreased cleavage on its targets, and led to the up-regulation of its targets, especially BnaA10g01450D gene. These results showed that bna-miR165a-5p might participate in wax biosynthesis process by regulating its putative target BnaA06g40560D (CYP96A2). The expression levels of a phosphate (Pi)-related miRNA, bna-miR827a, and its target genes were affected in wax-deficient rapeseeds. These results will promote the study of post-transcriptional regulation mechanisms of wax biosynthesis in B. napus and provide new directions for further research.
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Affiliation(s)
- Tingting Liu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jingquan Tang
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Li Chen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jiayue Zeng
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China.
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21
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Thody J, Folkes L, Medina-Calzada Z, Xu P, Dalmay T, Moulton V. PAREsnip2: a tool for high-throughput prediction of small RNA targets from degradome sequencing data using configurable targeting rules. Nucleic Acids Res 2019; 46:8730-8739. [PMID: 30007348 PMCID: PMC6158750 DOI: 10.1093/nar/gky609] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/25/2018] [Indexed: 12/25/2022] Open
Abstract
Small RNAs (sRNAs) are short, non-coding RNAs that play critical roles in many important biological pathways. They suppress the translation of messenger RNAs (mRNAs) by directing the RNA-induced silencing complex to their sequence-specific mRNA target(s). In plants, this typically results in mRNA cleavage and subsequent degradation of the mRNA. The resulting mRNA fragments, or degradome, provide evidence for these interactions, and thus degradome analysis has become an important tool for sRNA target prediction. Even so, with the continuing advances in sequencing technologies, not only are larger and more complex genomes being sequenced, but also degradome and associated datasets are growing both in number and read count. As a result, existing degradome analysis tools are unable to process the volume of data being produced without imposing huge resource and time requirements. Moreover, these tools use stringent, non-configurable targeting rules, which reduces their flexibility. Here, we present a new and user configurable software tool for degradome analysis, which employs a novel search algorithm and sequence encoding technique to reduce the search space during analysis. The tool significantly reduces the time and resources required to perform degradome analysis, in some cases providing more than two orders of magnitude speed-up over current methods.
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Affiliation(s)
| | - Leighton Folkes
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | | | - Ping Xu
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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22
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Abstract
Leaf senescence is an important developmental process involving orderly disassembly of macromolecules for relocating nutrients from leaves to other organs and is critical for plants' fitness. Leaf senescence is the response of an intricate integration of various environmental signals and leaf age information and involves a complex and highly regulated process with the coordinated actions of multiple pathways. Impressive progress has been made in understanding how senescence signals are perceived and processed, how the orderly degeneration process is regulated, how the senescence program interacts with environmental signals, and how senescence regulatory genes contribute to plant productivity and fitness. Employment of systems approaches using omics-based technologies and characterization of key regulators have been fruitful in providing newly emerging regulatory mechanisms. This review mainly discusses recent advances in systems understanding of leaf senescence from a molecular network dynamics perspective. Genetic strategies for improving the productivity and quality of crops are also described.
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Affiliation(s)
- Hye Ryun Woo
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea; ,
| | - Hyo Jung Kim
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu 42988, Republic of Korea
| | - Pyung Ok Lim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea; ,
| | - Hong Gil Nam
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea; ,
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu 42988, Republic of Korea
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23
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Micromanagement of Developmental and Stress-Induced Senescence: The Emerging Role of MicroRNAs. Genes (Basel) 2019; 10:genes10030210. [PMID: 30871088 PMCID: PMC6470504 DOI: 10.3390/genes10030210] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/22/2019] [Accepted: 03/06/2019] [Indexed: 01/13/2023] Open
Abstract
MicroRNAs are short (19⁻24-nucleotide-long), non-coding RNA molecules. They downregulate gene expression by triggering the cleavage or translational inhibition of complementary mRNAs. Senescence is a stage of development following growth completion and is dependent on the expression of specific genes. MicroRNAs control the gene expression responsible for plant competence to answer senescence signals. Therefore, they coordinate the juvenile-to-adult phase transition of the whole plant, the growth and senescence phase of each leaf, age-related cellular structure changes during vessel formation, and remobilization of resources occurring during senescence. MicroRNAs are also engaged in the ripening and postharvest senescence of agronomically important fruits. Moreover, the hormonal regulation of senescence requires microRNA contribution. Environmental cues, such as darkness or drought, induce senescence-like processes in which microRNAs also play regulatory roles. In this review, we discuss recent findings concerning the role of microRNAs in the senescence of various plant species.
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Kuo YW, Lin JS, Li YC, Jhu MY, King YC, Jeng ST. MicroR408 regulates defense response upon wounding in sweet potato. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:469-483. [PMID: 30403812 PMCID: PMC6322576 DOI: 10.1093/jxb/ery381] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/02/2018] [Indexed: 05/08/2023]
Abstract
MiRNAs play diverse roles in plant development and defense responses by binding to their mRNA targets based on sequence complementarity. Here, we investigated a wound-related miR408 and its target genes in sweet potato (Ipomoea batatas) by small RNA deep sequencing and transcriptome analysis. The expression patterns of miR408 and the miR408 precursor were significantly repressed by wounding and jasmonate (JA). In contrast, expression of the putative target genes IbKCS (3-ketoacyl-CoA synthase 4), IbPCL (plantacyanin), and IbGAUT (galacturonosyltransferase 7-like) of miR408 was increased following wounding, whereas only IbKCS was increased after JA treatment. Target cleavage site mapping and Agrobacterium-mediated transient assay demonstrated that IbKCS, IbPCL, and IbGAUT were the targets of miR408. The expression of miR408 target genes was repressed in transgenic sweet potatoes overexpressing miR408. These data indicated a relationship between miR408 and its target genes. Notably, miR408-overexpressing plants showed a semi-dwarf phenotype and attenuated resistance to insect feeding, while transgenic plants overexpressing IbKCS exhibited more insect resistance than plants overexpressing only the empty vector. Collectively, sweet potato reduces the abundance of miR408 upon wounding to elevate the expression of IbKCS, IbPCL, and IbGAUT. The expression of IbKCS enhances the defense system against herbivore wounding.
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Affiliation(s)
- Yun-Wei Kuo
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Jeng-Shane Lin
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Chi Li
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Min-Yao Jhu
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yu-Chi King
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Shih-Tong Jeng
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
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Vargas-Asencio JA, Perry KL. A Small RNA-Mediated Regulatory Network in Arabidopsis thaliana Demonstrates Connectivity Between phasiRNA Regulatory Modules and Extensive Co-Regulation of Transcription by miRNAs and phasiRNAs. FRONTIERS IN PLANT SCIENCE 2019; 10:1710. [PMID: 32082334 PMCID: PMC7001039 DOI: 10.3389/fpls.2019.01710] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 12/05/2019] [Indexed: 05/19/2023]
Abstract
Gene regulation involves the orchestrated action of multiple regulators to fine-tune the expression of genes. Hierarchical interactions and co-regulation among regulators are commonly observed in biological systems, leading to complex regulatory networks. Small RNA (sRNAs) have been shown to be important regulators of gene expression due to their involvement in multiple cellular processes. In plants, microRNA (miRNAs) and phased small interfering RNAs (phasiRNAs) correspond to two well-characterized types of sRNAs involved in the regulation of posttranscriptional gene expression, although information about their targets and interactions with other gene expression regulators is limited. We describe an extended sRNA-mediated regulatory network in Arabidopsis thaliana that provides a reference frame to understand sRNA biogenesis and activity at the genome-wide level. This regulatory network combines a comprehensive evaluation of phasiRNA production and sRNA targets supported by degradome data. The network includes ~17% of genes in the A. thaliana genome, representing ~50% annotated gene ontology (GO) functional categories. Approximately 14% of genes with GO annotations corresponding to regulation of gene expression were found to be under sRNA control. The unbiased bioinformatic approach used to produce the network was able to detect 107 PHAS loci (regions of phasiRNA production), 5,047 active phasiRNAs (~70% of which were non-canonical), and reconstruct 17 regulatory modules resulting from complex regulatory interactions between different sRNA-regulatory pathways. Known regulatory modules like miR173-TAS-PPR/TPR and miR390-TAS3-ARF/F-box were faithfully reconstructed and expanded, illustrating the accuracy and sensitivity of the methods and providing confidence for the validity of findings of previously unrecognized modules. The network presented here includes a 2X increase in the number of identified PHAS loci, a large complement (~70%) of non-canonical phasiRNAs, and the most comprehensive evaluation of sRNA cleavage activity in A. thaliana to date. Structural analysis showed similarities to networks of other biological systems and demonstrated connectivity between phasiRNA regulatory modules with extensive co-regulation of transcripts by miRNAs and phasiRNAs. The described regulatory network provides a reference that will facilitate global analyses of individual plant regulatory programs such as those that control homeostasis, development, and responses to biotic and abiotic environmental changes.
