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Tondepu SAG, Manova V, Vadivel D, Dondi D, Pagano A, Macovei A. MicroRNAs potentially targeting DDR-related genes are differentially expressed upon exposure to γ-rays during seed germination in wheat. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108771. [PMID: 38820913 DOI: 10.1016/j.plaphy.2024.108771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 05/08/2024] [Accepted: 05/22/2024] [Indexed: 06/02/2024]
Abstract
DNA damage response (DDR), a complex network of cellular pathways that cooperate to sense and repair DNA lesions, is regulated by several mechanisms, including microRNAs. As small, single-stranded RNA molecules, miRNAs post-transcriptionally regulate their target genes by mRNA cleavage or translation inhibition. Knowledge regarding miRNAs influence on DDR-associated genes is still scanty in plants. In this work, an in silico analysis was performed to identify putative miRNAs that could target DDR sensors, signal transducers and effector genes in wheat. Selected putative miRNA-gene pairs were tested in an experimental system where seeds from two wheat mutant lines were irradiated with 50 Gy and 300 Gy gamma(γ)-rays. To evaluate the effect of the treatments on wheat germination, phenotypic and molecular (DNA damage, ROS accumulation, gene/miRNA expression profile) analyses have been carried out. The results showed that in dry seeds ROS accumulated immediately after irradiation and decayed soon after while the negative impact on seedling growth was supported by enhanced accumulation of DNA damage. When a qRT-PCR analysis was performed, the selected miRNAs and DDR-related genes were differentially modulated by the γ-rays treatments in a dose-, time- and genotype-dependent manner. A significant negative correlation was observed between the expression of tae-miR5086 and the RAD50 gene, involved in double-strand break sensing and homologous recombination repair, one of the main processes that repairs DNA breaks induced by γ-rays. The results hereby reported can be relevant for wheat breeding programs and screening of the radiation response and tolerance of novel wheat varieties.
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Affiliation(s)
- Sri Amarnadh Gupta Tondepu
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Adolfo Ferrata 9, 27100, Pavia, Italy
| | - Vasilissa Manova
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences "Acad. G. Bonchev", Street Bldg. 21, 1113, Sofia, Bulgaria.
| | - Dhanalakshmi Vadivel
- Department of Chemistry, University of Pavia, Via Torquato Taramelli 12, 27100, Pavia, Italy
| | - Daniele Dondi
- Department of Chemistry, University of Pavia, Via Torquato Taramelli 12, 27100, Pavia, Italy
| | - Andrea Pagano
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Adolfo Ferrata 9, 27100, Pavia, Italy
| | - Anca Macovei
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Adolfo Ferrata 9, 27100, Pavia, Italy.
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Kaur A, Madhu, Sharma A, Singh K, Upadhyay SK. Investigation of two-pore K + (TPK) channels in Triticum aestivum L. suggests their role in stress response. Heliyon 2024; 10:e27814. [PMID: 38533012 PMCID: PMC10963239 DOI: 10.1016/j.heliyon.2024.e27814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 02/28/2024] [Accepted: 03/07/2024] [Indexed: 03/28/2024] Open
Abstract
Two-pore K+ (TPK) channels are voltage-independent and involved in stress response in plants. Herein, we identified 12 TaTPK genes located on nine chromosomes in the Triticum aestivum genome. The majority of TaTPK genes comprised two exons. Each TaTPK channel comprised four transmembrane (TM) helices, N- and C-terminal ion-channel domains, two EF-hand domains and one 14-3-3 binding site. Additionally, highly conserved 'GYGD' motif responsible for K+ ion specificity, was found in between the TMs in both the ion-channel domains. Nine TaTPK channels were predicted to be localised at the plasma membrane, while three were vacuolar. The protein-protein and protein-chemical interactions indicated the coordinated functioning of the TaTPK channels with the other K+ transporters and their possible interaction with the Ca2+-signaling pathway. Expression studies suggested their importance in both vegetative and reproductive tissues development. Significantly modulated expression of various TaTPK genes during heat, drought, combined heat and drought and salt stresses, and after fungal infestation, depicted their function in stress responses. The miRNAs and transcription factors interaction analyses suggested their role in the hormone, light, growth and development-related, and stress-responsive signaling cascades. The current study suggested vital functions of various TaTPK genes, especially in stress response, and would provide an opportunity for their detailed characterization in future studies.
