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Ma X, Nie Z, Huang H, Yan C, Li S, Hu Z, Wang Y, Yin H. Small RNA profiling reveals that an ovule-specific microRNA, cja-miR5179, targets a B-class MADS-box gene in Camellia japonica. ANNALS OF BOTANY 2023; 132:1007-1020. [PMID: 37831901 PMCID: PMC10808017 DOI: 10.1093/aob/mcad155] [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: 06/27/2023] [Accepted: 10/09/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND AND AIMS The functional specialization of microRNA and its target genes is often an important factor in the establishment of spatiotemporal patterns of gene expression that are essential to plant development and growth. In different plant lineages, understanding the functional conservation and divergence of microRNAs remains to be explored. METHODS To identify small regulatory RNAs underlying floral patterning, we performed a tissue-specific profiling of small RNAs in various floral organs from single and double flower varieties (flowers characterized by multiple layers of petals) in Camellia japonica. We identified cja-miR5179, which belongs to a deeply conserved microRNA family that is conserved between angiosperms and basal plants but frequently lost in eudicots. We characterized the molecular function of cja-miR5179 and its target - a B-function MADS-box gene - through gene expression analysis and transient expression assays. KEY RESULTS We showed that cja-miR5179 is exclusively expressed in ovule tissues at the early stage of floral development. We found that cja-miR5179 targets the coding sequences of a DEFICIENS-like B-class gene (CjDEF) mRNA, which is located in the K motif of the MADS-box domain; and the target sites of miR5179/MADS-box were consistent in Camellia and orchids. Furthermore, through a petal transient-expression assay, we showed that the BASIC PENTACYSTEINE proteins bind to the GA-rich motifs in the cja-miR5179 promoter region and suppresses its expression. CONCLUSIONS We propose that the regulation between miR5179 and a B-class MADS-box gene in C. japonica has a deep evolutionary origin before the separation of monocots and dicots. During floral development of C. japonica, cja-miR5179 is specifically expressed in the ovule, which may be required for the inhibition of CjDEF function. This work highlights the evolutionary conservation as well as functional divergence of small RNAs in floral development.
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Affiliation(s)
- Xianjin Ma
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Ziyan Nie
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Hu Huang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Chao Yan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
- Experimental Center for Subtropical Forestry, Chinese Academy of Forestry, Fenyi, Jiangxi 336600, China
| | - Sijia Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Zhikang Hu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Yupeng Wang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
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2
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Shi Q, Tian D, Wang J, Chen A, Miao Y, Chen Y, Li J, Wu X, Zheng B, Guo W, Shi X. Overexpression of miR390b promotes stem elongation and height growth in Populus. HORTICULTURE RESEARCH 2023; 10:uhac258. [PMID: 36778185 PMCID: PMC9907050 DOI: 10.1093/hr/uhac258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/18/2022] [Indexed: 06/18/2023]
Abstract
MicroRNA390 (miR390) is involved in plant growth and development by down-regulating the expression of the downstream genes trans-acting short interfering RNA3 (TAS3) and AUXIN RESPONSE FACTORs (ARFs). There is a scarcity of research on the involvement of the miR390-TAS3-ARFs pathway in the stem development of Populus. Here, differentially expressed miRNAs during poplar stem development were screened by small RNA sequencing analysis, and a novel function of miR390b in stem development was revealed. Overexpression of miR390b (OE-miR390b) resulted in a large increase in the number of xylem fiber cells and a slight decrease in the cell length at the longitudinal axis. Overall increases in stem elongation and plant height were observed in the OE-miR390b plants. According to transcriptome sequencing results and transient co-expression analysis, TAS3.1 and TAS3.2 were identified as the target genes of miR390 in poplar and were negatively regulated by miR390 in the apex. The transcription levels of ARF3.2 and ARF4 were significantly repressed in OE-miR390b plants and strongly negatively correlated with the number of xylem fiber cells along the longitudinal axis. These findings indicate that the conserved miR390-TAS3-ARFs pathway in poplar is involved in stem elongation and plant height growth.
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Affiliation(s)
- Qiaofang Shi
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Poplar Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Dongdong Tian
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Jieyu Wang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Poplar Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Aoli Chen
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuqing Miao
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiming Chen
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Poplar Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Jun Li
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Poplar Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaomeng Wu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Bo Zheng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Poplar Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenwu Guo
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
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3
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Farooqi MQU, Nawaz G, Wani SH, Choudhary JR, Rana M, Sah RP, Afzal M, Zahra Z, Ganie SA, Razzaq A, Reyes VP, Mahmoud EA, Elansary HO, El-Abedin TKZ, Siddique KHM. Recent developments in multi-omics and breeding strategies for abiotic stress tolerance in maize ( Zea mays L.). FRONTIERS IN PLANT SCIENCE 2022; 13:965878. [PMID: 36212378 PMCID: PMC9538355 DOI: 10.3389/fpls.2022.965878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/23/2022] [Indexed: 06/12/2023]
Abstract
High-throughput sequencing technologies (HSTs) have revolutionized crop breeding. The advent of these technologies has enabled the identification of beneficial quantitative trait loci (QTL), genes, and alleles for crop improvement. Climate change have made a significant effect on the global maize yield. To date, the well-known omic approaches such as genomics, transcriptomics, proteomics, and metabolomics are being incorporated in maize breeding studies. These approaches have identified novel biological markers that are being utilized for maize improvement against various abiotic stresses. This review discusses the current information on the morpho-physiological and molecular mechanism of abiotic stress tolerance in maize. The utilization of omics approaches to improve abiotic stress tolerance in maize is highlighted. As compared to single approach, the integration of multi-omics offers a great potential in addressing the challenges of abiotic stresses of maize productivity.
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Affiliation(s)
| | - Ghazala Nawaz
- Department of Botanical and Environmental Sciences, Kohat University of Science and Technology, Kohat, Pakistan
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Jeet Ram Choudhary
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Maneet Rana
- Division of Crop Improvement, ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Rameswar Prasad Sah
- Division of Crop Improvement, ICAR-National Rice Research Institute, Cuttack, India
| | - Muhammad Afzal
- College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Zahra Zahra
- Department of Civil and Environmental Engineering, University of California, Irvine, Irvine, CA, United States
| | | | - Ali Razzaq
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | | | - Eman A. Mahmoud
- Department of Food Industries, Faculty of Agriculture, Damietta University, Damietta, Egypt
| | - Hosam O. Elansary
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
- Floriculture, Ornamental Horticulture, and Garden Design Department, Faculty of Agriculture (El-Shatby), Alexandria University, Alexandria, Egypt
- Department of Geography, Environmental Management, and Energy Studies, University of Johannesburg, Johannesburg, South Africa
| | - Tarek K. Zin El-Abedin
- Department of Agriculture & Biosystems Engineering, Faculty of Agriculture (El-Shatby), Alexandria University, Alexandria, Egypt
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4
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Nakayama H, Leichty AR, Sinha NR. Molecular mechanisms underlying leaf development, morphological diversification, and beyond. THE PLANT CELL 2022; 34:2534-2548. [PMID: 35441681 PMCID: PMC9252486 DOI: 10.1093/plcell/koac118] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/13/2022] [Indexed: 05/13/2023]
Abstract
The basic mechanisms of leaf development have been revealed through a combination of genetics and intense analyses in select model species. The genetic basis for diversity in leaf morphology seen in nature is also being unraveled through recent advances in techniques and technologies related to genomics and transcriptomics, which have had a major impact on these comparative studies. However, this has led to the emergence of new unresolved questions about the mechanisms that generate the diversity of leaf form. Here, we provide a review of the current knowledge of the fundamental molecular genetic mechanisms underlying leaf development with an emphasis on natural variation and conserved gene regulatory networks involved in leaf development. Beyond that, we discuss open questions/enigmas in the area of leaf development, how recent technologies can best be deployed to generate a unified understanding of leaf diversity and its evolution, and what untapped fields lie ahead.