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26
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Wang Y, Guo S, Wang L, Wang L, He X, Shu S, Sun J, Lu N. Identification of microRNAs associated with the exogenous spermidine-mediated improvement of high-temperature tolerance in cucumber seedlings (Cucumis sativus L.). BMC Genomics 2018; 19:285. [PMID: 29690862 PMCID: PMC5937831 DOI: 10.1186/s12864-018-4678-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 04/16/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND High-temperature stress inhibited the growth of cucumber seedlings. Foliar spraying of 1.0 mmol·L- 1 exogenous spermidine (Spd) to the sensitive cucumber cultivar 'Jinchun No. 2' grown at high-temperature (42 °C/32 °C) in an artificial climate box improved the high-temperature tolerance. Although there have been many reports on the response of microRNAs (miRNAs) to high-temperature stress, the mechanism by which exogenous Spd may mitigate the damage of high-temperature stress through miRNA-mediated regulation has not been studied. RESULTS To elucidate the regulation of miRNAs in response to exogenous Spd-mediated improvement of high-temperature tolerance, four small RNA libraries were constructed from cucumber leaves and sequenced: untreated-control (CW), Spd-treated (CS), high-temperature stress (HW), and Spd-treated and high-temperature stress (HS). As a result, 107 known miRNAs and 79 novel miRNAs were identified. Eight common differentially expressed miRNAs (miR156d-3p, miR170-5p, miR2275-5p, miR394a, miR479b, miR5077, miR5222 and miR6475) were observed in CS/CW, HW/CW, HS/CW and HS/HW comparison pairs, which were the first set of miRNAs that responded to not only high-temperature stress but also exogenous Spd in cucumber seedlings. Five of the eight miRNAs were predicted to target 107 potential genes. Gene function and pathway analyses highlighted the integral role that these miRNAs and target genes probably play in the improvement of the high-temperature tolerance of cucumber seedlings through exogenous Spd application. CONCLUSIONS Our study identified the first set of miRNAs associated with the exogenous Spd-mediated improvement of high-temperature tolerance in cucumber seedlings. The results could help to promote further studies on the complex molecular mechanisms underlying high-temperature tolerance in cucumber and provide a theoretical basis for the high-quality and efficient cultivation of cucumber with high-temperature resistance.
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Affiliation(s)
- Ying Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Nanjing Agricultural University (Suqian) Academy of Protected Horticulture, Suqian, 223800, Jiangsu, China
| | - Shirong Guo
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Nanjing Agricultural University (Suqian) Academy of Protected Horticulture, Suqian, 223800, Jiangsu, China
| | - Lei Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Nanjing Agricultural University (Suqian) Academy of Protected Horticulture, Suqian, 223800, Jiangsu, China
| | - Liwei Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Nanjing Agricultural University (Suqian) Academy of Protected Horticulture, Suqian, 223800, Jiangsu, China
| | - Xueying He
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Nanjing Agricultural University (Suqian) Academy of Protected Horticulture, Suqian, 223800, Jiangsu, China
| | - Sheng Shu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Nanjing Agricultural University (Suqian) Academy of Protected Horticulture, Suqian, 223800, Jiangsu, China
| | - Jin Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
- Nanjing Agricultural University (Suqian) Academy of Protected Horticulture, Suqian, 223800, Jiangsu, China.
| | - Na Lu
- Center for Environment, Health and Field Sciences, Chiba University, Kashiwa-no-ha 6-2-1, Kashiwa, Chiba, Japan
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27
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Kim J, Kim JH, Lyu JI, Woo HR, Lim PO. New insights into the regulation of leaf senescence in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:787-799. [PMID: 28992051 DOI: 10.1093/jxb/erx287] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Plants undergo developmental changes throughout their life history. Senescence, the final stage in the life history of a leaf, is an important and unique developmental process whereby plants relocate nutrients from leaves to other developing organs, such as seeds, stems, or roots. Recent attempts to answer fundamental questions about leaf senescence have employed a combination of new ideas and advanced technologies. As senescence is an integral part of a plant's life history that is linked to earlier developmental stages, age-associated leaf senescence may be analysed from a life history perspective. The successful utilization of multi-omics approaches has resolved the complicated process of leaf senescence, replacing a component-based view with a network-based molecular mechanism that acts in a spatial-temporal manner. Senescence and death are critical for fitness and are thus evolved characters. Recent efforts have begun to focus on understanding the evolutionary basis of the developmental process that incorporates age information and environmental signals into a plant's survival strategy. This review describes recent insights into the regulatory mechanisms of leaf senescence in terms of systems-level spatiotemporal changes, presenting them from the perspectives of life history strategy and evolution.
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Affiliation(s)
- Jeongsik Kim
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea
| | - Jin Hee Kim
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea
| | - Jae Il Lyu
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea
| | - Hye Ryun Woo
- Department of New Biology, DGIST, Daegu, Republic of Korea
| | - Pyung Ok Lim
- Department of New Biology, DGIST, Daegu, Republic of Korea
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28
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Großkinsky DK, Syaifullah SJ, Roitsch T. Integration of multi-omics techniques and physiological phenotyping within a holistic phenomics approach to study senescence in model and crop plants. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:825-844. [PMID: 29444308 DOI: 10.1093/jxb/erx333] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The study of senescence in plants is complicated by diverse levels of temporal and spatial dynamics as well as the impact of external biotic and abiotic factors and crop plant management. Whereas the molecular mechanisms involved in developmentally regulated leaf senescence are very well understood, in particular in the annual model plant species Arabidopsis, senescence of other organs such as the flower, fruit, and root is much less studied as well as senescence in perennials such as trees. This review addresses the need for the integration of multi-omics techniques and physiological phenotyping into holistic phenomics approaches to dissect the complex phenomenon of senescence. That became feasible through major advances in the establishment of various, complementary 'omics' technologies. Such an interdisciplinary approach will also need to consider knowledge from the animal field, in particular in relation to novel regulators such as small, non-coding RNAs, epigenetic control and telomere length. Such a characterization of phenotypes via the acquisition of high-dimensional datasets within a systems biology approach will allow us to systematically characterize the various programmes governing senescence beyond leaf senescence in Arabidopsis and to elucidate the underlying molecular processes. Such a multi-omics approach is expected to also spur the application of results from model plants to agriculture and their verification for sustainable and environmentally friendly improvement of crop plant stress resilience and productivity and contribute to improvements based on postharvest physiology for the food industry and the benefit of its customers.
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Affiliation(s)
- Dominik K Großkinsky
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé, Taastrup, Denmark
| | - Syahnada Jaya Syaifullah
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé, Taastrup, Denmark
| | - Thomas Roitsch
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé, Taastrup, Denmark
- Department of Adaptive Biotechnologies, Global Change Research Institute, CAS, v.v.i., Drásov, Czech Republic
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29
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Yolcu S, Li X, Li S, Kim YJ. Beyond the genetic code in leaf senescence. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:801-810. [PMID: 29253191 DOI: 10.1093/jxb/erx401] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 05/10/2017] [Indexed: 06/07/2023]
Abstract
Leaf senescence is not only genetically programmed but also induced by exogenous stress to ensure completion of the plant life cycle, successful reproduction and environmental adaptability. Genetic reprogramming is a major aspect of leaf senescence, and the senescence signaling that follows is controlled by a complex regulatory network. Recent studies suggest that the activity of transcription factors together with epigenetic mechanisms ensures the robustness of this network, with the latter including chromatin remodeling, DNA modification, and RNA-mediated control of transcription factors and other senescence-associated genes. In this review, we provide an overview of the relevant epigenetic mechanisms and summarize recent findings of epigenetic regulators of plant leaf senescence involved in DNA methylation and histone modification along with the functions of small RNAs in this process.
