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Alves A, Confraria A, Lopes S, Costa B, Perdiguero P, Milhinhos A, Baena-González E, Correia S, Miguel CM. miR160 Interacts in vivo With Pinus pinaster AUXIN RESPONSE FACTOR 18 Target Site and Negatively Regulates Its Expression During Conifer Somatic Embryo Development. FRONTIERS IN PLANT SCIENCE 2022; 13:857611. [PMID: 35371172 PMCID: PMC8965291 DOI: 10.3389/fpls.2022.857611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
MicroRNAs (miRNAs) are key regulators of several plant developmental processes including embryogenesis. Most miRNA families are conserved across major groups of plant species, but their regulatory roles have been studied mainly in model species like Arabidopsis and other angiosperms. In gymnosperms, miRNA-dependent regulation has been less studied since functional approaches in these species are often difficult to establish. Given the fundamental roles of auxin signaling in somatic embryogenesis (SE) induction and embryo development, we investigated a previously predicted interaction between miR160 and a putative target encoding AUXIN RESPONSE FACTOR 18 in Pinus pinaster (PpARF18) embryonic tissues. Phylogenetic analysis of AUXIN RESPONSE FACTOR 18 (ARF18) from Pinus pinaster and Picea abies, used here as a model system of conifer embryogenesis, showed their close relatedness to AUXIN RESPONSE FACTOR (ARF) genes known to be targeted by miR160 in other species, including Arabidopsis ARF10 and ARF16. By using a luciferase (LUC) reporter system for miRNA activity in Arabidopsis protoplasts, we have confirmed that P. pinaster miR160 (ppi-miR160) interacts in vivo with PpARF18 target site. When the primary miR160 from P. pinaster was overexpressed in protoplasts under non-limiting levels of ARGONAUTE1, a significant increase of miR160 target cleavage activity was observed. In contrast, co-expression of the primary miRNA and the target mimic MIM160 led to a decrease of miR160 activity. Our results further support that this interaction is functional during consecutive stages of SE in the conifer model P. abies. Expression analyses conducted in five stages of development, from proembryogenic masses (PEMs) to the mature embryo, show that conifer ARF18 is negatively regulated by miR160 toward the fully developed mature embryo when miR160 reached its highest expression level. This study reports the first in vivo validation of a predicted target site of a conifer miRNA supporting the conservation of miR160 interaction with ARF targets in gymnosperms. The approach used here should be useful for future characterization of miRNA functions in conifer embryogenesis.
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Affiliation(s)
- Ana Alves
- Faculty of Sciences, BioISI—Biosystems and Integrative Sciences Institute, University of Lisbon, Lisbon, Portugal
| | - Ana Confraria
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras, Portugal
| | - Susana Lopes
- Faculty of Sciences, BioISI—Biosystems and Integrative Sciences Institute, University of Lisbon, Lisbon, Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras, Portugal
| | - Bruno Costa
- Faculty of Sciences, BioISI—Biosystems and Integrative Sciences Institute, University of Lisbon, Lisbon, Portugal
- INESC-ID, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Pedro Perdiguero
- Department of Genetics, Physiology and Microbiology, Faculty of Biological Sciences, Complutense University of Madrid (UCM), Madrid, Spain
| | - Ana Milhinhos
- Faculty of Sciences, BioISI—Biosystems and Integrative Sciences Institute, University of Lisbon, Lisbon, Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras, Portugal
| | - Elena Baena-González
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras, Portugal
| | - Sandra Correia
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| | - Célia M. Miguel
- Faculty of Sciences, BioISI—Biosystems and Integrative Sciences Institute, University of Lisbon, Lisbon, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
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2
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Li C, Jiang H, Li Y, Liu C, Qi Z, Wu X, Zhang Z, Hu Z, Zhu R, Guo T, Wang Z, Zheng W, Zhang Z, Zhao H, Wang N, Shan D, Xin D, Luan F, Chen Q. Identification of Finely Mapped Quantitative Trait Locus and Candidate Gene Mining for the Three-Seeded Pod Trait in Soybean. FRONTIERS IN PLANT SCIENCE 2021; 12:715488. [PMID: 34899770 PMCID: PMC8663486 DOI: 10.3389/fpls.2021.715488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/19/2021] [Indexed: 06/14/2023]
Abstract
The three-seeded pod number is an important trait that positively influences soybean yield. Soybean variety with increased three-seeded pod number contributes to the seed number/plant and higher yield. The candidate genes of the three-seeded pod may be the key for improving soybean yield. In this study, identification and validation of candidate genes for three-seeded pod has been carried out. First, a total of 36 quantitative trait locus (QTL) were detected from the investigation of recombinant inbred lines including 147 individuals derived from a cross between Charleston and Dongning 594 cultivars. Five consensus QTLs were integrated. Second, an introgressed line CSSL-182 carrying the target segment for the trait from the donor parent was selected to verify the consensus QTL based on its phenotype. Third, a secondary group was constructed by backcrossing with CSSL-182, and two QTLs were confirmed. There were a total of 162 genes in the two QTLs. The mining of candidate genes resulted in the annotation of eight genes with functions related to pod and seed sets. Finally, haplotype analysis and quantitative reverse transcriptase real-time PCR were carried to verify the candidate genes. Four of these genes had different haplotypes in the resource group, and the differences in the phenotype were highly significant. Moreover, the differences in the expression of the four genes during pod and seed development were also significant. These four genes were probably related to the development process underlying the three-seeded pod in soybean. Herein, we discuss the past and present studies related to the three-seeded pod trait in soybean.
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Affiliation(s)
- Candong Li
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
- College of Life Science, Northeast Agricultural University, Harbin, China
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Hongwei Jiang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yingying Li
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Chunyan Liu
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Zhaoming Qi
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Xiaoxia Wu
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Zhanguo Zhang
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Zhenbang Hu
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Rongsheng Zhu
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Tai Guo
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Zhixin Wang
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Wei Zheng
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Zhenyu Zhang
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Haihong Zhao
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Nannan Wang
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Dapeng Shan
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Dawei Xin
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Feishi Luan
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Qingshan Chen
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
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3
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Bertolotti G, Scintu D, Dello Ioio R. A small cog in a large wheel: crucial role of miRNAs in root apical meristem patterning. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6755-6767. [PMID: 34350947 DOI: 10.1093/jxb/erab332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
In both animal and plants, establishment of body axes is fundamental for proper organ development. Plant roots show two main developmental axes: the proximo-distal axis, which spans from the hypocotyl-root junction to the root tip; and the radial axis, which traverses from the vascular tissue to the epidermis. Root axes are determined in the root meristem. The root meristem occupies the tip of the root and contains self-renewing stem cells, which continuously produce new root cells. An intricate network of signalling pathways regulates meristem function and patterning to ensure proper root development and growth. In the last decade, miRNAs, 20-21 nucleotide-long molecules with morphogenetic activity, emerged as central regulators of root cell patterning. Their activity intersects with master regulators of meristematic activity, including phytohormones. In this review, we discuss the latest findings about the activity of miRNAs and their interaction with other molecular networks in the formation of root meristem axes. Furthermore, we describe how these small molecules allow root growth to adapt to changes in the environment, while maintaining the correct patterning.