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Affiliation(s)
- Hokuto Nakayama
- Graduate School of Science, Department of Biological Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Aaron R Leichty
- Department of Plant Biology, University of California Davis, Davis, California 95616, USA
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5
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Xu Z, Liu Q, Chen Y, He Y, Hu F. miR390 family of Cymbidium goeringii is involved in the development of reproductive organs in transgenic Arabidopsis. BMC PLANT BIOLOGY 2022; 22:149. [PMID: 35346036 PMCID: PMC8962573 DOI: 10.1186/s12870-022-03539-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND miR390s is an ancient family with a high level of conservation among plant miRNAs. Through the auxin signal transduction pathway, miR390 participates in diverse biological processes of plant growth and development. As an important Chinese traditional orchid, Cymbidium goeringii has unique flower shape and elegant fragrance. But its development has been greatly restricted because of the low flower bud differentiation and the difficult reproduction. This study aims to provide guidance for the role of cgo-miR390 in reproductive organ development to enhance the ornamental and economic value of Cymbidium. RESULTS MIR390a, MIR390b and MIR390c of C. goeringii were cloned, and their length ranged from 130 to 150 nt. Each precursor sequence of cgo-miR390 contains 2 to 3 mature miRNAs. Three kinds of cgo-miR390s displayed distinct temporal and spatial expression patterns during floral development in C. goeringii. The overexpression of MIR390s alters morphology and function of stamens and pistils in Arabidopsis, such as enlargement of anther aspect ratio and separation of stylar and stigmas, which affects the development of fruits and seeds. In particular, the pollen amount decreased and the seed abortion rate increased in cgo-MIR390c-overexpressed plants. CONCLUSIONS cgo-miR390 family affected the development of reproductive organs in transgenic Arabidopsis. The study provides references for the genetic improvement for orchid with potentially great economic benefit.
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Affiliation(s)
- Zihan Xu
- College of Landscape Architecture, Nanjing Forestry University, 210037, Nanjing, Jiangsu Province, China
| | - Qian Liu
- College of Landscape Architecture, Nanjing Forestry University, 210037, Nanjing, Jiangsu Province, China
| | - Yue Chen
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 310021, Hangzhou, Zhejiang Province, China
| | - Yuanhao He
- College of Landscape Architecture, Nanjing Forestry University, 210037, Nanjing, Jiangsu Province, China
| | - Fengrong Hu
- College of Landscape Architecture, Nanjing Forestry University, 210037, Nanjing, Jiangsu Province, China.
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6
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Richardson AE, Cheng J, Johnston R, Kennaway R, Conlon BR, Rebocho AB, Kong H, Scanlon MJ, Hake S, Coen E. Evolution of the grass leaf by primordium extension and petiole-lamina remodeling. Science 2021; 374:1377-1381. [PMID: 34882477 DOI: 10.1126/science.abf9407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- A E Richardson
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.,Agricultural Research Service/US Department of Agriculture Plant Gene Expression Center, Albany, CA 94710, USA.,Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - J Cheng
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.,State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - R Johnston
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.,The Elshire Group Limited, Palmerston North 4472, New Zealand
| | - R Kennaway
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - B R Conlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - A B Rebocho
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - H Kong
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - M J Scanlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - S Hake
- Agricultural Research Service/US Department of Agriculture Plant Gene Expression Center, Albany, CA 94710, USA
| | - E Coen
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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Barrera-Rojas CH, Otoni WC, Nogueira FTS. Shaping the root system: the interplay between miRNA regulatory hubs and phytohormones. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6822-6835. [PMID: 34259838 DOI: 10.1093/jxb/erab299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 06/19/2021] [Indexed: 06/13/2023]
Abstract
The root system commonly lies underground, where it provides anchorage for the aerial organs, as well as nutrients and water. Both endogenous and environmental cues contribute to the establishment of the root system. Among the endogenous cues, microRNAs (miRNAs), transcription factors, and phytohormones modulate root architecture. miRNAs belong to a subset of endogenous hairpin-derived small RNAs that post-transcriptionally control target gene expression, mostly transcription factors, comprising the miRNA regulatory hubs. Phytohormones are signaling molecules involved in most developmental processes. Some miRNAs and targets participate in more than one hormonal pathway, thereby providing new bridges in plant hormonal crosstalk. Unraveling the intricate network of molecular mechanisms underlying the establishment of root systems is a central aspect in the development of novel strategies for plant breeding to increase yield and optimize agricultural land use. In this review, we summarize recent findings describing the molecular mechanisms associated with the interplay between miRNA regulatory hubs and phytohormones to ensure the establishment of a proper root system. We focus on post-embryonic growth and development of primary, lateral, and adventitious roots. In addition, we discuss novel insights for future research on the interaction between miRNAs and phytohormones in root architecture.
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Affiliation(s)
- Carlos Hernán Barrera-Rojas
- Laboratory of Molecular Genetics of Plant Development, Department of Biological Sciences, Luiz de Queiroz College of Agriculture, University of Sao Paulo, Piracicaba, Sao Paulo, Brazil
| | - Wagner Campos Otoni
- Department of Plant Biology, Federal University of Viçosa, Viçosa, MG, Brazil
| | - Fabio Tebaldi Silveira Nogueira
- Laboratory of Molecular Genetics of Plant Development, Department of Biological Sciences, Luiz de Queiroz College of Agriculture, University of Sao Paulo, Piracicaba, Sao Paulo, Brazil
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8
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Li T, Lian H, Li H, Xu Y, Zhang H. HY5 regulates light-responsive transcription of microRNA163 to promote primary root elongation in Arabidopsis seedlings. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1437-1450. [PMID: 33860639 DOI: 10.1111/jipb.13099] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/12/2021] [Indexed: 05/25/2023]
Abstract
MicroRNAs (miRNAs) play key roles in the post-transcriptional regulation of gene expression in plants. Many miRNAs are responsive to environmental signals. Light is the first environmental signal perceived by plants after emergence from the soil. However, less is known about the roles and regulatory mechanism of miRNAs in response to light signal. Here, using small RNA sequencing, we determined that miR163 is significantly rapidly induced by light signaling in Arabidopsis thaliana seedlings. The light-inducible response of miR163 functions genetically downstream of LONG HYPOCOTYL 5 (HY5), a central positive regulator of photomorphogenesis. HY5 directly binds to the two G/C-hybrid elements in the miR163 promoter with unequal affinity; one of these elements, which is located next to the transcription start site, plays a major role in light-induced expression of miR163. Overexpression of miR163 rescued the defective primary root elongation of hy5 seedlings without affecting lateral root growth, whereas overexpressing of miR163 target PXMT1 inhibited primary root elongation. These findings provide insight into understanding the post-transcriptional regulation of root photomorphogenesis mediated by the HY5-miR163-PXMT1 network.
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Affiliation(s)
- Tao Li
- College of Life Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hongmei Lian
- College of Life Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Haojie Li
- College of Life Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yufang Xu
- College of Life Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Huiyong Zhang
- College of Life Science, Henan Agricultural University, Zhengzhou, 450002, China
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9
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Ma X, Denyer T, Javelle M, Feller A, Timmermans MCP. Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts. Genome Res 2021; 31:811-822. [PMID: 33863807 PMCID: PMC8092011 DOI: 10.1101/gr.270918.120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 03/04/2021] [Indexed: 01/12/2023]
Abstract
Development of complex organisms requires the delicate and dynamic spatiotemporal regulation of gene expression. Central to this are microRNAs (miRNAs). These mobile small RNAs offer specificity in conveying positional information and versatility in patterning the outcomes of gene expression. However, the parameters that shape miRNA output during development are still to be clarified. Here, we address this question on a genome-wide scale, using the maize shoot apex as a model. We show that patterns and levels of miRNA accumulation are largely determined at the transcriptional level, but are finessed post-transcriptionally in a tissue-dependent manner. The stem cell environments of the shoot apical meristem and vasculature appear particularly liable to this. Tissue-specific effects are also apparent at the level of target repression, with target cleavage products in the vasculature exceeding those of other tissues. Our results argue against a clearance mode of regulation purely at the level of transcript cleavage, leading us to propose that transcript cleavage provides a baseline level of target repression, onto which miRNA-driven translational repression can act to toggle the mode of target regulation between clearance and rheostat. Our data show how the inherent complexities of miRNA pathways allow the accumulation and activity of these small RNAs to be tailored in space and time to bring about the gene expression versatility needed during development.
