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Fan H, Wang X, Zhong H, Quan K, Yu R, Ma S, Song S, Lin M. Integrated analysis of miRNAs, transcriptome and phytohormones in the flowering time regulatory network of tea oil camellia. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:945-956. [PMID: 38974357 PMCID: PMC11222345 DOI: 10.1007/s12298-024-01473-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/16/2024] [Accepted: 06/17/2024] [Indexed: 07/09/2024]
Abstract
Camellia oleifera is a crucial cash crop in the southern region of China. Timely flowering is a crucial characteristic for maximizing crop productivity. Nevertheless, the cold temperature and wet weather throughout the fall and winter seasons in South China impact the timing of flowering and the yield produced by C. oleifera. This study examined the miRNAs, transcriptomes, and phytohormones that are part of the flowering time regulatory networks in distinct varieties of C. oleifera (Sep, Oct, and Nov). This study provides evidence that phytohormones significantly impact the timing of flowering in C. oleifera leaves. There is a positive correlation between the accumulation variations of zeatin (cZ), brassinolide (BL), salicylic acid (SA), 1-amino cyclopropane carboxylic acid (ACC), and jasmonic acid (JA) and flowering time. This means that blooming occurs earlier when the quantity of these substances in leaves increases. Abscisic acid (ABA), trans-zeatin-riboside (tZR), dihydrozeatin (dh-Z), and IP (N6-Isopentenyladenine) exhibit contrasting effects. Furthermore, both miR156 and miR172 play a crucial function in regulating flowering time in C. oleifera leaves by modulating the expression of SOC1, primarily through the miR156-SPL and miR172-AP2 pathways. These findings establish a strong basis for future research endeavors focused on examining the molecular network associated with the flowering period of C. oleifera and controlling flowering time management through external treatments. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01473-2.
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Affiliation(s)
- Haixiao Fan
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
| | - Xiaoling Wang
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
| | - Huiqi Zhong
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
| | - Kehui Quan
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
| | - Ruohan Yu
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
| | - Shiying Ma
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
| | - Siqiong Song
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
| | - Mengfei Lin
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
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Liu SJ, Cai C, Cai HY, Bai YQ, Wang DY, Zhang H, Peng JG, Xie LJ. Integrated analysis of transcriptome and small RNAome reveals regulatory network of rapid and long-term response to heat stress in Rhododendron moulmainense. PLANTA 2024; 259:104. [PMID: 38551672 PMCID: PMC10980653 DOI: 10.1007/s00425-024-04375-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/03/2024] [Indexed: 04/01/2024]
Abstract
MAIN CONCLUSION The post-transcriptional gene regulatory pathway and small RNA pathway play important roles in regulating the rapid and long-term response of Rhododendron moulmainense to high-temperature stress. The Rhododendron plays an important role in maintaining ecological balance. However, it is difficult to domesticate for use in urban ecosystems due to their strict optimum growth temperature condition, and its evolution and adaptation are little known. Here, we combined transcriptome and small RNAome to reveal the rapid response and long-term adaptability regulation strategies in Rhododendron moulmainense under high-temperature stress. The post-transcriptional gene regulatory pathway plays important roles in stress response, in which the protein folding pathway is rapidly induced at 4 h after heat stress, and alternative splicing plays an important role in regulating gene expression at 7 days after heat stress. The chloroplasts oxidative damage is the main factor inhibiting photosynthesis efficiency. Through WGCNA analysis, we identified gene association patterns and potential key regulatory genes responsible for maintaining the ROS steady-state under heat stress. Finally, we found that the sRNA synthesis pathway is induced under heat stress. Combined with small RNAome, we found that more miRNAs are significantly changed under long-term heat stress. Furthermore, MYBs might play a central role in target gene interaction network of differentially expressed miRNAs in R. moulmainense under heat stress. MYBs are closely related to ABA, consistently, ABA synthesis and signaling pathways are significantly inhibited, and the change in stomatal aperture is not obvious under heat stress. Taken together, we gained valuable insights into the transplantation and long-term conservation domestication of Rhododendron, and provide genetic resources for genetic modification and molecular breeding to improve heat resistance in Rhododendron.
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Affiliation(s)
- Si-Jia Liu
- College of Architectural Engineering, Shenzhen Polytechnic University, Shenzhen, 518055, China
| | - Chang Cai
- Guizhou Provincial Key Laboratory for Information Systems of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, Guiyang, 550001, China
| | - Hong-Yue Cai
- College of Architectural Engineering, Shenzhen Polytechnic University, Shenzhen, 518055, China
| | - Yu-Qing Bai
- Administrative Office of Wutong Mountain National Park, Shenzhen, 518004, China
| | - Ding-Yue Wang
- Administrative Office of Wutong Mountain National Park, Shenzhen, 518004, China
| | - Hua Zhang
- College of Architectural Engineering, Shenzhen Polytechnic University, Shenzhen, 518055, China
| | - Jin-Gen Peng
- College of Architectural Engineering, Shenzhen Polytechnic University, Shenzhen, 518055, China.
| | - Li-Juan Xie
- College of Architectural Engineering, Shenzhen Polytechnic University, Shenzhen, 518055, China.
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3
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Li XM, Jenke H, Strauss S, Bazakos C, Mosca G, Lymbouridou R, Kierzkowski D, Neumann U, Naik P, Huijser P, Laurent S, Smith RS, Runions A, Tsiantis M. Cell-cycle-linked growth reprogramming encodes developmental time into leaf morphogenesis. Curr Biol 2024; 34:541-556.e15. [PMID: 38244542 DOI: 10.1016/j.cub.2023.12.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/22/2024]
Abstract
How is time encoded into organ growth and morphogenesis? We address this question by investigating heteroblasty, where leaf development and form are modified with progressing plant age. By combining morphometric analyses, fate-mapping through live-imaging, computational analyses, and genetics, we identify age-dependent changes in cell-cycle-associated growth and histogenesis that underpin leaf heteroblasty. We show that in juvenile leaves, cell proliferation competence is rapidly released in a "proliferation burst" coupled with fast growth, whereas in adult leaves, proliferative growth is sustained for longer and at a slower rate. These effects are mediated by the SPL9 transcription factor in response to inputs from both shoot age and individual leaf maturation along the proximodistal axis. SPL9 acts by activating CyclinD3 family genes, which are sufficient to bypass the requirement for SPL9 in the control of leaf shape and in heteroblastic reprogramming of cellular growth. In conclusion, we have identified a mechanism that bridges across cell, tissue, and whole-organism scales by linking cell-cycle-associated growth control to age-dependent changes in organ geometry.
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Affiliation(s)
- Xin-Min Li
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Hannah Jenke
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Sören Strauss
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Christos Bazakos
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Gabriella Mosca
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Rena Lymbouridou
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Daniel Kierzkowski
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Ulla Neumann
- Central Microscopy (CeMic), Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Purva Naik
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Peter Huijser
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Stefan Laurent
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Richard S Smith
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Adam Runions
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany.
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Wang X, Zhou R, Zhao S, Niu S. An Integrated Analysis of microRNAs and the Transcriptome Reveals the Molecular Mechanisms Underlying the Regulation of Leaf Development in Xinyang Maojian Green Tea ( Camellia sinensis). PLANTS (BASEL, SWITZERLAND) 2023; 12:3665. [PMID: 37960023 PMCID: PMC10649745 DOI: 10.3390/plants12213665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/03/2023] [Accepted: 10/22/2023] [Indexed: 11/15/2023]
Abstract
Xinyang Maojian (XYMJ) tea is one of the world's most popular green teas; the development of new sprouts directly affects the yield and quality of tea products, especially for XYMJ, which has hairy tips. Here, we used transcriptome and small RNA sequencing to identify mRNAs and miRNAs, respectively, involved in regulating leaf development in different plant tissues (bud, leaf, and stem). We identified a total of 381 conserved miRNAs. Given that no genomic data for XYMJ green tea are available, we compared the sequencing data for XYMJ green tea with genomic data from a closely related species (Tieguanyin) and the Camellia sinensis var. sinensis database; we identified a total of 506 and 485 novel miRNAs, respectively. We also identified 11 sequence-identical novel miRNAs in the tissues of XYMJ tea plants. Correlation analyses revealed 97 miRNA-mRNA pairs involved in leaf growth and development; the csn-miR319-2/csnTCP2 and miR159-csnMYB modules were found to be involved in leaf development in XYMJ green tea. Quantitative real-time PCR was used to validate the expression levels of the miRNAs and mRNAs. The miRNAs and target genes identified in this study might shed new light on the molecular mechanisms underlying the regulation of leaf development in tea plants.
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Affiliation(s)
- Xianyou Wang
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang 453003, China
| | - Ruijin Zhou
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang 453003, China
| | - Shanshan Zhao
- School of Food Science, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Shengyang Niu
- School of Food Science, Henan Institute of Science and Technology, Xinxiang 453003, China
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Tang HB, Wang J, Wang L, Shang GD, Xu ZG, Mai YX, Liu YT, Zhang TQ, Wang JW. Anisotropic cell growth at the leaf base promotes age-related changes in leaf shape in Arabidopsis thaliana. THE PLANT CELL 2023; 35:1386-1407. [PMID: 36748203 PMCID: PMC10118278 DOI: 10.1093/plcell/koad031] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 05/17/2023]
Abstract
Plants undergo extended morphogenesis. The shoot apical meristem (SAM) allows for reiterative development and the formation of new structures throughout the life of the plant. Intriguingly, the SAM produces morphologically different leaves in an age-dependent manner, a phenomenon known as heteroblasty. In Arabidopsis thaliana, the SAM produces small orbicular leaves in the juvenile phase, but gives rise to large elliptical leaves in the adult phase. Previous studies have established that a developmental decline of microRNA156 (miR156) is necessary and sufficient to trigger this leaf shape switch, although the underlying mechanism is poorly understood. Here we show that the gradual increase in miR156-targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE transcription factors with age promotes cell growth anisotropy in the abaxial epidermis at the base of the leaf blade, evident by the formation of elongated giant cells. Time-lapse imaging and developmental genetics further revealed that the establishment of adult leaf shape is tightly associated with the longitudinal cell expansion of giant cells, accompanied by a prolonged cell proliferation phase in their vicinity. Our results thus provide a plausible cellular mechanism for heteroblasty in Arabidopsis, and contribute to our understanding of anisotropic growth in plants.