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Affiliation(s)
- Gaia Bertolotti
- University of Rome 'La Sapienza', Department of Biology and Biotechnology, 'Charles Darwin', Via dei Sardi 70, Rome, Italy
| | - Daria Scintu
- University of Rome 'La Sapienza', Department of Biology and Biotechnology, 'Charles Darwin', Via dei Sardi 70, Rome, Italy
| | - Raffaele Dello Ioio
- University of Rome 'La Sapienza', Department of Biology and Biotechnology, 'Charles Darwin', Via dei Sardi 70, Rome, Italy
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Dhaka N, Sharma R. MicroRNA-mediated regulation of agronomically important seed traits: a treasure trove with shades of grey! Crit Rev Biotechnol 2021; 41:594-608. [PMID: 33682533 DOI: 10.1080/07388551.2021.1873238] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Seed development is an intricate process with multiple levels of regulation. MicroRNAs (miRNAs) have emerged as one of the crucial components of molecular networks underlying agronomically important seed traits in diverse plant species. In fact, loss of function of the genes regulating miRNA biogenesis also exhibits defects in seed development. A total of 21 different miRNAs have experimentally been shown to regulate seed size, nutritional content, vigor, and shattering, and have been reviewed here. The mechanism details of the associated regulatory cascades mediated through transcriptional regulators, phytohormones, basic metabolic machinery, and secondary siRNAs are elaborated. Co-localization of miRNAs and their target regions with seed-related QTLs provides new avenues for engineering these traits using conventional breeding programs or biotechnological interventions. While global analysis of miRNAs using small RNA sequencing studies are expanding the repertoire of candidate miRNAs, recent revelations on their inheritance, transport, and mechanism of action would be instrumental in designing better strategies for optimizing agronomically relevant seed traits.
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Affiliation(s)
- Namrata Dhaka
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Haryana, India.,Crop Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rita Sharma
- Crop Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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5
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Luján-Soto E, Dinkova TD. Time to Wake Up: Epigenetic and Small-RNA-Mediated Regulation during Seed Germination. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10020236. [PMID: 33530470 PMCID: PMC7911344 DOI: 10.3390/plants10020236] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 05/03/2023]
Abstract
Plants make decisions throughout their lifetime based on complex networks. Phase transitions during seed growth are not an exception. From embryo development through seedling growth, several molecular pathways control genome stability, environmental signal transduction and the transcriptional landscape. Particularly, epigenetic modifications and small non-coding RNAs (sRNAs) have been extensively studied as significant handlers of these processes in plants. Here, we review key epigenetic (histone modifications and methylation patterns) and sRNA-mediated regulatory networks involved in the progression from seed maturation to germination, their relationship with seed traits and crosstalk with environmental inputs.
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6
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Armenta-Medina A, Gillmor CS, Gao P, Mora-Macias J, Kochian LV, Xiang D, Datla R. Developmental and genomic architecture of plant embryogenesis: from model plant to crops. PLANT COMMUNICATIONS 2021; 2:100136. [PMID: 33511346 PMCID: PMC7816075 DOI: 10.1016/j.xplc.2020.100136] [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: 10/12/2020] [Revised: 12/05/2020] [Accepted: 12/11/2020] [Indexed: 05/08/2023]
Abstract
Embryonic development represents an important reproductive phase of sexually reproducing plant species. The fusion of egg and sperm produces the plant zygote, a totipotent cell that, through cell division and cell identity specification in early embryogenesis, establishes the major cell lineages and tissues of the adult plant. The subsequent morphogenesis phase produces the full-sized embryo, while the late embryogenesis maturation process prepares the seed for dormancy and subsequent germination, ensuring continuation of the plant life cycle. In this review on embryogenesis, we compare the model eudicot Arabidopsis thaliana with monocot crops, focusing on genome activation, paternal and maternal regulation of early zygote development, and key organizers of patterning, such as auxin and WOX transcription factors. While the early stages of embryo development are apparently conserved among plant species, embryo maturation programs have diversified between eudicots and monocots. This diversification in crop species reflects the likely effects of domestication on seed quality traits that are determined during embryo maturation, and also assures seed germination in different environmental conditions. This review describes the most important features of embryonic development in plants, and the scope and applications of genomics in plant embryo studies.
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Affiliation(s)
- Alma Armenta-Medina
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - C. Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Peng Gao
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
| | - Javier Mora-Macias
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
| | - Leon V. Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
| | - Daoquan Xiang
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Raju Datla
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
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7
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Harnvanichvech Y, Gorelova V, Sprakel J, Weijers D. The Arabidopsis embryo as a quantifiable model for studying pattern formation. QUANTITATIVE PLANT BIOLOGY 2021; 2:e3. [PMID: 37077211 PMCID: PMC10095805 DOI: 10.1017/qpb.2021.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/15/2021] [Accepted: 02/21/2021] [Indexed: 05/03/2023]
Abstract
Phenotypic diversity of flowering plants stems from common basic features of the plant body pattern with well-defined body axes, organs and tissue organisation. Cell division and cell specification are the two processes that underlie the formation of a body pattern. As plant cells are encased into their cellulosic walls, directional cell division through precise positioning of division plane is crucial for shaping plant morphology. Since many plant cells are pluripotent, their fate establishment is influenced by their cellular environment through cell-to-cell signaling. Recent studies show that apart from biochemical regulation, these two processes are also influenced by cell and tissue morphology and operate under mechanical control. Finding a proper model system that allows dissecting the relationship between these aspects is the key to our understanding of pattern establishment. In this review, we present the Arabidopsis embryo as a simple, yet comprehensive model of pattern formation compatible with high-throughput quantitative assays.
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Affiliation(s)
- Yosapol Harnvanichvech
- Physical Chemistry and Soft Matter, Wageningen University, Wageningen, The Netherlands
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Vera Gorelova
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Joris Sprakel
- Physical Chemistry and Soft Matter, Wageningen University, Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
- Author for correspondence: Dolf Weijers, E-mail:
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8
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Poretska O, Yang S, Pitorre D, Poppenberger B, Sieberer T. AMP1 and CYP78A5/7 act through a common pathway to govern cell fate maintenance in Arabidopsis thaliana. PLoS Genet 2020; 16:e1009043. [PMID: 32960882 PMCID: PMC7531801 DOI: 10.1371/journal.pgen.1009043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 10/02/2020] [Accepted: 08/11/2020] [Indexed: 12/17/2022] Open
Abstract
Higher plants can continuously form new organs by the sustained activity of pluripotent stem cells. These stem cells are embedded in meristems, where they produce descendants, which undergo cell proliferation and differentiation programs in a spatiotemporally-controlled manner. Under certain conditions, pluripotency can be reestablished in descending cells and this reversion in cell fate appears to be actively suppressed by the existing stem cell pool. Mutation of the putative carboxypeptidase ALTERED MERISTEM PROGRAM1 (AMP1) in Arabidopsis causes defects in the suppression of pluripotency in cells normally programmed for differentiation, giving rise to unique hypertrophic phenotypes during embryogenesis as well as in the shoot apical meristem. A role of AMP1 in the miRNA-dependent control of translation has recently been established, however, how this activity is connected to its developmental functions is not resolved. Here we identify members of the cytochrome P450 clade CYP78A to act in parallel with AMP1 to control cell fate in Arabidopsis. Mutation of CYP78A5 and its close homolog CYP78A7 in a cyp78a5,7 double mutant caused suspensor-to-embryo conversion and ectopic stem cell pool formation in the shoot meristem, phenotypes characteristic for amp1. The tissues affected in the mutants showed pronounced expression levels of AMP1 and CYP78A5 in wild type. A comparison of mutant transcriptomic responses revealed an intriguing degree of overlap and highlighted alterations in protein lipidation processes. Moreover, we also found elevated protein levels of selected miRNA targets in cyp78a5,7. Based on comprehensive genetic interaction studies we propose a model in which both enzyme classes act on a common downstream process to sustain cell fate decisions in the early embryo and the shoot apical meristem.