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Affiliation(s)
- Xiaoli Ma
- Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Tom Denyer
- Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany
| | | | - Antje Feller
- Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Marja C P Timmermans
- Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany
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10
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Gautam V, Singh A, Yadav S, Singh S, Kumar P, Sarkar Das S, Sarkar AK. Conserved LBL1-ta-siRNA and miR165/166 -RLD1/2 modules regulate root development in maize. Development 2021; 148:dev.190033. [PMID: 33168582 DOI: 10.1242/dev.190033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 11/02/2020] [Indexed: 01/25/2023]
Abstract
Root system architecture and anatomy of monocotyledonous maize is significantly different from dicotyledonous model Arabidopsis The molecular role of non-coding RNA (ncRNA) is poorly understood in maize root development. Here, we address the role of LEAFBLADELESS1 (LBL1), a component of maize trans-acting short-interfering RNA (ta-siRNA), in maize root development. We report that root growth, anatomical patterning, and the number of lateral roots (LRs), monocot-specific crown roots (CRs) and seminal roots (SRs) are significantly affected in lbl1-rgd1 mutant, which is defective in production of ta-siRNA, including tasiR-ARF that targets AUXIN RESPONSE FACTOR3 (ARF3) in maize. Altered accumulation and distribution of auxin, due to differential expression of auxin biosynthesis and transporter genes, created an imbalance in auxin signalling. Altered expression of microRNA165/166 (miR165/166) and its targets, ROLLED1 and ROLLED2 (RLD1/2), contributed to the changes in lbl1-rgd1 root growth and vascular patterning, as was evident by the altered root phenotype of Rld1-O semi-dominant mutant. Thus, LBL1/ta-siRNA module regulates root development, possibly by affecting auxin distribution and signalling, in crosstalk with miR165/166-RLD1/2 module. We further show that ZmLBL1 and its Arabidopsis homologue AtSGS3 proteins are functionally conserved.
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Affiliation(s)
- Vibhav Gautam
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.,Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Archita Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sandeep Yadav
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sharmila Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Pramod Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shabari Sarkar Das
- Department of Botany and Forestry, Vidyasagar University, Midnapore, WB 721104, India
| | - Ananda K Sarkar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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11
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Maize microRNA166 Inactivation Confers Plant Development and Abiotic Stress Resistance. Int J Mol Sci 2020; 21:ijms21249506. [PMID: 33327508 PMCID: PMC7764941 DOI: 10.3390/ijms21249506] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/04/2020] [Accepted: 12/11/2020] [Indexed: 11/16/2022] Open
Abstract
MicroRNAs are important regulators in plant developmental processes and stress responses. In this study, we generated a series of maize STTM166 transgenic plants. Knock-down of miR166 resulted in various morphological changes, including rolled leaves, enhanced abiotic stress resistance, inferior yield-related traits, vascular pattern and epidermis structures, tassel architecture, as well as abscisic acid (ABA) level elevation and indole acetic acid (IAA) level reduction in maize. To profile miR166 regulated genes, we performed RNA-seq and qRT-PCR analysis. A total of 178 differentially expressed genes (DEGs) were identified, including 118 up-regulated and 60 down-regulated genes. These DEGs were strongly enriched in cell and intercellular components, cell membrane system components, oxidoreductase activity, single organism metabolic process, carbohydrate metabolic process, and oxidation reduction process. These results indicated that miR166 plays important roles in auxin and ABA interaction in monocots, yet the specific mechanism may differ from dicots. The enhanced abiotic stress resistance is partly caused via rolling leaves, high ABA content, modulated vascular structure, and the potential changes of cell membrane structure. The inferior yield-related traits and late flowering are partly controlled by the decreased IAA content, the interplay of miR166 with other miRNAs and AGOs. Taken together, the present study uncovered novel functions of miR166 in maize, and provide insights on applying short tandem target mimics (STTM) technology in plant breeding.
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Chen SY, Su MH, Kremling KA, Lepak NK, Romay MC, Sun Q, Bradbury PJ, Buckler ES, Ku HM. Identification of miRNA-eQTLs in maize mature leaf by GWAS. BMC Genomics 2020; 21:689. [PMID: 33023467 PMCID: PMC7541240 DOI: 10.1186/s12864-020-07073-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/14/2020] [Indexed: 11/28/2022] Open
Abstract
Background MiRNAs play essential roles in plant development and response to biotic and abiotic stresses through interaction with their target genes. The expression level of miRNAs shows great variations among different plant accessions, developmental stages, and tissues. Little is known about the content within the plant genome contributing to the variations in plants. This study aims to identify miRNA expression-related quantitative trait loci (miR-QTLs) in the maize genome. Results The miRNA expression level from next generation sequencing (NGS) small RNA libraries derived from mature leaf samples of the maize panel (200 maize lines) was estimated as phenotypes, and maize Hapmap v3.2.1 was chosen as the genotype for the genome-wide association study (GWAS). A total of four significant miR-eQTLs were identified contributing to miR156k-5p, miR159a-3p, miR390a-5p and miR396e-5p, and all of them are trans-eQTLs. In addition, a strong positive coexpression of miRNA was found among five miRNA families. Investigation of the effects of these miRNAs on the expression levels and target genes provided evidence that miRNAs control the expression of their targets by suppression and enhancement. Conclusions These identified significant miR-eQTLs contribute to the diversity of miRNA expression in the maize penal at the developmental stages of mature leaves in maize, and the positive and negative regulation between miRNA and its target genes has also been uncovered.
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Affiliation(s)
- Shu-Yun Chen
- Department of Life Science, National Cheng Kung University, Tainan, 701, Taiwan
| | - Mei-Hsiu Su
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Karl A Kremling
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, 14850, NY, USA
| | - Nicholas K Lepak
- United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, USA
| | - M Cinta Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
| | - Qi Sun
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
| | - Peter J Bradbury
- United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, USA
| | - Edward S Buckler
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, 14850, NY, USA.,United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, USA.,Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
| | - Hsin-Mei Ku
- Advanced Plant Biotechnology Center, National Chung Hsing University, No 145 Xingda Rd, South Dist, Taichung, 402, Taiwan.
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López-Ruiz BA, Juárez-González VT, Gómez-Felipe A, De Folter S, Dinkova TD. tasiR-ARFs Production and Target Regulation during In Vitro Maize Plant Regeneration. PLANTS (BASEL, SWITZERLAND) 2020; 9:E849. [PMID: 32640631 PMCID: PMC7411845 DOI: 10.3390/plants9070849] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 12/11/2022]
Abstract
During in vitro maize plant regeneration somatic cells change their normal fate and undergo restructuring to generate pluripotent cells able to originate new plants. Auxins are essential to achieve such plasticity. Their physiological effects are mediated by auxin response factors (ARFs) that bind auxin responsive elements within gene promoters. Small trans-acting (ta)-siRNAs, originated from miR390-guided TAS3 primary transcript cleavage, target ARF3/4 class (tasiR-ARFs). Here we found that TAS3b precursor as well as derived tasiR-ARFbD5 and tasiR-ARFbD6 display significantly lower levels in non-embryogenic callus (NEC), while TAS3g, miR390 and tasiR-ARFg are more abundant in the same tissue. However, Argonaute (AGO7) and leafbladeless 1 (LBLl) required for tasiR-ARF biogenesis showed significantly higher transcript levels in EC suggesting limited tasiR-ARF biogenesis in NEC. The five maize ARFs targeted by tasiR-ARFs were also significantly enriched in EC and accompanied by higher auxin accumulation with punctuate patterns in this tissue. At hormone half-reduction and photoperiod implementation, plant regeneration initiated from EC with transient TAS3g, miR390 and tasiR-ARFg increase. Upon complete hormone depletion, TAS3b became abundant and derived tasiR-ARFs gradually increased at further regeneration stages. ZmARF transcripts targeted by tasiR-ARFs, as well as AGO7 and LBL1 showed significantly lower levels during regeneration than in EC. These results indicate a dynamic tasiR-ARF mediated regulation throughout maize in vitro plant regeneration.
