101
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Tregear JW, Richaud F, Collin M, Esbelin J, Parrinello H, Cochard B, Nodichao L, Morcillo F, Adam H, Jouannic S. Micro-RNA-Regulated SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) Gene Expression and Cytokinin Accumulation Distinguish Early-Developing Male and Female Inflorescences in Oil Palm (Elaeis guineensis). PLANTS 2022; 11:plants11050685. [PMID: 35270155 PMCID: PMC8912876 DOI: 10.3390/plants11050685] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 11/16/2022]
Abstract
Sexual differentiation of inflorescences and flowers is important for reproduction and affects crop plant productivity. We report here on a molecular study of the process of sexual differentiation in the immature inflorescence of oil palm (Elaeis guineensis). This species is monoecious and exhibits gender diphasy, producing male and female inflorescences separately on the same plant in alternation. Three main approaches were used: small RNA-seq to characterise and study the expression of miRNA genes; RNA-seq to monitor mRNA accumulation patterns; hormone quantification to assess the role of cytokinins and auxins in inflorescence differentiation. Our study allowed the characterisation of 30 previously unreported palm MIRNA genes. In differential gene and miRNA expression studies, we identified a number of key developmental genes and miRNA-mRNA target modules previously described in relation to their developmental regulatory role in the cereal panicle, notably the miR156/529/535-SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL) gene regulatory module. Gene enrichment analysis highlighted the importance of hormone-related genes, and this observation was corroborated by the detection of much higher levels of cytokinins in the female inflorescence. Our data illustrate the importance of branching regulation within the developmental window studied, during which the female inflorescence, unlike its male counterpart, produces flower clusters on new successive axes by sympodial growth.
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Affiliation(s)
- James W. Tregear
- DIADE, University of Montpellier, CIRAD, IRD, 34394 Montpellier, France; (M.C.); (J.E.); (F.M.); (H.A.); (S.J.)
- Correspondence:
| | - Frédérique Richaud
- CIRAD, UMR AGAP, 34398 Montpellier, France;
- AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France
| | - Myriam Collin
- DIADE, University of Montpellier, CIRAD, IRD, 34394 Montpellier, France; (M.C.); (J.E.); (F.M.); (H.A.); (S.J.)
| | - Jennifer Esbelin
- DIADE, University of Montpellier, CIRAD, IRD, 34394 Montpellier, France; (M.C.); (J.E.); (F.M.); (H.A.); (S.J.)
| | - Hugues Parrinello
- MGX-Montpellier GenomiX, University of Montpellier, CNRS, INSERM, 34094 Montpellier, France;
| | | | | | - Fabienne Morcillo
- DIADE, University of Montpellier, CIRAD, IRD, 34394 Montpellier, France; (M.C.); (J.E.); (F.M.); (H.A.); (S.J.)
- CIRAD, UMR DIADE, 34394 Montpellier, France
| | - Hélène Adam
- DIADE, University of Montpellier, CIRAD, IRD, 34394 Montpellier, France; (M.C.); (J.E.); (F.M.); (H.A.); (S.J.)
| | - Stefan Jouannic
- DIADE, University of Montpellier, CIRAD, IRD, 34394 Montpellier, France; (M.C.); (J.E.); (F.M.); (H.A.); (S.J.)
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102
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Lokuge S, Jayasundara S, Ihalagedara P, Kahanda I, Herath D. miRNAFinder: A comprehensive web resource for plant Pre-microRNA classification. Biosystems 2022; 215-216:104662. [DOI: 10.1016/j.biosystems.2022.104662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 01/08/2022] [Accepted: 02/28/2022] [Indexed: 12/14/2022]
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103
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Yang K, Han H, Li Y, Ye J, Xu F. Significance of miRNA in enhancement of flavonoid biosynthesis. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:217-226. [PMID: 34806280 DOI: 10.1111/plb.13361] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 10/15/2021] [Indexed: 05/20/2023]
Abstract
Flavonoid metabolism shows very strong plasticity in plant development and coping with the changing environment. Flavonoid biosynthesis is regulated by many metabolic pathways, including transcriptional regulation, post-transcriptional control, post-translational regulationand epigenetic regulation. miRNA is a form of endogenous noncoding single-strand small molecule RNA that primarily regulates the expression of target genes horizontally after transcription through splicing and translational suppression. It also plays an important role in regulating plant growth and development, secondary metabolism and biotic and abiotic stress. miRNA can regulate the formation of flavonoids by acting on structural genes or indirectly by using an MBW transcription complex comprising MYB-bHLH-WD40. This study summarizes the biosynthesis and mechanisms of miRNA, and provides a summary of the mechanisms of miRNAs involved in production of flavonoids, in order to elucidate the biosynthesis pathway and complex regulatory network of plant flavonoids. We aim to provide new insights into improving the content of flavonoid active ingredients in plants.
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Affiliation(s)
- K Yang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - H Han
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - Y Li
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - J Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - F Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
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104
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Li Z, Li W, Guo M, Liu S, Liu L, Yu Y, Mo B, Chen X, Gao L. Origin, evolution and diversification of plant ARGONAUTE proteins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1086-1097. [PMID: 34845788 PMCID: PMC9208301 DOI: 10.1111/tpj.15615] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/13/2021] [Accepted: 11/22/2021] [Indexed: 05/26/2023]
Abstract
Argonaute (AGO) proteins are central players in RNA interference in eukaryotes. They associate with small RNAs (sRNA) and lead to transcriptional or posttranscriptional silencing of targets, thereby regulating diverse biological processes. The molecular and biological functions of AGO proteins have been extensively characterized, particularly in a few angiosperm species, leading to the recognition that the AGO family has expanded to accommodate diverse sRNAs thereby performing diverse biological functions. However, understanding of the expansion of AGO proteins in plants is still limited, due to a dearth of knowledge of AGO proteins in green algal groups. Here, we identified more than 2900 AGO proteins from 244 plant species, including green algae, and performed a large-scale phylogenetic analysis. The phylogeny shows that the plant AGO family gave rise to four clades after the emergence of hydrobiontic algae and prior to the emergence of land plants. Subsequent parallel expansion in ferns and angiosperms resulted in eight main clades in angiosperms: AGO2, AGO7, AGO6, AGO4, AGO1, AGO10a, AGO10b and AGO5. On the basis of this phylogeny, we identified two novel AGO4 orthologs that Arabidopsis does not have, and redefined AGO10, which is composed of AGO10a and AGO10b. Finally, we propose a hypothetical evolutionary model of AGO proteins in plants. Our studies provide a deeper understanding of the phylogenetic relationships of AGO family members in the green lineage, which would help to further reveal their roles as RNAi effectors.
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Affiliation(s)
- Zancong Li
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Wenqi Li
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Mingxi Guo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Simu Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Yu Yu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Lei Gao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
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105
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Jin L, Chen M, Xiang M, Guo Z. RNAi-Based Antiviral Innate Immunity in Plants. Viruses 2022; 14:v14020432. [PMID: 35216025 PMCID: PMC8875485 DOI: 10.3390/v14020432] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 12/13/2022] Open
Abstract
Multiple antiviral immunities were developed to defend against viral infection in hosts. RNA interference (RNAi)-based antiviral innate immunity is evolutionarily conserved in eukaryotes and plays a vital role against all types of viruses. During the arms race between the host and virus, many viruses evolve viral suppressors of RNA silencing (VSRs) to inhibit antiviral innate immunity. Here, we reviewed the mechanism at different stages in RNAi-based antiviral innate immunity in plants and the counteractions of various VSRs, mainly upon infection of RNA viruses in model plant Arabidopsis. Some critical challenges in the field were also proposed, and we think that further elucidating conserved antiviral innate immunity may convey a broad spectrum of antiviral strategies to prevent viral diseases in the future.
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106
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Jiang T, Zheng B. Epigenetic Regulation of Megaspore Mother Cell Formation. FRONTIERS IN PLANT SCIENCE 2022; 12:826871. [PMID: 35185968 PMCID: PMC8850924 DOI: 10.3389/fpls.2021.826871] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/31/2021] [Indexed: 05/31/2023]
Abstract
In flowering plants, the female gametophyte (FG) initiates from the formation of the megaspore mother cell (MMC). Among a pool of the somatic cells in the ovule primordium, only one hypodermal cell undergoes a transition of cell fate to become the MMC. Subsequently, the MMC undergoes a series of meiosis and mitosis to form the mature FG harboring seven cells with eight nuclei. Although SPL/NZZ, the core transcription factor for MMC formation, was identified several decades ago, which and why only one somatic cell is chosen as the MMC have long remained mysterious. A growing body of evidence reveal that MMC formation is associated with epigenetic regulation at multiple layers, including dynamic distribution of histone variants and histone modifications, small RNAs, and DNA methylation. In this review, we summarize the progress of epigenetic regulation in the MMC formation, emphasizing the roles of chromosome condensation, histone variants, histone methylation, small RNAs, and DNA methylation.
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107
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Analysis of the miRNA expression profile involved in the tomato spotted wilt orthotospovirus–pepper interaction. Virus Res 2022; 312:198710. [DOI: 10.1016/j.virusres.2022.198710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 02/12/2022] [Accepted: 02/12/2022] [Indexed: 11/30/2022]
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108
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Araújo PM, Grativol C. In silico Identification of Candidate miRNA-encoded Peptides in Four Fabaceae Species. Comput Biol Chem 2022; 97:107644. [DOI: 10.1016/j.compbiolchem.2022.107644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 01/26/2022] [Accepted: 02/16/2022] [Indexed: 11/29/2022]
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109
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Wang C, Jiang F, Zhu S. Complex Small RNA-mediated Regulatory Networks between Viruses/Viroids/Satellites and Host Plants. Virus Res 2022; 311:198704. [DOI: 10.1016/j.virusres.2022.198704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 01/16/2022] [Accepted: 01/29/2022] [Indexed: 12/26/2022]
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110
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Yu Y, Gui Y, Li Z, Jiang C, Guo J, Niu D. Induced Systemic Resistance for Improving Plant Immunity by Beneficial Microbes. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030386. [PMID: 35161366 PMCID: PMC8839143 DOI: 10.3390/plants11030386] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 05/05/2023]
Abstract
Plant beneficial microorganisms improve the health and growth of the associated plants. Application of beneficial microbes triggers an enhanced resistance state, also termed as induced systemic resistance (ISR), in the host, against a broad range of pathogens. Upon the activation of ISR, plants employ long-distance systemic signaling to provide protection for distal tissue, inducing rapid and strong immune responses against pathogens invasions. The transmission of ISR signaling was commonly regarded to be a jasmonic acid- and ethylene-dependent, but salicylic acid-independent, transmission. However, in the last decade, the involvement of both salicylic acid and jasmonic acid/ethylene signaling pathways and the regulatory roles of small RNA in ISR has been updated. In this review, the plant early recognition, responsive reactions, and the related signaling transduction during the process of the plant-beneficial microbe interaction was discussed, with reflection on the crucial regulatory role of small RNAs in the beneficial microbe-mediated ISR.