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Affiliation(s)
- Amandeep Kaur
- Department of Botany, Panjab University, Chandigarh, India, 160014
| | - Madhu
- Department of Botany, Panjab University, Chandigarh, India, 160014
| | - Alok Sharma
- Department of Botany, Panjab University, Chandigarh, India, 160014
- Regional Ayurveda Research Institute, Gwalior, Madhya Pradesh, 474001, India
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, Chandigarh, India
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Székely A, Gulyás Z, Balogh E, Payet R, Dalmay T, Kocsy G, Kalapos B. Identification of ascorbate- and salicylate-responsive miRNAs and verification of the spectral control of miR395 in Arabidopsis. PHYSIOLOGIA PLANTARUM 2023; 175:e14070. [PMID: 38148221 DOI: 10.1111/ppl.14070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 12/28/2023]
Abstract
We assumed that miRNAs might regulate the physiological and biochemical processes in plants through their effects on the redox system and phytohormones. To check this hypothesis, the transcriptome profile of wild-type Arabidopsis and lines with decreased ascorbate (Asc), glutathione (GSH), or salicylate (Sal) levels were compared. GSH deficiency did not influence the miRNA expression, whereas lower levels of Asc and Sal reduced the accumulation of 9 and 44 miRNAs, respectively, but only four miRNAs were upregulated. Bioinformatics analysis revealed that their over-represented target genes are associated with the synthesis of nitrogen-containing and aromatic compounds, nucleic acids, and sulphate assimilation. Among them, the sulphate reduction-related miR395 - ATP-sulfurylase couple was selected to check the assumed modulating role of the light spectrum. A greater induction of the Asc- and Sal-responsive miR395 was observed under sulphur starvation in far-red light compared to white and blue light in wild-type and GSH-deficient Arabidopsis lines. Sal deficiency inhibited the induction of miR395 by sulphur starvation in blue light, whereas Asc deficiency greatly reduced it independently of the spectrum. Interestingly, sulphur starvation decreased only the level of ATP sulfurylase 4 among the miR395 target genes in far-red light. The expression level of ATP sulfurylase 3 was higher in far-red light than in blue light in wild-type and Asc-deficient lines. The results indicate the coordinated control of miRNAs by the redox and hormonal system since 11 miRNAs were affected by both Asc and Sal deficiency. This process can be modulated by light spectrum, as shown for miR395.
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Affiliation(s)
- András Székely
- Agricultural Institute, Centre for Agricultural Research, HUN-REN, Martonvásár, Hungary
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Zsolt Gulyás
- Agricultural Institute, Centre for Agricultural Research, HUN-REN, Martonvásár, Hungary
| | - Eszter Balogh
- Agricultural Institute, Centre for Agricultural Research, HUN-REN, Martonvásár, Hungary
| | - Rocky Payet
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Tamás Dalmay
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Gábor Kocsy
- Agricultural Institute, Centre for Agricultural Research, HUN-REN, Martonvásár, Hungary
| | - Balázs Kalapos
- Agricultural Institute, Centre for Agricultural Research, HUN-REN, Martonvásár, Hungary
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Gulyás Z, Székely A, Kulman K, Kocsy G. Light-Dependent Regulatory Interactions between the Redox System and miRNAs and Their Biochemical and Physiological Effects in Plants. Int J Mol Sci 2023; 24:8323. [PMID: 37176028 PMCID: PMC10179207 DOI: 10.3390/ijms24098323] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
Light intensity and spectrum play a major role in the regulation of the growth, development, and stress response of plants. Changes in the light conditions affect the formation of reactive oxygen species, the activity of the antioxidants, and, consequently, the redox environment in the plant tissues. Many metabolic processes, thus the biogenesis and function of miRNAs, are redox-responsive. The miRNAs, in turn, can modulate various components of the redox system, and this process is also associated with the alteration in the intensity and spectrum of the light. In this review, we would like to summarise the possible regulatory mechanisms by which the alterations in the light conditions can influence miRNAs in a redox-dependent manner. Daily and seasonal fluctuations in the intensity and spectral composition of the light can affect the expression of miRNAs, which can fine-tune the various physiological and biochemical processes due to their effect on their target genes. The interactions between the redox system and miRNAs may be modulated by light conditions, and the proposed function of this regulatory network and its effect on the various biochemical and physiological processes will be introduced in plants.