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Affiliation(s)
- Brenda Anabel López-Ruiz
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de Mexico, 04510 Ciudad de Mexico, Mexico; (B.A.L.-R.); (V.T.J.-G.)
| | - Vasti Thamara Juárez-González
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de Mexico, 04510 Ciudad de Mexico, Mexico; (B.A.L.-R.); (V.T.J.-G.)
| | - Andrea Gómez-Felipe
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Unidad de Genómica Avanzada (UGA-LANGEBIO), 36821 Irapuato Gto., Mexico; (A.G.-F.); (S.D.F.)
| | - Stefan De Folter
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Unidad de Genómica Avanzada (UGA-LANGEBIO), 36821 Irapuato Gto., Mexico; (A.G.-F.); (S.D.F.)
| | - Tzvetanka D. Dinkova
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de Mexico, 04510 Ciudad de Mexico, Mexico; (B.A.L.-R.); (V.T.J.-G.)
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Abstract
The coordination of cell fate decisions within complex multicellular structures rests on intercellular communication. To generate ordered patterns, cells need to know their relative positions within the growing structure. This is commonly achieved via the production and perception of mobile signaling molecules. In animal systems, such positional signals often act as morphogens and subdivide a field of cells into domains of discrete cell identities using a threshold-based readout of their mobility gradient. Reflecting the independent origin of multicellularity, plants evolved distinct signaling mechanisms to drive cell fate decisions. Many of the basic principles underlying developmental patterning are, however, shared between animals and plants, including the use of signaling gradients to provide positional information. In plant development, small RNAs can act as mobile instructive signals, and similar to classical morphogens in animals, employ a threshold-based readout of their mobility gradient to generate precisely defined cell fate boundaries. Given the distinctive nature of peptide morphogens and small RNAs, how might mechanisms underlying the function of traditionally morphogens be adapted to create morphogen-like behavior using small RNAs? In this review, we highlight the contributions of mobile small RNAs to pattern formation in plants and summarize recent studies that have advanced our understanding regarding the formation, stability, and interpretation of small RNA gradients.
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Affiliation(s)
- Simon Klesen
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Kristine Hill
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
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15
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Tolstyko E, Lezzhov A, Solovyev A. Identification of miRNA precursors in the phloem of Cucurbita maxima. PeerJ 2019; 7:e8269. [PMID: 31844599 PMCID: PMC6911342 DOI: 10.7717/peerj.8269] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 11/22/2019] [Indexed: 01/14/2023] Open
Abstract
Plant development and responses to environmental cues largely depend on mobile signals including microRNAs (miRNAs) required for post-transcriptional silencing of specific genes. Short-range cell-to-cell transport of miRNA in developing tissues and organs is involved in transferring positional information essential for determining cell fate. Among other RNA species, miRNAs are found in the phloem sap. Long-distance transport of miRNA via the phloem takes a part in regulation of physiological responses to changing environmental conditions. As shown for regulation of inorganic phosphorus and sulfate homeostasis, mature miRNAs rather than miRNAs precursors are transported in the phloem as signaling molecules. Here, a bioinformatics analysis of transcriptomic data for Cucurbita maxima phloem exudate RNAs was carried out to elucidate whether miRNA precursors could also be present in the phloem. We demonstrated that the phloem transcriptome contained a subset of C. maxima pri-miRNAs that differed from a subset of pri-miRNA sequences abundant in a leaf transcriptome. Differential accumulation of pri-miRNA was confirmed by PCR analysis of C. maxima phloem exudate and leaf RNA samples. Therefore, the presented data indicate that a number of C. maxima pri-miRNAs are selectively recruited to the phloem translocation pathway. This conclusion was validated by inter-species grafting experiments, in which C. maxima pri-miR319a was found to be transported across the graft union via the phloem, confirming the presence of pri-miR319a in sieve elements and showing that phloem miRNA precursors could play a role in long-distance signaling in plants.
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Affiliation(s)
- Eugeny Tolstyko
- Department of Virology, Moscow State University, Moscow, Russia
| | - Alexander Lezzhov
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
| | - Andrey Solovyev
- Department of Virology, Moscow State University, Moscow, Russia.,Belozersky Institute, Moscow State University, Moscow, Russia.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
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16
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Brosnan CA, Sarazin A, Lim P, Bologna NG, Hirsch‐Hoffmann M, Voinnet O. Genome-scale, single-cell-type resolution of microRNA activities within a whole plant organ. EMBO J 2019; 38:e100754. [PMID: 31268601 PMCID: PMC6600646 DOI: 10.15252/embj.2018100754] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 05/03/2019] [Accepted: 05/07/2019] [Indexed: 01/27/2023] Open
Abstract
Loaded into ARGONAUTE(AGO) proteins, eukaryotic micro(mi)RNAs regulate gene expression via cleavage, translational repression, and/or accelerated decay of sequence-complementary target transcripts. Despite their importance in development, cell identity maintenance and stress responses, how individual miRNAs contribute to spatial gene regulation within the complex cell mosaics formed in tissues/organs has remained inaccessible in any organism to date. We have developed a non-invasive methodology to examine, at single-cell-type resolution, the AGO-loading and activity patterns of entire miRNA cohorts in intact organs, applied here to the Arabidopsis root tip. A dual miRNAome-targetome analytical interface allowing intuitive data integration/visualization was developed as the basis for in-depth investigations via single-cell-type experimentation. These uncovered an array of so far speculative or hitherto unknown types of spatial miRNA-mediated gene regulation schemes, including via widespread cell-to-cell movement between contiguous layers of distinct identities. This study provides the proof of principle that minimally invasive, genome-scale analysis of miRNA activities within and between single-cell types of whole organs is achievable.