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Affiliation(s)
- Hong-Bo Tang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Shanghai 200032, China
- University of Chinese Academy of Sciences (UCAS), Shanghai 200032, China
| | - Juan Wang
- School of Statistics and Mathematics, Inner Mongolia University of Finance and Economics, Huhehaote 010070, China
| | - Long Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Shanghai 200032, China
| | - Guan-Dong Shang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Shanghai 200032, China
- University of Chinese Academy of Sciences (UCAS), Shanghai 200032, China
| | - Zhou-Geng Xu
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Shanghai 200032, China
- University of Chinese Academy of Sciences (UCAS), Shanghai 200032, China
| | - Yan-Xia Mai
- Core Facility Center of CEMPS, Institute of Plant Physiology and Ecology (SIPPE), Shanghai 200032, China
| | - Ye-Tong Liu
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Shanghai 200032, China
- Shanghai Normal University, College of Life and Environmental Sciences, Shanghai 200234, China
| | - Tian-Qi Zhang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Shanghai 200032, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Shanghai 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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6
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Zhang Z, He C, Bao C, Li Z, Jin W, Li C, Chen Y. MiRNA Profiling and Its Potential Roles in Rapid Growth of Velvet Antler in Gansu Red Deer ( Cervus elaphus kansuensis). Genes (Basel) 2023; 14:424. [PMID: 36833351 PMCID: PMC9957509 DOI: 10.3390/genes14020424] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
A significant variety of cell growth factors are involved in the regulation of antler growth, and the fast proliferation and differentiation of various tissue cells occur during the yearly regeneration of deer antlers. The unique development process of velvet antlers has potential application value in many fields of biomedical research. Among them, the nature of cartilage tissue and the rapid growth and development process make deer antler a model for studying cartilage tissue development or rapid repair of damage. However, the molecular mechanisms underlying the rapid growth of antlers are still not well studied. MicroRNAs are ubiquitous in animals and have a wide range of biological functions. In this study, we used high-throughput sequencing technology to analyze the miRNA expression patterns of antler growth centers at three distinct growth phases, 30, 60, and 90 days following the abscission of the antler base, in order to determine the regulatory function of miRNA on the rapid growth of antlers. Then, we identified the miRNAs that were differentially expressed at various growth stages and annotated the functions of their target genes. The results showed that 4319, 4640, and 4520 miRNAs were found in antler growth centers during the three growth periods. To further identify the essential miRNAs that could regulate fast antler development, five differentially expressed miRNAs (DEMs) were screened, and the functions of their target genes were annotated. The results of KEGG pathway annotation revealed that the target genes of the five DEMs were significantly annotated to the "Wnt signaling pathway", "PI3K-Akt signaling pathway", "MAPK signaling pathway", and "TGF-β signaling pathway", which were associated with the rapid growth of velvet antlers. Therefore, the five chosen miRNAs, particularly ppy-miR-1, mmu-miR-200b-3p, and novel miR-94, may play crucial roles in rapid antler growth in summer.
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Affiliation(s)
- Zhenxiang Zhang
- Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland, Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, China
- College of Eco–Environmental Engineering, Qinghai University, Xining 810016, China
| | - Caixia He
- College of Eco–Environmental Engineering, Qinghai University, Xining 810016, China
| | - Changhong Bao
- College of Eco–Environmental Engineering, Qinghai University, Xining 810016, China
| | - Zhaonan Li
- College of Eco–Environmental Engineering, Qinghai University, Xining 810016, China
| | - Wenjie Jin
- College of Eco–Environmental Engineering, Qinghai University, Xining 810016, China
| | - Changzhong Li
- College of Eco–Environmental Engineering, Qinghai University, Xining 810016, China
| | - Yanxia Chen
- College of Eco–Environmental Engineering, Qinghai University, Xining 810016, China
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Kim Y, Takahashi S, Miyao M. Relationship between reduction in rice (Nipponbare) leaf blade size under elevated CO 2 and miR396- GRF module. PLANT SIGNALING & BEHAVIOR 2022; 17:2041280. [PMID: 35318879 PMCID: PMC8959511 DOI: 10.1080/15592324.2022.2041280] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/07/2022] [Accepted: 02/07/2022] [Indexed: 05/27/2023]
Abstract
Elevated CO2 (eCO2; 1000 ppm) influences developing rice leaf formation, reducing leaf blade length and width as compared to rice grown under ambient CO2 (aCO2; 400 ppm). Since micro RNAs (miRNAs) are known to play multiple roles in plant development, we hypothesized that miRNAs might be involved in modulating leaf size under eCO2 conditions. To identify miRNAs responding to eCO2, we profiled miRNA levels in developing rice leaves (P4; plastochron number of the fourth-youngest leaf) under eCO2 using small RNA-seq. We detected 18 mature miRNA sequences for which expression levels varied more than two-fold between the eCO2 and aCO2 conditions. Among them, only miR396e and miR396f significantly differed between the two conditions. Additionally, the expression of growth-regulating factors (GRFs), potential target mRNA of miR396s, were repressed under the eCO2 condition. We used an antisense oligonucleotide approach to confirm that single-strand DNA corresponding to the miR396e sequence effectively downregulated GRF expression in developing leaves, reducing the leaf blade length, such as for rice grown under eCO2. These results suggest that the miR396-GRF module is crucially relevant to controlling rice leaf blade length in eCO2 environments.
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Affiliation(s)
- Yonghyun Kim
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Sumire Takahashi
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Mitsue Miyao
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
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8
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Norouzi M, Bakhtiarizadeh MR, Salehi A. Investigation of the transability of dietary small non-coding RNAs to animals. Front Genet 2022; 13:933709. [PMID: 36134021 PMCID: PMC9483711 DOI: 10.3389/fgene.2022.933709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Our daily diet not only provides essential nutrients needed for survival and growth but also supplies bioactive ingredients to promote health and prevent disease. Recent studies have shown that exogenous microRNAs (miRNAs), xenomiRs, may enter the consumer’s body through dietary intake and regulate gene expression. This fascinating phenomenon suggests that xenomiRs can act as a new class of bioactive substances associated with mammalian systems. In contrast, several studies have failed to detect xenomiRs in consumers and reported that the observed diet-derived miRNAs in the previous studies can be related to the false positive effects of experiments. This discrepancy can be attributed to the potential artifacts related to the process of experiments, small sample size, and inefficient bioinformatics pipeline. Since this hypothesis is not generally accepted yet, more studies are required. Here, a stringent and reliable bioinformatics pipeline was used to analyze 133 miRNA sequencing data from seven different studies to investigate this phenomenon. Generally, our results do not support the transfer of diet-derived miRNAs into the animal/human tissues in every situation. Briefly, xenomiRs were absent from most samples, and also, their expressions were very low in the samples where they were present, which is unlikely to be sufficient to regulate cell transcripts. Furthermore, this study showed that the possibility of miRNAs being absorbed through animals’ diets and thus influencing gene expression during specific periods of biological development is not inconceivable. In this context, our results were in agreement with the theory of the transfer of small RNAs under certain conditions and periods as xenomiRs were found in colostrum which may modulate infants’ immune systems via post-transcriptional regulation. These findings provide evidence for the selective absorption of diet-derived small RNAs, which need to be investigated in future studies to shed light on the mechanisms underlying the transference of diet-derived miRNAs.
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Affiliation(s)
- Milad Norouzi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | | | - Abdolreza Salehi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
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9
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Li Y, Zhang D, Zhang S, Lou Y, An X, Jiang Z, Gao Z. Transcriptome and miRNAome analysis reveals components regulating tissue differentiation of bamboo shoots. PLANT PHYSIOLOGY 2022; 188:2182-2198. [PMID: 35157078 PMCID: PMC8968251 DOI: 10.1093/plphys/kiac018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/17/2021] [Indexed: 05/27/2023]
Abstract
Primary thickening determines bamboo yield and wood property. However, little is known about the regulatory networks involved in this process. This study identified a total of 58,652 genes and 150 miRNAs via transcriptome and small RNA sequencing using the underground thickening shoot samples of wild-type (WT) Moso bamboo (Phyllostachys edulis) and a thick wall (TW) variant (P. edulis "Pachyloen") at five developmental stages (WTS1/TWS1-WTS5/TWS5). A total of 14,029 (65.17%) differentially expressed genes and 68 (45.33%) differentially expressed miRNAs were identified from the WT, TW, and WTTW groups. The first two groups were composed of four pairwise combinations, each between two successive stages (WTS2/TWS2_versus_WTS1/TWS1, WTS3/TWS3_versus_WTS2/TWS2, WTS4/TWS4_versus_WTS3/TWS3, and WTS5/TWS5_versus_WTS4/TWS4), and the WTTW group was composed of five combinations, each between two relative stages (TWS1-5_versus_WTS1-5). Additionally, among the phytohormones, zeatin showed more remarkable changes in concentrations than indole-3-acetic acid, gibberellic acid, and abscisic acid throughout the five stages in the WT and the TW groups. Moreover, 125 cleavage sites were identified for 387 miRNA-mRNA pairs via degradome sequencing (P < 0.05). The dual-luciferase reporter assay confirmed that 13 miRNAs bound to 12 targets. Fluorescence in situ hybridization localized miR166 and miR160 in the shoot apical meristem and the procambium of Moso bamboo shoots at the S1 stage. Thus, primary thickening is a complex process regulated by miRNA-gene-phytohormone networks, and the miRNAome and transcriptome dynamics regulate phenotypic plasticity. These findings provide insights into the molecular mechanisms underlying wood formation and properties and propose targets for bamboo breeding.