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Affiliation(s)
- Seher Yolcu
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea
| | - Xiaojie Li
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shengben Li
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yun Ju Kim
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea
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30
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Huang D, Lan W, Li D, Deng B, Lin W, Ren Y, Miao Y. WHIRLY1 Occupancy Affects Histone Lysine Modification and WRKY53 Transcription in Arabidopsis Developmental Manner. FRONTIERS IN PLANT SCIENCE 2018; 9:1503. [PMID: 30405658 PMCID: PMC6202938 DOI: 10.3389/fpls.2018.01503] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 09/26/2018] [Indexed: 05/21/2023]
Abstract
Single-stranded DNA-binding proteins (SSBs) are assumed to involve in DNA replication, DNA repairmen, and gene transcription. Here, we provide the direct evidence on the functionality of an Arabidopsis SSB, WHIRLY1, by using loss- or gain-of-function lines. We show that WHIRLY1 binding to the promoter of WRKY53 represses the enrichment of H3K4me3, but enhances the enrichment of H3K9ac at the region contained WHIRLY1-binding sequences and TATA box or the translation start region of WRKY53, coincided with a recruitment of RNAPII. In vitro ChIP assays confirm that WHIRLY1 inhibits H3K4me3 enrichment at the preinitiation complex formation stage, while promotes H3K9ac enrichment and RNAPII recruitment at the elongation stage, consequently affecting the transcription of WRKY53. These results further explore the molecular actions underlying SSB-mediated gene transcription through epigenetic regulation in plant senescence.
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31
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Yu D, Ma X, Zuo Z, Shao W, Wang H, Meng Y. Bioinformatics resources for deciphering the biogenesis and action pathways of plant small RNAs. RICE (NEW YORK, N.Y.) 2017; 10:38. [PMID: 28786034 PMCID: PMC5545994 DOI: 10.1186/s12284-017-0177-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 08/03/2017] [Indexed: 05/31/2023]
Abstract
The next-generation sequencing (NGS) technology has revolutionized our previous understanding of the plant genomes, relying on its innate advantages, such as high throughput and deep sequencing depth. In addition to the protein-coding gene loci, massive transcription signals have been detected within intergenic or intragenic regions. Most of these signals belong to non-coding ones, considering their weak protein-coding potential. Generally, these transcripts could be divided into long non-coding RNAs and small non-coding RNAs (sRNAs) based on their sequence length. In addition to the well-known microRNAs (miRNAs), many plant endogenous sRNAs were collectively referred to as small interfering RNAs. However, an increasing number of unclassified sRNA species are being discovered by NGS. The high heterogeneity of these novel sRNAs greatly hampered the mechanistic studies, especially on the clear description of their biogenesis and action pathways. Fortunately, public databases, bioinformatics softwares and NGS datasets are increasingly available for plant sRNA research. Here, by summarizing these valuable resources, we proposed a general workflow to decipher the RDR (RNA-dependent RNA polymerase)- and DCL (Dicer-like)-dependent biogenesis pathways, and the Argonaute-mediated action modes (such as target cleavages and chromatin modifications) for specific sRNA species in plants. Taken together, we hope that by summarizing a list of the public resources, this work will facilitate the plant biologists to perform classification and functional characterization of the interesting sRNA species.
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Affiliation(s)
- Dongliang Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Xiaoxia Ma
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Ziwei Zuo
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Weishan Shao
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China.
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China.
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32
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Koyama T, Sato F, Ohme-Takagi M. Roles of miR319 and TCP Transcription Factors in Leaf Development. PLANT PHYSIOLOGY 2017; 175:874-885. [PMID: 28842549 PMCID: PMC5619901 DOI: 10.1104/pp.17.00732] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/23/2017] [Indexed: 05/19/2023]
Abstract
Sophisticated regulation of gene expression, including microRNAs (miRNAs) and their target genes, is required for leaf differentiation, growth, and senescence. The impact of miR319 and its target TEOSINTE BRANCHED1, CYCLOIDEA, and PROLIFERATING CELL NUCLEAR ANTIGEN BINDING FACTOR (TCP) genes on leaf development has been extensively investigated, but the redundancies of these gene families often interfere with the evaluation of their function and regulation in the developmental context. Here, we present the genetic evidence of the involvement of the MIR319 and TCP gene families in Arabidopsis (Arabidopsis thaliana) leaf development. Single mutations in MIR319A and MIR319B genes moderately inhibited the formation of leaf serrations, whereas double mutations increased the extent of this inhibition and resulted in the formation of smooth leaves. Mutations in MIR319 and gain-of-function mutations in the TCP4 gene conferred resistance against miR319 and impaired the cotyledon boundary and leaf serration formation. These mutations functionally associated with CUP-SHAPED COTYLEDON genes, which regulate the cotyledon boundary and leaf serration formation. In contrast, loss-of-function mutations in miR319-targeted and nontargeted TCP genes cooperatively induced the formation of serrated leaves in addition to changes in the levels of their downstream gene transcript. Taken together, these findings demonstrate that the MIR319 and TCP gene families underlie robust and multilayer control of leaf development. This study also provides a framework toward future researches on redundant miRNAs and transcription factors in Arabidopsis and crop plants.
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Affiliation(s)
- Tomotsugu Koyama
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Seikacho, Kyoto 619-0284, Japan
| | - Fumihiko Sato
- Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Masaru Ohme-Takagi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8562, Japan
- Institute for Environmental Science and Technology, Saitama University, Sakura, Saitama 388-8570, Japan
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33
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Li M, Liang Z, He S, Zeng Y, Jing Y, Fang W, Wu K, Wang G, Ning X, Wang L, Li S, Tan H, Tan F. Genome-wide identification of leaf abscission associated microRNAs in sugarcane (Saccharum officinarum L.). BMC Genomics 2017; 18:754. [PMID: 28946845 PMCID: PMC5613641 DOI: 10.1186/s12864-017-4053-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/11/2017] [Indexed: 11/16/2022] Open
Abstract
Background Sugarcane (Saccharum officinarum L.) is an economically important crop, mainly due to the production of sugar and biofuel (Azevedo RA, Carvalho RF, Cia MC, & Gratão PL, Trop Plant Biol 4:42-51, 2011). Grown mainly in tropical and subtropical countries, sugarcane is a highly polyploid plant with up to ten copies of each chromosome, which increases the difficulties of genome assembly and genetic, physiologic and biochemical analyses. The increasing demands of sugar and the increasing cost of sugarcane harvest require sugarcane varieties which can shed their leaves during the maturity time, so it is important to study the mechanism of leaf abscission in sugarcane. Results To improve the understanding of miRNA roles in sugarcane leaf abscission, we reported the genome-wide characterization of miRNAs and their putative targets in sugarcane using deep sequencing for six small RNA libraries. In total, 93 conserved miRNAs and 454 novel miRNAs were identified in sugarcane using previously reported transcriptome as reference. Among them, 25 up-regulated and 13 down-regulated miRNAs were identified in leaf abscission sugarcane plants (LASP) compared to leaf packaging sugarcane plants (LPSP). Target prediction revealed several miRNA-mRNA modules including miR156-SPL, miR319-TPR2, miR396-GRF and miR408-LAC3 might be involved in the sugarcane leaf abscission. KEGG pathway enrichment analysis showed differentially expressed miRNAs may regulate pathways like “plant hormone signal transduction” and “plant-pathogen interaction”, which is consistent with previous transcriptome study. In addition, we identified 96 variant miRNAs with 135 single nucleotide polymorphisms (SNPs). The expression of sugarcane miRNAs and variant miRNAs were confirmed by qRT-PCR. We identified a possible poaceae specific miRNA called miR5384 for the first time in sugarcane. Conclusions We not only reported miR5384, a possible poaceae specific miRNA, for the first time in sugarcane but also presented some miRNA-mRNA modules including miR156-SPL, miR319-TPR2, miR396-GRF and miR408-LAC in sugarcane. These modules might be involved in the regulation of sugarcane leaf abscission during the maturity time. All of these findings may lay ground work for future application of sugarcane breeding program and benefit research studies of sugarcane miRNAs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4053-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ming Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China.