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Affiliation(s)
- Yiyang Yu
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (Y.G.); (Z.L.); (C.J.); (J.G.)
- State Key Laboratory of Biological Interactions and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Ying Gui
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (Y.G.); (Z.L.); (C.J.); (J.G.)
- State Key Laboratory of Biological Interactions and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Zijie Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (Y.G.); (Z.L.); (C.J.); (J.G.)
- State Key Laboratory of Biological Interactions and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Chunhao Jiang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (Y.G.); (Z.L.); (C.J.); (J.G.)
- State Key Laboratory of Biological Interactions and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Jianhua Guo
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (Y.G.); (Z.L.); (C.J.); (J.G.)
- State Key Laboratory of Biological Interactions and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Dongdong Niu
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (Y.G.); (Z.L.); (C.J.); (J.G.)
- State Key Laboratory of Biological Interactions and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
- Correspondence:
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111
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Luo L, Yang X, Guo M, Lan T, Yu Y, Mo B, Chen X, Gao L, Liu L. TRANS-ACTING SIRNA3-derived short interfering RNAs confer cleavage of mRNAs in rice. PLANT PHYSIOLOGY 2022; 188:347-362. [PMID: 34599593 PMCID: PMC8774828 DOI: 10.1093/plphys/kiab452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/29/2021] [Indexed: 05/11/2023]
Abstract
Plant TRANS-ACTING SIRNA3 (TAS3)-derived short interfering RNAs (siRNAs) include tasiR-AUXIN RESPONSE FACTORs (ARFs), which are functionally conserved in targeting ARF genes, and a set of non-tasiR-ARF siRNAs, which have rarely been studied. In this study, TAS3 siRNAs were systematically characterized in rice (Oryza sativa). Small RNA sequencing results showed that an overwhelming majority of TAS3 siRNAs belong to the non-tasiR-ARF group, while tasiR-ARFs occupy a diminutive fraction. Phylogenetic analysis of TAS3 genes across dicot and monocot plants revealed that the siRNA-generating regions were highly conserved in grass species, especially in the Oryzoideae. Target genes were identified for not only tasiR-ARFs but also non-tasiR-ARF siRNAs by analyzing rice Parallel Analysis of RNA Ends datasets, and some of these siRNA-target interactions were experimentally confirmed using tas3 mutants generated by genome editing. Consistent with the de-repression of target genes, phenotypic alterations were observed for mutants in three TAS3 loci in comparison to wild-type rice. The regulatory role of ribosomes in the TAS3 siRNA-target interactions was further revealed by the fact that TAS3 siRNA-mediated target cleavage, in particular tasiR-ARFs targeting ARF2/3/14/15, occurred extensively in rice polysome samples. Altogether, our study sheds light into TAS3 genes in plants and expands our knowledge about rice TAS3 siRNA-target interactions.
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Affiliation(s)
- Linlin Luo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Guangdong Province, Shenzhen 518060, China
| | - Xiaoyu Yang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Mingxi Guo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
| | - Ting Lan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
| | - Yu Yu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 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, Guangdong Province, Shenzhen 518060, China
| | - Xuemei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521, USA
| | - Lei Gao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
- Author for communication:
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112
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Luo X, Luo S, Fu Y, Kong C, Wang K, Sun D, Li M, Yan Z, Shi Q, Zhang Y. Genome-Wide Identification and Comparative Profiling of MicroRNAs Reveal Flavonoid Biosynthesis in Two Contrasting Flower Color Cultivars of Tree Peony. FRONTIERS IN PLANT SCIENCE 2022; 12:797799. [PMID: 35058956 PMCID: PMC8763678 DOI: 10.3389/fpls.2021.797799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/19/2021] [Indexed: 05/08/2023]
Abstract
MicroRNA (miRNA)-mediated gene regulation is involved in various physiological processes in plants. Flower color is one of the vital ornamental traits of tree peony (Paeonia suffruticosa Andr.). However, the yellow-flowered tree peony cultivars are particularly rare. To elucidate the miRNA-mediated gene regulatory mechanism underlying yellow pigmentation in tree peony, we combined pigment assessment, miRNA identification, expression analysis, and gene functional verification in two contrasting flower color cultivars "High Noon" and "Roufurong." Flavones/flavonols and anthocyanins were found to be the main contributors to the coloration of "High Noon" and "Roufurong" petals, respectively. Subsequently, miRNA analysis based on available genome data identified 9 differentially expressed miRNAs and 12 relevant target genes implicated in flavonoid biosynthesis. Their dynamic expression patterns determined the key role of mdm-miR156b-PsSPL2 module in yellow pigmentation of tree peony flowers. The sequence analysis and subcellular localization validated that PsSPL2 might function as a nuclear-localized transcription factor. Overexpression of PsSPL2 in tobacco resulted in a decrease of anthocyanin content and down-regulation of NtF3'H and NtDFR transcripts. PsSPL2-silenced petals exhibited lighter yellow color, and the contents of THC, Ap, and Ch decreased significantly. Meanwhile, expression levels of PsCHS, PsCHI, and PsF3H were significantly decreased in the petals with PsSPL2 silencing, while those of PsF3'H and PsDFR were remarkably increased. This study offers a novel insight into yellow pigmentation-related miRNA regulation network in tree peony, and further provides the valuable information on physiological changes during yellow coloring process of tree peony.
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Affiliation(s)
- Xiaoning Luo
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, China
| | - Sha Luo
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, China
| | - Yaqi Fu
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, China
| | - Chen Kong
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, China
| | - Kai Wang
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, China
| | - Daoyang Sun
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, China
| | - Mengchen Li
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, China
| | - Zhenguo Yan
- Academy of Agricultural Planning and Engineering, MARA, Beijing, China
| | - Qianqian Shi
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, China
| | - Yanlong Zhang
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, China
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113
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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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114
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Dełeńko K, Nuc P, Kubiak D, Bielewicz D, Dolata J, Niedojadło K, Górka S, Jarmołowski A, Szweykowska-Kulińska Z, Niedojadło J. MicroRNA biogenesis and activity in plant cell dedifferentiation stimulated by cell wall removal. BMC PLANT BIOLOGY 2022; 22:9. [PMID: 34979922 PMCID: PMC8722089 DOI: 10.1186/s12870-021-03323-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/05/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Despite the frequent use of protoplast-to-plant system in in vitro cultures of plants, the molecular mechanisms regulating the first and most limiting stages of this process, i.e., protoplast dedifferentiation and the first divisions leading to the formation of a microcallus, have not been elucidated. RESULTS In this study, we investigated the function of miRNAs in the dedifferentiation of A. thaliana mesophyll cells in a process stimulated by the enzymatic removal of the cell wall. Leaf cells, protoplasts and CDPs (cells derived from protoplasts) cultured for 24, 72 and 120 h (first cell division). In protoplasts, a strong decrease in the amount of AGO1 in both the nucleus and the cytoplasm, as well as dicing bodies (DBs), which are considered to be sites of miRNA biogenesis, was shown. However during CDPs division, the amounts of AGO1 and DBs strongly increased. MicroRNA transcriptome studies demonstrated that lower amount of differentially expressed miRNAs are present in protoplasts than in CDPs cultured for 120 h. Then analysis of differentially expressed miRNAs, selected pri-miRNA and mRNA targets were performed. CONCLUSION This result indicates that miRNA function is not a major regulation of gene expression in the initial but in later steps of dedifferentiation during CDPs divisions. miRNAs participate in organogenesis, oxidative stress, nutrient deficiencies and cell cycle regulation in protoplasts and CDPs. The important role played by miRNAs in the process of dedifferentiation of mesophyll cells was confirmed by the increased mortality and reduced cell division of CDPs derived from mutants with defective miRNA biogenesis and miR319b expression.
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Affiliation(s)
- Konrad Dełeńko
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100, Torun, Poland
| | - Przemysław Nuc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Dawid Kubiak
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100, Torun, Poland
| | - Dawid Bielewicz
- Center for Advanced Technology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 10, 61-614, Poznań, Poland
| | - Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Katarzyna Niedojadło
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
| | - Sylwia Górka
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100, Torun, Poland
| | - Artur Jarmołowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Zofia Szweykowska-Kulińska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Janusz Niedojadło
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland.
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100, Torun, Poland.
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115
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Hu X, Persson Hodén K, Liao Z, Åsman A, Dixelius C. Phytophthora infestans Ago1-associated miRNA promotes potato late blight disease. THE NEW PHYTOLOGIST 2022; 233:443-457. [PMID: 34605025 DOI: 10.1111/nph.17758] [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: 07/06/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Phytophthora spp. cause serious damage to plants by exploiting a large number of effector proteins and small RNAs (sRNAs). Several reports have described modulation of host RNA biogenesis and defence gene expression. Here, we analysed Phytophthora infestans Argonaute (Ago) 1 associated small RNAs during potato leaf infection. Small RNAs were co-immunoprecipitated, deep sequenced and analysed against the P. infestans and potato genomes, followed by transcript analyses and transgenic assays on a predicted target. Extensive targeting of potato and pathogen-derived sRNAs to a range of mRNAs was observed, including 638 sequences coding for resistance (R) proteins in the host genome. The single miRNA encoded by P. infestans (miR8788) was found to target a potato alpha/beta hydrolase-type encoding gene (StABH1), a protein localized to the plasma membrane. Analyses of stable transgenic potato lines harbouring overexpressed StABH1 or artificial miRNA gene constructs demonstrated the importance of StABH1 during infection by P. infestans. miR8788 knock-down strains showed reduced growth on potato, and elevated StABH1 expression levels were observed when plants were inoculated with the two knock-down strains compared to the wild-type strain 88069. The findings of our study suggest that sRNA encoded by P. infestans can affect potato mRNA, thereby expanding our knowledge of the multifaceted strategies this species uses to facilitate infection.