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Affiliation(s)
- Olena Poretska
- Research Unit Plant Growth Regulation, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
- Department for Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Saiqi Yang
- Research Unit Plant Growth Regulation, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Delphine Pitorre
- Department for Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Brigitte Poppenberger
- Biotechnology of Horticultural Crops, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Tobias Sieberer
- Research Unit Plant Growth Regulation, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
- Department for Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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9
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Wójcik AM. Research Tools for the Functional Genomics of Plant miRNAs During Zygotic and Somatic Embryogenesis. Int J Mol Sci 2020; 21:E4969. [PMID: 32674459 PMCID: PMC7420248 DOI: 10.3390/ijms21144969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022] Open
Abstract
During early plant embryogenesis, some of the most fundamental decisions on fate and identity are taken making it a fascinating process to study. It is no surprise that higher plant embryogenesis was intensively analysed during the last century, while somatic embryogenesis is probably the most studied regeneration model. Encoded by the MIRNA, short, single-stranded, non-coding miRNAs, are commonly present in all Eukaryotic genomes and are involved in the regulation of the gene expression during the essential developmental processes such as plant morphogenesis, hormone signaling, and developmental phase transition. During the last few years dedicated to miRNAs, analytical methods and tools have been developed, which have afforded new opportunities in functional analyses of plant miRNAs, including (i) databases for in silico analysis; (ii) miRNAs detection and expression approaches; (iii) reporter and sensor lines for a spatio-temporal analysis of the miRNA-target interactions; (iv) in situ hybridisation protocols; (v) artificial miRNAs; (vi) MIM and STTM lines to inhibit miRNA activity, and (vii) the target genes resistant to miRNA. Here, we attempted to summarise the toolbox for functional analysis of miRNAs during plant embryogenesis. In addition to characterising the described tools/methods, examples of the applications have been presented.
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Affiliation(s)
- Anna Maria Wójcik
- University of Silesia in Katowice, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland
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10
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Plotnikova A, Kellner MJ, Schon MA, Mosiolek M, Nodine MD. MicroRNA Dynamics and Functions During Arabidopsis Embryogenesis. THE PLANT CELL 2019; 31:2929-2946. [PMID: 31562217 PMCID: PMC6925019 DOI: 10.1105/tpc.19.00395] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/16/2019] [Accepted: 09/25/2019] [Indexed: 05/19/2023]
Abstract
MicroRNAs (miRNAs) are short noncoding RNAs that mediate the repression of target transcripts in plants and animals. Although miRNAs are required throughout plant development, relatively little is known regarding their embryonic functions. To systematically characterize embryonic miRNAs in Arabidopsis (Arabidopsis thaliana), we developed or applied high-throughput sequencing-based methods to profile hundreds of miRNAs and associated targets throughout embryogenesis. We discovered dozens of miRNAs that dynamically cleave and repress target transcripts, including 30 that encode transcription factors. Transcriptome analyses indicated that these miRNA:target interactions have profound effects on embryonic gene expression programs. Moreover, we demonstrated that the miRNA-mediated repression of six transcription factors are individually required for proper division patterns of various embryonic cell lineages. These data indicate that the miRNA-directed repression of multiple transcription factors is critically important for the establishment of the plant body plan, and they provide a foundation to further investigate how miRNAs contribute to these initial cellular differentiation events.
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Affiliation(s)
- Alexandra Plotnikova
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Max J Kellner
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Michael A Schon
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Magdalena Mosiolek
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Michael D Nodine
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
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11
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Juárez-González VT, López-Ruiz BA, Baldrich P, Luján-Soto E, Meyers BC, Dinkova TD. The explant developmental stage profoundly impacts small RNA-mediated regulation at the dedifferentiation step of maize somatic embryogenesis. Sci Rep 2019; 9:14511. [PMID: 31601893 PMCID: PMC6786999 DOI: 10.1038/s41598-019-50962-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 09/23/2019] [Indexed: 01/22/2023] Open
Abstract
Maize somatic embryogenesis (SE) requires the induction of embryogenic callus and establishment of proliferation before plant regeneration. The molecular mechanisms underlying callus embryogenic potential are not well understood. Here we explored the role of small RNAs (sRNAs) and the accumulation of their target transcripts in maize SE at the dedifferentiation step using VS-535 zygotic embryos collected at distinct developmental stages and displaying contrasting in vitro embryogenic potential and morphology. MicroRNAs (miRNAs), trans-acting siRNAs (tasiRNAs), heterochromatic siRNAs (hc-siRNAs) populations and their RNA targets were analyzed by high-throughput sequencing. Abundances of specific miRNAs, tasiRNAs and targets were validated by qRT-PCR. Unique accumulation patterns were found for immature embryo at 15 Days After Pollination (DAP) and for the callus induction from this explant, as compared to 23 DAP and mature embryos. miR156, miR164, miR166, tasiARFs and the 24 nt hc-siRNAs displayed the most strikingly different patterns between explants and during dedifferentiation. According to their role in auxin responses and developmental cues, we conclude that sRNA-target regulation operating within the 15 DAP immature embryo explant provides key molecular hints as to why this stage is relevant for callus induction with successful proliferation and plant regeneration.
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Affiliation(s)
- Vasti T Juárez-González
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, CDMX, 04510, México
| | - Brenda A López-Ruiz
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, CDMX, 04510, México
| | - Patricia Baldrich
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
| | - Eduardo Luján-Soto
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, CDMX, 04510, México
| | - Blake C Meyers
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, 65211, USA
| | - Tzvetanka D Dinkova
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, CDMX, 04510, México.
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12
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Trolet A, Baldrich P, Criqui MC, Dubois M, Clavel M, Meyers BC, Genschik P. Cell Cycle-Dependent Regulation and Function of ARGONAUTE1 in Plants. THE PLANT CELL 2019; 31:1734-1750. [PMID: 31189739 PMCID: PMC6713298 DOI: 10.1105/tpc.19.00069] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/07/2019] [Accepted: 06/07/2019] [Indexed: 05/04/2023]
Abstract
Regulated gene expression is key to the orchestrated progression of the cell cycle. Many genes are expressed at specific points in the cell cycle, including important cell cycle regulators, plus factors involved in signal transduction, hormonal regulation, and metabolic control. We demonstrate that post-embryonic depletion of Arabidopsis (Arabidopsis thaliana) ARGONAUTE1 (AGO1), the main effector of plant microRNAs (miRNAs), impairs cell division in the root meristem. We utilized the highly synchronizable tobacco (Nicotiana tabacum) Bright yellow 2 (BY2) cell suspension to analyze mRNA, small RNAs, and mRNA cleavage products of synchronized BY2 cells at S, G2, M, and G1 phases of the cell cycle. This revealed that in plants, only a few miRNAs show differential accumulation during the cell cycle, and miRNA-target pairs were only identified for a small proportion of the more than 13,000 differentially expressed genes during the cell cycle. However, this unique set of miRNA-target pairs could be key to attenuate the expression of several transcription factors and disease resistance genes. We also demonstrate that AGO1 binds to a set of 19-nucleotide, tRNA-derived fragments during the cell cycle progression.