| | - Zhaoxu Liang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Shanshan He
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Yuan Zeng
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Yan Jing
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Weikuan Fang
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Kaichao Wu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Guanyu Wang
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Xia Ning
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Lunwang Wang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Song Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Hongwei Tan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Fang Tan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
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Picard CL, Gehring M. Proximal methylation features associated with nonrandom changes in gene body methylation. Genome Biol 2017; 18:73. [PMID: 28446217 PMCID: PMC5406939 DOI: 10.1186/s13059-017-1206-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/04/2017] [Indexed: 11/10/2022] Open
Abstract
Background Gene body methylation at CG dinucleotides is a widely conserved feature of methylated genomes but remains poorly understood. The Arabidopsis thaliana strain Cvi has depleted gene body methylation relative to the reference strain Col. Here, we leverage this natural epigenetic difference to investigate gene body methylation stability. Results Recombinant inbred lines derived from Col and Cvi were used to examine the transmission of distinct gene body methylation states. The vast majority of genic CG methylation patterns are faithfully transmitted over nine generations according to parental genotype, with only 1–4% of CGs either losing or gaining methylation relative to the parent. Genic CGs that fail to maintain the parental methylation state are shared among independent lines, suggesting that these are not random occurrences. We use a logistic regression framework to identify features that best predict sites that fail to maintain parental methylation state. Intermediate levels of CG methylation around a dynamic CG site and high methylation variability across many A. thaliana strains at that site are the strongest predictors. These data suggest that the dynamic CGs we identify are not specific to the Col–Cvi recombinant inbred lines but have an epigenetic state that is inherently less stable within the A. thaliana species. Extending this, variably methylated genic CGs in maize and Brachypodium distachyon are also associated with intermediate local CG methylation. Conclusions These results provide new insights into the features determining the inheritance of gene body methylation and demonstrate that two different methylation equilibria can be maintained within single individuals. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1206-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Colette L Picard
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.,Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Mary Gehring
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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Wang B, Wang J, Wang C, Shen W, Jia H, Zhu X, Li X. Study on Expression Modes and Cleavage Role of miR156b/c/d and its Target Gene Vv-SPL9 During the Whole Growth Stage of Grapevine. J Hered 2016; 107:626-634. [PMID: 27660497 DOI: 10.1093/jhered/esw030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 04/29/2016] [Indexed: 11/14/2022] Open
Abstract
miR156 regulates the expression of its target SPL (PROMOTER BINDING-LIKE) genes during flower and fruit development, diverse developmental stage transitions, especially from vegetative to reproductive growth phases, by cleaving the target mRNA SPL of one plant-specific transcription factor. However, systematic reports on grapevine have yet to be presented. Here, the precise sequence of miR156 (vvi-miR156b/c/d) in grapevine "Takatsuma" was cloned with a previously cloned grapevine SPL (Vv-SPL9). Expression profiles in 18 grapevine tissues were identified through stem-loop RT-PCR. The interaction mode between vvi-miR156b/c/d and Vv-SPL9 was further validated by detecting the cleavage site and cleavage products of 3'- and 5'-ends via an integrated approach of 5'-RLM-RACE (RNA ligase-mediated 5'-rapid amplification of cDNA ends), 3'-PPM-RACE (poly(A) polymerase-mediated 3'-rapid amplification of cDNA ends), and qRT-PCR (real time reverse transcriptase-polymerase chain reaction). The variation in their cleavage roles in the whole growth stage of grapevine was also systematically investigated. Results showed that vvi-miR156b/c/d exhibited typical temporal-spatial-specific expression levels. The expression levels were higher in vegetative organs, such as leaf, than in reproductive organs, such as tendrils, flowers, and berries. A significant variation was observed during vegetative-to-reproductive transition. The expression patterns of Vv-SPL9 showed the opposite trends with those of vvi-miR156b. We confirmed that the cleavage site was at the 10th site of vvi-miR156b/c/d complementary to Vv-SPL9 in "Takatsuma" grapevine. We also identified the temporal-spatial variation of the cleavage products. This variation can indicate the regulatory function of miR156 on SPL in grapevines. Our findings provide further insights into the functions of vvi-miR156b/c/d and its target Vv-SPL9, and also help enrich our knowledge of small RNA-mediated regulation in grapevine.
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Affiliation(s)
- Baoju Wang
- From the College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China (B. Wang, J. Wang, C. Wang, Jia, Zhu, and Li); and College of Life Science, Nanjing Agricultural University, Nanjing 210095, China (Shen)
| | - Jian Wang
- From the College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China (B. Wang, J. Wang, C. Wang, Jia, Zhu, and Li); and College of Life Science, Nanjing Agricultural University, Nanjing 210095, China (Shen)
| | - Chen Wang
- From the College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China (B. Wang, J. Wang, C. Wang, Jia, Zhu, and Li); and College of Life Science, Nanjing Agricultural University, Nanjing 210095, China (Shen).
| | - Wenbiao Shen
- From the College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China (B. Wang, J. Wang, C. Wang, Jia, Zhu, and Li); and College of Life Science, Nanjing Agricultural University, Nanjing 210095, China (Shen)
| | - Haifeng Jia
- From the College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China (B. Wang, J. Wang, C. Wang, Jia, Zhu, and Li); and College of Life Science, Nanjing Agricultural University, Nanjing 210095, China (Shen)
| | - Xudong Zhu
- From the College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China (B. Wang, J. Wang, C. Wang, Jia, Zhu, and Li); and College of Life Science, Nanjing Agricultural University, Nanjing 210095, China (Shen)
| | - Xiaopeng Li
- From the College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China (B. Wang, J. Wang, C. Wang, Jia, Zhu, and Li); and College of Life Science, Nanjing Agricultural University, Nanjing 210095, China (Shen)
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Kim J, Woo HR, Nam HG. Toward Systems Understanding of Leaf Senescence: An Integrated Multi-Omics Perspective on Leaf Senescence Research. MOLECULAR PLANT 2016; 9:813-25. [PMID: 27174403 DOI: 10.1016/j.molp.2016.04.017] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 04/15/2016] [Accepted: 04/27/2016] [Indexed: 05/20/2023]
Abstract
Leaf senescence is a complex but tightly regulated developmental process involving a coordinated sequence of multiple molecular events, which ultimately leads to death of the leaf. Efforts to understand the mechanistic principles underlying leaf senescence have been largely made by transcriptomic, proteomic, and metabolomic studies over the past decade. This review focuses on recent milestones in leaf senescence research obtained using multi-omics technologies, as well as future endeavors toward systems understanding of leaf senescence processes. In particular, we discuss recent advances in understanding molecular events during leaf senescence through genome-wide transcriptome analyses in Arabidopsis. We also describe comparative transcriptome analyses used to unveil the commonality and diversity of regulatory mechanisms governing leaf senescence in the plant kingdom. Finally, we provide current illustrations of epigenomic, proteomic, and metabolomic landscapes of leaf senescence. We envisage that integration of multi-omics leaf senescence data will enable us to address unresolved questions regarding leaf senescence, including determining the molecular principles that coordinate concurrent and ordered changes in biological events during leaf senescence.
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Affiliation(s)
- Jeongsik Kim
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Republic of Korea
| | - Hye Ryun Woo
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea.
| | - Hong Gil Nam
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Republic of Korea; Department of New Biology, DGIST, Daegu, 42988, Republic of Korea.
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Woo HR, Koo HJ, Kim J, Jeong H, Yang JO, Lee IH, Jun JH, Choi SH, Park SJ, Kang B, Kim YW, Phee BK, Kim JH, Seo C, Park C, Kim SC, Park S, Lee B, Lee S, Hwang D, Nam HG, Lim PO. Programming of Plant Leaf Senescence with Temporal and Inter-Organellar Coordination of Transcriptome in Arabidopsis. PLANT PHYSIOLOGY 2016; 171:452-67. [PMID: 26966169 PMCID: PMC4854694 DOI: 10.1104/pp.15.01929] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/07/2016] [Indexed: 05/20/2023]
Abstract
Plant leaves, harvesting light energy and fixing CO2, are a major source of foods on the earth. Leaves undergo developmental and physiological shifts during their lifespan, ending with senescence and death. We characterized the key regulatory features of the leaf transcriptome during aging by analyzing total- and small-RNA transcriptomes throughout the lifespan of Arabidopsis (Arabidopsis thaliana) leaves at multidimensions, including age, RNA-type, and organelle. Intriguingly, senescing leaves showed more coordinated temporal changes in transcriptomes than growing leaves, with sophisticated regulatory networks comprising transcription factors and diverse small regulatory RNAs. The chloroplast transcriptome, but not the mitochondrial transcriptome, showed major changes during leaf aging, with a strongly shared expression pattern of nuclear transcripts encoding chloroplast-targeted proteins. Thus, unlike animal aging, leaf senescence proceeds with tight temporal and distinct interorganellar coordination of various transcriptomes that would be critical for the highly regulated degeneration and nutrient recycling contributing to plant fitness and productivity.