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Affiliation(s)
- Xinyi Hu
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO Box 7080, S-75007, Uppsala, Sweden
| | - Kristian Persson Hodén
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO Box 7080, S-75007, Uppsala, Sweden
| | - Zhen Liao
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO Box 7080, S-75007, Uppsala, Sweden
| | - Anna Åsman
- Department of Molecular Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO Box 7015, S-75007, Uppsala, Sweden
| | - Christina Dixelius
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO Box 7080, S-75007, Uppsala, Sweden
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116
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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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117
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Genomics Associated Interventions for Heat Stress Tolerance in Cool Season Adapted Grain Legumes. Int J Mol Sci 2021; 23:ijms23010399. [PMID: 35008831 PMCID: PMC8745526 DOI: 10.3390/ijms23010399] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022] Open
Abstract
Cool season grain legumes occupy an important place among the agricultural crops and essentially provide multiple benefits including food supply, nutrition security, soil fertility improvement and revenue for farmers all over the world. However, owing to climate change, the average temperature is steadily rising, which negatively affects crop performance and limits their yield. Terminal heat stress that mainly occurred during grain development phases severely harms grain quality and weight in legumes adapted to the cool season, such as lentils, faba beans, chickpeas, field peas, etc. Although, traditional breeding approaches with advanced screening procedures have been employed to identify heat tolerant legume cultivars. Unfortunately, traditional breeding pipelines alone are no longer enough to meet global demands. Genomics-assisted interventions including new-generation sequencing technologies and genotyping platforms have facilitated the development of high-resolution molecular maps, QTL/gene discovery and marker-assisted introgression, thereby improving the efficiency in legumes breeding to develop stress-resilient varieties. Based on the current scenario, we attempted to review the intervention of genomics to decipher different components of tolerance to heat stress and future possibilities of using newly developed genomics-based interventions in cool season adapted grain legumes.
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118
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Hajieghrari B, Farrokhi N. Plant RNA-mediated gene regulatory network. Genomics 2021; 114:409-442. [PMID: 34954000 DOI: 10.1016/j.ygeno.2021.12.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/21/2021] [Accepted: 12/20/2021] [Indexed: 11/26/2022]
Abstract
Not all transcribed RNAs are protein-coding RNAs. Many of them are non-protein-coding RNAs in diverse eukaryotes. However, some of them seem to be non-functional and are resulted from spurious transcription. A lot of non-protein-coding transcripts have a significant function in the translation process. Gene expressions depend on complex networks of diverse gene regulatory pathways. Several non-protein-coding RNAs regulate gene expression in a sequence-specific system either at the transcriptional level or post-transcriptional level. They include a significant part of the gene expression regulatory network. RNA-mediated gene regulation machinery is evolutionarily ancient. They well-evolved during the evolutionary time and are becoming much more complex than had been expected. In this review, we are trying to summarizing the current knowledge in the field of RNA-mediated gene silencing.
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Affiliation(s)
- Behzad Hajieghrari
- Department of Agricultural Biotechnology, College of Agriculture, Jahrom University, Jahrom, Iran.
| | - Naser Farrokhi
- Department of Cell, Molecular Biology Faculty of Life Sciences, Biotechnology, Shahid Beheshti University, G. C Evin, Tehran, Iran.
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119
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Dalmadi Á, Miloro F, Bálint J, Várallyay É, Havelda Z. Controlled RISC loading efficiency of miR168 defined by miRNA duplex structure adjusts ARGONAUTE1 homeostasis. Nucleic Acids Res 2021; 49:12912-12928. [PMID: 34850097 PMCID: PMC8682782 DOI: 10.1093/nar/gkab1138] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 10/25/2021] [Accepted: 11/16/2021] [Indexed: 11/12/2022] Open
Abstract
Micro RNAs (miRNAs) are processed from precursor RNA molecules with precisely defined secondary stem-loop structures. ARGONAUTE1 (AGO1) is the main executor component of miRNA pathway and its expression is controlled via the auto-regulatory feedback loop activity of miR168 in plants. Previously we have shown that AGO1 loading of miR168 is strongly restricted leading to abundant cytoplasmic accumulation of AGO-unbound miR168. Here, we report, that intrinsic RNA secondary structure of MIR168a precursor not only defines the processing of miR168, but also precisely adjusts AGO1 loading efficiency determining the biologically active subset of miR168 pool. Our results show, that modification of miRNA duplex structure of MIR168a precursor fragment or expression from artificial precursors can alter the finely adjusted loading efficiency of miR168. In dcl1-9 mutant where, except for miR168, production of most miRNAs is severely reduced this mechanism ensures the elimination of unloaded AGO1 proteins via enhanced AGO1 loading of miR168. Based on this data, we propose a new competitive loading mechanism model for miR168 action: the miR168 surplus functions as a molecular buffer for controlled AGO1 loading continuously adjusting the amount of AGO1 protein in accordance with the changing size of the cellular miRNA pool.
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Affiliation(s)
- Ágnes Dalmadi
- Hungarian University of Agriculture and Life Sciences, Institute of Genetics and Biotechnology, Páter Károly Street 1, Gödöllő 2100, Hungary
| | - Fabio Miloro
- Hungarian University of Agriculture and Life Sciences, Institute of Genetics and Biotechnology, Páter Károly Street 1, Gödöllő 2100, Hungary
| | - Jeannette Bálint
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert Street 4, Gödöllő 2100, Hungary
| | - Éva Várallyay
- Hungarian University of Agriculture and Life Sciences, Institute of Plant Protection, Ménesi Street 44, Budapest 1118, Hungary
| | - Zoltán Havelda
- Hungarian University of Agriculture and Life Sciences, Institute of Genetics and Biotechnology, Páter Károly Street 1, Gödöllő 2100, Hungary
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120
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Patil S, Joshi S, Jamla M, Zhou X, Taherzadeh MJ, Suprasanna P, Kumar V. MicroRNA-mediated bioengineering for climate-resilience in crops. Bioengineered 2021; 12:10430-10456. [PMID: 34747296 PMCID: PMC8815627 DOI: 10.1080/21655979.2021.1997244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 12/24/2022] Open
Abstract
Global projections on the climate change and the dynamic environmental perturbations indicate severe impacts on food security in general, and crop yield, vigor and the quality of produce in particular. Sessile plants respond to environmental challenges such as salt, drought, temperature, heavy metals at transcriptional and/or post-transcriptional levels through the stress-regulated network of pathways including transcription factors, proteins and the small non-coding endogenous RNAs. Amongs these, the miRNAs have gained unprecedented attention in recent years as key regulators for modulating gene expression in plants under stress. Hence, tailoring of miRNAs and their target pathways presents a promising strategy for developing multiple stress-tolerant crops. Plant stress tolerance has been successfully achieved through the over expression of microRNAs such as Os-miR408, Hv-miR82 for drought tolerance; OsmiR535A and artificial DST miRNA for salinity tolerance; and OsmiR535 and miR156 for combined drought and salt stress. Examples of miR408 overexpression also showed improved efficiency of irradiation utilization and carbon dioxide fixation in crop plants. Through this review, we present the current understanding about plant miRNAs, their roles in plant growth and stress-responses, the modern toolbox for identification, characterization and validation of miRNAs and their target genes including in silico tools, machine learning and artificial intelligence. Various approaches for up-regulation or knock-out of miRNAs have been discussed. The main emphasis has been given to the exploration of miRNAs for development of bioengineered climate-smart crops that can withstand changing climates and stressful environments, including combination of stresses, with very less or no yield penalties.
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Affiliation(s)
- Suraj Patil
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Pune, India
| | - Shrushti Joshi
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Pune, India
| | - Monica Jamla
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Pune, India
| | - Xianrong Zhou
- School of Life Science and Biotechnology, Yangtze Normal University, Ch-ongqing, China
| | | | - Penna Suprasanna
- Bhabha Atomic Research Centre, Homi Bhabha National Institute, Mumbai, India
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Pune, India
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121
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Li J, Duan Y, Sun N, Wang L, Feng S, Fang Y, Wang Y. The miR169n-NF-YA8 regulation module involved in drought resistance in Brassica napus L. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 313:111062. [PMID: 34763855 DOI: 10.1016/j.plantsci.2021.111062] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/10/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
As an ancient and conserved plant microRNA (miRNA) family, miR169 targets nuclear factor Y subunit alpha (NF-YA) family members. The miR169-NF-YA module is associated with plant development and various stress responses. However, the function of miR169 in response to drought stress in rapeseed (Brassica napus L.) is unclear. In the present study, we showed that miR169n acted as a negative regulator of drought resistance in rapeseed by targeting a nuclear factor Y-A gene, NF-YA8. miR169n was strongly down-regulated by drought stress. Expression of a miR169n target mimicry construct (MIM169n) which functioned as a sponge to trap miR169n resulted in enhanced resistance of transgenic plants to both osmotic stress at the post-germination stage and drought stress at the seedling stage. MIM169n plants had a higher relative water content (RWC) and proline content, lower relative electrolyte leakage (REL), and showed higher antioxidative capability compared with those of control (CK) plants under drought stress. Moreover, NF-YA8 was verified as a target of miR169n, and overexpression of NF-YA8 led to improved tolerance of rapeseed to osmotic stress at the post-germination stage. Overall, our findings implied that the miR169n-NF-YA8 regulatory module could serve as a potential target for genetic improvement of drought resistance in B. napus.
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Affiliation(s)
- Jian Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, 225009, Yangzhou, China
| | - Yujing Duan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, 225009, Yangzhou, China
| | - Nianli Sun
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, 225009, Yangzhou, China
| | - Lu Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, 225009, Yangzhou, China
| | - Shanshan Feng
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, 225009, Yangzhou, China
| | - Yujie Fang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, 225009, Yangzhou, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, 225009, Yangzhou, China.
| | - Youping Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, 225009, Yangzhou, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, 225009, Yangzhou, China.