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Affiliation(s)
- Christopher Andrew Brosnan
- Department of BiologySwiss Federal Institute of Technology (ETH)ZürichSwitzerland
- Present address:
Queensland Brain InstituteThe University of QueenslandBrisbaneQldAustralia
| | - Alexis Sarazin
- Department of BiologySwiss Federal Institute of Technology (ETH)ZürichSwitzerland
| | - PeiQi Lim
- Department of BiologySwiss Federal Institute of Technology (ETH)ZürichSwitzerland
- Present address:
QIAGEN Singapore Pte. Ltd.SingaporeSingapore
| | - Nicolas Gerardo Bologna
- Department of BiologySwiss Federal Institute of Technology (ETH)ZürichSwitzerland
- Present address:
Center for Research in Agricultural Genomics (CRAG)BarcelonaSpain
| | | | - Olivier Voinnet
- Department of BiologySwiss Federal Institute of Technology (ETH)ZürichSwitzerland
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17
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Xia Z, Zhao Z, Gao X, Jiao Z, Wu Y, Zhou T, Fan Z. Characterization of Maize miRNAs in Response to Synergistic Infection of Maize Chlorotic Mottle Virus and Sugarcane Mosaic Virus. Int J Mol Sci 2019; 20:ijms20133146. [PMID: 31252649 PMCID: PMC6650953 DOI: 10.3390/ijms20133146] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/20/2019] [Accepted: 06/25/2019] [Indexed: 01/09/2023] Open
Abstract
The synergistic infection of maize chlorotic mottle virus (MCMV) and sugarcane mosaic virus (SCMV) causes maize lethal necrosis, with considerable losses to global maize production. microRNAs (miRNAs) are conserved non-coding small RNAs that play essential regulatory roles in plant development and environmental stress responses, including virus infection. However, the characterization of maize miRNAs in response to synergistic infection of MCMV and SCMV remains largely unknown. In this study, the profiles of small RNAs from MCMV and SCMV single- and co-infected (S + M) maize plants were obtained by high-throughput sequencing. A total of 173 known miRNAs, belonging to 26 miRNA families, and 49 novel miRNAs were profiled. The expression patterns of most miRNAs in S + M-infected maize plants were similar to that in SCMV-infected maize plants, probably due to the existence of RNA silencing suppressor HC-Pro. Northern blotting and quantitative real-time PCR were performed to validate the accumulation of miRNAs and their targets in different experimental treatments, respectively. The down-regulation of miR159, miR393, and miR394 might be involved in antiviral defense to synergistic infection. These results provide novel insights into the regulatory networks of miRNAs in maize plants in response to the synergistic infection of MCMV and SCMV.
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Affiliation(s)
- Zihao Xia
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China.
| | - Zhenxing Zhao
- State Key Laboratory of Agro-Biotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, China
| | - Xinran Gao
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhiyuan Jiao
- State Key Laboratory of Agro-Biotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, China
| | - Yuanhua Wu
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Tao Zhou
- State Key Laboratory of Agro-Biotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, China
| | - Zaifeng Fan
- State Key Laboratory of Agro-Biotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, China.
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18
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Perspectives on microRNAs and Phased Small Interfering RNAs in Maize ( Zea mays L.): Functions and Big Impact on Agronomic Traits Enhancement. PLANTS 2019; 8:plants8060170. [PMID: 31212808 PMCID: PMC6630462 DOI: 10.3390/plants8060170] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 02/05/2023]
Abstract
Small RNA (sRNA) population in plants comprises of primarily micro RNAs (miRNAs) and small interfering RNAs (siRNAs). MiRNAs play important roles in plant growth and development. The miRNA-derived secondary siRNAs are usually known as phased siRNAs, including phasiRNAs and tasiRNAs. The miRNA and phased siRNA biogenesis mechanisms are highly conserved in plants. However, their functional conservation and diversification may differ in maize. In the past two decades, lots of miRNAs and phased siRNAs have been functionally identified for curbing important maize agronomic traits, such as those related to developmental timing, plant architecture, sex determination, reproductive development, leaf morphogenesis, root development and nutrition, kernel development and tolerance to abiotic stresses. In contrast to Arabidopsis and rice, studies on maize miRNA and phased siRNA biogenesis and functions are limited, which restricts the small RNA-based fundamental and applied studies in maize. This review updates the current status of maize miRNA and phased siRNA mechanisms and provides a survey of our knowledge on miRNA and phased siRNA functions in controlling agronomic traits. Furthermore, improvement of those traits through manipulating the expression of sRNAs or their targets is discussed.
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19
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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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20
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Singh A, Gautam V, Singh S, Sarkar Das S, Verma S, Mishra V, Mukherjee S, Sarkar AK. Plant small RNAs: advancement in the understanding of biogenesis and role in plant development. PLANTA 2018; 248:545-558. [PMID: 29968061 DOI: 10.1007/s00425-018-2927-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 04/12/2018] [Indexed: 05/07/2023]
Abstract
Present review addresses the advances made in the understanding of biogenesis of plant small RNAs and their role in plant development. We discuss the elaborate role of microRNAs (miRNAs) and trans-acting small interfering RNAs (ta-siRNAs) in various aspects of plant growth and development and highlight relevance of small RNA mobility. Small non-coding RNAs regulate various aspects of plant development. Small RNAs (sRNAs) of 21-24 nucleotide length are derived from double-stranded RNAs through the combined activity of several biogenesis and processing components. These sRNAs function by negatively regulating the expression of target genes. miRNAs and ta-siRNAs constitute two important classes of endogenous small RNAs in plants, which play important roles in plant growth and developmental processes like embryogenesis, organ formation and patterning, shoot and root growth, and reproductive development. Biogenesis of miRNAs is a multistep process which includes transcription, processing and modification, and their loading onto RNA-induced silencing complex (RISC). RISC-loaded miRNAs carry out post-transcriptional silencing of their target(s). Recent studies identified orthologues of different biogenesis components of novel and conserved small RNAs from different model plants. Although many small RNAs have been identified from diverse plant species, only a handful of them have been functionally characterized. In this review, we discuss the advances made in understanding the biogenesis, functional conservation/divergence in miRNA-mediated gene regulation, and the developmental role of small RNAs in different plant species.
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Affiliation(s)
- Archita Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Vibhav Gautam
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sharmila Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shabari Sarkar Das
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Swati Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Vishnu Mishra
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shalini Mukherjee
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ananda K Sarkar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Fard EM, Bakhshi B, Farsi M, Kakhki AM, Nikpay N, Ebrahimi MA, Mardi M, Salekdeh GH. MicroRNAs regulate the main events in rice drought stress response by manipulating the water supply to shoots. MOLECULAR BIOSYSTEMS 2018; 13:2289-2302. [PMID: 28872648 DOI: 10.1039/c7mb00298j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
MicroRNAs (miRNAs) are small endogenous regulatory RNAs that are involved in a variety of biological processes related to proliferation, development, and response to biotic and abiotic stresses. miRNA profiles of rice (Oryza sativa L. cv. IR64.) leaves in a partial root zone drying (PRD) system were analysed using a high-throughput sequencing approach to identify miRNAs associated with drought signalling. The treatments performed in this study were as follows: well-watered ("wet" roots, WW), wherein both halves of the pot were watered daily; drought ("dry" roots, DD), wherein water was withheld from both halves of the pot; and well-watered/drought ("wet" and "dry" roots, WD), wherein one half of each pot was watered daily, the same as in WW, and water was withheld from the other part, the same as in DD. High-throughput sequencing enabled us to detect novel miRNAs and study the differential expression of known miRNAs. A total of 209 novel miRNAs were detected in this study. Differential miRNA profiling of the DD, WD and WW conditions showed differential expression of 159 miRNAs, among which 83, 44 and 32 miRNAs showed differential expression under both DD and WD conditions. The detection of putative targets of the differentially expressed miRNAs and investigation of their functions showed that most of these genes encode transcription factors involved in growth and development, leaf morphology, regulation of hormonal homeostasis, and stress response. The most important differences between the DD and WD conditions involved regulation of the levels of hormones such as auxin, cytokinin, abscisic acid, and jasmonic acid and also regulation of phosphor homeostasis. Overall, differentially expressed miRNAs under WD conditions were found to differ from those under DD conditions, with such differences playing a role in adaptation and inducing the normal condition. The mechanisms involved in regulating hormonal homeostasis and involved in energy production and consumption were found to be the most important regulatory pathways distinguishing the DD and WD conditions.
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Affiliation(s)
- Ehsan Mohseni Fard
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Tehran, Iran.