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Affiliation(s)
- Ying Li
- National State Forestry and Grassland Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shuqin Zhang
- National State Forestry and Grassland Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China
| | - Yongfeng Lou
- Jiangxi Academy of Forestry, Jiangxi 330032, China
| | - Xinmin An
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
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10
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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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11
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Qu H, Liu Y, Jiang H, Liu Y, Song W, Chen L. Identification and characterization of miRNAs associated with sterile flower buds in the tea plant based on small RNA sequencing. Hereditas 2021; 158:26. [PMID: 34271985 PMCID: PMC8285856 DOI: 10.1186/s41065-021-00188-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/07/2021] [Indexed: 11/18/2022] Open
Abstract
Background miRNAs are a type of conserved, small RNA molecule that regulate gene expression and play an important role in the growth and development of plants. miRNAs are involved in seed germination, root development, shoot apical meristem maintenance, leaf development, and flower development by regulating various target genes. However, the role of miRNAs in the mechanism of tea plant flower sterility remains unclear. Therefore, we performed miRNA sequencing on the flowers of fertile male parents, female parents, and sterile offspring. Results A total of 55 known miRNAs and 90 unknown miRNAs were identified. In the infertile progeny, 37 miRNAs were differentially expressed; 18 were up-regulated and 19 were down-regulated. miR156, miR157, miR164, miR167, miR169, miR2111 and miR396 family members were down-regulated, and miR160, miR172 and miR319 family members were up-regulated. Moreover, we predicted that the 37 differentially expressed miRNAs target a total of 363 genes, which were enriched in 31 biological functions. We predicted that miR156 targets 142 genes, including ATD1A, SPL, ACA1, ACA2, CKB22 and MADS2. Conclusion We detected a large number of differentially expressed miRNAs in the sterile tea plant flowers, and their target genes were involved in complex biological processes. Among these miRNAs, the down-regulation of miR156 may be one of the factor in the formation of sterile floral buds in tea plants. Supplementary Information The online version contains supplementary material available at 10.1186/s41065-021-00188-8.
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Affiliation(s)
- Hao Qu
- Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai, Xishuangbanna, 666201, China.,Yunnan Provincial Key Laboratory of Tea Science, Menghai, Xishuangbanna, 666201, China
| | - Yue Liu
- Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai, Xishuangbanna, 666201, China.,Yunnan Provincial Key Laboratory of Tea Science, Menghai, Xishuangbanna, 666201, China
| | - Huibing Jiang
- Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai, Xishuangbanna, 666201, China.,Yunnan Provincial Key Laboratory of Tea Science, Menghai, Xishuangbanna, 666201, China
| | - Yufei Liu
- Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai, Xishuangbanna, 666201, China.,Yunnan Provincial Key Laboratory of Tea Science, Menghai, Xishuangbanna, 666201, China
| | - Weixi Song
- Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai, Xishuangbanna, 666201, China.,Yunnan Provincial Key Laboratory of Tea Science, Menghai, Xishuangbanna, 666201, China
| | - Linbo Chen
- Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai, Xishuangbanna, 666201, China. .,Yunnan Provincial Key Laboratory of Tea Science, Menghai, Xishuangbanna, 666201, China.
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12
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Owusu Adjei M, Zhou X, Mao M, Rafique F, Ma J. MicroRNAs Roles in Plants Secondary Metabolism. PLANT SIGNALING & BEHAVIOR 2021; 16:1915590. [PMID: 33938393 PMCID: PMC8205019 DOI: 10.1080/15592324.2021.1915590] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 05/20/2023]
Abstract
Plant growth and development is dependent on the regulation of classes of microRNAs (miRNAs) that have emerged as important gene regulators. These miRNAs can regulate plant gene expression to function. They play an important roles in biological homeostasis and environmental response controls. A wide range of plant biological and metabolic processes, including developmental timing, tissues specific development, and differentiation, depends on miRNAs. They perpetually regulate secondary metabolite functions in different plant family lines. Mapping of molecular phylogenies shows the distribution of secondary metabolism in the plant territory. More importantly, a lot of information related to miRNA regulatory processes in plants is revealed, but the role of miRNAs in secondary metabolism regulation and functions of the metabolites are still unclear. In this review, we pinnacle some potential miRNAs regulating the secondary metabolite biosynthesis activities in plants. This will provide an alternative knowledge for functional studies of secondary metabolism.
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Affiliation(s)
- Mark Owusu Adjei
- College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xuzixin Zhou
- College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Meiqin Mao
- College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Fatima Rafique
- College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jun Ma
- College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China
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13
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Molecular Cloning, Transcriptional Profiling, Subcellular Localization, and miRNA-Binding Site Analysis of Six SCL9 Genes in Poplar. PLANTS 2021; 10:plants10071338. [PMID: 34208997 PMCID: PMC8309000 DOI: 10.3390/plants10071338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/25/2021] [Accepted: 06/27/2021] [Indexed: 11/16/2022]
Abstract
The SCL9 subfamily is a key member of the GRAS family that regulates plant development and stress responses. Nevertheless, the functional role of these genes in the growth and development of poplar still unclear. Here, we reported the six SCL9 genes, which were found to be differentially expressed during poplar adventitious root formation. The full-length sequences of PeSCL9 genes of ‘Nanlin895’ poplar (Populus deltoids × Populus euramericana) were cloned by the RACE technique All PeSCL9 genes lacked introns. RT-qPCR revealed that PeSCL9 genes displayed a dynamic expression pattern in the adventitious root of poplar, according to RT-qPCR data. A series of comprehensive genes characteristics analysis were carried out for six genes by bioinformation. Meanwhile, transient expression analysis of the Populus protoplasts showed that all the PeSCL9 proteins were localized in the nucleus. In addition, the degradome and sRNA of ‘Nanlin895’ poplar in combination were used to predict miRNAs that regulate PeSCL9. It was found that miR396a and miR396c may affect PeSCL9 expression via cleavage, which was further verified by a transient expression experiment in Populus protoplasts. Overall, the development of poplar adventitious root and other tissues was closely related to these six SCL9 genes, and they serve as a starting point for further research into the mechanisms regulating poplar growth and development.
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14
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Yang X, Zhao X, Dai Z, Ma F, Miao X, Shi Z. OsmiR396/growth regulating factor modulate rice grain size through direct regulation of embryo-specific miR408. PLANT PHYSIOLOGY 2021; 186:519-533. [PMID: 33620493 PMCID: PMC8154042 DOI: 10.1093/plphys/kiab084] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/08/2021] [Indexed: 05/23/2023]
Abstract
microRNAs (miRNAs) are promising targets for crop improvement of complex agricultural traits. Coordinated activity between/among different miRNAs may fine-tune specific developmental processes in diverse organisms. Grain size is a main factor determining rice (Oryza sativa L.) crop yield, but the network of miRNAs influencing this trait remains uncharacterized. Here we show that sequestering OsmiR396 through target mimicry (MIM396) can substantially increase grain size in several japonica and indica rice subspecies and in plants with excessive tillers and a high panicle density. Thus, OsmiR396 has a major role related to the regulation of rice grain size. The grain shape of Growth Regulating Factor8 (OsGRF8)-overexpressing transgenic plants was most similar to that of MIM396 plants, suggesting OsGRF8 is a major mediator of OsmiR396 in grain size regulation. A miRNA microarray analysis revealed changes to the expression of many miRNAs, including OsmiR408, in the MIM396 plants. Analyses of gene expression patterns and functions indicated OsmiR408 is an embryo-specific miRNA that positively regulates grain size. Silencing OsmiR408 expression (miR408KO) using CRISPR technology resulted in small grains. Moreover, we revealed the direct regulatory effects of OsGRF8 on OsMIR408 expression. A genetic analysis further showed that the large-grain phenotype of MIM396 plants could be complemented by miR408KO. Also, several hormone signaling pathways might be involved in the OsmiR396/GRF-meditated grain size regulation. Our findings suggest that genetic regulatory networks comprising various miRNAs, such as OsmiR396 and OsmiR408, may be crucial for controlling rice grain size. Furthermore, the OsmiR396/GRF module may be important for breeding new high-yielding rice varieties.
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Affiliation(s)
- Xiaofang Yang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiaoling Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhengyan Dai
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Feilong Ma
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Xuexia Miao
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhenying Shi
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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15
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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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16
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Lu Y, Zeng J, Liu Q. The Rice miR396-GRF-GIF-SWI/SNF Module: A Player in GA Signaling. FRONTIERS IN PLANT SCIENCE 2021; 12:786641. [PMID: 35087553 PMCID: PMC8786800 DOI: 10.3389/fpls.2021.786641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/13/2021] [Indexed: 05/13/2023]
Abstract
Rice Growth-Regulating Factors (GRFs) were originally identified to be gibberellin (GA)-induced, but the nature of GA induction has remained unknown because most reports thereafter focused on revealing their roles in growth-promoting activities. GRFs have the WRC (Trp, Arg, Cys) domain to target DNA and contain the QLQ (Gln, Leu, Gln) domain to interact with GRF-Interacting Factor (GIF), which recruits ATP-dependent DNA translocase Switch/Sucrose Non-fermenting (SWI/SNF) for chromatin remodeling. Both GRFs and GIFs exhibit transcriptional activities but GIFs lack a DNA-binding domain. So, GRFs act like a navigator in the GRF-GIF-SWI/SNF complex, determining when and where the complex should work on. The levels of most rice GRFs can be sensitively regulated by miR396, which responds to many developmental and environmental factors. Recent clues from several studies highlight the original question of how GRFs participate in GA signaling. DELLA (contain DELLA motif) protein plays dual roles in controlling the level of GRFs by regulating the level of miR396 and interacting with GRFs. Here we address the question of why this complex plays an essential role in controlling plant growth focusing on the action of GA signaling pivot, DELLA.