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122
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The THO/TREX Complex Active in Alternative Splicing Mediates Plant Responses to Salicylic Acid and Jasmonic Acid. Int J Mol Sci 2021; 22:ijms222212197. [PMID: 34830079 PMCID: PMC8619553 DOI: 10.3390/ijms222212197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 12/12/2022] Open
Abstract
Salicylic acid (SA) and jasmonic acid (JA) are essential plant immune hormones, which could induce plant resistance to multiple pathogens. However, whether common components are employed by both SA and JA to induce defense is largely unknown. In this study, we found that the enhanced disease susceptibility 8 (EDS8) mutant was compromised in plant defenses to hemibiotrophic pathogen Pseudomonas syringae pv. maculicola ES4326 and necrotrophic pathogen Botrytis cinerea, and was deficient in plant responses to both SA and JA. The EDS8 was identified to be THO1, which encodes a subunit of the THO/TREX complex, by using mapping-by-sequencing. To check whether the EDS8 itself or the THO/TREX complex mediates SA and JA signaling, the mutant of another subunit of the THO/TREX complex, THO3, was tested. THO3 mutation reduced both SA and JA induced defenses, indicating that the THO/TREX complex is critical for plant responses to these two hormones. We further proved that the THO/TREX interacting protein SERRATE, a factor regulating alternative splicing (AS), was involved in plant responses to SA and JA. Thus, the AS events in the eds8 mutant after SA or JA treatment were determined, and we found that the SA and JA induced different alternative splicing events were majorly modulated by EDS8. In summary, our study proves that the THO/TREX complex active in AS is involved in both SA and JA induced plant defenses.
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123
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Wang M, Yang C, Wei K, Zhao M, Shen L, Ji J, Wang L, Zhang D, Guo J, Zheng Y, Yu J, Zhu M, Liu H, Li YF. Temporal expression study of miRNAs in the crown tissues of winter wheat grown under natural growth conditions. BMC Genomics 2021; 22:793. [PMID: 34736408 PMCID: PMC8567549 DOI: 10.1186/s12864-021-08048-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 09/30/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Winter wheat requires prolonged exposure to low temperature to initiate flowering (vernalization). Shoot apical meristem of the crown is the site of cold perception, which produces leaf primordia during vegetative growth before developing into floral primordia at the initiation of the reproductive phase. Although many essential genes for winter wheat cold acclimation and floral initiation have been revealed, the importance of microRNA (miRNA) meditated post-transcriptional regulation in crowns is not well understood. To understand the potential roles of miRNAs in crown tissues, we performed a temporal expression study of miRNAs in crown tissues at the three-leaf stage, winter dormancy stage, spring green-up stage, and jointing stage of winter wheat grown under natural growth conditions. RESULTS In total, 348 miRNAs belonging to 298 miRNA families, were identified in wheat crown tissues. Among them, 92 differentially expressed miRNAs (DEMs) were found to be significantly regulated from the three-leaf stage to the jointing stage. Most of these DEMs were highly expressed at the three-leaf stage and winter dormancy stage, and then declined in later stages. Six DEMs, including miR156a-5p were markedly induced during the winter dormancy stage. Eleven DEMs, including miR159a.1, miR390a-5p, miR393-5p, miR160a-5p, and miR1436, were highly expressed at the green-up stage. Twelve DEMs, such as miR172a-5p, miR394a, miR319b-3p, and miR9676-5p were highly induced at the jointing stage. Moreover, 14 novel target genes of nine wheat or Pooideae-specific miRNAs were verified using RLM-5' RACE assay. Notably, six mTERFs and two Rf1 genes, which are associated with mitochondrial gene expression, were confirmed as targets of three wheat-specific miRNAs. CONCLUSIONS The present study not only confirmed the known miRNAs associated with phase transition and floral development, but also identified a number of wheat or Pooideae-specific miRNAs critical for winter wheat cold acclimation and floral development. Most importantly, this study provided experimental evidence that miRNA could regulate mitochondrial gene expression by targeting mTERF and Rf1 genes. Our study provides valuable information for further exploration of the mechanism of miRNA mediated post-transcriptional regulation during winter wheat vernalization and inflorescent initiation.
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Affiliation(s)
- Menglei Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China.,Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, 453007, China.,Present address: National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Chenhui Yang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Kangning Wei
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Miao Zhao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Liqiang Shen
- Jindal School of Management, University of Texas at Dallas, 800 W Campbell RD, Richardson, TX, 75080, USA
| | - Jie Ji
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Li Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China.,Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, 453007, China
| | - Daijing Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Junqiang Guo
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Yun Zheng
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Juanjuan Yu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China.,Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, 453007, China
| | - Mo Zhu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China.,Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, 453007, China
| | - Haiying Liu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Yong-Fang Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China. .,Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, 453007, China.
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Li J, Fan R, Wu B, Ji X, Hao C. Genome-Wide Identification and Functional Exploration of SBP-Box Gene Family in Black Pepper ( Piper nigrum L.). Genes (Basel) 2021; 12:genes12111740. [PMID: 34828347 PMCID: PMC8625754 DOI: 10.3390/genes12111740] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/23/2021] [Accepted: 10/28/2021] [Indexed: 11/16/2022] Open
Abstract
Black pepper (Piper nigrum L.), is dubbed "the King of Spices". However, the lack of genic knowledge has limited the understanding of its physiological processes and hindered the development of its molecular breeding. The SBP-box gene family is an important family in plant development and integrates multiple physiological processes. Here, we made a genome-wide identification of the pepper SBP-box gene family to provide evolutionary and functional information about this conserved transcription factor. In total, 34 SBP genes were identified in pepper. All these pepper SBP genes were clustered into eight groups, and one pepper group was not found in Arabidopsis thaliana. Segment duplications played the most important role in the expansion process of pepper SBP genes, and all these duplications were subjected to purifying selection. Half of pepper SBP genes were found miR156 target sites, and 17 miR156s were predicted. The tissue expression analysis revealed the differential expression of pepper SBP genes. Eleven SBP genes were found in four co-expression networks, and the GO enrichment further provides a functional prediction for pepper SBP genes. This study lays a foundation for further studies of pepper and provides a valuable reference for functional mining of pepper SBP genes.
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Affiliation(s)
- Jing Li
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (J.L.); (R.F.); (B.W.); (X.J.)
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulatioin for Tropical Spice and Beverage Crops, Wanning 571533, China
- Academician Sim Soonliang of Hainan Province Research Station, Wanning 571533, China
| | - Rui Fan
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (J.L.); (R.F.); (B.W.); (X.J.)
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulatioin for Tropical Spice and Beverage Crops, Wanning 571533, China
- Academician Sim Soonliang of Hainan Province Research Station, Wanning 571533, China
| | - Baoduo Wu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (J.L.); (R.F.); (B.W.); (X.J.)
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulatioin for Tropical Spice and Beverage Crops, Wanning 571533, China
- Academician Sim Soonliang of Hainan Province Research Station, Wanning 571533, China
| | - Xunzhi Ji
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (J.L.); (R.F.); (B.W.); (X.J.)
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulatioin for Tropical Spice and Beverage Crops, Wanning 571533, China
- Academician Sim Soonliang of Hainan Province Research Station, Wanning 571533, China
| | - Chaoyun Hao
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (J.L.); (R.F.); (B.W.); (X.J.)
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulatioin for Tropical Spice and Beverage Crops, Wanning 571533, China
- Academician Sim Soonliang of Hainan Province Research Station, Wanning 571533, China
- Correspondence:
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125
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Distinct Evolutionary Profiles and Functions of microRNA156 and microRNA529 in Land Plants. Int J Mol Sci 2021; 22:ijms222011100. [PMID: 34681763 PMCID: PMC8541648 DOI: 10.3390/ijms222011100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/23/2021] [Accepted: 10/11/2021] [Indexed: 01/14/2023] Open
Abstract
MicroRNA156 (miR156) and miR529 have high sequence similarity and recognize overlapping sites in the same target genes, SQUAMOSA promoter binding protein-like (SPL or SBP box) genes, making it difficult to accurately distinguish their roles in regulatory networks that affect numerous biological functions. Here, we collected data about miR156 and miR529 family members from representative land plants and performed sequence comparisons, phylogenetic analysis, small RNA sequencing, and parallel analysis of RNA ends (PARE) analysis to dissect their evolutionary and functional differences. Although miR156 and miR529 are highly similar, there are differences in their mismatch-sensitive regions, which are essential for target recognition. In land plants, miR156 precursors are conserved mainly within the hairpin region, whereas miR529 precursors are conserved outside the hairpin region, including both the 5’ and 3’ arms. Phylogenetic analysis showed that MIR156 and MIR529 evolved independently, through divergent evolutionary patterns. The two genes also exhibit different expression patterns, with MIR529 preferentially expressed in reproductive tissues and MIR156 in other tissues. PARE analysis revealed that miR156 and miR529 possess specific targets in addition to common targets in maize, pointing to functional differences between them. Based on our findings, we developed a method for the rapid identification of miR529 and miR156 family members and uncovered the evolutionary divergence of these families, providing insights into their different regulatory roles in plant growth and development.
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126
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Zhou Q, Shi J, Li Z, Zhang S, Zhang S, Zhang J, Bao M, Liu G. miR156/157 Targets SPLs to Regulate Flowering Transition, Plant Architecture and Flower Organ Size in Petunia. PLANT & CELL PHYSIOLOGY 2021; 62:839-857. [PMID: 33768247 DOI: 10.1093/pcp/pcab041] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/19/2021] [Indexed: 05/15/2023]
Abstract
miR156/157 plays multiple pivotal roles during plant growth and development. In this study, we identified 11 miR156- and 5 miR157-encoding loci from the genome of Petunia axillaris and Petunia inflata, designated as PaMIR0156/157s and PiMIR0156/157s, respectively. Real-time quantitative reverse transcription PCR (qRT-PCR) analysis indicated that PhmiR156/157 was expressed predominantly in cotyledons, germinating seeds, flower buds, young fruits and seedlings. PhmiR156/157 levels declined in shoot apical buds and leaves of petunia before flowering as the plant ages; moreover, the temporal expression patterns of most miR156/157-targeted PhSPLs were complementary to that of PhmiR156/157. Ectopic expression of PhMIR0157a in Arabidopsis and petunia resulted in delayed flowering, dwarf plant stature, increased branches and reduced organ size. However, PhMIR0156f-overexpressing Arabidopsis and petunia plants showed only delayed flowering. In addition, downregulation of PhmiR156/157 level by overexpressing STTM156/157 led to taller plants with less branches, longer internodes and precocious flowering. qRT-PCR analysis indicated that PhmiR156/157 modulates these traits mainly by downregulating their PhSPL targets and subsequently decreasing the expression of flowering regulatory genes. Our results demonstrate that the PhmiR156/157-PhSPL module has conserved but also divergent functions in growth and development, which will help us decipher the genetic basis for the improvement of flower transition, plant architecture and organ development in petunia.