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Dong J, Huang H. Auxin polar transport flanking incipient primordium initiates leaf adaxial-abaxial polarity patterning. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:455-464. [PMID: 29405646 DOI: 10.1111/jipb.12640] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 02/05/2018] [Indexed: 05/08/2023]
Abstract
The leaves of most higher plants are polar along their adaxial-abaxial axis, and the development of the adaxial domain (upper side) and the abaxial domain (lower side) makes the leaf a highly efficient photosynthetic organ. It has been proposed that a hypothetical signal transported from the shoot apical meristem (SAM) to the incipient leaf primordium, or conversely, the plant hormone auxin transported from the leaf primordium to the SAM, initiates leaf adaxial-abaxial patterning. This hypothetical signal has been referred to as the Sussex signal, because the research of Ian Sussex published in 1951 was the first to imply its existence. Recent results, however, have shown that auxin polar transport flanking the incipient leaf primordium, but not the Sussex signal, is the key to initiate leaf polarity. Here, we review the new findings and integrate them with other recently published results in the field of leaf development, mainly focusing on the early steps of leaf polarity establishment.
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Affiliation(s)
- Jiaqiang Dong
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Hai Huang
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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23
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Liu H, Yu H, Tang G, Huang T. Small but powerful: function of microRNAs in plant development. PLANT CELL REPORTS 2018; 37:515-528. [PMID: 29318384 DOI: 10.1007/s00299-017-2246-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/15/2017] [Indexed: 05/02/2023]
Abstract
MicroRNAs (miRNAs) are a group of endogenous noncoding small RNAs frequently 21 nucleotides long. miRNAs act as negative regulators of their target genes through sequence-specific mRNA cleavage, translational repression, or chromatin modifications. Alterations of the expression of a miRNA or its targets often result in a variety of morphological and physiological abnormalities, suggesting the strong impact of miRNAs on plant development. Here, we review the recent advances on the functional studies of plant miRNAs. We will summarize the regulatory networks of miRNAs in a series of developmental processes, including meristem development, establishment of lateral organ polarity and boundaries, vegetative and reproductive organ growth, etc. We will also conclude the conserved and species-specific roles of plant miRNAs in evolution and discuss the strategies for further elucidating the functional mechanisms of miRNAs during plant development.
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Affiliation(s)
- Haiping Liu
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, 49931, USA
| | - Hongyang Yu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Guiliang Tang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, 49931, USA
| | - Tengbo Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China.
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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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26
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Taochy C, Gursanscky NR, Cao J, Fletcher SJ, Dressel U, Mitter N, Tucker MR, Koltunow AMG, Bowman JL, Vaucheret H, Carroll BJ. A Genetic Screen for Impaired Systemic RNAi Highlights the Crucial Role of DICER-LIKE 2. PLANT PHYSIOLOGY 2017; 175:1424-1437. [PMID: 28928141 PMCID: PMC5664484 DOI: 10.1104/pp.17.01181] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 09/14/2017] [Indexed: 05/17/2023]
Abstract
Posttranscriptional gene silencing (PTGS) of transgenes involves abundant 21-nucleotide small interfering RNAs (siRNAs) and low-abundance 22-nucleotide siRNAs produced from double-stranded RNA (dsRNA) by DCL4 and DCL2, respectively. However, DCL2 facilitates the recruitment of RNA-DEPENDENT RNA POLYMERASE 6 (RDR6) to ARGONAUTE 1-derived cleavage products, resulting in more efficient amplification of secondary and transitive dsRNA and siRNAs. Here, we describe a reporter system where RDR6-dependent PTGS is initiated by restricted expression of an inverted-repeat dsRNA specifically in the Arabidopsis (Arabidopsis thaliana) root tip, allowing a genetic screen to identify mutants impaired in RDR6-dependent systemic PTGS. Our screen identified dcl2 but not dcl4 mutants. Moreover, grafting experiments showed that DCL2, but not DCL4, is required in both the source rootstock and the recipient shoot tissue for efficient RDR6-dependent systemic PTGS. Furthermore, dcl4 rootstocks produced more DCL2-dependent 22-nucleotide siRNAs than the wild type and showed enhanced systemic movement of PTGS to grafted shoots. Thus, along with its role in recruiting RDR6 for further amplification of PTGS, DCL2 is crucial for RDR6-dependent systemic PTGS.
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Affiliation(s)
- Christelle Taochy
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Institut National de la Recherche Agronomique AgroParisTech Centre National de la Recherche Scientifique, Université Paris-Saclay, 78000 Versailles, France
| | - Nial R Gursanscky
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jiangling Cao
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Stephen J Fletcher
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Uwe Dressel
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Neena Mitter
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Matthew R Tucker
- Commonwealth Scientific and Industrial Research Organization Agriculture, Waite Campus, Urrbrae, South Australia 5064, Australia
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Campus, Adelaide, South Australia 5064, Australia
| | - Anna M G Koltunow
- Commonwealth Scientific and Industrial Research Organization Agriculture, Waite Campus, Urrbrae, South Australia 5064, Australia
| | - John L Bowman
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria 3800, Australia
| | - Hervé Vaucheret
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Institut National de la Recherche Agronomique AgroParisTech Centre National de la Recherche Scientifique, Université Paris-Saclay, 78000 Versailles, France
| | - Bernard J Carroll
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
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Abstract
The differentiation of a leaf - from its inception as a semicircular bulge on the surface of the shoot apical meristem into a flattened structure with specialized upper and lower surfaces - is one of the most intensely studied processes in plant developmental biology. The large body of contemporary data on leaf dorsiventrality has its origin in the pioneering experiments of Ian Sussex, who carried out these studies as a PhD student in the early 1950s. Here, we review his original experiments in their historical context and describe our current understanding of this surprisingly complex process. Finally, we postulate possible candidates for the 'Sussex signal' - the elusive meristem-derived factor that first ignited interest in this important developmental problem.
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Affiliation(s)
- Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, Bern CH-3013, Switzerland
| | - Marja C P Timmermans
- Center for Plant Molecular Biology, University of Tübingen, Tübingen D-72076, Germany
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Yu Y, Ji L, Le BH, Zhai J, Chen J, Luscher E, Gao L, Liu C, Cao X, Mo B, Ma J, Meyers BC, Chen X. ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis. PLoS Biol 2017; 15:e2001272. [PMID: 28231321 PMCID: PMC5322904 DOI: 10.1371/journal.pbio.2001272] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 01/26/2017] [Indexed: 01/05/2023] Open
Abstract
The degradation of small RNAs in plants and animals is associated with small RNA 3′ truncation and 3′ uridylation and thus relies on exonucleases and nucleotidyl transferases. ARGONAUTE (AGO) proteins associate with small RNAs in vivo and are essential for not only the activities but also the stability of small RNAs. AGO1 is the microRNA (miRNA) effector in Arabidopsis, and its closest homolog, AGO10, maintains stem cell homeostasis in meristems by sequestration of miR165/6, a conserved miRNA acting through AGO1. Here, we show that SMALL RNA DEGRADING NUCLEASES (SDNs) initiate miRNA degradation by acting on AGO1-bound miRNAs to cause their 3′ truncation, and the truncated species are uridylated and degraded. We report that AGO10 reduces miR165/6 accumulation by enhancing its degradation by SDN1 and SDN2 in vivo. In vitro, AGO10-bound miR165/6 is more susceptible to SDN1-mediated 3′ truncation than AGO1-bound miR165/6. Thus, AGO10 promotes the degradation of miR165/6, which is contrary to the stabilizing effect of AGO1. Our work identifies a class of exonucleases responsible for miRNA 3′ truncation in vivo and uncovers a mechanism of specificity determination in miRNA turnover. This work, together with previous studies on AGO10, suggests that spatially regulated miRNA degradation underlies stem cell maintenance in plants. MicroRNAs (miRNAs) are 21–24 nucleotide regulatory RNAs that impact nearly all biological processes in plants and animals. The abundance of miRNAs is determined by their biogenesis and degradation. miRNA degradation is associated with trimming and tailing of their 3′ ends. The relationship between 3′ trimming and 3′ tailing as well as the enzyme(s) responsible for 3′ trimming was unknown in Arabidopsis. Mechanisms that protect miRNAs from degradation include 3′ terminal methylation and association with ARGONAUTE (AGO) proteins. In this study, we show that two members of the SMALL RNA DEGRADING NUCLEASE (SDN) family, SDN1 and SDN2, are partly responsible for the miRNA 3′ trimming activities in Arabidopsis. We further elucidate the relationship between 3′ trimming and 3′ tailing—miRNAs are first trimmed by SDNs, and the 3′ trimmed-and-unmethylated miRNAs are tailed by the nucleotidyl transferase HESO1. Furthermore, we demonstrate that SDN1 is able to act on AGO1-bound and methylated miRNAs. We also reveal a special function of AGO10, which has the highest affinity for miR165/6 in vivo. We show that AGO10-bound miR165/6 is more susceptible to SDN-mediated degradation than AGO1-bound miR165/6. This study provides a general molecular framework for miRNA degradation and an example of specificity determination in miRNA degradation.