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Affiliation(s)
- Adrien Trolet
- Institut de Biologie Moléculaire des Plantes (IBMP-CNRS), 12, Rue du Général Zimmer, 67084 Strasbourg Cedex, France
| | - Patricia Baldrich
- Donald Danforth Plant Science Center, 975 N Warson Road, St. Louis, Missouri 63132
| | - Marie-Claire Criqui
- Institut de Biologie Moléculaire des Plantes (IBMP-CNRS), 12, Rue du Général Zimmer, 67084 Strasbourg Cedex, France
| | - Marieke Dubois
- Institut de Biologie Moléculaire des Plantes (IBMP-CNRS), 12, Rue du Général Zimmer, 67084 Strasbourg Cedex, France
| | - Marion Clavel
- Institut de Biologie Moléculaire des Plantes (IBMP-CNRS), 12, Rue du Général Zimmer, 67084 Strasbourg Cedex, France
| | - Blake C Meyers
- Donald Danforth Plant Science Center, 975 N Warson Road, St. Louis, Missouri 63132
- Division of Plant Sciences, 52 Agriculture Lab, University of Missouri, Columbia, Missouri 65211
| | - Pascal Genschik
- Institut de Biologie Moléculaire des Plantes (IBMP-CNRS), 12, Rue du Général Zimmer, 67084 Strasbourg Cedex, France
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13
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Development-Related miRNA Expression and Target Regulation during Staggered In Vitro Plant Regeneration of Tuxpeño VS-535 Maize Cultivar. Int J Mol Sci 2019; 20:ijms20092079. [PMID: 31035580 PMCID: PMC6539278 DOI: 10.3390/ijms20092079] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 11/17/2022] Open
Abstract
In vitro plant regeneration addresses basic questions of molecular reprogramming in the absence of embryonic positional cues. The process is highly dependent on the genotype and explant characteristics. However, the regulatory mechanisms operating during organ differentiation from in vitro cultures remain largely unknown. Recently, miRNAs have emerged as key regulators during embryogenic callus induction, plant differentiation, auxin responses and totipotency. Here, we explored how development-related miRNA switches the impact on their target regulation depending on physiological and molecular events taking place during maize Tuxpeño VS-535 in vitro plant regeneration. Three callus types with distinctive regeneration potential were characterized by microscopy and histological preparations. The embryogenic calli (EC) showed higher miRNA levels than non-embryogenic tissues (NEC). An inverse correlation for miR160 and miR166 targets was found during EC callus induction, whereas miR156, miR164 and miR394 displayed similar to their targets RNA accumulation levels. Most miRNA accumulation switches took place early at regenerative spots coincident with shoot apical meristem (SAM) establishment, whereas miR156, miR160 and miR166 increased at further differentiation stages. Our data uncover particular miRNA-mediated regulation operating for maize embryogenic tissues, supporting their regulatory role in early SAM establishment and basipetala growth during the in vitro regeneration process.
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14
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Gao P, Xiang D, Quilichini TD, Venglat P, Pandey PK, Wang E, Gillmor CS, Datla R. Gene expression atlas of embryo development in Arabidopsis. PLANT REPRODUCTION 2019; 32:93-104. [PMID: 30762127 DOI: 10.1007/s00497-019-00364-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 02/01/2019] [Indexed: 05/24/2023]
Abstract
Embryogenesis represents a critical phase in the life cycle of flowering plants. Here, we characterize transcriptome landscapes associated with key stages of embryogenesis by combining an optimized method for the isolation of developing Arabidopsis embryos with high-throughput RNA-seq. The resulting RNA-seq datasets identify distinct overlapping patterns of gene expression, as well as temporal shifts in gene activity across embryogenesis. Network analysis revealed stage-specific and multi-stage gene expression clusters and biological functions associated with key stages of embryo development. Methylation-related gene expression was associated with early- and middle-stage embryos, initiation of photosynthesis components with the late embryogenesis stage, and storage/energy-related protein activation with late and mature embryos. These results provide a comprehensive understanding of transcriptome programming in Arabidopsis embryogenesis and identify modules of gene expression corresponding to key stages of embryo development. This dataset and analysis are a unique resource to advance functional genetic analysis of embryo development in plants.
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Affiliation(s)
- Peng Gao
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada
| | - Daoquan Xiang
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Teagen D Quilichini
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Prakash Venglat
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Prashant K Pandey
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Edwin Wang
- Center for Health Genomics and Informatics, University of Calgary Cumming School of Medicine, Calgary, AB, T2N 4N1, Canada
| | - C Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Raju Datla
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada.
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada.
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15
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Armenta-Medina A, Gillmor CS. Genetic, molecular and parent-of-origin regulation of early embryogenesis in flowering plants. Curr Top Dev Biol 2019; 131:497-543. [DOI: 10.1016/bs.ctdb.2018.11.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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16
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Siddiqui ZH, Abbas ZK, Ansari MW, Khan MN. The role of miRNA in somatic embryogenesis. Genomics 2018; 111:1026-1033. [PMID: 30476555 DOI: 10.1016/j.ygeno.2018.11.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/14/2018] [Accepted: 11/17/2018] [Indexed: 02/04/2023]
Abstract
Somatic embryogenesis (SEG) is one of the best techniques for mass production of economically important plants. It is also used for the study of morphology, anatomy, physiology, genetics and molecular mechanism of embryo development. Somatic Embryos (SE) are bipolar structures that develop from a cell other than a gamete or zygote. SEG reflects the unique developmental potential of plant somatic cells, resulting in the transition of the differentiated somatic cells to embryogenic cells to follow the zygotic embryo stages. There are several biochemical and physiological processes that transformed a single somatic cell to a whole plant. SE studies provide insight into cell mechanisms governing the totipotency process in plants. Previously, in vitro studies have suggested the role of various regulatory genes in embryogenic transition that are triggered by plant hormones in response to stress. The omic studies identify the specific genes, transcripts, and proteins required for somatic embryogenesis development. MicroRNAs (miRNAs) are small, 19-24 nucleotides (nt), non-coding small RNA regulatory molecules controlling a large number of biological processes. In addition to their role in SEG, miRNAs play vital role in plant development, secondary metabolite synthesis and metabolism of macromolecules, hormone signal transduction, and tolerance of plants to biotic and abiotic stresses. During last decade several types of miRNAs involved in SEG have been reported. Among these miRNAs, miR156, miR162, miR166a, miR167, miR168, miR171a/b, miR171c, miR393, miR397 and miR398 played very active role during various stages of SEG. In this review, we highlighted the role of these as well as other miRNAs in some economically important plants.