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Affiliation(s)
- Yuzhu Lu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
- *Correspondence: Yuzhu Lu
| | - Jia Zeng
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Qiaoquan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Qiaoquan Liu
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17
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Wang L, Yin Y, Jing X, Wang M, Zhao M, Yu J, Qiu Z, Li YF. Profiling of MicroRNAs Involved in Mepiquat Chloride-Mediated Inhibition of Internode Elongation in Cotton ( Gossypium hirsutum L.) Seedlings. FRONTIERS IN PLANT SCIENCE 2021; 12:643213. [PMID: 33719323 PMCID: PMC7943613 DOI: 10.3389/fpls.2021.643213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/01/2021] [Indexed: 05/06/2023]
Abstract
Mepiquat chloride (MC) is the most important plant growth retardant that is widely used in cotton (Gossypium hirsutum L.) production to suppress excessive vegetative growth and improve plant architecture. MicroRNAs (miRNAs) are important gene expression regulators that control plant growth and development. However, miRNA-mediated post-transcriptional regulation in MC-induced growth inhibition remains unclear. In this study, the dynamic expression profiles of miRNAs responsive to MC in cotton internodes were investigated. A total of 508 known miRNAs belonging to 197 families and five novel miRNAs were identified. Among them, 104 miRNAs were differentially expressed at 48, 72, or 96 h post MC treatment compared with the control (0 h); majority of them were highly conserved miRNAs. The number of differentially expressed miRNAs increased with time after treatment. The expression of 14 known miRNAs was continuously suppressed, whereas 12 known miRNAs and one novel miRNA were continuously induced by MC. The expression patterns of the nine differentially expressed miRNAs were verified using qRT-PCR. The targets of the known and novel miRNAs were predicted. Four conserved and six novel targets were validated using the RLM-5' RACE assay. This study revealed that miRNAs play crucial regulatory roles in the MC-induced inhibition of internode elongation. It can improve our understanding of post-transcriptional gene regulation in MC-mediated growth inhibition and could potentially facilitate the breeding of dwarf cotton.
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Affiliation(s)
- Li Wang
- College of Life Sciences, Henan Normal University, Xinxiang, China
- Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, China
- Li Wang,
| | - Ying Yin
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Xiuxiu Jing
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Menglei Wang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Miao Zhao
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Juanjuan Yu
- College of Life Sciences, Henan Normal University, Xinxiang, China
- Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, China
| | - Zongbo Qiu
- College of Life Sciences, Henan Normal University, Xinxiang, China
- Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, China
| | - Yong-Fang Li
- College of Life Sciences, Henan Normal University, Xinxiang, China
- Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, China
- *Correspondence: Yong-Fang Li,
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18
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Salih H, Wang X, Chen B, Jia Y, Gong W, Du X. Identification, characterization and expression profiling of circular RNAs in the early cotton fiber developmental stages. Genomics 2020; 113:356-365. [PMID: 33338632 DOI: 10.1016/j.ygeno.2020.12.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 11/29/2020] [Accepted: 12/13/2020] [Indexed: 11/27/2022]
Abstract
Circular RNA is one of the endogenous non-coding RNAs with a covalently closed loop structure and largely involved in regulating gene expression. However, the abundance of circular RNAs and their regulatory functions during the early stages of fiber development are still not known. In this work, we conducted high-throughput sequencing of the Ligonlintless-1 and its wild-type at 0 DPA, 8 DPA and stem. A total of 2811 circular RNAs were identified and unevenly distributed across cotton chromosomes. We found 34, 142 and 27 circular RNAs were differentially expressed between Ligonlintless-1 and wild-type at 0 DPA, 8 DPA and stem, respectively. Both circular RNA-microRNA-mRNA network and MeJA treatment results in Ligonlintless-1 and wild-type might provide a strong indication of four circular RNAs and ghr_miR169b being important biological molecular associating with fiber development. The results provide new insight into the putative molecular function of circular RNAs in the regulation of fiber development.
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Affiliation(s)
- Haron Salih
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, China; Crop Sciences department, Zalingei University, Central Darfur, Sudan
| | - Xiao Wang
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, China
| | - Baojun Chen
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, China
| | - Yinhua Jia
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, China
| | - Wenfang Gong
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, China.
| | - Xiongming Du
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, China.
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19
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Hongkuan Z, Karsoon T, Shengkang L, Hongyu M, Huaiping Z. The functional roles of the non-coding RNAs in molluscs. Gene 2020; 768:145300. [PMID: 33207256 DOI: 10.1016/j.gene.2020.145300] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/01/2020] [Accepted: 11/04/2020] [Indexed: 01/10/2023]
Abstract
This review focus on the current knowledge of non-coding RNAs (ncRNAs) in molluscs. In this review, we provide an overview of long ncRNAs (lncRNA), microRNAs (miRNA) and piwi-interacting RNAs (piRNA), followed by evidence for the regulation of ncRNAs in variety of biological process in molluscs, including development, biomineralization and innate immune response. This review advances our understanding on the roles of ncRNAs in molluscs and suggest the future direction to fully understand the epigenetic regulatory network of molluscs.
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Affiliation(s)
- Zhang Hongkuan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou 515063, China; Mariculture Research Center for Subtropical Shellfish & Algae of Guangdong Province, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Tan Karsoon
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou 515063, China; Mariculture Research Center for Subtropical Shellfish & Algae of Guangdong Province, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Li Shengkang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou 515063, China; Mariculture Research Center for Subtropical Shellfish & Algae of Guangdong Province, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Ma Hongyu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou 515063, China; Mariculture Research Center for Subtropical Shellfish & Algae of Guangdong Province, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Zheng Huaiping
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou 515063, China; Mariculture Research Center for Subtropical Shellfish & Algae of Guangdong Province, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China.
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MAC5, an RNA-binding protein, protects pri-miRNAs from SERRATE-dependent exoribonuclease activities. Proc Natl Acad Sci U S A 2020; 117:23982-23990. [PMID: 32887800 DOI: 10.1073/pnas.2008283117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
MAC5 is a component of the conserved MOS4-associated complex. It plays critical roles in development and immunity. Here we report that MAC5 is required for microRNA (miRNA) biogenesis. MAC5 interacts with Serrate (SE), which is a core component of the microprocessor that processes primary miRNA transcripts (pri-miRNAs) into miRNAs and binds the stem-loop region of pri-miRNAs. MAC5 is essential for both the efficient processing and the stability of pri-miRNAs. Interestingly, the reduction of pri-miRNA levels in mac5 is partially caused by XRN2/XRN3, the nuclear-localized 5'-to-3' exoribonucleases, and depends on SE. These results reveal that MAC5 plays a dual role in promoting pri-miRNA processing and stability through its interaction with SE and/or pri-miRNAs. This study also uncovers that pri-miRNAs need to be protected from nuclear RNA decay machinery, which is connected to the microprocessor.
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Fard EM, Moradi S, Salekdeh NN, Bakhshi B, Ghaffari MR, Zeinalabedini M, Salekdeh GH. Plant isomiRs: origins, biogenesis, and biological functions. Genomics 2020; 112:3382-3395. [DOI: 10.1016/j.ygeno.2020.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/22/2020] [Accepted: 06/10/2020] [Indexed: 12/14/2022]
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22
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Lu Y, Meng Y, Zeng J, Luo Y, Feng Z, Bian L, Gao S. Coordination between GROWTH-REGULATING FACTOR1 and GRF-INTERACTING FACTOR1 plays a key role in regulating leaf growth in rice. BMC PLANT BIOLOGY 2020; 20:200. [PMID: 32384927 PMCID: PMC7206744 DOI: 10.1186/s12870-020-02417-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/29/2020] [Indexed: 05/29/2023]
Abstract
BACKGROUND The interactions between Growth-regulating factors (GRFs) and GRF-Interacting Factors (GIFs) have been well demonstrated but it remains unclear whether different combinations of GRF and GIF play distinctive roles in the pathway downstream of the complex. RESULTS Here we showed that OsGRF1 and OsGIF1 synergistically regulate leaf growth in rice. The expression of OsGIF1 emerged in all tissues with much higher level while that of OsGRF1 appeared preferentially only in the stem tips containing shoot apical meristem (SAM) and younger leaves containing leaf primordium. Overexpression of an OsmiR396-resistant version of mOsGRF1 resulted in expanded leaves due to increased cell proliferation while knockdown of OsGRF1 displayed an opposite phenotype. Overexpression of OsGIF1 did not exhibit new phenotype while knockdown lines displayed pleiotropic growth defects including shrunken leaves. The crossed lines of mOsGRF1 overexpression and OsGIF1 knockdown still exhibited shrunk leaves, indicating that OsGIF1 is indispensable in leaf growth regulated by OsGRF1. The expression of OsGRF1 could be upregulated by gibberellins (GAs) and downregulated by various stresses while that of OsGIF1 could not. CONCLUSION Our results suggest that OsGIF1 is in an excessive expression in various tissues and play roles in various aspects of growth while OsGRF1 may specifically involve in leaf growth through titrating OsGIF1. Both internal and external conditions impacting leaf growth are likely via way of regulating the expression of OsGRF1.
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Affiliation(s)
- Yuzhu Lu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009 China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009 Jiangsu China
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009 China
| | - Yunlong Meng
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009 China
| | - Jia Zeng
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009 China
| | - Ying Luo
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009 China
| | - Zhen Feng
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009 China
| | - Liying Bian
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009 China
| | - Suyun Gao
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009 China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009 Jiangsu China
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Kurihara Y, Makita Y, Shimohira H, Fujita T, Iwasaki S, Matsui M. Translational Landscape of Protein-Coding and Non-Protein-Coding RNAs upon Light Exposure in Arabidopsis. PLANT & CELL PHYSIOLOGY 2020; 61:536-545. [PMID: 31794029 DOI: 10.1093/pcp/pcz219] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/22/2019] [Indexed: 06/10/2023]
Abstract
Light is one of the most essential environmental clues for plant growth and morphogenesis. Exposure to blue monochromatic light from darkness is a turning point for plant biological activity, and as a result dramatic changes in gene expression occur. To understand the translational impacts of blue light, we have performed ribosome profiling analysis and called translated open reading frames (ORFs) de novo within not only mRNAs but also non-coding RNAs (ncRNAs). Translation efficiency of 3,823 protein-coding ORFs, such as nuclear chloroplast-related genes, was up-regulated by blue light exposure. Moreover, the translational activation of the microRNA biogenesis-related genes, DCL1 and HYL1, was induced by blue light. Considering the 3-nucleotide codon periodicity of ribosome footprints, a few hundred short ORFs lying on ncRNAs and upstream ORFs (uORFs) on mRNAs were found that had differential translation status between blue light and dark. uORFs are known to have a negative effect on the expression of the main ORFs (mORFs) on the same mRNAs. Our analysis suggests that the translation of uORFs is likely to be more stimulated than that of the corresponding mORFs, and uORF-mediated translational repression of the mORFs in five genes was alleviated by blue light exposure. With data-based annotation of the ORFs, our analysis provides insights into the translatome in response to environmental changes, such as those involving light.