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Affiliation(s)
- Hye Ryun Woo
- Department of New Biology, DGIST, Daegu, Republic of Korea (H.R.W., D.H., H.G.N., P.O.L.);Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea (H.J.K., J.K., H.J., I.H.L., S.H.C., S.J.P., B.K., Y.W.K., B.-K.P., J.H.K., D.H., H.G.N.);School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea (H.J.K.);Korean Bioinformation Center, KRIBB, Daejeon, Republic of Korea (J.O.Y., S.C.K., S.P., B.L.);Division of Molecular Life Sciences, POSTECH, Pohang, Republic of Korea (I.H.L., J.H.J., S.H.C.);Division of Integrative Biosciences and Biotechnologies, POSTECH, Pohang, Republic of Korea (S.J.P.);DNA Link Inc., Seoul, Republic of Korea (C.S.); andEwha Research Center for Systems Biology and Department of Life Science, Ewha Womans University, Seoul, Republic of Korea (C.P., S.L.)
| | - Hee Jung Koo
- Department of New Biology, DGIST, Daegu, Republic of Korea (H.R.W., D.H., H.G.N., P.O.L.);Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea (H.J.K., J.K., H.J., I.H.L., S.H.C., S.J.P., B.K., Y.W.K., B.-K.P., J.H.K., D.H., H.G.N.);School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea (H.J.K.);Korean Bioinformation Center, KRIBB, Daejeon, Republic of Korea (J.O.Y., S.C.K., S.P., B.L.);Division of Molecular Life Sciences, POSTECH, Pohang, Republic of Korea (I.H.L., J.H.J., S.H.C.);Division of Integrative Biosciences and Biotechnologies, POSTECH, Pohang, Republic of Korea (S.J.P.);DNA Link Inc., Seoul, Republic of Korea (C.S.); andEwha Research Center for Systems Biology and Department of Life Science, Ewha Womans University, Seoul, Republic of Korea (C.P., S.L.)
| | - Jeongsik Kim
- Department of New Biology, DGIST, Daegu, Republic of Korea (H.R.W., D.H., H.G.N., P.O.L.);Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea (H.J.K., J.K., H.J., I.H.L., S.H.C., S.J.P., B.K., Y.W.K., B.-K.P., J.H.K., D.H., H.G.N.);School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea (H.J.K.);Korean Bioinformation Center, KRIBB, Daejeon, Republic of Korea (J.O.Y., S.C.K., S.P., B.L.);Division of Molecular Life Sciences, POSTECH, Pohang, Republic of Korea (I.H.L., J.H.J., S.H.C.);Division of Integrative Biosciences and Biotechnologies, POSTECH, Pohang, Republic of Korea (S.J.P.);DNA Link Inc., Seoul, Republic of Korea (C.S.); andEwha Research Center for Systems Biology and Department of Life Science, Ewha Womans University, Seoul, Republic of Korea (C.P., S.L.)
| | - Hyobin Jeong
- Department of New Biology, DGIST, Daegu, Republic of Korea (H.R.W., D.H., H.G.N., P.O.L.);Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea (H.J.K., J.K., H.J., I.H.L., S.H.C., S.J.P., B.K., Y.W.K., B.-K.P., J.H.K., D.H., H.G.N.);School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea (H.J.K.);Korean Bioinformation Center, KRIBB, Daejeon, Republic of Korea (J.O.Y., S.C.K., S.P., B.L.);Division of Molecular Life Sciences, POSTECH, Pohang, Republic of Korea (I.H.L., J.H.J., S.H.C.);Division of Integrative Biosciences and Biotechnologies, POSTECH, Pohang, Republic of Korea (S.J.P.);DNA Link Inc., Seoul, Republic of Korea (C.S.); andEwha Research Center for Systems Biology and Department of Life Science, Ewha Womans University, Seoul, Republic of Korea (C.P., S.L.)
| | - Jin Ok Yang
- Department of New Biology, DGIST, Daegu, Republic of Korea (H.R.W., D.H., H.G.N., P.O.L.);Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea (H.J.K., J.K., H.J., I.H.L., S.H.C., S.J.P., B.K., Y.W.K., B.-K.P., J.H.K., D.H., H.G.N.);School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea (H.J.K.);Korean Bioinformation Center, KRIBB, Daejeon, Republic of Korea (J.O.Y., S.C.K., S.P., B.L.);Division of Molecular Life Sciences, POSTECH, Pohang, Republic of Korea (I.H.L., J.H.J., S.H.C.);Division of Integrative Biosciences and Biotechnologies, POSTECH, Pohang, Republic of Korea (S.J.P.);DNA Link Inc., Seoul, Republic of Korea (C.S.); andEwha Research Center for Systems Biology and Department of Life Science, Ewha Womans University, Seoul, Republic of Korea (C.P., S.L.)
| | - Il Hwan Lee
- Department of New Biology, DGIST, Daegu, Republic of Korea (H.R.W., D.H., H.G.N., P.O.L.);Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea (H.J.K., J.K., H.J., I.H.L., S.H.C., S.J.P., B.K., Y.W.K., B.-K.P., J.H.K., D.H., H.G.N.);School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea (H.J.K.);Korean Bioinformation Center, KRIBB, Daejeon, Republic of Korea (J.O.Y., S.C.K., S.P., B.L.);Division of Molecular Life Sciences, POSTECH, Pohang, Republic of Korea (I.H.L., J.H.J., S.H.C.);Division of Integrative Biosciences and Biotechnologies, POSTECH, Pohang, Republic of Korea (S.J.P.);DNA Link Inc., Seoul, Republic of Korea (C.S.); andEwha Research Center for Systems Biology and Department of Life Science, Ewha Womans University, Seoul, Republic of Korea (C.P., S.L.)
| | - Ji Hyung Jun
- Department of New Biology, DGIST, Daegu, Republic of Korea (H.R.W., D.H., H.G.N., P.O.L.);Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea (H.J.K., J.K., H.J., I.H.L., S.H.C., S.J.P., B.K., Y.W.K., B.-K.P., J.H.K., D.H., H.G.N.);School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea (H.J.K.);Korean Bioinformation Center, KRIBB, Daejeon, Republic of Korea (J.O.Y., S.C.K., S.P., B.L.);Division of Molecular Life Sciences, POSTECH, Pohang, Republic of Korea (I.H.L., J.H.J., S.H.C.);Division of Integrative Biosciences and Biotechnologies, POSTECH, Pohang, Republic of Korea (S.J.P.);DNA Link Inc., Seoul, Republic of Korea (C.S.); andEwha Research Center for Systems Biology and Department of Life Science, Ewha Womans University, Seoul, Republic of Korea (C.P., S.L.)
| | - Seung Hee Choi
- Department of New Biology, DGIST, Daegu, Republic of Korea (H.R.W., D.H., H.G.N., P.O.L.);Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea (H.J.K., J.K., H.J., I.H.L., S.H.C., S.J.P., B.K., Y.W.K., B.-K.P., J.H.K., D.H., H.G.N.);School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea (H.J.K.);Korean Bioinformation Center, KRIBB, Daejeon, Republic of Korea (J.O.Y., S.C.K., S.P., B.L.);Division of Molecular Life Sciences, POSTECH, Pohang, Republic of Korea (I.H.L., J.H.J., S.H.C.);Division of Integrative Biosciences and Biotechnologies, POSTECH, Pohang, Republic of Korea (S.J.P.);DNA Link Inc., Seoul, Republic of Korea (C.S.); andEwha Research Center for Systems Biology and Department of Life Science, Ewha Womans University, Seoul, Republic of Korea (C.P., S.L.)