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Affiliation(s)
- Zsolt Gulyás
- Agricultural Institute, Centre for Agricultural Research ELKH, Department of Biological Resources, 2462 Martonvásár, Hungary
| | - András Székely
- Agricultural Institute, Centre for Agricultural Research ELKH, Department of Biological Resources, 2462 Martonvásár, Hungary
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Kitti Kulman
- Agricultural Institute, Centre for Agricultural Research ELKH, Department of Biological Resources, 2462 Martonvásár, Hungary
| | - Gábor Kocsy
- Agricultural Institute, Centre for Agricultural Research ELKH, Department of Biological Resources, 2462 Martonvásár, Hungary
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5
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Gulyás Z, Moncsek B, Hamow KÁ, Stráner P, Tolnai Z, Badics E, Incze N, Darkó É, Nagy V, Perczel A, Kovács L, Soós V. D27-LIKE1 isomerase has a preference towards trans/cis and cis/cis conversions of carotenoids in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1377-1395. [PMID: 36308414 DOI: 10.1111/tpj.16017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/20/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Carotenoids contribute to a variety of physiological processes in plants, functioning also as biosynthesis precursors of ABA and strigolactones (SLs). SL biosynthesis starts with the enzymatic conversion of all-trans-β-carotene to 9-cis-β-carotene by the DWARF27 (D27) isomerase. In Arabidopsis, D27 has two closely related paralogs, D27-LIKE1 and D27-LIKE2, which were predicted to be β-carotene-isomerases. In the present study, we characterised D27-LIKE1 and identified some key aspects of its physiological and enzymatic functions in Arabidopsis. d27-like1-1 mutant does not display any strigolactone-deficient traits and exhibits a substantially higher 9-cis-violaxanthin content, which is accompanied by a slightly higher ABA level. In vitro feeding assays with recombinant D27-LIKE1 revealed that the protein exhibits affinity to all β-carotene isoforms but with an exclusive preference towards trans/cis conversions and the interconversion between 9-cis, 13-cis and 15-cis-β-carotene forms, and accepts zeaxanthin and violaxanthin as substrates. Finally, we present evidence showing that D27-LIKE1 mRNA is phloem mobile and D27-LIKE1 is an ancient isomerase with a long evolutionary history. In summary, we demonstrate that D27-LIKE1 is a carotenoid isomerase with multi-substrate specificity and has a characteristic preference towards the catalysation of cis/cis interconversion of carotenoids. Therefore, D27-LIKE1 is a potential regulator of carotenoid cis pools and, eventually, SL and ABA biosynthesis pathways.
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Affiliation(s)
- Zsolt Gulyás
- Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, Martonvásár, 2462, Hungary
| | - Blanka Moncsek
- Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, Martonvásár, 2462, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter s. 1/A, Budapest, 1117, Hungary
| | - Kamirán Áron Hamow
- Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, Martonvásár, 2462, Hungary
| | - Pál Stráner
- Laboratory of Structural Chemistry and Biology, MTA-ELTE Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter s. 1/A, Budapest, 1117, Hungary
| | - Zoltán Tolnai
- Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, Martonvásár, 2462, Hungary
| | - Eszter Badics
- Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, Martonvásár, 2462, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter s. 1/A, Budapest, 1117, Hungary
| | - Norbert Incze
- Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, Martonvásár, 2462, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter s. 1/A, Budapest, 1117, Hungary
| | - Éva Darkó
- Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, Martonvásár, 2462, Hungary
| | - Valéria Nagy
- Biological Research Centre, ELKH, 6726, Szeged, Temesvári krt. 62, Hungary
| | - András Perczel
- Laboratory of Structural Chemistry and Biology, MTA-ELTE Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter s. 1/A, Budapest, 1117, Hungary
| | - László Kovács
- Biological Research Centre, ELKH, 6726, Szeged, Temesvári krt. 62, Hungary
| | - Vilmos Soós
- Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, Martonvásár, 2462, Hungary