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Affiliation(s)
- Yukio Kurihara
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045 Japan
| | - Yuko Makita
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045 Japan
| | - Haruka Shimohira
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045 Japan
- Graduate School of Nanobioscience Department of Life and Environmental System Science, Yokohama City University, Yokohama, Kanagawa, 236-0027 Japan
| | - Tomoya Fujita
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198 Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8503 Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198 Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561 Japan
| | - Minami Matsui
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045 Japan
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24
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Liebsch D, Palatnik JF. MicroRNA miR396, GRF transcription factors and GIF co-regulators: a conserved plant growth regulatory module with potential for breeding and biotechnology. CURRENT OPINION IN PLANT BIOLOGY 2020; 53:31-42. [PMID: 31726426 DOI: 10.1016/j.pbi.2019.09.008] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/19/2019] [Accepted: 09/23/2019] [Indexed: 05/23/2023]
Abstract
Multicellular life relies on complex regulatory mechanisms ensuring proper growth and development. In plants, these mechanisms construct a body plan that is both reproducible, and highly flexible for adaptation to different environmental conditions. A crucial regulatory module - consisting of microRNA miR396, GROWTH REGULATING FACTORS (GRFs) and GRF-INTERACTING FACTORS (GIFs) - has been shown to control growth of multiple tissues and organs in a variety of species. Especially in the last few years, research has expanded our knowledge of miR396-GRF/GIF function to crops, where it affects agronomically important traits, and highlighted its role in coordinating growth with endogenous and environmental factors. Special properties make the miR396-GRF/GIF system highly efficient in growth regulation and a promising target for improving plant yield.
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Affiliation(s)
- Daniela Liebsch
- IBR (Instituto de Biologia Molecular y Celular de Rosario), UNR/CONICET, Ocampo y Esmeralda s/n, 2000 Rosario, Argentina.
| | - Javier F Palatnik
- IBR (Instituto de Biologia Molecular y Celular de Rosario), UNR/CONICET, Ocampo y Esmeralda s/n, 2000 Rosario, Argentina; Centro de Estudios Interdisciplinarios, Universidad Nacional de Rosario, Rosario, Argentina.
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25
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Seeve CM, Sunkar R, Zheng Y, Liu L, Liu Z, McMullen M, Nelson S, Sharp RE, Oliver MJ. Water-deficit responsive microRNAs in the primary root growth zone of maize. BMC PLANT BIOLOGY 2019; 19:447. [PMID: 31651253 PMCID: PMC6814125 DOI: 10.1186/s12870-019-2037-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/12/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND MicroRNA-mediated gene regulatory networks play a significant role in plant growth and development and environmental stress responses. RESULTS We identified 79 microRNAs (miRNAs) and multiple miRNA variants (isomiRs) belonging to 26 miRNA families in the primary root growth zone of maize seedlings grown at one of three water potentials: well-watered (- 0.02 MPa), mild water deficit stress (- 0.3 MPa), and severe water deficit stress (- 1.6 MPa). The abundances of 3 miRNAs (mild stress) and 34 miRNAs representing 17 families (severe stress) were significantly different in water-deficit stressed relative to well-watered controls (FDR < 0.05 and validated by stem loop RT-qPCR). Degradome sequencing revealed 213 miRNA-regulated transcripts and trancriptome profiling revealed that the abundance of 77 (miRNA-regulated) were regulated by water-defecit stress. miR399e,i,j-3p was strongly regulated by water-defcit stress implicating the possibility of nutrient deficiency during stress. CONCLUSIONS We have identified a number of maize miRNAs that respond to specific water deficits applied to the primary root growth zone. We have also identified transcripts that are targets for miRNA regulation in the root growth zone under water-deficit stress. The miR399e,i,j-3p that is known to regulate phosphate uptake in response to nutrient deficiencies responds to water-deficit stress, however, at the seedling stage the seed provides adequate nutrients for root growth thus miR399e,i,j-3p may play a separate role in water-deficit responses. A water-deficit regulated maize transcript, similar to known miR399 target mimics, was identified and we hypothesized that it is another regulatory player, moderating the role of miR399e,i,j-3p, in primary root growth zone water deficit responses.
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Affiliation(s)
- Candace M. Seeve
- USDA-ARS, Plant Genetics Research Unit, Columbia, MO 65211 USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211 USA
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078 USA
| | - Yun Zheng
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, 650500 Yunnan China
| | - Li Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500 Yunnan China
| | - Zhijie Liu
- Huazhong Agricultural University, Wuhan, 430070 Hubei Province China
| | - Michael McMullen
- Division of Plant Sciences, Columbia, University of Missouri, Columbia, MO 65211 USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211 USA
| | - Sven Nelson
- USDA-ARS, Plant Genetics Research Unit, Columbia, MO 65211 USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211 USA
| | - Robert E. Sharp
- Division of Plant Sciences, Columbia, University of Missouri, Columbia, MO 65211 USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211 USA
| | - Melvin J. Oliver
- USDA-ARS, Plant Genetics Research Unit, Columbia, MO 65211 USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211 USA
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26
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Szczygieł-Sommer A, Gaj MD. The miR396-GRF Regulatory Module Controls the Embryogenic Response in Arabidopsis via an Auxin-Related Pathway. Int J Mol Sci 2019; 20:ijms20205221. [PMID: 31640280 PMCID: PMC6829408 DOI: 10.3390/ijms20205221] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 10/18/2019] [Indexed: 01/26/2023] Open
Abstract
In plants, microRNAs have been indicated to control various developmental processes, including somatic embryogenesis (SE), which is triggered in the in vitro cultured somatic cells of plants. Although a transcriptomic analysis has indicated that numerous MIRNAs are differentially expressed in the SE of different plants, the role of specific miRNAs in the embryogenic reprogramming of the somatic cell transcriptome is still poorly understood. In this study, we focused on performing a functional analysis of miR396 in SE given that the transcripts of MIR396 genes and the mature molecules of miR396 were found to be increased during an SE culture of Arabidopsis. In terms of miR396 in embryogenic induction, we observed the SE-associated expression pattern of MIR396b in explants of the β-glucuronidase (GUS) reporter line. In order to gain insight into the miR396-controlled mechanism that is involved in SE induction, the embryogenic response of mir396 mutants and the 35S:MIR396b overexpressor line to media with different 2,4-Dichlorophenoxyacetic acid (2,4-D) concentrations was evaluated. The results suggested that miR396 might contribute to SE induction by controlling the sensitivity of tissues to auxin treatment. Within the targets of miR396 that are associated with SE induction, we identified genes encoding the GROWTH-REGULATING FACTOR (GRF) transcription factors, including GRF1, GRF4, GRF7, GRF8, and GRF9. Moreover, the study suggested a regulatory relationship between miR396, GRF, and the PLETHORA (PLT1 and PLT2) genes during SE induction. A complex regulatory relationship within the miR396–GRF1/4/8/9–PLT1/2 module that involves the negative and positive control of GRFs and PLT (respectively) by miR396 might be assumed.
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Affiliation(s)
- Aleksandra Szczygieł-Sommer
- Department of Genetics, University of Silesia, Faculty of Biology and Environmental Protection, 40-032 Katowice, Poland.
| | - Małgorzata D Gaj
- Department of Genetics, University of Silesia, Faculty of Biology and Environmental Protection, 40-032 Katowice, Poland.
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27
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Chen X, Jiang L, Zheng J, Chen F, Wang T, Wang M, Tao Y, Wang H, Hong Z, Huang Y, Huang R. A missense mutation in Large Grain Size 1 increases grain size and enhances cold tolerance in rice. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3851-3866. [PMID: 31020332 PMCID: PMC6685659 DOI: 10.1093/jxb/erz192] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/25/2019] [Indexed: 05/04/2023]
Abstract
Grain shape is controlled by quantitative trait loci (QTLs) in rice (Oryza sativa L.). A rice mutant (JF178) with long and large grains has been used in a breeding program for over a decade, but its genetic basis has been unclear. Here, a semi-dominant QTL, designated Large Grain Size 1 (LGS1), was cloned and the potential molecular mechanism of LGS1 function was studied. Near-isogenic lines (NILs) and a map-based approach were employed to clone the LGS1 locus. LGS1 encodes the OsGRF4 transcription factor and contains a 2 bp missense mutation in the coding region that coincides with the putative pairing site of miRNA396. The LGS1 transcript levels in the mutant line were found to be higher than the lgs1 transcript levels in the control plants, suggesting that the mutation might disrupt the pairing of the LGS1 mRNA with miR396. In addition to producing larger grains, LGS1 also enhanced cold tolerance at the seedling stage and increased the survival rate of seedlings after cold stress treatment. These findings indicate that the mutation in LGS1 appears to disturb the GRF4-miR396 stress response network and results in the development of enlarged grains and enhancement of cold tolerance in rice.