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Affiliation(s)
- Qin Zhou
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiewei Shi
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhineng Li
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education; College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Sisi Zhang
- Wuhan Institute of Landscape Architecture, Peace Avenue No. 1240, Wuhan 430081, China
| | - Shuting Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiaqi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Guofeng Liu
- Department of Botany, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, China
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127
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Xiong F, Groot EP, Zhang Y, Li S. Functions of plant importin β proteins beyond nucleocytoplasmic transport. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6140-6149. [PMID: 34089597 DOI: 10.1093/jxb/erab263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/04/2021] [Indexed: 06/12/2023]
Abstract
In eukaryotic cells, nuclear activities are isolated from other cellular functions by the nuclear envelope. Because the nuclear envelope provides a diffusion barrier for macromolecules, a complex nuclear transport machinery has evolved that is highly conserved from yeast to plants and mammals. Among those components, the importin β family is the most important one. In this review, we summarize recent findings on the biological function of importin β family members, including development, reproduction, abiotic stress responses, and plant immunity. In addition to the traditional nuclear transport function, we highlight the new molecular functions of importin β, including protein turnover, miRNA regulation, and signaling. Taken together, our review will provide a systematic view of this versatile protein family in plants.
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Affiliation(s)
- Feng Xiong
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Edwin P Groot
- Sino-German Joint Research Center for Agricultural Biology, State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Yan Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Sha Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
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128
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Abstract
Plants cannot move, so they must endure abiotic stresses such as drought, salinity and extreme temperatures. These stressors greatly limit the distribution of plants, alter their growth and development, and reduce crop productivity. Recent progress in our understanding of the molecular mechanisms underlying the responses of plants to abiotic stresses emphasizes their multilevel nature; multiple processes are involved, including sensing, signalling, transcription, transcript processing, translation and post-translational protein modifications. This improved knowledge can be used to boost crop productivity and agricultural sustainability through genetic, chemical and microbial approaches.
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129
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Guo Z, Kuang Z, Zhao Y, Deng Y, He H, Wan M, Tao Y, Wang D, Wei J, Li L, Yang X. PmiREN2.0: from data annotation to functional exploration of plant microRNAs. Nucleic Acids Res 2021; 50:D1475-D1482. [PMID: 34554254 PMCID: PMC8728213 DOI: 10.1093/nar/gkab811] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/31/2021] [Accepted: 09/08/2021] [Indexed: 11/21/2022] Open
Abstract
Nearly 200 plant genomes have been sequenced over the last two years, and new functions of plant microRNAs (miRNAs) have been revealed. Therefore, timely update of the plant miRNA databases by incorporating miRNAs from the newly sequenced species and functional information is required to provide useful resources for advancing plant miRNA research. Here we report the update of PmiREN2.0 (https://pmiren.com/) with an addition of 19 363 miRNA entries from 91 plants, doubling the amount of data in the original version. Meanwhile, abundant regulatory information centred on miRNAs was added, including predicted upstream transcription factors through binding motifs scanning and elaborate annotation of miRNA targets. As an example, a genome-wide regulatory network centred on miRNAs was constructed for Arabidopsis. Furthermore, phylogenetic trees of conserved miRNA families were built to expand the understanding of miRNA evolution across the plant lineages. These data are helpful to deduce the regulatory relationships concerning miRNA functions in diverse plants. Beside the new data, a suite of design tools was incorporated to facilitate experimental practice. Finally, a forum named ‘PmiREN Community’ was added for discussion and resource and new discovery sharing. With these upgrades, PmiREN2.0 should serve the community better and accelerate miRNA research in plants.
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Affiliation(s)
- Zhonglong Guo
- Beijing Agro-biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China.,State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, P.R. China
| | - Zheng Kuang
- Beijing Agro-biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China.,State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, P.R. China
| | - Yongxin Zhao
- Beijing Agro-biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China
| | - Yang Deng
- Beijing Agro-biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China
| | - Hao He
- Beijing Agro-biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China
| | - Miaomiao Wan
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, P.R. China
| | - Yihan Tao
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, P.R. China
| | - Dong Wang
- WeiRan Biotech, Beijing 100085, P.R. China
| | - Jianhua Wei
- Beijing Agro-biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China
| | - Lei Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, P.R. China
| | - Xiaozeng Yang
- Beijing Agro-biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China
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130
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Identification and expression analysis of miRNAs in germination and seedling growth of Tibetan hulless barley. Genomics 2021; 113:3735-3749. [PMID: 34517091 DOI: 10.1016/j.ygeno.2021.08.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 01/30/2023]
Abstract
Germination and seedling growth are crucial for plant development and agricultural production. While, the regulatory mechanisms during these processes in Tibetan hulless barley (Hordeum vulgare L. var. nudum) are not well understood. Given the regulatory roles of microRNAs (miRNAs) in crop plants and the irreplaceability of barley in the highland area of China, we herein presented a genome-wide survey of miRNAs to reveal a potential regulatory network in the early developmental stages of two Tibetan hulless barleys, from which a total of 156 miRNAs was identified including 35 known and 121 novel ones. Six of the identified novel miRNAs were further experimentally validated. According to the evolutionary analysis, miR156, miR166, miR168, and miR171 were conserved across Tibetan hulless barleys and eight other seed plants. Expression profiles of ten known miRNAs showed that they were involved in phytohormone signaling, carbohydrate and lipid metabolism, as well as juvenile-adult transition during barley development. Moreover, a total of 1280 genes targeted by 101 miRNAs were predicted from both barley libraries. Three genes (PLN03212, MATE eukaryotic, and GRAS) were validated via the RNA ligase-mediated 5'-rapid amplification of cDNA ends (RLM-5' RACE) to be the targets of hvu-miR159a, hvu-miR166a, and hvu-miR171-3p, respectively. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of putative targets, the most abundant pathways were related to "metabolism". These results revealed that miRNA-target pairs participating in the regulation of multigene expression and the embryonic development of Tibetan hulless barleys were controlled by complex mechanisms involving the concordant expression of different miRNAs and feedback loops among miRNAs as well as their targets. The study provides insight into the regulatory network of barley miRNAs for better understanding of miRNA functions during germination and seedling growth.
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131
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Dong X, Liu C, Wang Y, Dong Q, Gai Y, Ji X. MicroRNA Profiling During Mulberry ( Morus atropurpurea Roxb) Fruit Development and Regulatory Pathway of miR477 for Anthocyanin Accumulation. FRONTIERS IN PLANT SCIENCE 2021; 12:687364. [PMID: 34567022 PMCID: PMC8455890 DOI: 10.3389/fpls.2021.687364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
To understand the mechanism of small non-coding RNAs (miRNA)-mediated development and ripening of mulberry fruits, three small RNA libraries from mulberry fruits at different development stages were constructed, and 159 conserved miRNAs as well as 86 novel miRNAs were successfully identified. Among the miRNAs identified, there were 90 miRNAs which showed differential expression patterns at different stages of fruit development and ripening. The target genes of these differential expressed (DE) miRNAs were involved in growth and development, transcription and regulation of transcription, metabolic processes, and etc. Interestingly, it was found that the expression level of mul-miR477 was increased with fruit ripening, and it can target the antisense lncRNA (Mul-ABCB19AS) of the ATP binding cassette (ABC) transporter B 19 gene (Mul-ABCB19). Our results showed that mul-miR477 can repress the expression of Mul-ABCB19AS and increase the expression of Mul-ABCB19, and it acted as a positive regulator participating anthocyanin accumulation through the regulatory network of mul-miR477-Mul-ABCB19AS-Mul-ABCB19.
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Affiliation(s)
- Xiaonan Dong
- College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Chaorui Liu
- College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Yuqi Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
| | - Qing Dong
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
| | - Yingping Gai
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
| | - Xianling Ji
- College of Forestry, Shandong Agricultural University, Tai’an, China
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132
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Zhu Y, Li G, Singh J, Khan A, Fazio G, Saltzgiver M, Xia R. Laccase Directed Lignification Is One of the Major Processes Associated With the Defense Response Against Pythium ultimum Infection in Apple Roots. FRONTIERS IN PLANT SCIENCE 2021; 12:629776. [PMID: 34557205 PMCID: PMC8453155 DOI: 10.3389/fpls.2021.629776] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Apple replant disease (ARD), incited by a pathogen complex including Pythium ultimum, causes stunted growth or death of newly planted trees at replant sites. Development and deployment of resistant or tolerant rootstocks offers a cost-effective, ecologically friendly, and durable approach for ARD management. Maximized exploitation of natural resistance requires integrated efforts to identify key regulatory mechanisms underlying resistance traits in apple. In this study, miRNA profiling and degradome sequencing identified major miRNA pathways and candidate genes using six apple rootstock genotypes with contrasting phenotypes to P. ultimum infection. The comprehensive RNA-seq dataset offered an expansive view of post-transcriptional regulation of apple root defense activation in response to infection from P. ultimum. Several pairs of miRNA families and their corresponding targets were identified for their roles in defense response in apple roots, including miR397-laccase, miR398-superoxide dismutase, miR10986-polyphenol oxidase, miR482-resistance genes, and miR160-auxin response factor. Of these families, the genotype-specific expression patterns of miR397 indicated its fundamental role in developing defense response patterns to P. ultimum infection. Combined with other identified copper proteins, the importance of cellular fortification, such as lignification of root tissues by the action of laccase, may critically contribute to genotype-specific resistance traits. Our findings suggest that quick and enhanced lignification of apple roots may significantly impede pathogen penetration and minimize the disruption of effective defense activation in roots of resistant genotypes. The identified target miRNA species and target genes consist of a valuable resource for subsequent functional analysis of their roles during interaction between apple roots and P. ultimum.