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Affiliation(s)
- Zahid Hameed Siddiqui
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia.
| | - Zahid Khorshid Abbas
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Mohammad Wahid Ansari
- Department of Botany, Zakir Husain Delhi College, University of Delhi, JLN Marg, New Delhi 110002, India
| | - Mohammad Nasir Khan
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
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17
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Lepiniec L, Devic M, Roscoe TJ, Bouyer D, Zhou DX, Boulard C, Baud S, Dubreucq B. Molecular and epigenetic regulations and functions of the LAFL transcriptional regulators that control seed development. PLANT REPRODUCTION 2018; 31:291-307. [PMID: 29797091 DOI: 10.1007/s00497-018-0337-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 05/10/2018] [Indexed: 05/20/2023]
Abstract
The LAFL (i.e. LEC1, ABI3, FUS3, and LEC2) master transcriptional regulators interact to form different complexes that induce embryo development and maturation, and inhibit seed germination and vegetative growth in Arabidopsis. Orthologous genes involved in similar regulatory processes have been described in various angiosperms including important crop species. Consistent with a prominent role of the LAFL regulators in triggering and maintaining embryonic cell fate, their expression appears finely tuned in different tissues during seed development and tightly repressed in vegetative tissues by a surprisingly high number of genetic and epigenetic factors. Partial functional redundancies and intricate feedback regulations of the LAFL have hampered the elucidation of the underpinning molecular mechanisms. Nevertheless, genetic, genomic, cellular, molecular, and biochemical analyses implemented during the last years have greatly improved our knowledge of the LALF network. Here we summarize and discuss recent progress, together with current issues required to gain a comprehensive insight into the network, including the emerging function of LEC1 and possibly LEC2 as pioneer transcription factors.
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Affiliation(s)
- L Lepiniec
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France.
| | - M Devic
- Régulations Epigénétiques et Développement de la Graine, ERL 5300 CNRS-IRD UMR DIADE, IRD centre de Montpellier, 911 Avenue Agropolis, BP 64501, 34394, Montpellier, France
- Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Sorbonne Universités, Université Pierre et Marie Curie (Paris 06) & Centre National pour la Recherche Scientifique CNRS UMR 7621, 66650, Banyuls-sur-Mer, France
| | - T J Roscoe
- Régulations Epigénétiques et Développement de la Graine, ERL 5300 CNRS-IRD UMR DIADE, IRD centre de Montpellier, 911 Avenue Agropolis, BP 64501, 34394, Montpellier, France
- Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Sorbonne Universités, Université Pierre et Marie Curie (Paris 06) & Centre National pour la Recherche Scientifique CNRS UMR 7621, 66650, Banyuls-sur-Mer, France
| | - D Bouyer
- Institut de Biologie de l'ENS, CNRS UMR8197, Ecole Normale Supérieure, 46 rue d'Ulm, 75230, Paris Cedex 05, France
| | - D-X Zhou
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Sud 11, Université Paris-Saclay, 91405, Orsay, France
| | - C Boulard
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France
| | - S Baud
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France
| | - B Dubreucq
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France
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18
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Wójcik AM, Mosiolek M, Karcz J, Nodine MD, Gaj MD. Whole Mount in situ Localization of miRNAs and mRNAs During Somatic Embryogenesis in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:1277. [PMID: 30233621 PMCID: PMC6131960 DOI: 10.3389/fpls.2018.01277] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 08/15/2018] [Indexed: 05/11/2023]
Abstract
Somatic embryogenesis (SE) results from the transition of differentiated plant somatic cells into embryogenic cells that requires the extensive reprogramming of the somatic cell transcriptome. Commonly, the SE-involved genes are identified by analyzing the heterogeneous population of explant cells and thus, it is necessary to validate the expression of the candidate genes in the cells that are competent for embryogenic transition. Here, we optimized and implemented the whole mount in situ hybridization (WISH) method (Bleckmann and Dresselhaus, 2016; Dastidar et al., 2016) in order to analyze the spatiotemporal localization of miRNAs (miR156, miR166, miR390, miR167) and mRNAs such as WOX5 and PHABULOSA-target of miR165/166 during the SE that is induced in Arabidopsis explants. This study presents a detailed step-by-step description of the WISH procedure in which DIG-labeled LNA and RNA probes were used to detect miRNAs and mRNAs, respectively. The usefulness of the WISH in the functional analysis of the SE-involved regulatory pathways is demonstrated and the advantages of this method are highlighted: (i) the ability to analyze intact non-sectioned plant tissue; (ii) the specificity of transcript detection; (iii) the detection of miRNA; and (iv) a semi-quantitative assessment of the RNA abundance.
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Affiliation(s)
- Anna M. Wójcik
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Magdalena Mosiolek
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Jagna Karcz
- Scanning Electron Microscopy Laboratory, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Michael D. Nodine
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Małgorzata D. Gaj
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
- *Correspondence: Małgorzata D. Gaj,
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19
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MicroRNA and Putative Target Discoveries in Chrysanthemum Polyploidy Breeding. Int J Genomics 2017; 2017:6790478. [PMID: 29387713 PMCID: PMC5745731 DOI: 10.1155/2017/6790478] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 10/30/2017] [Indexed: 11/24/2022] Open
Abstract
MicroRNAs (miRNAs), around 22 nucleotides (nt) in length, are a class of endogenous and noncoding RNA molecule that play an essential role in plant development, either by suppressing the transcription of target genes at a transcriptional level or inhibiting translation at a posttranscriptional level. To understand the roles of miRNAs and their target genes in chrysanthemum polyploidy breeding, three sRNA libraries of normal and abnormal embryos after hybridization were performed by RNA-Seq. As a result, a total of 170 miRNAs were identified and there are 41 special miRNAs in cross of paternal chromosome doubling, such as miR169b, miR440, and miR528-5p. miR164c and miR159a were highly expressed in a normal embryo at 18 days after pollination, suggesting the regulatory role at the late stage of embryonic development. miR172c was only detected in the normal embryo at 18 days after pollination, which means that miR172c mainly mediates gene expression in postembryonic development and these genes may promote embryo maturation. Other miRNAs, including miR414, miR2661, and miR5021, may regulate the genes participated in pathways of auxin response and energy metabolism; then they regulate the complex embryonic development together.
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20
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Wójcik AM, Nodine MD, Gaj MD. miR160 and miR166/165 Contribute to the LEC2-Mediated Auxin Response Involved in the Somatic Embryogenesis Induction in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2017; 8:2024. [PMID: 29321785 PMCID: PMC5732185 DOI: 10.3389/fpls.2017.02024] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 11/14/2017] [Indexed: 05/04/2023]
Abstract
MicroRNAs are non-coding small RNA molecules that are involved in the post-transcriptional regulation of the genes that control various developmental processes in plants, including zygotic embryogenesis (ZE). miRNAs are also believed to regulate somatic embryogenesis (SE), a counterpart of the ZE that is induced in vitro in plant somatic cells. However, the roles of specific miRNAs in the regulation of the genes involved in SE, in particular those encoding transcription factors (TFs) with an essential function during SE including LEAFY COTYLEDON2 (LEC2), remain mostly unknown. The aim of the study was to reveal the function of miR165/166 and miR160 in the LEC2-controlled pathway of SE that is induced in in vitro cultured Arabidopsis explants.In ZE, miR165/166 controls the PHABULOSA/PHAVOLUTA (PHB/PHV) genes, which are the positive regulators of LEC2, while miR160 targets the AUXIN RESPONSE FACTORS (ARF10, ARF16, ARF17) that control the auxin signaling pathway, which plays key role in LEC2-mediated SE. We found that a deregulated expression/function of miR165/166 and miR160 resulted in a significant accumulation of auxin in the cultured explants and the spontaneous formation of somatic embryos. Our results show that miR165/166 might contribute to SE induction via targeting PHB, a positive regulator of LEC2 that controls embryogenic induction via activation of auxin biosynthesis pathway (Wójcikowska et al., 2013). Similar to miR165/166, miR160 was indicated to control SE induction through auxin-related pathways and the negative impact of miR160 on ARF10/ARF16/ARF17 was shown in an embryogenic culture. Altogether, the results suggest that the miR165/166- and miR160-node contribute to the LEC2-mediated auxin-related pathway of embryogenic transition that is induced in the somatic cells of Arabidopsis. A model summarizing the suggested regulatory interactions between the miR165/166-PHB and miR160-ARF10/ARF16/ARF17 nodes that control SE induction in Arabidopsis was proposed.