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Affiliation(s)
- Xiaolong Chen
- School of Life Sciences, Xiamen University, Xiamen, China
| | | | | | - Fangyu Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tiansheng Wang
- Quanzhou Institute of Agricultural Sciences, Quanzhou, China
| | - Meiling Wang
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Yi Tao
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Houcong Wang
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Zonglie Hong
- School of Life Sciences, Xiamen University, Xiamen, China
- Department of Plant Sciences, University of Idaho, Moscow, ID, USA
- Correspondence: , , and
| | - Yumin Huang
- School of Life Sciences, Xiamen University, Xiamen, China
- Correspondence: , , and
| | - Rongyu Huang
- School of Life Sciences, Xiamen University, Xiamen, China
- Correspondence: , , and
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28
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Cerruti E, Comino C, Acquadro A, Marconi G, Repetto AM, Pisanu AB, Pilia R, Albertini E, Portis E. Analysis of DNA Methylation Patterns Associated with In Vitro Propagated Globe Artichoke Plants Using an EpiRADseq-Based Approach. Genes (Basel) 2019; 10:E263. [PMID: 30939865 PMCID: PMC6523903 DOI: 10.3390/genes10040263] [Citation(s) in RCA: 5] [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: 02/27/2019] [Revised: 03/22/2019] [Accepted: 03/26/2019] [Indexed: 01/16/2023] Open
Abstract
Globe artichoke represents one of the main horticultural species of the Mediterranean basin, and 'Spinoso sardo' is the most widespread and economically relevant varietal type in Sardinia, Italy. In the last decades, in vitro culture of meristematic apices has increased the frequency of aberrant plants in open-field production. These off-type phenotypes showed highly pinnate-parted leaves and late inflorescence budding, and emerged from some branches of the true-to-type 'Spinoso sardo' plants. This phenomenon cannot be foreseen and is reversible through generations, suggesting the occurrence of epigenetic alterations. Here, we report an exploratory study on DNA methylation patterns in off-type/true-to-type globe artichoke plants, using a modified EpiRADseq technology, which allowed the identification of 2,897 differentially methylated loci (DML): 1,998 in CG, 458 in CHH, and 441 in CHG methylation contexts of which 720, 88, and 152, respectively, were in coding regions. Most of them appeared involved in primary metabolic processes, mostly linked to photosynthesis, regulation of flower development, and regulation of reproductive processes, coherently with the observed phenotype. Differences in the methylation status of some candidate genes were integrated with transcriptional analysis to test whether these two regulation levels might interplay in the emergence and spread of the 'Spinoso sardo' non-conventional phenotype.
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Affiliation(s)
- Elisa Cerruti
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, 10095 Grugliasco, Italy.
| | - Cinzia Comino
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, 10095 Grugliasco, Italy.
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, 10095 Grugliasco, Italy.
| | - Gianpiero Marconi
- Department of Agricultural, Food, and Environmental Sciences, University of Perugia, 06121 Perugia, Italy.
| | - Anna Maria Repetto
- Agris Sardegna-Agenzia Regionale per la Ricerca in Agricoltura-Servizio Ricerca sui Sistemi Colturali Erbacei, 09123 Cagliari, Italy.
| | - Anna Barbara Pisanu
- Agris Sardegna-Agenzia Regionale per la Ricerca in Agricoltura-Servizio Ricerca sui Sistemi Colturali Erbacei, 09123 Cagliari, Italy.
| | - Roberto Pilia
- Agris Sardegna-Agenzia Regionale per la Ricerca in Agricoltura-Servizio Ricerca sui Sistemi Colturali Erbacei, 09123 Cagliari, Italy.
| | - Emidio Albertini
- Department of Agricultural, Food, and Environmental Sciences, University of Perugia, 06121 Perugia, Italy.
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, 10095 Grugliasco, Italy.
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Ren T, Weraduwage SM, Sharkey TD. Prospects for enhancing leaf photosynthetic capacity by manipulating mesophyll cell morphology. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1153-1165. [PMID: 30590670 DOI: 10.1093/jxb/ery448] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 12/25/2018] [Indexed: 06/09/2023]
Abstract
Leaves are beautifully specialized organs designed to maximize the use of light and CO2 for photosynthesis. Engineering leaf anatomy therefore holds great potential to enhance photosynthetic capacity. Here we review the effect of the dominant leaf anatomical traits on leaf photosynthesis and confirm that a high chloroplast surface area exposed to intercellular airspace per unit leaf area (Sc) is critical for efficient photosynthesis. The possibility of improving Sc through appropriately increasing mesophyll cell density is further analyzed. The potential influences of modifying mesophyll cell morphology on CO2 diffusion, light distribution within the leaf, and other physiological processes are also discussed. Some potential target genes regulating leaf mesophyll cell proliferation and expansion are explored. Indeed, more comprehensive research is needed to understand how manipulating mesophyll cell morphology through editing the potential target genes impacts leaf photosynthetic capacity and related physiological processes. This will pinpoint the targets for engineering leaf anatomy to maximize photosynthetic capacity.
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Affiliation(s)
- Tao Ren
- College of Resources and Environment, Huazhong Agricultural University, China
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, USA
| | - Sarathi M Weraduwage
- Department of Energy Plant Research Laboratory and Plant Resiience Institute, Michigan State University, East Lansing, USA
| | - Thomas D Sharkey
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, USA
- Department of Energy Plant Research Laboratory and Plant Resiience Institute, Michigan State University, East Lansing, USA
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30
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Liu XX, Luo XF, Luo KX, Liu YL, Pan T, Li ZZ, Duns GJ, He FL, Qin ZD. Small RNA sequencing reveals dynamic microRNA expression of important nutrient metabolism during development of Camellia oleifera fruit. Int J Biol Sci 2019; 15:416-429. [PMID: 30745831 PMCID: PMC6367553 DOI: 10.7150/ijbs.26884] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 11/10/2018] [Indexed: 12/13/2022] Open
Abstract
To obtain insight into the function of miRNAs in the synthesis and storage of important nutrients during the development of Camellia oleifera fruit, Illumina sequencing of flower and fruit small-RNA was conducted. The results revealed that 797 miRNAs were significantly differentially expressed between flower and fruit samples of Camellia oleifera. Through integrated GO and KEGG function annotations, it was determined that the miRNA target genes were mainly involved in metabolic pathways, plant hormone signal transduction, fruit development, mitosis and regulation of biosynthetic processes. Carbohydrate accumulation genes were differentially regulated by miR156, miR390 and miR395 in the fruit growth and development process. MiR477 is the key miRNA functioning in regulation of genes and involved in fatty acid synthesis. Additionally, miR156 also has the function of regulating glycolysis and nutrient transformation genes.
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Affiliation(s)
- Xiao-Xia Liu
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Xiao-Fang Luo
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Ke-Xin Luo
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Ya-Lin Liu
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Ting Pan
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Zhi-Zhang Li
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Gregory J Duns
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Fu-Lin He
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Zuo-Dong Qin
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
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31
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Abstract
MicroRNAs (miRNA) are small RNAs of 20-22 nt that regulate diverse biological pathways through the modulation of gene expression. miRNAs recognize target RNAs by base complementarity and guide them to degradation or translational arrest. They are transcribed as longer precursors with extensive secondary structures. In plants, these precursors are processed by a complex harboring DICER-LIKE1 (DCL1), which cuts on the precursor stem region to release the mature miRNA together with the miRNA*. In both plants and animals, the miRNA precursors contain spatial clues that determine the position of the miRNA along their sequences. DCL1 is assisted by several proteins, such as the double-stranded RNA binding protein, HYPONASTIC LEAVES1 (HYL1), and the zinc finger protein SERRATE (SE). The precise biogenesis of miRNAs is of utter importance since it determines the exact nucleotide sequence of the mature small RNAs and therefore the identity of the target genes. miRNA processing itself can be regulated and therefore can determine the final small RNA levels and activity. Here, we describe methods to analyze miRNA processing intermediates in plants. These approaches can be used in wild-type or mutant plants, as well as in plants grown under different conditions, allowing a molecular characterization of the miRNA biogenesis from the RNA precursor perspective.
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Aydinoglu F, Lucas SJ. Identification and expression profiles of putative leaf growth related microRNAs in maize (Zea mays L.) hybrid ADA313. Gene 2018; 690:57-67. [PMID: 30597233 DOI: 10.1016/j.gene.2018.12.042] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 10/17/2018] [Accepted: 12/13/2018] [Indexed: 02/06/2023]
Abstract
Throughout the plant life cycle, growth of new leaves is governed by cell division and cell expansion. During steady-state growth of the maize leaf, these processes are spatially separated between the meristem zone, consisting of dividing cells at the leaf base, the elongation zone, consisting of expanding cells moving upwards from the meristem, and the mature zone containing differentiated mature cells. Increased leaf size can be achieved through increasing cell number or cell size, for example by manipulating the genes controlling the transition between those zones. In this study, microRNA (miRNA) genes, which are a class of endogenous small, non-coding gene regulatory RNAs, were investigated in the growth zones, to gain insight into their role in the transition between cell division and cell expansion. A genome-wide survey was conducted using a miRNA-microarray and 59 miRNA genes were detected to be differentially expressed between the growth zones. miR160, miR166, miR168, miR172, miR319 and miR390 families were significantly up-regulated in the meristem relative to the elongation and mature zones. In contrast, expression of the miR167 and miR396 families was lower in the meristem and higher in the mature zone. Therefore, these were considered to be candidate growth-regulated miRNAs that control cell division processes indirectly by repressing target genes. The miR156, miR166, miR167, miR399, miR408 and miR2275 families were expressed most highly in the elongation zone, and so were classified as elongation-specific, with possible roles in switching from cell division to cell elongation during leaf differentiation. In silico target prediction analysis showed that these miRNAs target several transcription factors and metabolic genes, and a reciprocal relationship between the expression levels of miR319 and miR396 and their targets was confirmed by qRT-PCR. Furthermore, 12 candidate novel miRNAs were identified from the microarray data and computationally verified. Three out of twelve were also validated by qRT-PCR. These findings provide important information regarding the regulatory functions of miRNAs in controlling progression of growth mechanisms.
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Affiliation(s)
- Fatma Aydinoglu
- Gebze Technical University, Molecular Biology and Genetics Department, Kocaeli, Turkey.
| | - Stuart James Lucas
- Sabanci University Nanotechnology Research & Application Center (SUNUM), Istanbul, Turkey
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Abstract
Plant leaves are differentiated organs that arise sequentially from a population of pluripotent stem cells at the shoot apical meristem (SAM). There is substantial diversity in leaf shape, much of which depends on the size and arrangement of outgrowths at the leaf margin. These outgrowths are generated by a patterning mechanism similar to the phyllotactic processes producing organs at the SAM, which involves the transcription factors CUP-SHAPED COTYLEDON and the phytohormone auxin. In the leaf, this patterning mechanism creates sequential protrusions and indentations along the margin. The size, shape, and distribution of these protrusions also depend on the overall growth of the leaf lamina. Globally, growth is regulated by a complex genetic network controlling the distribution of cell proliferation and the timing of differentiation. Evolutionary changes in margin form arise from changes in two different classes of homeobox genes that modify the outcome of marginal patterning in diverse ways, and are under intense investigation.