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Affiliation(s)
- Yu Yu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California, United States of America
| | - Lijuan Ji
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California, United States of America
| | - Brandon H. Le
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California, United States of America
| | - Jixian Zhai
- Department of Plant and Soil Sciences, and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Jiayi Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California, United States of America
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Elizabeth Luscher
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California, United States of America
| | - Lei Gao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California, United States of America
| | - Chunyan Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, West Lincui Road, Chaoyang District, Beijing, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, West Lincui Road, Chaoyang District, Beijing, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Blake C. Meyers
- Department of Plant and Soil Sciences, and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California, United States of America
- Howard Hughes Medical Institute, University of California, Riverside, California, United States of America
- * E-mail:
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29
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Roodbarkelari F, Groot EP. Regulatory function of homeodomain-leucine zipper (HD-ZIP) family proteins during embryogenesis. THE NEW PHYTOLOGIST 2017; 213:95-104. [PMID: 27523393 DOI: 10.1111/nph.14132] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 07/04/2016] [Indexed: 05/26/2023]
Abstract
Homeodomain-leucine zipper proteins (HD-ZIPs) form a plant-specific family of transcription factors functioning as homo- or heterodimers. Certain members of all four classes of this family are involved in embryogenesis, the focus of this review. They support auxin biosynthesis, transport and response, which are in turn essential for the apical-basal patterning of the embryo, radicle formation and outgrowth of the cotyledons. They transcriptionally regulate meristem regulators to maintain the shoot apical meristem once it is initiated. Some members are specific to the protoderm, the outermost layer of the embryo, and play a role in shoot apical meristem function. Within classes, homeodomain-leucine zippers tend to act redundantly during embryo development, and there are many examples of regulation within and between classes of homeodomain-leucine zippers. This indicates a complex network of regulation that awaits future experiments to uncover.
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Affiliation(s)
| | - Edwin P Groot
- Institute of Biology III, Albert-Ludwigs-Universität, Freiburg 79104, Germany
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30
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Ramachandran P, Carlsbecker A, Etchells JP. Class III HD-ZIPs govern vascular cell fate: an HD view on patterning and differentiation. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:55-69. [PMID: 27794018 DOI: 10.1093/jxb/erw370] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Plant vasculature is required for the transport of water and solutes throughout the plant body. It is constituted of xylem, specialized for transport of water, and phloem, that transports photosynthates. These two differentiated tissues are specified early in development and arise from divisions in the procambium, which is the vascular meristem during primary growth. During secondary growth, the xylem and phloem are further expanded via differentiation of cells derived from divisions in the cambium. Almost all of the developmental fate decisions in this process, including vascular specification, patterning, and differentiation, are regulated by transcription factors belonging to the class III homeodomain-leucine zipper (HD-ZIP III) family. This review draws together the literature describing the roles that these genes play in vascular development, looking at how HD-ZIP IIIs are regulated, and how they in turn influence other regulators of vascular development. Themes covered vary, from interactions between HD-ZIP IIIs and auxin, cytokinin, and brassinosteroids, to the requirement for exquisite spatial and temporal regulation of HD-ZIP III expression through miRNA-mediated post-transcriptional regulation, and interactions with other transcription factors. The literature described places the HD-ZIP III family at the centre of a complex network required for initiating and maintaining plant vascular tissues.
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Affiliation(s)
- Prashanth Ramachandran
- Physiological Botany, Department of Organismal Biology and Linnean Centre for Plant Biology in Uppsala, Uppsala University, Ulls väg 24E, SE-756 51 Uppsala, Sweden
| | - Annelie Carlsbecker
- Physiological Botany, Department of Organismal Biology and Linnean Centre for Plant Biology in Uppsala, Uppsala University, Ulls väg 24E, SE-756 51 Uppsala, Sweden
| | - J Peter Etchells
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
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31
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Szyrajew K, Bielewicz D, Dolata J, Wójcik AM, Nowak K, Szczygieł-Sommer A, Szweykowska-Kulinska Z, Jarmolowski A, Gaj MD. MicroRNAs Are Intensively Regulated during Induction of Somatic Embryogenesis in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2017; 8:18. [PMID: 28167951 PMCID: PMC5253390 DOI: 10.3389/fpls.2017.00018] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 01/04/2017] [Indexed: 05/06/2023]
Abstract
Several genes encoding transcription factors (TFs) were indicated to have a key role in the induction of somatic embryogenesis (SE), which is triggered in the somatic cells of plants. In order to further explore the genetic regulatory network that is involved in the embryogenic transition induced in plant somatic cells, micro-RNA (miRNAs) molecules, the products of MIRNA (MIR) genes and the common regulators of TF transcripts, were analyzed in an embryogenic culture of Arabidopsis thaliana. In total, the expression of 190 genes of the 114 MIRNA families was monitored during SE induction and the levels of the primary (pri-miRNAs) transcripts vs. the mature miRNAs were investigated. The results revealed that the majority (98%) of the MIR genes were active and that most of them (64%) were differentially expressed during SE. A distinct attribute of the MIR expression in SE was the strong repression of MIR transcripts at the early stage of SE followed by their significant up-regulation in the advanced stage of SE. Comparison of the mature miRNAs vs. pri-miRNAs suggested that the extensive post-transcriptional regulation of miRNA is associated with SE induction. Candidate miRNA molecules of the assumed function in the embryogenic response were identified among the mature miRNAs that had a differential expression in SE, including miR156, miR157, miR159, miR160, miR164, miR166, miR169, miR319, miR390, miR393, miR396, and miR398. Consistent with the central role of phytohormones and stress factors in SE induction, the functions of the candidate miRNAs were annotated to phytohormone and stress responses. To confirm the functions of the candidate miRNAs in SE, the expression patterns of the mature miRNAs and their presumed targets were compared and regulatory relation during SE was indicated for most of the analyzed miRNA-target pairs. The results of the study contribute to the refinement of the miRNA-controlled regulatory pathways that operate during embryogenic induction in plants and provide a valuable platform for the identification of the genes that are targeted by the candidate miRNAs in SE induction.