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Affiliation(s)
- Anna M. Wójcik
- Department of Genetics, University of Silesia, Faculty of Biology and Environmental Protection, Katowice, Poland
| | - Michael D. Nodine
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Małgorzata D. Gaj
- Department of Genetics, University of Silesia, Faculty of Biology and Environmental Protection, Katowice, Poland
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21
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Arabidopsis thaliana miRNAs promote embryo pattern formation beginning in the zygote. Dev Biol 2017; 431:145-151. [DOI: 10.1016/j.ydbio.2017.09.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 09/05/2017] [Accepted: 09/06/2017] [Indexed: 11/20/2022]
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22
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Rodrigues AS, Miguel CM. The pivotal role of small non-coding RNAs in the regulation of seed development. PLANT CELL REPORTS 2017; 36:653-667. [PMID: 28289886 DOI: 10.1007/s00299-017-2120-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 02/09/2017] [Indexed: 05/27/2023]
Abstract
Seeds represent a crucial stage of the seed plants life cycle. It is during seed development that the foundations of the future plant body, and the ability to give rise to a new plant capable of growing under sometimes adverse environmental conditions, are established. Small non-coding RNAs are major regulators of gene expression both at the post-transcriptional and transcriptional levels and, not surprisingly, these elements play major roles in seed development and germination. We review here the current knowledge about small RNA expression and functions in seed development, going from the morphogenesis phase comprehending embryo development and patterning, to the several steps of the maturation phase, ending in the transition to the germination. A special focus is given to the small RNAs for which functional studies have been conducted and their participation in regulatory networks operating in seeds. Many challenges remain ahead for dissecting the complex small RNA landscape in seeds, but this is a highly relevant issue in plant biology and advances in this area will most certainly impact plant breeding.
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Affiliation(s)
- Andreia S Rodrigues
- Instituto de Biologia Experimental e Tecnológica (iBET), Apartado 12, 2780-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157, Oeiras, Portugal
| | - Célia M Miguel
- Instituto de Biologia Experimental e Tecnológica (iBET), Apartado 12, 2780-901, Oeiras, Portugal.
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157, Oeiras, Portugal.
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa (FCUL), Campo Grande, 1749-016, Lisbon, Portugal.
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23
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Li S, Castillo-González C, Yu B, Zhang X. The functions of plant small RNAs in development and in stress responses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:654-670. [PMID: 27943457 DOI: 10.1111/tpj.13444] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/29/2016] [Accepted: 12/06/2016] [Indexed: 05/22/2023]
Abstract
Like metazoans, plants use small regulatory RNAs (sRNAs) to direct gene expression. Several classes of sRNAs, which are distinguished by their origin and biogenesis, exist in plants. Among them, microRNAs (miRNAs) and trans-acting small interfering RNAs (ta-siRNAs) mainly inhibit gene expression at post-transcriptional levels. In the past decades, plant miRNAs and ta-siRNAs have been shown to be essential for numerous developmental processes, including growth and development of shoots, leaves, flowers, roots and seeds, among others. In addition, miRNAs and ta-siRNAs are also involved in the plant responses to abiotic and biotic stresses, such as drought, temperature, salinity, nutrient deprivation, bacteria, virus and others. This review summarizes the roles of miRNAs and ta-siRNAs in plant physiology and development.
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Affiliation(s)
- Shengjun Li
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588-0660, USA
| | - Claudia Castillo-González
- Department of Biochemistry and Biophysics & Institute of Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, 77843, USA
| | - Bin Yu
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588-0660, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics & Institute of Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, 77843, USA
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24
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Couzigou JM, Combier JP. Plant microRNAs: key regulators of root architecture and biotic interactions. THE NEW PHYTOLOGIST 2016; 212:22-35. [PMID: 27292927 DOI: 10.1111/nph.14058] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/08/2016] [Indexed: 05/24/2023]
Abstract
Contents 22 I. 22 II. 24 III. 25 IV. 27 V. 29 VI. 10 31 References 32 SUMMARY: Plants have evolved a remarkable faculty of adaptation to deal with various and changing environmental conditions. In this context, the roots have taken over nutritional aspects and the root system architecture can be modulated in response to nutrient availability or biotic interactions with soil microorganisms. This adaptability requires a fine tuning of gene expression. Indeed, root specification and development are highly complex processes requiring gene regulatory networks involved in hormonal regulations and cell identity. Among the different molecular partners governing root development, microRNAs (miRNAs) are key players for the fast regulation of gene expression. miRNAs are small RNAs involved in most developmental processes and are required for the normal growth of organisms, by the negative regulation of key genes, such as transcription factors and hormone receptors. Here, we review the known roles of miRNAs in root specification and development, from the embryonic roots to the establishment of root symbioses, highlighting the major roles of miRNAs in these processes.
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Affiliation(s)
- Jean-Malo Couzigou
- UMR5546, Laboratoire de Recherche en Sciences Végétales, UPS, CNRS, Université de Toulouse, Castanet-Tolosan, 31326, France
| | - Jean-Philippe Combier
- UMR5546, Laboratoire de Recherche en Sciences Végétales, UPS, CNRS, Université de Toulouse, Castanet-Tolosan, 31326, France
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25
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Wójcik AM, Gaj MD. miR393 contributes to the embryogenic transition induced in vitro in Arabidopsis via the modification of the tissue sensitivity to auxin treatment. PLANTA 2016; 244:231-43. [PMID: 27040841 PMCID: PMC4903112 DOI: 10.1007/s00425-016-2505-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 03/18/2016] [Indexed: 05/06/2023]
Abstract
miR393 was found to control embryogenic transition in somatic cells in Arabidopsis via control of the TIR1 and AFB2 auxin receptors genes of the F-box family. miR393 molecules are believed to regulate the expression of the auxin receptors of the TAAR clade. Considering the central role of auxin in the induction of somatic embryogenesis (SE) in plant explants cultured in vitro, the involvement of miR393 in the embryogenic transition of somatic cells has been hypothesised. To verify this assumption, the reporter, overexpressor and mutant lines in genes encoded MIR393 and TIR1/AFB proteins of the F-box family were analysed during SE in Arabidopsis. Expression profiling of MIR393a and MIR393b, mature miR393 and the target genes (TIR1, AFB1, AFB2, AFB3) were investigated in explants undergoing SE. In addition, the embryogenic potential of various genotypes with a modified activity of the MIR393 and TIR1/AFB targets was evaluated. The distinct increase in the accumulation of miR393 that was coupled with a notable down-regulation of TIR1 and AFB2 targets was observed at the early phase of SE induction. Relevant to this observation, the GUS/GFP monitored expression of MIR393, TIR1 and AFB2 transcripts was localised in explant tissue undergoing SE induction. The results suggest the miR393-mediated regulation of TIR1 and AFB2 during embryogenic transition induced in Arabidopsis and a modification of the explant sensitivity to auxin treatment is proposed as underlying this regulatory pathway.