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Affiliation(s)
- Yanmin Zhu
- Tree Fruit Research Laboratory, USDA-ARS, Wenatchee, WA, United States
| | - Guanliang Li
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jugpreet Singh
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY, United States
| | - Awais Khan
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY, United States
| | - Gennaro Fazio
- Plant Genetic Resources Unit, USDA-ARS, Geneva, NY, United States
| | - Melody Saltzgiver
- Tree Fruit Research Laboratory, USDA-ARS, Wenatchee, WA, United States
| | - Rui Xia
- College of Horticulture, South China Agricultural University, Guangzhou, China
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133
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Srivastava S, Suprasanna P. MicroRNAs: Tiny, powerful players of metal stress responses in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:928-938. [PMID: 34246107 DOI: 10.1016/j.plaphy.2021.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 06/14/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
Metal contamination of the environment is a widespread problem threatening sustainable and safe crop production. Physio-biochemical and molecular mechanisms of plant responses to metal exposure have been studied to establish the best possible agronomical or biotechnological methods to tackle metal contamination. Metal stress tolerance is regulated by several molecular effectors among which microRNAs are one of the key master regulators of plant growth and stress responses in plants. MicroRNAs are known to coordinate multitude of plant responses to metal stress through antioxidant functions, root growth, hormonal signalling, transcription factors and metal transporters. The present review discusses integrative functions of microRNAs in the regulation of metal stress in plants, which will be useful for engineering stress tolerance traits for improved plant growth and productivity in metal stressed situations.
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Affiliation(s)
- Sudhakar Srivastava
- Plant Stress Biology Laboratory, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005, UP, India.
| | - Penna Suprasanna
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, Maharashtra, India
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134
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Campo S, Sánchez‐Sanuy F, Camargo‐Ramírez R, Gómez‐Ariza J, Baldrich P, Campos‐Soriano L, Soto‐Suárez M, San Segundo B. A novel Transposable element-derived microRNA participates in plant immunity to rice blast disease. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1798-1811. [PMID: 33780108 PMCID: PMC8428829 DOI: 10.1111/pbi.13592] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 02/15/2021] [Accepted: 03/02/2021] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that direct post-transcriptional gene silencing in plant development and stress responses through cleavage or translational repression of target mRNAs. Here, we report the identification and functional characterization of a new member of the miR812 family in rice (named as miR812w) involved in disease resistance. miR812w is present in cultivated Oryza species, both japonica and indica subspecies, and wild rice species within the Oryza genus, but not in dicotyledonous species. miR812w is a 24nt-long that requires DCL3 for its biogenesis and is loaded into AGO4 proteins. Whereas overexpression of miR812w increased resistance to infection by the rice blast fungus Magnaporthe oryzae, CRISPR/Cas9-mediated MIR812w editing enhances disease susceptibility, supporting that miR812w plays a role in blast resistance. We show that miR812w derives from the Stowaway type of rice MITEs (Miniature Inverted-Repeat Transposable Elements). Moreover, miR812w directs DNA methylation in trans at target genes that have integrated a Stowaway MITE copy into their 3' or 5' untranslated region (ACO3, CIPK10, LRR genes), as well as in cis at the MIR812w locus. The target genes of miR812 were found to be hypo-methylated around the miR812 recognition site, their expression being up-regulated in transgene-free CRISPR/Cas9-edited miR812 plants. These findings further support that, in addition to post-transcriptional regulation of gene expression, miRNAs can exert their regulatory function at the transcriptional level. This relationship between miR812w and Stowaway MITEs integrated into multiple coding genes might eventually create a network for miR812w-mediated regulation of gene expression with implications in rice immunity.
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Affiliation(s)
- Sonia Campo
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
| | - Ferran Sánchez‐Sanuy
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
| | - Rosany Camargo‐Ramírez
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
| | - Jorge Gómez‐Ariza
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
| | - Patricia Baldrich
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
- Present address:
Donald Danforth Plant Science Center975 N Warson RoadSt. LouisMO63132USA
| | - Lidia Campos‐Soriano
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
| | - Mauricio Soto‐Suárez
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
- Present address:
Corporación Colombiana de Investigación Agropecuaria. AGROSAVIAKm 14 vía Mosquera‐BogotáMosquera250047Colombia
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
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135
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Qiao Y, Xia R, Zhai J, Hou Y, Feng L, Zhai Y, Ma W. Small RNAs in Plant Immunity and Virulence of Filamentous Pathogens. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:265-288. [PMID: 34077241 DOI: 10.1146/annurev-phyto-121520-023514] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Gene silencing guided by small RNAs governs a broad range of cellular processes in eukaryotes. Small RNAs are important components of plant immunity because they contribute to pathogen-triggered transcription reprogramming and directly target pathogen RNAs. Recent research suggests that silencing of pathogen genes by plant small RNAs occurs not only during viral infection but also in nonviral pathogens through a process termed host-induced gene silencing, which involves trans-species small RNA trafficking. Similarly, small RNAs are also produced by eukaryotic pathogens and regulate virulence. This review summarizes the small RNA pathways in both plants and filamentous pathogens, including fungi and oomycetes, and discusses their role in host-pathogen interactions. We highlight secondarysmall interfering RNAs of plants as regulators of immune receptor gene expression and executors of host-induced gene silencing in invading pathogens. The current status and prospects of trans-species gene silencing at the host-pathogen interface are discussed.
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Affiliation(s)
- Yongli Qiao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China;
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou 510640, China
| | - Jixian Zhai
- School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yingnan Hou
- Department of Microbiology and Plant Pathology, University of California, Riverside, California 92521, USA
| | - Li Feng
- School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yi Zhai
- Department of Microbiology and Plant Pathology, University of California, Riverside, California 92521, USA
| | - Wenbo Ma
- Department of Microbiology and Plant Pathology, University of California, Riverside, California 92521, USA
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK;
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Wang T, Zheng Y, Tang Q, Zhong S, Su W, Zheng B. Brassinosteroids inhibit miRNA-mediated translational repression by decreasing AGO1 on the endoplasmic reticulum. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1475-1490. [PMID: 34020507 DOI: 10.1111/jipb.13139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/12/2021] [Indexed: 05/20/2023]
Abstract
Translational repression is a conserved mechanism in microRNA (miRNA)-guided gene silencing. In Arabidopsis, ARGONAUTE1 (AGO1), the major miRNA effector, localizes in the cytoplasm for mRNA cleavage and at the endoplasmic reticulum (ER) for translational repression of target genes. However, the mechanism underlying miRNA-mediated translational repression is poorly understood. In particular, how the subcellular partitioning of AGO1 is regulated is largely unexplored. Here, we show that the plant hormone brassinosteroids (BRs) inhibit miRNA-mediated translational repression by negatively regulating the distribution of AGO1 at the ER in Arabidopsis thaliana. We show that the protein levels rather than the transcript levels of miRNA target genes were reduced in BR-deficient mutants but increased under BR treatments. The localization of AGO1 at the ER was significantly decreased under BR treatments while it was increased in the BR-deficient mutants. Moreover, ROTUNDIFOLIA3 (ROT3), an enzyme involved in BR biosynthesis, co-localizes with AGO1 at the ER and interacts with AGO1 in a GW motif-dependent manner. Complementation analysis showed that the AGO1-ROT3 interaction is necessary for the function of ROT3. Our findings provide new clues to understand how miRNA-mediated gene silencing is regulated by plant endogenous hormones.
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Affiliation(s)
- Taiyun Wang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yanhua Zheng
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qi Tang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Songxiao Zhong
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Wei Su
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
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137
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Šečić E, Kogel KH, Ladera-Carmona MJ. Biotic stress-associated microRNA families in plants. JOURNAL OF PLANT PHYSIOLOGY 2021; 263:153451. [PMID: 34119743 DOI: 10.1016/j.jplph.2021.153451] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 06/12/2023]
Abstract
Plants and animals utilize various regulatory mechanisms for control of gene expression during development in different tissues and cell types. About 30 years ago, a new mechanism of gene regulation, termed RNA interference (RNAi), was discovered and proved revolutionary for the mechanistic understanding of gene regulation. Noncoding RNAs, including short, 21-24 nucleotide (nt) long microRNAs (miRNAs), endogenously-generated from MIR genes, are key components of RNAi processes, by post-transcriptionally controlling transcripts with antisense complementarity through either translational repression or mRNA degradation. Since their discovery, important roles in regulation of ontogenetic development, cell differentiation, proliferation, and apoptosis in eukaryotes have been elucidated. In plants, miRNAs are known regulatory elements of basic endogenous functions and responses to the environmental stimuli. While the role of miRNAs in regulation of nutrient uptake, circadian clock and general response to abiotic stress is already well understood, a comprehensive understanding of their immune-regulatory roles in response to various biotic stress factors has not yet been achieved. This review summarizes the current understanding of the function of miRNAs and their targets in plants during interaction with microbial pathogens and symbionts. Additionally, we provide a consensus conclusion regarding the typical induction or repression response of conserved miRNA families to pathogenic and beneficial fungi, bacteria, and oomycetes, as well as an outlook of agronomic application of miRNAs in plants. Further investigation of plant miRNAs responsive to microbes, aided with novel sequencing and bioinformatics approaches for discovery and prediction in non-model organisms holds great potential for development of new forms of plant protection.
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Affiliation(s)
- Ena Šečić
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26, D-35392, Giessen, Germany.
| | - Karl-Heinz Kogel
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26, D-35392, Giessen, Germany.
| | - Maria Jose Ladera-Carmona
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26, D-35392, Giessen, Germany.
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138
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Zou H, Guo X, Yang R, Wang S, Li L, Niu J, Wang D, Cao X. MiR408- SmLAC3 Module Participates in Salvianolic Acid B Synthesis in Salvia miltiorrhiza. Int J Mol Sci 2021; 22:ijms22147541. [PMID: 34299156 PMCID: PMC8306038 DOI: 10.3390/ijms22147541] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 11/21/2022] Open
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression involved in plant development and abiotic stress responses. Recently, miRNAs have also been reported to be engaged in the regulation of secondary plant metabolism. However, there are few functional studies of miRNAs in medicinal plants. For this study, we obtained Sm-miR408 interference lines to investigate the function of Sm-miR408 in a medicinal model plant (Salvia miltiorrhiza). It was found that inhibiting the expression of Sm-miR408 could increase the content of salvianolic acid B and rosmarinic acid in the roots. The SmLAC3 and Sm-miR408 expression patterns were analyzed by qRT-PCR. A 5’ RLM-RACE assay confirmed that Sm-miR408 targets and negatively regulates SmLAC3. Moreover, the overexpression of SmLAC3 in S. miltiorrhiza promoted the accumulation of salvianolic acids in the roots. Furthermore, the lignin content of the roots in overexpressed SmLAC3 lines was decreased. Taken together, these findings indicated that Sm-miR408 modulates the accumulation of phenolic acids in S. miltiorrhiza by targeting SmLAC3 expression levels.