| | - Su Jin Park
- Department of New Biology, DGIST, Daegu, Republic of Korea (H.R.W., D.H., H.G.N., P.O.L.);Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea (H.J.K., J.K., H.J., I.H.L., S.H.C., S.J.P., B.K., Y.W.K., B.-K.P., J.H.K., D.H., H.G.N.);School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea (H.J.K.);Korean Bioinformation Center, KRIBB, Daejeon, Republic of Korea (J.O.Y., S.C.K., S.P., B.L.);Division of Molecular Life Sciences, POSTECH, Pohang, Republic of Korea (I.H.L., J.H.J., S.H.C.);Division of Integrative Biosciences and Biotechnologies, POSTECH, Pohang, Republic of Korea (S.J.P.);DNA Link Inc., Seoul, Republic of Korea (C.S.); andEwha Research Center for Systems Biology and Department of Life Science, Ewha Womans University, Seoul, Republic of Korea (C.P., S.L.)
| | - Byeongsoo Kang
- Department of New Biology, DGIST, Daegu, Republic of Korea (H.R.W., D.H., H.G.N., P.O.L.);Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea (H.J.K., J.K., H.J., I.H.L., S.H.C., S.J.P., B.K., Y.W.K., B.-K.P., J.H.K., D.H., H.G.N.);School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea (H.J.K.);Korean Bioinformation Center, KRIBB, Daejeon, Republic of Korea (J.O.Y., S.C.K., S.P., B.L.);Division of Molecular Life Sciences, POSTECH, Pohang, Republic of Korea (I.H.L., J.H.J., S.H.C.);Division of Integrative Biosciences and Biotechnologies, POSTECH, Pohang, Republic of Korea (S.J.P.);DNA Link Inc., Seoul, Republic of Korea (C.S.); andEwha Research Center for Systems Biology and Department of Life Science, Ewha Womans University, Seoul, Republic of Korea (C.P., S.L.)
| | - You Wang Kim
- Department of New Biology, DGIST, Daegu, Republic of Korea (H.R.W., D.H., H.G.N., P.O.L.);Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea (H.J.K., J.K., H.J., I.H.L., S.H.C., S.J.P., B.K., Y.W.K., B.-K.P., J.H.K., D.H., H.G.N.);School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea (H.J.K.);Korean Bioinformation Center, KRIBB, Daejeon, Republic of Korea (J.O.Y., S.C.K., S.P., B.L.);Division of Molecular Life Sciences, POSTECH, Pohang, Republic of Korea (I.H.L., J.H.J., S.H.C.);Division of Integrative Biosciences and Biotechnologies, POSTECH, Pohang, Republic of Korea (S.J.P.);DNA Link Inc., Seoul, Republic of Korea (C.S.); andEwha Research Center for Systems Biology and Department of Life Science, Ewha Womans University, Seoul, Republic of Korea (C.P., S.L.)
| | - Bong-Kwan Phee
- Department of New Biology, DGIST, Daegu, Republic of Korea (H.R.W., D.H., H.G.N., P.O.L.);Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea (H.J.K., J.K., H.J., I.H.L., S.H.C., S.J.P., B.K., Y.W.K., B.-K.P., J.H.K., D.H., H.G.N.);School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea (H.J.K.);Korean Bioinformation Center, KRIBB, Daejeon, Republic of Korea (J.O.Y., S.C.K., S.P., B.L.);Division of Molecular Life Sciences, POSTECH, Pohang, Republic of Korea (I.H.L., J.H.J., S.H.C.);Division of Integrative Biosciences and Biotechnologies, POSTECH, Pohang, Republic of Korea (S.J.P.);DNA Link Inc., Seoul, Republic of Korea (C.S.); andEwha Research Center for Systems Biology and Department of Life Science, Ewha Womans University, Seoul, Republic of Korea (C.P., S.L.)
| | - Jin Hee Kim
- Department of New Biology, DGIST, Daegu, Republic of Korea (H.R.W., D.H., H.G.N., P.O.L.);Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea (H.J.K., J.K., H.J., I.H.L., S.H.C., S.J.P., B.K., Y.W.K., B.-K.P., J.H.K., D.H., H.G.N.);School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea (H.J.K.);Korean Bioinformation Center, KRIBB, Daejeon, Republic of Korea (J.O.Y., S.C.K., S.P., B.L.);Division of Molecular Life Sciences, POSTECH, Pohang, Republic of Korea (I.H.L., J.H.J., S.H.C.);Division of Integrative Biosciences and Biotechnologies, POSTECH, Pohang, Republic of Korea (S.J.P.);DNA Link Inc., Seoul, Republic of Korea (C.S.); andEwha Research Center for Systems Biology and Department of Life Science, Ewha Womans University, Seoul, Republic of Korea (C.P., S.L.)
| | - Chaehwa Seo
- Department of New Biology, DGIST, Daegu, Republic of Korea (H.R.W., D.H., H.G.N., P.O.L.);Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea (H.J.K., J.K., H.J., I.H.L., S.H.C., S.J.P., B.K., Y.W.K., B.-K.P., J.H.K., D.H., H.G.N.);School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea (H.J.K.);Korean Bioinformation Center, KRIBB, Daejeon, Republic of Korea (J.O.Y., S.C.K., S.P., B.L.);Division of Molecular Life Sciences, POSTECH, Pohang, Republic of Korea (I.H.L., J.H.J., S.H.C.);Division of Integrative Biosciences and Biotechnologies, POSTECH, Pohang, Republic of Korea (S.J.P.);DNA Link Inc., Seoul, Republic of Korea (C.S.); andEwha Research Center for Systems Biology and Department of Life Science, Ewha Womans University, Seoul, Republic of Korea (C.P., S.L.)
| | - Charny Park
- Department of New Biology, DGIST, Daegu, Republic of Korea (H.R.W., D.H., H.G.N., P.O.L.);Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea (H.J.K., J.K., H.J., I.H.L., S.H.C., S.J.P., B.K., Y.W.K., B.-K.P., J.H.K., D.H., H.G.N.);School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea (H.J.K.);Korean Bioinformation Center, KRIBB, Daejeon, Republic of Korea (J.O.Y., S.C.K., S.P., B.L.);Division of Molecular Life Sciences, POSTECH, Pohang, Republic of Korea (I.H.L., J.H.J., S.H.C.);Division of Integrative Biosciences and Biotechnologies, POSTECH, Pohang, Republic of Korea (S.J.P.);DNA Link Inc., Seoul, Republic of Korea (C.S.); andEwha Research Center for Systems Biology and Department of Life Science, Ewha Womans University, Seoul, Republic of Korea (C.P., S.L.)
| | - Sang Cheol Kim
- Department of New Biology, DGIST, Daegu, Republic of Korea (H.R.W., D.H., H.G.N., P.O.L.);Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea (H.J.K., J.K., H.J., I.H.L., S.H.C., S.J.P., B.K., Y.W.K., B.-K.P., J.H.K., D.H., H.G.N.);School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea (H.J.K.);Korean Bioinformation Center, KRIBB, Daejeon, Republic of Korea (J.O.Y., S.C.K., S.P., B.L.);Division of Molecular Life Sciences, POSTECH, Pohang, Republic of Korea (I.H.L., J.H.J., S.H.C.);Division of Integrative Biosciences and Biotechnologies, POSTECH, Pohang, Republic of Korea (S.J.P.);DNA Link Inc., Seoul, Republic of Korea (C.S.); andEwha Research Center for Systems Biology and Department of Life Science, Ewha Womans University, Seoul, Republic of Korea (C.P., S.L.)