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Xiong C, Pei H, Zhang Y, Ren W, Ma Z, Tang Y, Huang J. Integrative analysis of transcriptome and miRNAome reveals molecular mechanisms regulating pericarp thickness in sweet corn during kernel development. FRONTIERS IN PLANT SCIENCE 2022; 13:945379. [PMID: 35958194 PMCID: PMC9361504 DOI: 10.3389/fpls.2022.945379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/27/2022] [Indexed: 06/18/2023]
Abstract
Pericarp thickness affects the edible quality of sweet corn (Zea mays L. saccharata Sturt.). Therefore, breeding varieties with a thin pericarp is important for the quality breeding of sweet corn. However, the molecular mechanisms underlying the pericarp development remain largely unclear. We performed an integrative analysis of mRNA and miRNA sequencing to elucidate the genetic mechanism regulating pericarp thickness during kernel development (at 15 days, 19 days, and 23 days after pollination) of two sweet corn inbred lines with different pericarp thicknesses (M03, with a thinner pericarp and M08, with a thicker pericarp). A total of 2,443 and 1,409 differentially expressed genes (DEGs) were identified in M03 and M08, respectively. Our results indicate that phytohormone-mediated programmed cell death (PCD) may play a critical role in determining pericarp thickness in sweet corn. Auxin (AUX), gibberellin (GA), and brassinosteroid (BR) signal transduction may indirectly mediate PCD to regulate pericarp thickness in M03 (the thin pericarp variety). In contrast, abscisic acid (ABA), cytokinin (CK), and ethylene (ETH) signaling may be the key regulators of pericarp PCD in M08 (the thick pericarp variety). Furthermore, 110 differentially expressed microRNAs (DEMIs) and 478 differentially expressed target genes were identified. miRNA164-, miRNA167-, and miRNA156-mediated miRNA-mRNA pairs may participate in regulating pericarp thickness. The expression results of DEGs were validated by quantitative real-time PCR. These findings provide insights into the molecular mechanisms regulating pericarp thickness and propose the objective of breeding sweet corn varieties with a thin pericarp.
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Balogh E, Kalapos B, Ahres M, Boldizsár Á, Gierczik K, Gulyás Z, Gyugos M, Szalai G, Novák A, Kocsy G. Far-Red Light Coordinates the Diurnal Changes in the Transcripts Related to Nitrate Reduction, Glutathione Metabolism and Antioxidant Enzymes in Barley. Int J Mol Sci 2022; 23:ijms23137479. [PMID: 35806480 PMCID: PMC9267158 DOI: 10.3390/ijms23137479] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 11/16/2022] Open
Abstract
Spectral quality, intensity and period of light modify many regulatory and stress signaling pathways in plants. Both nitrate and sulfate assimilations must be synchronized with photosynthesis, which ensures energy and reductants for these pathways. However, photosynthesis is also a source of reactive oxygen species, whose levels are controlled by glutathione and other antioxidants. In this study, we investigated the effect of supplemental far-red (735 nm) and blue (450 nm) lights on the diurnal expression of the genes related to photoreceptors, the circadian clock, nitrate reduction, glutathione metabolism and various antioxidants in barley. The maximum expression of the investigated four photoreceptor and three clock-associated genes during the light period was followed by the peaking of the transcripts of the three redox-responsive transcription factors during the dark phase, while most of the nitrate and sulfate reduction, glutathione metabolism and antioxidant-enzyme-related genes exhibited high expression during light exposure in plants grown in light/dark cycles for two days. These oscillations changed or disappeared in constant white light during the subsequent two days. Supplemental far-red light induced the activation of most of the studied genes, while supplemental blue light did not affect or inhibited them during light/dark cycles. However, in constant light, several genes exhibited greater expression in blue light than in white and far-red lights. Based on a correlation analysis of the gene expression data, we propose a major role of far-red light in the coordinated transcriptional adjustment of nitrate reduction, glutathione metabolism and antioxidant enzymes to changes of the light spectrum.