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Affiliation(s)
- Anna M Wójcik
- Department of Genetics, University of Silesia, Jagiellońska 28, 40-032, Katowice, Poland
| | - Małgorzata D Gaj
- Department of Genetics, University of Silesia, Jagiellońska 28, 40-032, Katowice, Poland.
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dos Santos ALW, Elbl P, Navarro BV, de Oliveira LF, Salvato F, Balbuena TS, Floh EIS. Quantitative proteomic analysis of Araucaria angustifolia (Bertol.) Kuntze cell lines with contrasting embryogenic potential. J Proteomics 2016; 130:180-9. [DOI: 10.1016/j.jprot.2015.09.027] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 08/26/2015] [Accepted: 09/22/2015] [Indexed: 12/21/2022]
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Baroux C, Grossniklaus U. The Maternal-to-Zygotic Transition in Flowering Plants: Evidence, Mechanisms, and Plasticity. Curr Top Dev Biol 2015; 113:351-71. [PMID: 26358878 DOI: 10.1016/bs.ctdb.2015.06.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The maternal-to-zygotic transition (MZT) defines a developmental phase during which the embryo progressively emancipates itself from a developmental control relying largely on maternal information. The MZT is a functional readout of two processes: the clearance of maternally derived information and the de novo expression of the inherited, parental alleles enabled by zygotic genome activation (ZGA). In plants, for many years the debate about whether the MZT exists at all focused on the ZGA alone. However, several recent studies provide evidence for a progressive alleviation of the maternal control over embryogenesis that is correlated with a gradual ZGA, a process that is itself maternally controlled. Yet, several examples of zygotic genes that are expressed and/or functionally required early in embryogenesis demonstrate a certain flexibility in the dynamics and kinetics of the MZT among plant species and also intraspecific hybrids.
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Affiliation(s)
- Célia Baroux
- Institute of Plant Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Ueli Grossniklaus
- Institute of Plant Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland.
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Kurdyukov S, Song Y, Tiew TWY, Wang XD, Nolan KE, Rose RJ. Protocols for Obtaining Zygotic and Somatic Embryos for Studying the Regulation of Early Embryo Development in the Model Legume Medicago truncatula. J Vis Exp 2015:e52635. [PMID: 26131626 DOI: 10.3791/52635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Early embryogenesis starting from a single cell zygote goes through rapid cell division and morphogenesis, and is morphologically characterized by pre-globular, globular, heart, torpedo and cotyledon stages. This progressive development is under the tight regulation of a complex molecular network. Harvesting sufficient early embryos at a similar stage of development is essential for investigating the cellular and molecular regulation of early embryogenesis. This is not straightforward since early embryogenesis undergoes rapid morphogenesis in a short while e.g. 8 days for Medicago truncatula to reach the early cotyledon stage. Here, we address the issue by two approaches. The first one establishes a linkage between embryo development and pod morphology in helping indicate the stage of the zygotic embryo. This is particularly based on the number of pod spirals and development of the spines. An alternative way to complement the in vivo studies is via culturing leaf explants to produce somatic embryos. The medium includes an unusual hormone combination - an auxin (1-naphthaleneacetic acid), a cytokinin (6-benzylaminopurine), abscisic acid and gibberellic acid. The different stages can be discerned growing out of the callus without dissection.
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Affiliation(s)
- Sergey Kurdyukov
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - Youhong Song
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - Terence W-Y Tiew
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - Xin-Ding Wang
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - Kim E Nolan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - Ray J Rose
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia;
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Song JB, Shu XX, Shen Q, Li BW, Song J, Yang ZM. Altered Fruit and Seed Development of Transgenic Rapeseed (Brassica napus) Over-Expressing MicroRNA394. PLoS One 2015; 10:e0125427. [PMID: 25978066 PMCID: PMC4433277 DOI: 10.1371/journal.pone.0125427] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/23/2015] [Indexed: 02/02/2023] Open
Abstract
Fruit and seed development in plants is a complex biological process mainly involved in input and biosynthesis of many storage compounds such as proteins and oils. Although the basic biochemical pathways for production of the storage metabolites in plants are well characterized, their regulatory mechanisms are not fully understood. In this study, we functionally identified rapeseed (Brassica napus) miR394 with its target gene Brassica napus LEAF CURLING RESPONSIVENESS (BnLCR) to dissect a role of miR394 during the fruit and seed development. Transgenic rapeseed plants over-expressing miR394 under the control of the cauliflower mosaic virus 35S promoter were generated. miR394 over-expression plants exhibited a delayed flowering time and enlarged size of plants, leaf blade, pods and seed body, but developed seeds with higher contents of protein and glucosinolates (GLS) and lower levels of oil accumulation as compared to wild-type. Over-expression of miR394 altered the fatty acid (FA) composition by increasing several FA species such as C16:0 and C18:0 and unsaturated species of C20:1 and C22:1 but lowering C18:3. This change was accompanied by induction of genes coding for transcription factors of FA synthesis including LEAFY COTYLEDON1 (BnLEC1), BnLEC2, and FUSCA3 (FUS3). Because the phytohormone auxin plays a crucial role in fruit development and seed patterning, the DR5-GUS reporter was used for monitoring the auxin response in Arabidopsis siliques and demonstrated that the DR5 gene was strongly expressed. These results suggest that BnmiR394 is involved in rapeseed fruit and seed development.
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Affiliation(s)
- Jian Bo Song
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, China
- Department of Biochemistry and Molecular Biology, College of Life Science, Jiangxi Agricultural University, Nanchang, China
| | - Xia Xia Shu
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Qi Shen
- The Rapeseed Institute of Guizhou Province, Gui Yang, China
| | - Bo Wen Li
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Jun Song
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Zhi Min Yang
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, China
- * E-mail:
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Zhang F, Dong W, Huang L, Song A, Wang H, Fang W, Chen F, Teng N. Identification of MicroRNAs and their Targets Associated with Embryo Abortion during Chrysanthemum Cross Breeding via High-Throughput Sequencing. PLoS One 2015; 10:e0124371. [PMID: 25909659 PMCID: PMC4409343 DOI: 10.1371/journal.pone.0124371] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 02/27/2015] [Indexed: 12/22/2022] Open
Abstract
Background MicroRNAs (miRNAs) are important regulators in plant development. They post-transcriptionally regulate gene expression during various biological and metabolic processes by binding to the 3’-untranslated region of target mRNAs to facilitate mRNA degradation or inhibit translation. Chrysanthemum (Chrysanthemum morifolium) is one of the most important ornamental flowers with increasing demand each year. However, embryo abortion is the main reason for chrysanthemum cross breeding failure. To date, there have been no experiments examining the expression of miRNAs associated with chrysanthemum embryo development. Therefore, we sequenced three small RNA libraries to identify miRNAs and their functions. Our results will provide molecular insights into chrysanthemum embryo abortion. Results Three small RNA libraries were built from normal chrysanthemum ovules at 12 days after pollination (DAP), and normal and abnormal chrysanthemum ovules at 18 DAP. We validated 228 miRNAs with significant changes in expression frequency during embryonic development. Comparative profiling revealed that 69 miRNAs exhibited significant differential expression between normal and abnormal embryos at 18 DAP. In addition, a total of 1037 miRNA target genes were predicted, and their annotations were defined by transcriptome data. Target genes associated with metabolic pathways were most highly represented according to the annotation. Moreover, 52 predicted target genes were identified to be associated with embryonic development, including 31 transcription factors and 21 additional genes. Gene ontology (GO) annotation also revealed that high-ranking miRNA target genes related to cellular processes and metabolic processes were involved in transcription regulation and the embryo developmental process. Conclusions The present study generated three miRNA libraries and gained information on miRNAs and their targets in the chrysanthemum embryo. These results enrich the growing database of new miRNAs and lay the foundation for the further understanding of miRNA biological function in the regulation of chrysanthemum embryo abortion.