| | - Seongjin Park
- Department of New Biology, DGIST, Daegu, Republic of Korea (H.R.W., D.H., H.G.N., P.O.L.);Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea (H.J.K., J.K., H.J., I.H.L., S.H.C., S.J.P., B.K., Y.W.K., B.-K.P., J.H.K., D.H., H.G.N.);School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea (H.J.K.);Korean Bioinformation Center, KRIBB, Daejeon, Republic of Korea (J.O.Y., S.C.K., S.P., B.L.);Division of Molecular Life Sciences, POSTECH, Pohang, Republic of Korea (I.H.L., J.H.J., S.H.C.);Division of Integrative Biosciences and Biotechnologies, POSTECH, Pohang, Republic of Korea (S.J.P.);DNA Link Inc., Seoul, Republic of Korea (C.S.); andEwha Research Center for Systems Biology and Department of Life Science, Ewha Womans University, Seoul, Republic of Korea (C.P., S.L.)
| | - Byungwook Lee
- Department of New Biology, DGIST, Daegu, Republic of Korea (H.R.W., D.H., H.G.N., P.O.L.);Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea (H.J.K., J.K., H.J., I.H.L., S.H.C., S.J.P., B.K., Y.W.K., B.-K.P., J.H.K., D.H., H.G.N.);School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea (H.J.K.);Korean Bioinformation Center, KRIBB, Daejeon, Republic of Korea (J.O.Y., S.C.K., S.P., B.L.);Division of Molecular Life Sciences, POSTECH, Pohang, Republic of Korea (I.H.L., J.H.J., S.H.C.);Division of Integrative Biosciences and Biotechnologies, POSTECH, Pohang, Republic of Korea (S.J.P.);DNA Link Inc., Seoul, Republic of Korea (C.S.); andEwha Research Center for Systems Biology and Department of Life Science, Ewha Womans University, Seoul, Republic of Korea (C.P., S.L.)
| | - Sanghyuk Lee
- Department of New Biology, DGIST, Daegu, Republic of Korea (H.R.W., D.H., H.G.N., P.O.L.);Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea (H.J.K., J.K., H.J., I.H.L., S.H.C., S.J.P., B.K., Y.W.K., B.-K.P., J.H.K., D.H., H.G.N.);School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea (H.J.K.);Korean Bioinformation Center, KRIBB, Daejeon, Republic of Korea (J.O.Y., S.C.K., S.P., B.L.);Division of Molecular Life Sciences, POSTECH, Pohang, Republic of Korea (I.H.L., J.H.J., S.H.C.);Division of Integrative Biosciences and Biotechnologies, POSTECH, Pohang, Republic of Korea (S.J.P.);DNA Link Inc., Seoul, Republic of Korea (C.S.); andEwha Research Center for Systems Biology and Department of Life Science, Ewha Womans University, Seoul, Republic of Korea (C.P., S.L.)
| | - Daehee Hwang
- Department of New Biology, DGIST, Daegu, Republic of Korea (H.R.W., D.H., H.G.N., P.O.L.);Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea (H.J.K., J.K., H.J., I.H.L., S.H.C., S.J.P., B.K., Y.W.K., B.-K.P., J.H.K., D.H., H.G.N.);School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea (H.J.K.);Korean Bioinformation Center, KRIBB, Daejeon, Republic of Korea (J.O.Y., S.C.K., S.P., B.L.);Division of Molecular Life Sciences, POSTECH, Pohang, Republic of Korea (I.H.L., J.H.J., S.H.C.);Division of Integrative Biosciences and Biotechnologies, POSTECH, Pohang, Republic of Korea (S.J.P.);DNA Link Inc., Seoul, Republic of Korea (C.S.); andEwha Research Center for Systems Biology and Department of Life Science, Ewha Womans University, Seoul, Republic of Korea (C.P., S.L.)
| | - Hong Gil Nam
- Department of New Biology, DGIST, Daegu, Republic of Korea (H.R.W., D.H., H.G.N., P.O.L.);Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea (H.J.K., J.K., H.J., I.H.L., S.H.C., S.J.P., B.K., Y.W.K., B.-K.P., J.H.K., D.H., H.G.N.);School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea (H.J.K.);Korean Bioinformation Center, KRIBB, Daejeon, Republic of Korea (J.O.Y., S.C.K., S.P., B.L.);Division of Molecular Life Sciences, POSTECH, Pohang, Republic of Korea (I.H.L., J.H.J., S.H.C.);Division of Integrative Biosciences and Biotechnologies, POSTECH, Pohang, Republic of Korea (S.J.P.);DNA Link Inc., Seoul, Republic of Korea (C.S.); andEwha Research Center for Systems Biology and Department of Life Science, Ewha Womans University, Seoul, Republic of Korea (C.P., S.L.)
| | - Pyung Ok Lim
- Department of New Biology, DGIST, Daegu, Republic of Korea (H.R.W., D.H., H.G.N., P.O.L.);Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea (H.J.K., J.K., H.J., I.H.L., S.H.C., S.J.P., B.K., Y.W.K., B.-K.P., J.H.K., D.H., H.G.N.);School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea (H.J.K.);Korean Bioinformation Center, KRIBB, Daejeon, Republic of Korea (J.O.Y., S.C.K., S.P., B.L.);Division of Molecular Life Sciences, POSTECH, Pohang, Republic of Korea (I.H.L., J.H.J., S.H.C.);Division of Integrative Biosciences and Biotechnologies, POSTECH, Pohang, Republic of Korea (S.J.P.);DNA Link Inc., Seoul, Republic of Korea (C.S.); andEwha Research Center for Systems Biology and Department of Life Science, Ewha Womans University, Seoul, Republic of Korea (C.P., S.L.)
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Huo X, Wang C, Teng Y, Liu X. Identification of miRNAs associated with dark-induced senescence in Arabidopsis. BMC PLANT BIOLOGY 2015; 15:266. [PMID: 26530097 PMCID: PMC4632659 DOI: 10.1186/s12870-015-0656-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/28/2015] [Indexed: 05/25/2023]
Abstract
BACKGROUND microRNAs (miRNAs) are endogenous small (~21 nucleotide) single-stranded non-coding RNAs that typically function by guiding cleavage of target genes. To find the miRNAs that may be involved in dark-induced leaf senescence, we identified miRNAs by microarray platform using Arabidopsis thaliana leaves from both whole darkened plants (DPs) and individually darkened leaves (IDLs). RESULTS We found that the expressions of 137 miRNAs (P < 0.01, signal intensity >0) were significantly changed both in DP and IDL leaves. Among them, the expression levels of 44 miRNAs were relative higher than others (P < 0.01, signal intensity > 500). Of these differentially expressed miRNAs, 6 miRNAs (miR319a, 319c, miR159, miR164a, miR164c and miR390a) have been previously reported to be involved in dark-induced leaf senescence, and the remaining 38 miRNAs have not been implicated in leaf senescence before. Target genes of all 44 miRNAs were predicted, and some of them, such as NAC1, At3g28690, At2g17640 and At2g45160, were found in the Leaf Senescence Database (LSD). GO and KEGG analysis of 137 miRNAs showed that the predicted target genes were significantly enriched in transcription regulation, development-related biological processes and metabolic pathways. Expression levels of some of the corresponding miRNA targets (At1g73440, At2g03220 and At5g54810) were analysed and found to be significantly different in DP/IDL than that in WT. CONCLUSIONS A microarray analysis about dark-induced miRNAs involved in leaf senescence are present here. Further expression analysis revealed that some new founding miRNAs maybe regulate leaf senescence in Arabidopsis, and the findings highlight the important role of miRNAs in dark-induced leaf senescence.
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Affiliation(s)
- Xiaoying Huo
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, P. R. China.
| | - Chao Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, P. R. China.
| | - Yibo Teng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, P. R. China.
| | - Xunyan Liu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, P. R. China.