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139
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Erokhina TN, Ryazantsev DY, Samokhvalova LV, Mozhaev AA, Orsa AN, Zavriev SK, Morozov SY. Activity of Chemically Synthesized Peptide Encoded by the miR156A Precursor and Conserved in the Brassicaceae Family Plants. BIOCHEMISTRY (MOSCOW) 2021; 86:551-562. [PMID: 33993858 DOI: 10.1134/s0006297921050047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
It was recently found that the primary transcripts of some microRNA genes (pri-miRNAs) are able to express peptides with 12 to 40 residues in length. These peptides, called miPEPs, participate in the transcriptional regulation of their own pri-miRNAs. In our previous studies, we used bioinformatic approach for comparative analysis of pri-miRNA sequences in plant genomes to identify a new group of miPEPs (miPEP-156a peptides) encoded by pri-miR156a in several dozen species of the Brassicaceae family. Exogenous miPEP-156a peptides could efficiently penetrate into the plant seedlings through the root system and spread systemically to the leaves. The peptides produced moderate morphological effect accelerating primary root growth. In parallel, the miPEP-156a peptides upregulated expression of their own pri-miR156a. Importantly, the observed effects at both morphological and molecular levels correlated with the peptide ability to quickly translocate into the cell nucleus and to bind chromatin. In this work, we established secondary structure of the miPEP-156a and demonstrated its changes induced by formation of the peptide complex with DNA.
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Affiliation(s)
- Tatiana N Erokhina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Dmitry Yu Ryazantsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Larisa V Samokhvalova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Andrey A Mozhaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alexander N Orsa
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Sergey K Zavriev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Sergey Yu Morozov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.
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140
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Selvi A, Devi K, Manimekalai R, Prathima PT, Valiyaparambth R, Lakshmi K. High-throughput miRNA deep sequencing in response to drought stress in sugarcane. 3 Biotech 2021; 11:312. [PMID: 34109097 DOI: 10.1007/s13205-021-02857-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/22/2021] [Indexed: 12/14/2022] Open
Abstract
Drought is a major factor which reduces cane growth and productivity. In the present study, we sequenced drought susceptible (V1) and drought tolerant (V2) sugarcane varieties using high-throughput miRNA deep sequencing method to study the regulation of gene expression by miRNAs during drought stress in sugarcane. A total of 1224 conserved miRNAs which belong to 89 miRNA families were identified and 38% of the differentially regulated miRNAs were common for both varieties. Additionally 435 novel miRNAs were also identified from four small RNA libraries. We identified 145 miRNAs that were differentially expressed in susceptible variety (V1-31) and 143 miRNAs differentially expressed in the tolerant variety (V2-31). Target prediction revealed that the genes mainly encoded transcription factors, proteins, phosphatase and kinases involved in signal transduction pathways, integral component of membrane and inorganic ion transport metabolism, enzymes involved in carbohydrate transport and metabolism and drought-stress-related proteins involved in defense mechanisms. Pathway analysis of targets revealed that "General function prediction only" was the most significant pathway observed in both tolerant and susceptible genotypes followed by "signal transduction mechanisms". Functional annotation of the transcripts revealed genes like calcium-dependent protein kinase, respiratory burst oxidase, caffeic acid 3-O-methyltransferase, peroxidase, calmodulin, glutathione S-transferase and transcription factors like MYB, WRKY that are involved in drought tolerant pathways. qRT-PCR was used to verify the expression levels of miRNAs and their potential targets obtained from RNA sequencing results. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-021-02857-x.
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Affiliation(s)
- Athiappan Selvi
- Biotechnology Section, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| | - Kaliannan Devi
- Biotechnology Section, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| | - Ramaswamy Manimekalai
- Biotechnology Section, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| | | | - Rabisha Valiyaparambth
- Biotechnology Section, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| | - Kasirajan Lakshmi
- Biotechnology Section, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
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141
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Hang N, Shi T, Liu Y, Ye W, Taier G, Sun Y, Wang K, Zhang W. Overexpression of Os-microRNA408 enhances drought tolerance in perennial ryegrass. PHYSIOLOGIA PLANTARUM 2021; 172:733-747. [PMID: 33215699 DOI: 10.1111/ppl.13276] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/26/2020] [Accepted: 11/10/2020] [Indexed: 05/29/2023]
Abstract
As a conserved microRNA (miRNA) family in plants, miR408 is known to be involved in different abiotic stress responses, including drought. Interestingly, some studies indicated a species- and/or cultivar-specific drought-responsive characteristic of miR408 in plant drought stress. Moreover, the functions of miR408 in perennial grass species are unknown. In this study, we investigated the role of miR408 in perennial ryegrass (Lolium perenne L.) by withholding water for 10 days for both wild type and transgenic plants with heterologous expression of rice (Oryza sativa L.) miR408 gene, Os-miR408. The results showed that transgenic perennial ryegrass plants displayed morphological changes under normal growth conditions, such as curl leaves and sunken stomata, which could be related to decreased leaf water loss. Moreover, transgenic perennial ryegrass exhibited improved drought tolerance, as demonstrated by maintaining higher leaf relative water content (RWC), lower electrolyte leakage (EL), and less lipid peroxidation compared to WT plants under drought stress. Furthermore, the transgenic plants showed higher antioxidative capacity under drought. These results showed that the improved drought tolerance in Os-miR408 transgenic plants could be due to leaf morphological changes favoring the maintenance of water status and to increased antioxidative capacity protecting against the reactive oxygen species damages under stress. These findings implied that miR408 could serve as a potential target for genetic manipulations to engineer perennial grass plants for improved water stress tolerance.
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Affiliation(s)
- Nan Hang
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Tianran Shi
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Yanrong Liu
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wenxin Ye
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Huhehaote, China
| | - Geli Taier
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Yan Sun
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Kehua Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Wanjun Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
- National Energy R&D Center for Biomass, China Agricultural University, Beijing, China
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142
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Bhogireddy S, Mangrauthia SK, Kumar R, Pandey AK, Singh S, Jain A, Budak H, Varshney RK, Kudapa H. Regulatory non-coding RNAs: a new frontier in regulation of plant biology. Funct Integr Genomics 2021; 21:313-330. [PMID: 34013486 PMCID: PMC8298231 DOI: 10.1007/s10142-021-00787-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 11/27/2022]
Abstract
Beyond the most crucial roles of RNA molecules as a messenger, ribosomal, and transfer RNAs, the regulatory role of many non-coding RNAs (ncRNAs) in plant biology has been recognized. ncRNAs act as riboregulators by recognizing specific nucleic acid targets through homologous sequence interactions to regulate plant growth, development, and stress responses. Regulatory ncRNAs, ranging from small to long ncRNAs (lncRNAs), exert their control over a vast array of biological processes. Based on the mode of biogenesis and their function, ncRNAs evolved into different forms that include microRNAs (miRNAs), small interfering RNAs (siRNAs), miRNA variants (isomiRs), lncRNAs, circular RNAs (circRNAs), and derived ncRNAs. This article explains the different classes of ncRNAs and their role in plant development and stress responses. Furthermore, the applications of regulatory ncRNAs in crop improvement, targeting agriculturally important traits, have been discussed.
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Affiliation(s)
- Sailaja Bhogireddy
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
| | | | - Rakesh Kumar
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Life Sciences, Central University of Karnataka, Karnataka, India
| | - Arun K Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Sadhana Singh
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Ankit Jain
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, Western Australia, Australia
| | - Himabindu Kudapa
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
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143
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Esposito S, Aversano R, Tripodi P, Carputo D. Whole-Genome Doubling Affects Pre-miRNA Expression in Plants. PLANTS 2021; 10:plants10051004. [PMID: 34069771 PMCID: PMC8157229 DOI: 10.3390/plants10051004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/09/2021] [Accepted: 05/10/2021] [Indexed: 11/16/2022]
Abstract
Whole-genome doubling (polyploidy) is common in angiosperms. Several studies have indicated that it is often associated with molecular, physiological, and phenotypic changes. Mounting evidence has pointed out that micro-RNAs (miRNAs) may have an important role in whole-genome doubling. However, an integrative approach that compares miRNA expression in polyploids is still lacking. Here, a re-analysis of already published RNAseq datasets was performed to identify microRNAs’ precursors (pre-miRNAs) in diploids (2x) and tetraploids (4x) of five species (Arabidopsis thaliana L., Morus alba L., Brassica rapa L., Isatis indigotica Fort., and Solanum commersonii Dun). We found 3568 pre-miRNAs, three of which (pre-miR414, pre-miR5538, and pre-miR5141) were abundant in all 2x, and were absent/low in their 4x counterparts. They are predicted to target more than one mRNA transcript, many belonging to transcription factors (TFs), DNA repair mechanisms, and related to stress. Sixteen pre-miRNAs were found in common in all 2x and 4x. Among them, pre-miRNA482, pre-miRNA2916, and pre-miRNA167 changed their expression after polyploidization, being induced or repressed in 4x plants. Based on our results, a common ploidy-dependent response was triggered in all species under investigation, which involves DNA repair, ATP-synthesis, terpenoid biosynthesis, and several stress-responsive transcripts. In addition, an ad hoc pre-miRNA expression analysis carried out solely on 2x vs. 4x samples of S. commersonii indicated that ploidy-dependent pre-miRNAs seem to actively regulate the nucleotide metabolism, probably to cope with the increased requirement for DNA building blocks caused by the augmented DNA content. Overall, the results outline the critical role of microRNA-mediated responses following autopolyploidization in plants.