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Affiliation(s)
| | - Adam Runions
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Mainak Das Gupta
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Miltos Tsiantis
- Max Planck Institute for Plant Breeding Research, Cologne, Germany.
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Sieburth LE, Vincent JN. Beyond transcription factors: roles of mRNA decay in regulating gene expression in plants. F1000Res 2018; 7. [PMID: 30613385 PMCID: PMC6305221 DOI: 10.12688/f1000research.16203.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/05/2018] [Indexed: 12/16/2022] Open
Abstract
Gene expression is typically quantified as RNA abundance, which is influenced by both synthesis (transcription) and decay. Cytoplasmic decay typically initiates by deadenylation, after which decay can occur through any of three cytoplasmic decay pathways. Recent advances reveal several mechanisms by which RNA decay is regulated to control RNA abundance. mRNA can be post-transcriptionally modified, either indirectly through secondary structure or through direct modifications to the transcript itself, sometimes resulting in subsequent changes in mRNA decay rates. mRNA abundances can also be modified by tapping into pathways normally used for RNA quality control. Regulated mRNA decay can also come about through post-translational modification of decapping complex subunits. Likewise, mRNAs can undergo changes in subcellular localization (for example, the deposition of specific mRNAs into processing bodies, or P-bodies, where stabilization and destabilization occur in a transcript- and context-dependent manner). Additionally, specialized functions of mRNA decay pathways were implicated in a genome-wide mRNA decay analysis in Arabidopsis. Advances made using plants are emphasized in this review, but relevant studies from other model systems that highlight RNA decay mechanisms that may also be conserved in plants are discussed.
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Affiliation(s)
- Leslie E Sieburth
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Jessica N Vincent
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
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Koyama T. A hidden link between leaf development and senescence. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 276:105-110. [PMID: 30348308 DOI: 10.1016/j.plantsci.2018.08.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/04/2018] [Accepted: 08/13/2018] [Indexed: 05/21/2023]
Abstract
Leaf senescence is the final step of leaf development and is usually accompanied by visible color changes from green to yellow or brown. Unlike the senescence of the whole body of animals and unicellular organisms, which is often associated with death, leaf senescence in plants requires highly integrative processes towards cell death with nutrient recycling and storage. Since leaf senescence plays pivotal roles in the production of plant biomass and grain yield, the mechanisms of degradation and relocation of macromolecules as well as the regulation of signaling and biosynthetic pathways have received much attention. The importance of the plant hormone ethylene in the onset of leaf senescence has been clearly documented. However, research has increasingly demonstrated that the function of ethylene in the regulation of leaf senescence is dependent on leaf development. This review raises the issue of how ethylene requires developmental regulators and focuses on the developmental aspect of leaf senescence. It also emphasizes the remarkable impact that developmental regulators have on regulating the onset of leaf senescence.
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Affiliation(s)
- Tomotsugu Koyama
- Bioorganic Research Institute Suntory Foundation for Life Sciences, Japan.
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36
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Das Gupta M, Tsiantis M. Gene networks and the evolution of plant morphology. CURRENT OPINION IN PLANT BIOLOGY 2018; 45:82-87. [PMID: 29885565 DOI: 10.1016/j.pbi.2018.05.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/07/2018] [Accepted: 05/15/2018] [Indexed: 05/19/2023]
Abstract
Elaboration of morphology depends on the precise orchestration of gene expression by key regulatory genes. The hierarchy and relationship among the participating genes is commonly known as gene regulatory network (GRN). Therefore, the evolution of morphology ultimately occurs by the rewiring of gene network structures or by the co-option of gene networks to novel domains. The availability of high-resolution expression data combined with powerful statistical tools have opened up new avenues to formulate and test hypotheses on how diverse gene networks influence trait development and diversity. Here we summarize recent studies based on both big-data and genetics approaches to understand the evolution of plant form and physiology. We also discuss recent genome-wide investigations on how studying open-chromatin regions may help study the evolution of gene expression patterns.
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Affiliation(s)
- Mainak Das Gupta
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany.
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37
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Li Z, Xu R, Li N. MicroRNAs from plants to animals, do they define a new messenger for communication? Nutr Metab (Lond) 2018; 15:68. [PMID: 30302122 PMCID: PMC6167836 DOI: 10.1186/s12986-018-0305-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 09/21/2018] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs), a class of single-stranded non-coding RNA of about 22 nucleotides, are potent regulators of gene expression existing in both plants and animals. Recent studies showed that plant miRNAs could enter mammalian bloodstream via gastrointestinal tract, through which access a variety of tissues and cells of recipients to exert therapeutic effects. This intriguing phenomenon indicates that miRNAs of diet/plant origin may act as a new class of bioactive ingredients communicating with mammalian systems. In this review, in order to pinpoint the reason underlying discrepancies of miRNAs transmission from diet/plant to animals, the pathways that generate miRNAs and machineries involved in the functions of miRNAs in both kingdoms were outlined and compared. Then, the current controversies concerning cross-kingdom regulations and the potential mechanisms responsible for absorption and transfer of diet/plant-derived miRNAs were interpreted. Furthermore, the hormone-like action of miRNAs and the intricate interplay between miRNAs and hormones were implicated. Finally, how these findings may impact nutrition and medicine were briefly discussed.
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Affiliation(s)
- Zhiqing Li
- 1State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Tsinghua University, Beijing, 100005 People's Republic of China
| | - Ruodan Xu
- 2Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700 People's Republic of China.,3Department of Engineering, Aarhus University, 8000 Aarhus, Denmark
| | - Ning Li
- 2Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700 People's Republic of China
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Patwa N, Nithin C, Bahadur RP, Basak J. Identification and characterization of differentially expressed Phaseolus vulgaris miRNAs and their targets during mungbean yellow mosaic India virus infection reveals new insight into Phaseolus-MYMIV interaction. Genomics 2018; 111:1333-1342. [PMID: 30237075 DOI: 10.1016/j.ygeno.2018.09.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/17/2018] [Accepted: 09/09/2018] [Indexed: 02/06/2023]
Abstract
Phaseolus vulgaris is an economically important legume in tropical and subtropical regions of Asia, Africa, Latin-America and parts of USA and Europe. However, its production gets severely affected by mungbean yellow mosaic India virus (MYMIV). We aim to identify and characterize differentially expressed miRNAs during MYMIV-infection in P. vulgaris. A total of 422 miRNAs are identified of which 292 are expressed in both MYMIV-treated and mock-treated samples, 109 are expressed only in MYMIV-treated and 21 are expressed only in mock-treated samples. Selected up- and down-regulated miRNAs are validated by RT-qPCR. 3367 target ORFs are identified for 270 miRNAs. Selected targets are validated by 5' RLM-RACE. Differentially expressed miRNAs regulate transcription factors and are involved in improving stress tolerance to MYMIV. These findings will provide an insight into the role of miRNAs during MYMIV infection in P. vulgaris in particular and during any biotic stress conditions in Leguminosae family in general.
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Affiliation(s)
- Nisha Patwa
- Laboratory of Plant Stress Biology, Department of Biotechnology, Visva-Bharati, Santiniketan 731235, India
| | - Chandran Nithin
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, 721302, India
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, 721302, India
| | - Jolly Basak
- Laboratory of Plant Stress Biology, Department of Biotechnology, Visva-Bharati, Santiniketan 731235, India.
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39
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Liang Y, Xu P, Zou Q, Luo H, Yu W. An epigenetic perspective on tumorigenesis: Loss of cell identity, enhancer switching, and NamiRNA network. Semin Cancer Biol 2018; 57:1-9. [PMID: 30213688 DOI: 10.1016/j.semcancer.2018.09.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/26/2018] [Accepted: 09/06/2018] [Indexed: 02/09/2023]
Abstract
Various tumorigenic theories have been proposed in the past century, which contribute to the prevention and treatment of cancer clinically. However, the underlying mechanisms of the initiation of cancer, drug resistance, neoplasm relapse, and metastasis are still challenging to be panoramically addressed. Based on the abundant evidence provided by others and us, we postulate that Tumor Initiated by Loss of Cell Identity (LOCI), which is an inevitable initiating event of tumorigenesis. As a result, normal cells are transformed into the cancerous cell. In this process, epigenetic regulatory program, especially NamiRNA (Nuclear activating miRNA)-enhancer-gene activation network, is vital for the cell identity. The disorganization of NamiRNA-enhancer-gene activation network is a causal predisposition to the cell identity loss, and the altered cell identity is stabilized by genetic variations of the NamiRNA-enhancer-gene activation network. Furthermore, the additional genetic or epigenetic abnormities confer those cells to carcinogenic characteristics, such as growth advantage over normal cells, and finally yield cancer. In this review, we literally explain our tumor initiation hypothesis based on the corresponding evidence, which will not only help to refresh our understanding of tumorigenesis but also bring benefits to developing "cell identity reversing" based therapies.
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Affiliation(s)
- Ying Liang
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China; Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, Shanghai Medical College, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Molecular Biology, Fudan University, Shanghai, 200032, China; Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Peng Xu
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China; Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, Shanghai Medical College, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Molecular Biology, Fudan University, Shanghai, 200032, China; Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Qingping Zou
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China; Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, Shanghai Medical College, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Molecular Biology, Fudan University, Shanghai, 200032, China; Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Huaibing Luo
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China; Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, Shanghai Medical College, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Molecular Biology, Fudan University, Shanghai, 200032, China; Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Wenqiang Yu
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China; Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, Shanghai Medical College, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Molecular Biology, Fudan University, Shanghai, 200032, China; Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.