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Ma C, Burd S, Lers A. miR408 is involved in abiotic stress responses in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:169-87. [PMID: 26312768 DOI: 10.1111/tpj.12999] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 08/08/2015] [Accepted: 08/13/2015] [Indexed: 05/22/2023]
Abstract
MicroRNAs (miRNAs) are small RNAs that regulate the expression of target genes post-transcriptionally; they are known to play major roles in development and responses to abiotic stress. miR408 is a highly conserved miRNA in plants that responds to the availability of copper and targets genes encoding copper-containing proteins. It was recently recognized to be an important component of the HY5-SPL7 gene network that mediates a coordinated response to light and copper, illustrating its central role in the response of plants to the environment. Expression of miR408 is significantly affected by a variety of developmental and environmental conditions; however, its biological function is unknown. Involvement of miR408 in the abiotic stress response was investigated in Arabidopsis. Expression of miR408, as well as its target genes, was investigated in response to salinity, cold, oxidative stress, drought and osmotic stress. Analyses of transgenic plants with modulated miR408 expression revealed that higher miR408 expression leads to improved tolerance to salinity, cold and oxidative stress, but enhanced sensitivity to drought and osmotic stress. Cellular antioxidant capacity was enhanced in plants with elevated miR408 expression, as manifested by reduced levels of reactive oxygen species and induced expression of genes associated with antioxidative functions, including Cu/Zn superoxide dismutases (CSD1 and CSD2) and glutathione-S-transferase (GST-U25), as well as auxiliary genes: the copper chaperone CCS1 and the redox stress-associated gene SAP12. Overall, the results demonstrate significant involvement of miR408 in abiotic stress responses, emphasizing the central function of miR408 in plant survival.
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Affiliation(s)
- Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Bet Dagan, 50250, Israel
| | - Shaul Burd
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Bet Dagan, 50250, Israel
| | - Amnon Lers
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Bet Dagan, 50250, Israel
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Zavallo D, Debat HJ, Conti G, Manacorda CA, Rodriguez MC, Asurmendi S. Differential mRNA Accumulation upon Early Arabidopsis thaliana Infection with ORMV and TMV-Cg Is Associated with Distinct Endogenous Small RNAs Level. PLoS One 2015; 10:e0134719. [PMID: 26237414 PMCID: PMC4597857 DOI: 10.1371/journal.pone.0134719] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 07/13/2015] [Indexed: 12/04/2022] Open
Abstract
Small RNAs (sRNAs) play important roles in plant development and host-pathogen interactions. Several studies have highlighted the relationship between viral infections, endogenous sRNA accumulation and transcriptional changes associated with symptoms. However, few studies have described a global analysis of endogenous sRNAs by comparing related viruses at early stages of infection, especially before viral accumulation reaches systemic tissues. An sRNA high-throughput sequencing of Arabidopsis thaliana leaf samples infected either with Oilseed rape mosaic virus (ORMV) or crucifer-infecting Tobacco mosaic virus (TMV-Cg) with slightly different symptomatology at two early stages of infection (2 and 4dpi) was performed. At early stages, both viral infections strongly alter the patterns of several types of endogenous sRNA species in distal tissues with no virus accumulation suggesting a systemic signaling process foregoing to virus spread. A correlation between sRNAs derived from protein coding genes and the associated mRNA transcripts was also detected, indicating that an unknown recursive mechanism is involved in a regulatory circuit encompassing this sRNA/mRNA equilibrium. This work represents the initial step in uncovering how differential accumulation of endogenous sRNAs contributes to explain the massive alteration of the transcriptome associated with plant-virus interactions.
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Affiliation(s)
- Diego Zavallo
- Instituto de Biotecnología, CICVyA-INTA, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Humberto Julio Debat
- Instituto de Patología Vegetal (IPAVE), Centro de Investigaciones Agropecuarias (CIAP), INTA, Córdoba, Argentina
| | - Gabriela Conti
- Instituto de Biotecnología, CICVyA-INTA, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | | | - Maria Cecilia Rodriguez
- Instituto de Biotecnología, CICVyA-INTA, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Sebastian Asurmendi
- Instituto de Biotecnología, CICVyA-INTA, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- * E-mail:
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Brusslan JA, Bonora G, Rus-Canterbury AM, Tariq F, Jaroszewicz A, Pellegrini M. A Genome-Wide Chronological Study of Gene Expression and Two Histone Modifications, H3K4me3 and H3K9ac, during Developmental Leaf Senescence. PLANT PHYSIOLOGY 2015; 168:1246-61. [PMID: 25802367 PMCID: PMC4528724 DOI: 10.1104/pp.114.252999] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 03/20/2015] [Indexed: 05/19/2023]
Abstract
The genome-wide abundance of two histone modifications, H3K4me3 and H3K9ac (both associated with actively expressed genes), was monitored in Arabidopsis (Arabidopsis thaliana) leaves at different time points during developmental senescence along with expression in the form of RNA sequencing data. H3K9ac and H3K4me3 marks were highly convergent at all stages of leaf aging, but H3K4me3 marks covered nearly 2 times the gene area as H3K9ac marks. Genes with the greatest fold change in expression displayed the largest positively correlated percentage change in coverage for both marks. Most senescence up-regulated genes were premarked by H3K4me3 and H3K9ac but at levels below the whole-genome average, and for these genes, gene expression increased without a significant increase in either histone mark. However, for a subset of genes showing increased or decreased expression, the respective gain or loss of H3K4me3 marks was found to closely match the temporal changes in mRNA abundance; 22% of genes that increased expression during senescence showed accompanying changes in H3K4me3 modification, and they include numerous regulatory genes, which may act as primary response genes.
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Affiliation(s)
- Judy A Brusslan
- Department of Biological Sciences, California State University, Long Beach, California 90840-9502 (J.A.B., A.M.R.-C., F.T.); andDepartment of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (G.B., A.J., M.P.)
| | - Giancarlo Bonora
- Department of Biological Sciences, California State University, Long Beach, California 90840-9502 (J.A.B., A.M.R.-C., F.T.); andDepartment of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (G.B., A.J., M.P.)
| | - Ana M Rus-Canterbury
- Department of Biological Sciences, California State University, Long Beach, California 90840-9502 (J.A.B., A.M.R.-C., F.T.); andDepartment of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (G.B., A.J., M.P.)
| | - Fayha Tariq
- Department of Biological Sciences, California State University, Long Beach, California 90840-9502 (J.A.B., A.M.R.-C., F.T.); andDepartment of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (G.B., A.J., M.P.)
| | - Artur Jaroszewicz
- Department of Biological Sciences, California State University, Long Beach, California 90840-9502 (J.A.B., A.M.R.-C., F.T.); andDepartment of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (G.B., A.J., M.P.)
| | - Matteo Pellegrini
- Department of Biological Sciences, California State University, Long Beach, California 90840-9502 (J.A.B., A.M.R.-C., F.T.); andDepartment of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (G.B., A.J., M.P.)
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Bhardwaj D, Medici A, Gojon A, Lacombe B, Tuteja N. A new insight into root responses to external cues: Paradigm shift in nutrient sensing. PLANT SIGNALING & BEHAVIOR 2015; 10:e1049791. [PMID: 26146897 PMCID: PMC4854350 DOI: 10.1080/15592324.2015.1049791] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 05/06/2015] [Accepted: 05/06/2015] [Indexed: 05/25/2023]
Abstract
Higher plants are sessile and their growth relies on nutrients present in the soil. The acquisition of nutrients is challenging for plants. Phosphate and nitrate sensing and signaling cascades play significant role during adverse conditions of nutrient unavailability. Therefore, it is important to dissect the mechanism by which plant roots acquire nutrients from the soil. Root system architecture (RSA) exhibits extensive developmental flexibility and changes during nutrient stress conditions. Growth of root system in response to external concentration of nutrients is a joint operation of sensor or receptor proteins along with several other cytoplasmic accessory proteins. After nutrient sensing, sensor proteins start the cellular relay involving transcription factors, kinases, ubiquitin ligases and miRNA. The complexity of nutrient sensing is still nebulous and many new players need to be better studied. This review presents a survey of recent paradigm shift in the advancements in nutrient sensing in relation to plant roots.
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Affiliation(s)
- Deepak Bhardwaj
- International Center for Genetic Engineering & Biotechnology; Aruna Asaf Ali Marg; New Delhi, India
| | - Anna Medici
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes; UMR CNRS/INRA/SupAgro/UM; Institut de Biologie Intégrative des Plantes “Claude Grignon”; Montpellier cedex, France
| | - Alain Gojon
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes; UMR CNRS/INRA/SupAgro/UM; Institut de Biologie Intégrative des Plantes “Claude Grignon”; Montpellier cedex, France
| | - Benoît Lacombe
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes; UMR CNRS/INRA/SupAgro/UM; Institut de Biologie Intégrative des Plantes “Claude Grignon”; Montpellier cedex, France
| | - Narendra Tuteja
- International Center for Genetic Engineering & Biotechnology; Aruna Asaf Ali Marg; New Delhi, India
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