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Cimini S, Locato V, Giacinti V, Molinari M, De Gara L. A Multifactorial Regulation of Glutathione Metabolism behind Salt Tolerance in Rice. Antioxidants (Basel) 2022; 11:antiox11061114. [PMID: 35740011 PMCID: PMC9219684 DOI: 10.3390/antiox11061114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/01/2022] [Accepted: 06/01/2022] [Indexed: 02/01/2023] Open
Abstract
Knowledge of the stress-induced metabolic alterations in tolerant and sensitive plants is pivotal for identifying interesting traits that improve plant resilience toward unfavorable environmental conditions. This represents a hot topic area of plant science, particularly for crops, due to its implication in food security. Two rice varieties showing dissimilar resistance to salt, Baldo and Vialone Nano, have been studied to investigate the mechanisms underpinning tolerance toward salinity, and these studies have focused on the root system. A detailed analysis of the salt stress-dependent modulation of the redox network is here presented. The different phenotype observed after salt exposure in the two rice varieties is coherent with a differential regulation of cell-cycle progression and cell-death patterns observed at root level. Baldo, the tolerant variety, already showed a highly responsive antioxidative capacity in control conditions. Consistently, stressed Baldo plants showed a different pattern of H2O2 accumulation compared to Vialone Nano. Moreover, glutathione metabolism was finely modulated at transcriptional, post-transcriptional, and post-translational levels in Baldo. These results contribute to highlight the role of ROS and antioxidative pathways as a part of a complex redox network activated in rice toward salt stress.
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Ramakrishnan M, Papolu PK, Satish L, Vinod KK, Wei Q, Sharma A, Emamverdian A, Zou LH, Zhou M. Redox status of the plant cell determines epigenetic modifications under abiotic stress conditions and during developmental processes. J Adv Res 2022; 42:99-116. [PMID: 35690579 PMCID: PMC9788946 DOI: 10.1016/j.jare.2022.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/30/2022] [Accepted: 04/12/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The oxidation-reduction (redox) status of the cell influences or regulates transcription factors and enzymes involved in epigenetic changes, such as DNA methylation, histone protein modifications, and chromatin structure and remodeling. These changes are crucial regulators of chromatin architecture, leading to differential gene expression in eukaryotes. But the cell's redox homeostasis is difficult to sustain since the production of reactive oxygen species (ROS) and reactive nitrogen species (RNS) is not equal in plants at different developmental stages and under abiotic stress conditions. Exceeding optimum ROS and RNS levels leads to oxidative stress and thus alters the redox status of the cell. Consequently, this alteration modulates intracellular epigenetic modifications that either mitigate or mediate the plant growth and stress response. AIM OF REVIEW Recent studies suggest that the altered redox status of the cell reform the cellular functions and epigenetic changes. Recent high-throughput techniques have also greatly advanced redox-mediated gene expression discovery, but the integrated view of the redox status, and its associations with epigenetic changes and subsequent gene expression in plants are still scarce. In this review, we accordingly focus on how the redox status of the cell affects epigenetic modifications in plants under abiotic stress conditions and during developmental processes. This is a first comprehensive review on the redox status of the cell covering the redox components and signaling, redox status alters the post-translational modification of proteins, intracellular epigenetic modifications, redox interplay during DNA methylation, redox regulation of histone acetylation and methylation, redox regulation of miRNA biogenesis, redox regulation of chromatin structure and remodeling and conclusion, future perspectives and biotechnological opportunities for the future development of the plants. KEY SCIENTIFIC CONCEPTS OF REVIEW The interaction of redox mediators such as ROS, RNS and antioxidants regulates redox homeostasis and redox-mediated epigenetic changes. We discuss how redox mediators modulate epigenetic changes and show the opportunities for smart use of the redox status of the cell in plant development and abiotic stress adaptation. However, how a redox mediator triggers epigenetic modification without activating other redox mediators remains yet unknown.
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Affiliation(s)
- Muthusamy Ramakrishnan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, Jiangsu, China; Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, Jiangsu, China.
| | - Pradeep K Papolu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Lakkakula Satish
- Department of Biotechnology Engineering, & The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva - 84105, Israel; Applied Phycology and Biotechnology Division, Marine Algal Research Station, CSIR - Central Salt and Marine Chemicals Research Institute, Mandapam 623519, Tamil Nadu, India
| | | | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, Jiangsu, China; Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
| | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China; Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Abolghassem Emamverdian
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, Jiangsu, China; Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
| | - Long-Hai Zou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China; Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High-efficiency Utilization, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China.