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Affiliation(s)
- Fengjiao Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology & Equipment, Nanjing, China
| | - Wen Dong
- China Rural Technology Development Center, Beijing, China
| | - Lulu Huang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Aiping Song
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Haibin Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Nianjun Teng
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology & Equipment, Nanjing, China
- * E-mail:
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Wu XM, Kou SJ, Liu YL, Fang YN, Xu Q, Guo WW. Genomewide analysis of small RNAs in nonembryogenic and embryogenic tissues of citrus: microRNA- and siRNA-mediated transcript cleavage involved in somatic embryogenesis. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:383-94. [PMID: 25615015 DOI: 10.1111/pbi.12317] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 11/23/2014] [Accepted: 11/25/2014] [Indexed: 05/20/2023]
Abstract
Somatic embryogenesis (SE) is a process of somatic cells becoming dedifferentiated and generating embryos. SE has been widely used in biotechnology as a powerful way of regeneration and a model system for studying plant embryogenesis, but the controlling mechanisms of SE are far from clear. Here, we show the genomewide profiles of miRNAs/siRNAs and their target genes in nonembryogenic and embryogenic tissues of 'Valencia' sweet orange. By high-throughput sequencing (HTS) of small RNAs and RNA degradome tags, we identified 50 known and 45 novel miRNAs, 130 miniature inverted-repeat transposable elements (MITEs) derived, 94 other and 235 phased small interfering RNAs (siRNAs), as well as 203 target genes. The majority of the abundantly expressed miRNAs/siRNAs exhibit lower expression levels in embryogenic callus (EC) or during SE process than in nonembryogenic callus (NEC), which is supposed to derepress the target genes that are involved in development and stress response, thus to activate the biological processes required for cell differentiation. However, the conserved csi-miR156a/b, miR164b and 171c directed suppression of specific transcription factors (TFs) are supposed to inactivate the postembryonic growth thus to maintain normal SE. In this study, miRNA- and siRNA-mediated silencing of target genes was found under sophisticated regulation in citrus SE system; the enhancement effect of specific conserved miRNAs on SE was discussed, providing new clues for future investigation of mechanisms that control SE.
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Affiliation(s)
- Xiao-Meng Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
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Boke H, Ozhuner E, Turktas M, Parmaksiz I, Ozcan S, Unver T. Regulation of the alkaloid biosynthesis by miRNA in opium poppy. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:409-20. [PMID: 25735537 DOI: 10.1111/pbi.12346] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 12/23/2014] [Accepted: 12/23/2014] [Indexed: 05/21/2023]
Abstract
Opium poppy (Papaver somniferum) is an important medicinal plant producing benzylisoquinoline alkaloids (BIA). MicroRNAs (miRNAs) are endogenous small RNAs (sRNAs) of approximately 21 nucleotides. They are noncoding, but regulate gene expression in eukaryotes. Although many studies have been conducted on the identification and functions of plant miRNA, scarce researches on miRNA regulation of alkaloid biosynthesis have been reported. In this study, a total of 316 conserved and 11 novel miRNAs were identified in opium poppy using second-generation sequencing and direct cloning. Tissue-specific regulation of miRNA expression was comparatively analysed by miRNA microarray assays. A total of 232 miRNAs were found to be differentially expressed among four tissues. Likewise, 1469 target transcripts were detected using in silico and experimental approaches. The Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that miRNA putatively regulates carbohydrate metabolism and genetic-information processing. Additionally, miRNA target transcripts were mostly involved in response to stress against various factors and secondary-metabolite biosynthesis processes. Target transcript identification analyses revealed that some of the miRNAs might be involved in BIA biosynthesis, such as pso-miR13, pso-miR2161 and pso-miR408. Additionally, three putatively mature miRNA sequences were predicted to be targeting BIA-biosynthesis genes.
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Affiliation(s)
- Hatice Boke
- Department of Biology, Faculty of Science, Cankiri Karatekin University, Cankiri, Turkey
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Locascio A, Roig-Villanova I, Bernardi J, Varotto S. Current perspectives on the hormonal control of seed development in Arabidopsis and maize: a focus on auxin. FRONTIERS IN PLANT SCIENCE 2014; 5:412. [PMID: 25202316 PMCID: PMC4142864 DOI: 10.3389/fpls.2014.00412] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 08/03/2014] [Indexed: 05/18/2023]
Abstract
The seed represents the unit of reproduction of flowering plants, capable of developing into another plant, and to ensure the survival of the species under unfavorable environmental conditions. It is composed of three compartments: seed coat, endosperm and embryo. Proper seed development depends on the coordination of the processes that lead to seed compartments differentiation, development and maturation. The coordination of these processes is based on the constant transmission/perception of signals by the three compartments. Phytohormones constitute one of these signals; gradients of hormones are generated in the different seed compartments, and their ratios comprise the signals that induce/inhibit particular processes in seed development. Among the hormones, auxin seems to exert a central role, as it is the only one in maintaining high levels of accumulation from fertilization to seed maturation. The gradient of auxin generated by its PIN carriers affects several processes of seed development, including pattern formation, cell division and expansion. Despite the high degree of conservation in the regulatory mechanisms that lead to seed development within the Spermatophytes, remarkable differences exist during seed maturation between Monocots and Eudicots species. For instance, in Monocots the endosperm persists until maturation, and constitutes an important compartment for nutrients storage, while in Eudicots it is reduced to a single cell layer, as the expanding embryo gradually replaces it during the maturation. This review provides an overview of the current knowledge on hormonal control of seed development, by considering the data available in two model plants: Arabidopsis thaliana, for Eudicots and Zea mays L., for Monocots. We will emphasize the control exerted by auxin on the correct progress of seed development comparing, when possible, the two species.
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Affiliation(s)
- Antonella Locascio
- Department of Agronomy Food Natural Resources Animals Environment - University of PadovaPadova, Italy
- IBMCP-CSIC, Universidad Politécnica de ValenciaValencia, Spain
- *Correspondence: Antonella Locascio, IBMCP-CSIC, Universidad Politécnica de Valencia, Avda de los Naranjos s/n, ed.8E, 46020 Valencia, Spain e-mail:
| | | | - Jamila Bernardi
- Istituto di Agronomia Genetica e Coltivazioni Erbacee, Università Cattolica del Sacro CuorePiacenza, Italy
| | - Serena Varotto
- Department of Agronomy Food Natural Resources Animals Environment - University of PadovaPadova, Italy
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