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40
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Liang Y, Xu P, Zou Q, Luo H, Yu W. An epigenetic perspective on tumorigenesis: Loss of cell identity, enhancer switching, and NamiRNA network. Semin Cancer Biol 2018; 83:596-604. [PMID: 30208341 DOI: 10.1016/j.semcancer.2018.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 09/07/2018] [Indexed: 02/09/2023]
Abstract
Various tumorigenic theories have been proposed in the past century, which contribute to the prevention and treatment of cancer clinically. However, the underlying mechanisms of the initiation of cancer, drug resistance, neoplasm relapse, and metastasis are still challenging to be panoramically addressed. Based on the abundant evidence provided by others and us, we postulate that Tumor Initiated by Loss of Cell Identity (LOCI), which is an inevitable initiating event of tumorigenesis. As a result, normal cells are transformed into the cancerous cell. In this process, epigenetic regulatory program, especially NamiRNA (Nuclear activating miRNA)-enhancer-gene activation network, is vital for the cell identity. The disorganization of NamiRNA-enhancer-gene activation network is a causal predisposition to the cell identity loss, and the altered cell identity is stabilized by genetic variations of the NamiRNA-enhancer-gene activation network. Furthermore, the additional genetic or epigenetic abnormities confer those cells to carcinogenic characteristics, such as growth advantage over normal cells, and finally yield cancer. In this review, we literally explain our tumor imitation hypothesis based on the corresponding evidence, which will not only help to refresh our understanding of tumorigenesis but also bring benefits to developing "cell identity reversing" based therapies.
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Affiliation(s)
- Ying Liang
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China; Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, Shanghai Medical College, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Molecular Biology, Fudan University, Shanghai, 200032, China; Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Peng Xu
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China; Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, Shanghai Medical College, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Molecular Biology, Fudan University, Shanghai, 200032, China; Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Qingping Zou
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China; Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, Shanghai Medical College, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Molecular Biology, Fudan University, Shanghai, 200032, China; Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Huaibing Luo
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China; Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, Shanghai Medical College, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Molecular Biology, Fudan University, Shanghai, 200032, China; Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Wenqiang Yu
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China; Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, Shanghai Medical College, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Molecular Biology, Fudan University, Shanghai, 200032, China; Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.
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41
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Beltramino M, Ercoli MF, Debernardi JM, Goldy C, Rojas AML, Nota F, Alvarez ME, Vercruyssen L, Inzé D, Palatnik JF, Rodriguez RE. Robust increase of leaf size by Arabidopsis thaliana GRF3-like transcription factors under different growth conditions. Sci Rep 2018; 8:13447. [PMID: 30194309 PMCID: PMC6128883 DOI: 10.1038/s41598-018-29859-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 07/17/2018] [Indexed: 02/03/2023] Open
Abstract
An increase in crop yield is essential to reassure food security to meet the accelerating global demand. Several genetic modifications can increase organ size, which in turn might boost crop yield. Still, only in a few cases their performance has been evaluated under stress conditions. MicroRNA miR396 repress the expression of GROWTH-REGULATING FACTOR (GRF) genes that codes for transcription factors that promote organ growth. Here, we show that both Arabidopsis thaliana At-GRF2 and At-GRF3 genes resistant to miR396 activity (rGRF2 and rGRF3) increased organ size, but only rGRF3 can produce this effect without causing morphological defects. Furthermore, introduction of At-rGRF3 in Brassica oleracea can increase organ size, and when At-rGRF3 homologs from soybean and rice are introduced in Arabidopsis, leaf size is also increased. This suggests that regulation of GRF3 activity by miR396 is important for organ growth in a broad range of species. Plants harboring rGRF3 have larger leaves also under drought stress, a condition that stimulates miR396 accumulation. These plants also showed an increase in the resistance to virulent bacteria, suggesting that the size increment promoted by rGRF3 occurs without an obvious cost on plant defenses. Our findings indicate that rGRF3 can increase plant organ size under both normal and stress conditions and is a valuable tool for biotechnological applications.
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Affiliation(s)
- Matías Beltramino
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, Argentina
| | - María Florencia Ercoli
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, Argentina
| | - Juan Manuel Debernardi
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, Argentina
| | - Camila Goldy
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, Argentina
| | - Arantxa M L Rojas
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, Argentina
| | - Florencia Nota
- CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Córdoba, Argentina
| | - María Elena Alvarez
- CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Córdoba, Argentina
| | - Liesbeth Vercruyssen
- VIB-UGent Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - Dirk Inzé
- VIB-UGent Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - Javier F Palatnik
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, Argentina.
- Centro de Estudios Interdisciplinarios, Universidad Nacional de Rosario, Rosario, Argentina.
| | - Ramiro E Rodriguez
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, Argentina.
- Centro de Estudios Interdisciplinarios, Universidad Nacional de Rosario, Rosario, Argentina.
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42
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Takanashi H, Sumiyoshi H, Mogi M, Hayashi Y, Ohnishi T, Tsutsumi N. miRNAs control HAM1 functions at the single-cell-layer level and are essential for normal embryogenesis in Arabidopsis. PLANT MOLECULAR BIOLOGY 2018; 96:627-640. [PMID: 29574557 DOI: 10.1007/s11103-018-0719-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 03/14/2018] [Indexed: 05/22/2023]
Abstract
KEY MESSAGE: miR171a controls HAM1 functions within the protodermal cells of the embryo, and these controls are essential for normal embryogenesis in Arabidopsis. Arabidopsis thaliana miR171a is known to bind to and cleave mRNAs of three HAIRY MERISTEM (HAM) genes that encode members of the GRAS family transcriptional regulators. The molecular functions of the HAM genes are still being elucidated in Arabidopsis. However, detailed expression patterns of miR171a and the effects of the failure of miR171a to suppress HAM genes were unknown till now. Here, we show the detailed expression patterns of miR171a and HAM1 using green fluorescent protein and confocal scanning microscopy. Our observations revealed that miR171a was expressed in the surface cell layer of the embryo and shoot apical meristem, and it controlled HAM1 functions. To determine the impact of the failure of miR171a to suppress of HAM1, we introduced seven synonymous mutations into the miR171a target site of the HAM1 gene (modified HAM1, mHAM1) and generated transgenic plants that had mHAM1 driven by HAM1 native promoter. The mHAM1 transgenic plants showed organogenic defects. These results indicate that the control of HAM1 functions at the single-cell-layer level by miR171a is essential for proper organ formation in Arabidopsis.
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Affiliation(s)
- Hideki Takanashi
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hikari Sumiyoshi
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Mirai Mogi
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yoshikazu Hayashi
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takayuki Ohnishi
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
- Faculty of Agriculture, Utsunomiya University, Utsunomioya, Tochigi, 321-8505, Japan
| | - Nobuhiro Tsutsumi
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.
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43
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Chen L, Chen L, Zhang X, Liu T, Niu S, Wen J, Yi B, Ma C, Tu J, Fu T, Shen J. Identification of miRNAs that regulate silique development in Brassica napus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 269:106-117. [PMID: 29606207 DOI: 10.1016/j.plantsci.2018.01.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/05/2018] [Accepted: 01/22/2018] [Indexed: 05/08/2023]
Abstract
MicroRNAs (miRNAs) are a class of non-coding small RNAs (sRNAs) that play crucial regulatory roles in various developmental processes. Silique length indirectly influences seed yield in rapeseed (Brassica napus); however, the molecular roles of miRNAs in silique length are largely unknown. Here, backcross progenies of rapeseed with long siliques (LS) and short siliques (SS) were used to elucidate these roles. Four small RNA libraries from siliques in an early stage of development were sequenced, and a total of 814 non-redundant miRNA precursors were identified, representing 65 known and 394 novel miRNAs. Expression analyses revealed that 17 miRNAs were differentially expressed in LS and SS lines. Furthermore, through degradome sequencing, we identified 522 cleavage events. Correlation analysis of the differentially expressed miRNAs and their targets suggested that miR159 and miR319 represses cell proliferation and miR160 regulates auxin signal transduction to control silique length. Additionally, the upregulation of miR2111, miR399, miR827, and miR408 reflected restricted silique development due to inorganic phosphate/copper deficiency. More significantly, high expression of miR160 in rapeseed may repress auxin response factors and result in increased silique length, illustrating that silique length might be regulated via an auxin-response pathway.
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Affiliation(s)
- Li Chen
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Lei Chen
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Xiangxiang Zhang
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Tingting Liu
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Sailun Niu
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
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Liang Y, Zou Q, Yu W. Steering Against Wind: A New Network of NamiRNAs and Enhancers. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:331-337. [PMID: 28882787 PMCID: PMC5673672 DOI: 10.1016/j.gpb.2017.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 05/19/2017] [Accepted: 06/14/2017] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) are a class of endogenous non-coding RNAs with regulatory functions. Traditionally, miRNAs are thought to play a negative regulatory role in the cytoplasm by binding to the 3′UTR of target genes to degrade mRNA or inhibit translation. However, it remains a challenge to interpret the potential function of many miRNAs located in the nucleus. Recently, we reported a new type of miRNAs present in the nucleus, which can activate gene expression by binding to the enhancer, and named them nuclear activating miRNAs (NamiRNAs). The discovery of NamiRNAs showcases a complementary regulatory mechanism of miRNA, demonstrating their differential roles in the nucleus and cytoplasm. Here, we reviewed miRNAs in nucleus to better understand the function of NamiRNAs in their interactions with the enhancers. Accordingly, we propose a NamiRNA–enhancer–target gene activation network model to better understand the crosstalk between NamiRNAs and enhancers in regulating gene transcription. Moreover, we hypothesize that NamiRNAs may be involved in cell identity or cell fate determination during development, although further study is needed to elucidate the underlying mechanisms in detail.
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Affiliation(s)
- Ying Liang
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, Shanghai Medical College, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Molecular Biology, Fudan University, Shanghai 200032, China; Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Qingping Zou
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, Shanghai Medical College, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Molecular Biology, Fudan University, Shanghai 200032, China; Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Wenqiang Yu
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, Shanghai Medical College, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Molecular Biology, Fudan University, Shanghai 200032, China; Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China.
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