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Ding C, Shen T, Ran N, Zhang H, Pan H, Su X, Xu M. Integrated Degradome and Srna Sequencing Revealed miRNA-mRNA Regulatory Networks between the Phloem and Developing Xylem of Poplar. Int J Mol Sci 2022; 23:ijms23094537. [PMID: 35562928 PMCID: PMC9100975 DOI: 10.3390/ijms23094537] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/27/2022] [Accepted: 04/14/2022] [Indexed: 02/04/2023] Open
Abstract
Lignin and cellulose are the most abundant natural organic polymers in nature. MiRNAs are a class of regulatory RNAs discovered in mammals, plants, viruses, and bacteria. Studies have shown that miRNAs play a role in lignin and cellulose biosynthesis by targeting key enzymes. However, the specific miRNAs functioning in the phloem and developing xylem of Populus deltoides are still unknown. In this study, a total of 134 miRNAs were identified via high-throughput small RNA sequencing, including 132 known and two novel miRNAs, six of which were only expressed in the phloem. A total of 58 differentially expressed miRNAs (DEmiRNAs) were identified between the developing xylem and the phloem. Among these miRNAs, 21 were significantly upregulated in the developing xylem in contrast to the phloem and 37 were significantly downregulated. A total of 2431 target genes of 134 miRNAs were obtained via high-throughput degradome sequencing. Most target genes of these miRNAs were transcription factors, including AP2, ARF, bHLH, bZIP, GRAS, GRF, MYB, NAC, TCP, and WRKY genes. Furthermore, 13 and nine miRNAs were involved in lignin and cellulose biosynthesis, respectively, and we validated the miRNAs via qRT-PCR. Our study explores these miRNAs and their regulatory networks in the phloem and developing xylem of P.deltoides and provides new insight into wood formation.
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Affiliation(s)
- Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China;
| | - Tengfei Shen
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (T.S.); (N.R.); (H.Z.); (H.P.)
| | - Na Ran
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (T.S.); (N.R.); (H.Z.); (H.P.)
| | - Heng Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (T.S.); (N.R.); (H.Z.); (H.P.)
| | - Huixin Pan
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (T.S.); (N.R.); (H.Z.); (H.P.)
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China;
- Correspondence: (X.S.); (M.X.); Tel.: +86-136-4130-7199 (X.S.); +86-150-9430-7586 (M.X.)
| | - Meng Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (T.S.); (N.R.); (H.Z.); (H.P.)
- Correspondence: (X.S.); (M.X.); Tel.: +86-136-4130-7199 (X.S.); +86-150-9430-7586 (M.X.)
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Chaudhary S, Grover A, Sharma PC. MicroRNAs: Potential Targets for Developing Stress-Tolerant Crops. Life (Basel) 2021; 11:life11040289. [PMID: 33800690 PMCID: PMC8066829 DOI: 10.3390/life11040289] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/24/2022] Open
Abstract
Crop yield is challenged every year worldwide by changing climatic conditions. The forecasted climatic scenario urgently demands stress-tolerant crop varieties to feed the ever-increasing global population. Molecular breeding and genetic engineering approaches have been frequently exploited for developing crops with desired agronomic traits. Recently, microRNAs (miRNAs) have emerged as powerful molecules, which potentially serve as expression markers during stress conditions. The miRNAs are small non-coding endogenous RNAs, usually 20-24 nucleotides long, which mediate post-transcriptional gene silencing and fine-tune the regulation of many abiotic- and biotic-stress responsive genes in plants. The miRNAs usually function by specifically pairing with the target mRNAs, inducing their cleavage or repressing their translation. This review focuses on the exploration of the functional role of miRNAs in regulating plant responses to abiotic and biotic stresses. Moreover, a methodology is also discussed to mine stress-responsive miRNAs from the enormous amount of transcriptome data available in the public domain generated using next-generation sequencing (NGS). Considering the functional role of miRNAs in mediating stress responses, these molecules may be explored as novel targets for engineering stress-tolerant crop varieties.
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Affiliation(s)
- Saurabh Chaudhary
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
- Correspondence: (S.C.); (P.C.S.)
| | - Atul Grover
- Defence Institute of Bio-Energy Research, Defence Research and Development Organisation (DRDO), Haldwani 263139, India;
| | - Prakash Chand Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi 110078, India
- Correspondence: (S.C.); (P.C.S.)
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