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Affiliation(s)
- Salvatore Esposito
- CREA Research Centre for Cereal and Industrial Crops, 71122 Foggia, Italy;
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy;
| | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy;
| | - Pasquale Tripodi
- CREA Research Centre for Vegetable and Ornamental Crops, 84098 Pontecagnano, Italy;
| | - Domenico Carputo
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy;
- Correspondence: ; Tel.: +39-08-1252-9225
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144
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Zhang H, Guo Z, Zhuang Y, Suo Y, Du J, Gao Z, Pan J, Li L, Wang T, Xiao L, Qin G, Jiao Y, Cai H, Li L. MicroRNA775 regulates intrinsic leaf size and reduces cell wall pectin levels by targeting a galactosyltransferase gene in Arabidopsis. THE PLANT CELL 2021; 33:581-602. [PMID: 33955485 PMCID: PMC8136896 DOI: 10.1093/plcell/koaa049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/16/2020] [Indexed: 05/10/2023]
Abstract
Plants possess unique primary cell walls made of complex polysaccharides that play critical roles in determining intrinsic cell and organ size. How genes responsible for synthesizing and modifying the polysaccharides in the cell wall are regulated by microRNAs (miRNAs) to control plant size remains largely unexplored. Here we identified 23 putative cell wall-related miRNAs, termed as CW-miRNAs, in Arabidopsis thaliana and characterized miR775 as an example. We showed that miR775 post-transcriptionally silences GALT9, which encodes an endomembrane-located galactosyltransferase belonging to the glycosyltransferase 31 family. Over-expression of miR775 and deletion of GALT9 led to significantly enlarged leaf-related organs, primarily due to increased cell size. Monosaccharide quantification, confocal Raman imaging, and immunolabeling combined with atomic force microscopy revealed that the MIR775A-GALT9 circuit modulates pectin levels and the elastic modulus of the cell wall. We also showed that MIR775A is directly repressed by the transcription factor ELONGATED HYPOCOTYL5 (HY5). Genetic analysis confirmed that HY5 is a negative regulator of leaf size that acts through the HY5-MIR775A-GALT9 repression cascade to control pectin levels. These findings demonstrate that miR775-regulated cell wall remodeling is an integral determinant of intrinsic leaf size in A. thaliana. Studying other CW-miRNAs would provide more insights into cell wall biology.
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Affiliation(s)
- He Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Zhonglong Guo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yan Zhuang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yuanzhen Suo
- Biomedical Pioneering Innovation Center, School of Life Sciences and Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
| | - Jianmei Du
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Zhaoxu Gao
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Jiawei Pan
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Li Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Tianxin Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Liang Xiao
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Genji Qin
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, 100101 Beijing, China
| | - Huaqing Cai
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Author for correspondence:
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145
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Jodder J. Regulation of pri-MIRNA processing: mechanistic insights into the miRNA homeostasis in plant. PLANT CELL REPORTS 2021; 40:783-798. [PMID: 33454802 DOI: 10.1007/s00299-020-02660-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
miRNAs in plant plays crucial role in controlling proper growth, development and fitness by modulating the expression of their target genes. Therefore to modulate the expression of any stress/development related gene specifically, it is better to modulate expression of the miRNA that can target that gene. To modulate the expression level of miRNA, it is prerequisite to uncover the underlying molecular mechanism of its biogenesis. The biogenesis pathway consists of two major steps, transcription of MIR gene to pri-MIRNA and processing of pri-MIRNA into mature miRNA via sequential cleavage steps. Both of these pathways are tightly controlled by several different factors involving structural and functional molecules. This review is mainly focused on different aspects of pri-MIRNA processing mechanism to emphasize on the fact that to modulate the level of a miRNA in the cell only over-expression or knock-down of that MIR gene is not always sufficient rather it is also crucial to take processing regulation into consideration. The data collected from the recent and relevant literatures depicts that processing regulation is controlled by several aspects like structure and size of the pri-MIRNA, presence of introns in MIR gene and their location, interaction of processing factors with the core components of processing machinery etc. These detailed information can be utilized to figure out the particular point which can be utilized to modulate the expression of the miRNA which would ultimately be beneficial for the scientist and researcher working in this field to generate protocol for engineering plant with improved yield and stress tolerance.
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Affiliation(s)
- Jayanti Jodder
- School of Biotechnology, Presidency University (Rajarhat Campus), Canal Bank 7 Road, DG Block, Action Area 1D, Newtown, Kolkata, West Bengal, 700156, India.
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146
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Lunardon A, Kariuki SM, Axtell MJ. Expression and processing of polycistronic artificial microRNAs and trans-acting siRNAs from transiently introduced transgenes in Solanum lycopersicum and Nicotiana benthamiana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1087-1104. [PMID: 33655542 DOI: 10.1111/tpj.15221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 06/12/2023]
Abstract
Targeted gene silencing using small regulatory RNAs is a widely used technique for genetic studies in plants. Artificial microRNAs are one common approach, as they have the advantage of producing just a single functional small RNA, which can be designed for high target specificity and low off-target effects. Simultaneous silencing of multiple targets with artificial microRNAs can be achieved by producing polycistronic microRNA precursors. Alternatively, specialized trans-acting short interfering RNA (tasiRNA) precursors can be designed to produce several specific tasiRNAs at once. Here we tested several artificial microRNA- and tasiRNA-based methods for multiplexed gene silencing in Solanum lycopersicum (tomato) and Nicotiana benthamiana. All analyses used transiently expressed transgenes delivered by infiltration of leaves with Agrobacterium tumefacians. Small RNA sequencing analyses revealed that many previously described approaches resulted in poor small RNA processing. The 5'-most microRNA precursor hairpins on polycistronic artificial microRNA precursors were generally processed more accurately than precursors at the 3'-end. Polycistronic artificial microRNAs where the hairpin precursors were separated by transfer RNAs had the best processing precision. Strikingly, artificial tasiRNA precursors failed to be processed in the expected phased manner in our system. These results highlight the need for further development of multiplexed artificial microRNA and tasiRNA strategies. The importance of small RNA sequencing, as opposed to single-target assays such as RNA blots or real-time polymerase chain reaction, is also discussed.
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Affiliation(s)
- Alice Lunardon
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Samwel Muiruri Kariuki
- International Institute of Tropical Agriculture, Nairobi, PO Box 30709-00100, Kenya
- Department of Plant Sciences, Kenyatta University, Nairobi, PO Box 43844-00100, Kenya
| | - Michael J Axtell
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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147
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Zhang Q, Zhao YQ, Gao X, Jia GX. Analysis of miRNA-mediated regulation of flowering induction in Lilium × formolongi. BMC PLANT BIOLOGY 2021; 21:190. [PMID: 33879043 PMCID: PMC8058995 DOI: 10.1186/s12870-021-02961-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND MicroRNAs play pivotal roles in plant vegetative phase change and flowering induction via integrating into multiple flowering pathways. Lilium × formolongi is an important ornamental lily cultivar that can flower within one year after sowing. However, it remains unresolved how miRNA-mediated regulation networks contribute to the L. × formolongi characteristics of a short vegetative growth period and rapid flowering. RESULTS In this study, the small RNA libraries and one degradome library were constructed for L. × formolongi during vegetative growth and flowering initiation, and 366 conserved miRNAs and 32 novel miRNAs were identified. Additionally, 84 miRNAs were significantly differentially expressed during development. A total of 396 targets of 185 miRNAs were identified and validated through degradome sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that functions of the targets were top enriched in the cold and cadmium ion responses, pentose phosphate pathway and carbon fixation in photosynthetic organisms. Furthermore, among 23 differentially expressed miRNA-target pairs, the miR156s-LfSPL2, miR172a-LfAP2 and miR164a-LfNAC pairs as well as miR159a-LfSPL2 were found to be relevant to flowering based on the correlation analysis of expression profiles in the miRNA libraries, degradome and transcriptome. A coexpression regulatory network focused on differentially expressed pairs was also constructed by WGCNA, and 14 miRNAs were considered putative key miRNAs during vegetative development and flowering induction. miR156a/ d/ e showed particularly strong relationships with other miRNAs in the coexpression network. CONCLUSIONS This study provides cues for the further exploration of the regulatory mechanisms of short vegetative development and flowering in L. × formolongi.
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Affiliation(s)
- Qian Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Yu-Qian Zhao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Xue Gao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Gui-Xia Jia
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, China.
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148
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Persson Hodén K, Hu X, Martinez G, Dixelius C. smartPARE: An R Package for Efficient Identification of True mRNA Cleavage Sites. Int J Mol Sci 2021; 22:4267. [PMID: 33924042 PMCID: PMC8073297 DOI: 10.3390/ijms22084267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/14/2021] [Accepted: 04/17/2021] [Indexed: 11/30/2022] Open
Abstract
Degradome sequencing is commonly used to generate high-throughput information on mRNA cleavage sites mediated by small RNAs (sRNA). In our datasets of potato (Solanum tuberosum, St) and Phytophthora infestans (Pi), initial predictions generated high numbers of cleavage site predictions, which highlighted the need of improved analytic tools. Here, we present an R package based on a deep learning convolutional neural network (CNN) in a machine learning environment to optimize discrimination of false from true cleavage sites. When applying smartPARE to our datasets on potato during the infection process by the late blight pathogen, 7.3% of all cleavage windows represented true cleavages distributed on 214 sites in P. infestans and 444 sites in potato. The sRNA landscape of the two organisms is complex with uneven sRNA production and cleavage regions widespread in the two genomes. Multiple targets and several cases of complex regulatory cascades, particularly in potato, was revealed. We conclude that our new analytic approach is useful for anyone working on complex biological systems and with the interest of identifying cleavage sites particularly inferred by sRNA classes beyond miRNAs.
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Affiliation(s)
| | | | | | - Christina Dixelius
- The Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, Sweden; (K.P.H.); (X.H.); (G.M.)
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149
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Gan L, Yu B. Forkhead-associated domain 2 links light signal to miRNA biogenesis. MOLECULAR PLANT 2021; 14:541-543. [PMID: 33647479 PMCID: PMC8278648 DOI: 10.1016/j.molp.2021.02.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 05/15/2023]
Affiliation(s)
- Lu Gan
- School of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588-0666, USA
| | - Bin Yu
- School of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588-0666, USA.
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150
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Pagano L, Rossi R, Paesano L, Marmiroli N, Marmiroli M. miRNA regulation and stress adaptation in plants. ENVIRONMENTAL AND EXPERIMENTAL BOTANY 2021. [PMID: 0 DOI: 10.1016/j.envexpbot.2020.104369] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
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