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Affiliation(s)
- Katarzyna Szyrajew
- Department of Genetics, Faculty of Biology and Environmental Protection, University of SilesiaKatowice, Poland
| | - Dawid Bielewicz
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Jakub Dolata
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Anna M. Wójcik
- Department of Genetics, Faculty of Biology and Environmental Protection, University of SilesiaKatowice, Poland
| | - Katarzyna Nowak
- Department of Genetics, Faculty of Biology and Environmental Protection, University of SilesiaKatowice, Poland
| | - Aleksandra Szczygieł-Sommer
- Department of Genetics, Faculty of Biology and Environmental Protection, University of SilesiaKatowice, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Małgorzata D. Gaj
- Department of Genetics, Faculty of Biology and Environmental Protection, University of SilesiaKatowice, Poland
- *Correspondence: Małgorzata D. Gaj
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Aravind J, Rinku S, Pooja B, Shikha M, Kaliyugam S, Mallikarjuna MG, Kumar A, Rao AR, Nepolean T. Identification, Characterization, and Functional Validation of Drought-responsive MicroRNAs in Subtropical Maize Inbreds. FRONTIERS IN PLANT SCIENCE 2017; 8:941. [PMID: 28626466 PMCID: PMC5454542 DOI: 10.3389/fpls.2017.00941] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
MicroRNA-mediated gene regulation plays a crucial role in controlling drought tolerance. In the present investigation, 13 drought-associated miRNA families consisting of 65 members and regulating 42 unique target mRNAs were identified from drought-associated microarray expression data in maize and were subjected to structural and functional characterization. The largest number of members (14) was found in the zma-miR166 and zma-miR395 families, with several targets. However, zma-miR160, zma-miR390, zma-miR393, and zma-miR2275 each showed a single target. Twenty-three major drought-responsive cis-regulatory elements were found in the upstream regions of miRNAs. Many drought-related transcription factors, such as GAMYB, HD-Zip III, and NAC, were associated with the target mRNAs. Furthermore, two contrasting subtropical maize genotypes (tolerant: HKI-1532 and sensitive: V-372) were used to understand the miRNA-assisted regulation of target mRNA under drought stress. Approximately 35 and 31% of miRNAs were up-regulated in HKI-1532 and V-372, respectively. The up-regulation of target mRNAs was as high as 14.2% in HKI-1532 but was only 2.38% in V-372. The expression patterns of miRNA-target mRNA pairs were classified into four different types: Type I- up-regulation, Type II- down-regulation, Type III- neutral regulation, and Type IV- opposite regulation. HKI-1532 displayed 46 Type I, 13 Type II, and 23 Type III patterns, whereas V-372 had mostly Type IV interactions (151). A low level of negative regulations of miRNA associated with a higher level of mRNA activity in the tolerant genotype helped to maintain crucial biological functions such as ABA signaling, the auxin response pathway, the light-responsive pathway and endosperm expression under stress conditions, thereby leading to drought tolerance. Our study identified candidate miRNAs and mRNAs operating in important pathways under drought stress conditions, and these candidates will be useful in the development of drought-tolerant maize hybrids.
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Affiliation(s)
- Jayaraman Aravind
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
- Division of Germplasm Conservation, National Bureau of Plant Genetic ResourcesNew Delhi, India
| | - Sharma Rinku
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
- Department of Life Sciences, Shiv Nadar UniversityGautam Buddha Nagar, India
| | - Banduni Pooja
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
| | - Mittal Shikha
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
| | - Shiriga Kaliyugam
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
| | | | - Arun Kumar
- National Phytotron Facility, Indian Agricultural Research InstituteNew Delhi, India
| | - Atmakuri Ramakrishna Rao
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research InstituteNew Delhi, India
| | - Thirunavukkarasu Nepolean
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
- *Correspondence: Thirunavukkarasu Nepolean ;
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33
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Ghosh Dastidar M, Mosiolek M, Bleckmann A, Dresselhaus T, Nodine MD, Maizel A. Sensitive whole mount in situ localization of small RNAs in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:694-702. [PMID: 27411563 DOI: 10.1111/tpj.13270] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 07/11/2016] [Accepted: 07/11/2016] [Indexed: 05/25/2023]
Abstract
Small RNAs, such as microRNAs (miRNAs), regulate gene expression and play important roles in many plant processes. Although our knowledge of their biogenesis and mode of action has significantly progressed, we still have comparatively little information about their biological functions. In particular, knowledge about their spatio-temporal expression patterns rely on either indirect detection by use of reporter constructs or labor-intensive direct detection by in situ hybridization on sectioned material. None of the current approaches allows a systematic investigation of small RNA expression patterns. Here, we present a sensitive method for in situ detection of miRNAs and siRNAs in intact plant tissues that utilizes both double-labeled probes and a specific cross-linker. We determined the expression patterns of several small RNAs in diverse plant tissues.
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Affiliation(s)
- Mouli Ghosh Dastidar
- Center for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Magdalena Mosiolek
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Andrea Bleckmann
- Institute for Cell Biology and Plant Biochemistry, University of Regensburg, Universitaetsstrasse 31, 93053, Regensburg, Germany
| | - Thomas Dresselhaus
- Institute for Cell Biology and Plant Biochemistry, University of Regensburg, Universitaetsstrasse 31, 93053, Regensburg, Germany
| | - Michael D Nodine
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Alexis Maizel
- Center for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
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34
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Fouracre JP, Poethig RS. The role of small RNAs in vegetative shoot development. CURRENT OPINION IN PLANT BIOLOGY 2016; 29:64-72. [PMID: 26745378 PMCID: PMC4753120 DOI: 10.1016/j.pbi.2015.11.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 11/12/2015] [Accepted: 11/18/2015] [Indexed: 05/02/2023]
Abstract
Shoot development consists of the production of lateral organs in predictable spatial and temporal patterns at the shoot apex. To properly integrate such programs of growth across different cell and tissue types, plants require highly complex and robust genetic networks. Over the last twenty years, the roles of small, non-coding RNAs (sRNAs) in these networks have become increasingly apparent, not least in vegetative shoot growth. In this review, we describe recent progress in understanding the contribution of sRNAs to the regulation of vegetative shoot growth, and outline persisting experimental limitations in the field.
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Affiliation(s)
- Jim P Fouracre
- Biology Department, University of Pennsylvania, 433 S. University Ave, Philadelphia, PA 19104, USA
| | - R Scott Poethig
- Biology Department, University of Pennsylvania, 433 S. University Ave, Philadelphia, PA 19104, USA.
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35
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Petsch K, Manzotti PS, Tam OH, Meeley R, Hammell M, Consonni G, Timmermans MCP. Novel DICER-LIKE1 siRNAs Bypass the Requirement for DICER-LIKE4 in Maize Development. THE PLANT CELL 2015; 27. [PMID: 26209554 PMCID: PMC4568500 DOI: 10.1105/tpc.15.00194] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Dicer enzymes function at the core of RNA silencing to defend against exogenous RNA or to regulate endogenous genes. Plant DICER-LIKE4 (DCL4) performs dual functions, acting in antiviral defense and in development via the biogenesis of trans-acting short-interfering RNAs (siRNAs) termed tasiR-ARFs. These small RNAs play an essential role in the grasses, spatially defining the expression domain of AUXIN RESPONSE FACTOR3 (ARF3) transcription factors. However, contrary to tasiR-ARFs' essential function in development, DCL4 proteins exhibit strong evidence of recurrent adaptation typical of host factors involved in antiviral immunity. Here, we address how DCL4 balances its role in development with pressures to diversify in response to viral attack. We show that, in contrast to other tasiR-ARF biogenesis mutants, dcl4 null alleles have an uncharacteristically mild phenotype, correlated with normal expression of select arf3 targets. Loss of DCL4 activity yields a class of 22-nucleotide tasiR-ARF variants associated with the processing of arf3 transcripts into 22-nucleotide secondary siRNAs by DCL1. Our findings reveal a DCL1-dependent siRNA pathway that bypasses the otherwise adverse developmental effects of mutations in DCL4. This pathway is predicted to have important implications for DCL4's role in antiviral defense by reducing the selective constraints on DCL4 and allowing it to diversify in response to viral suppressors.
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Affiliation(s)
- Katherine Petsch
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Priscilla S Manzotti
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, 20133 Milan, Italy
| | - Oliver H Tam
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Robert Meeley
- DuPont Pioneer Ag Biotech Research, Johnston, Iowa 50131
| | - Molly Hammell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Gabriella Consonni
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, 20133 Milan, Italy
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Urbanek MO, Nawrocka AU, Krzyzosiak WJ. Small RNA Detection by in Situ Hybridization Methods. Int J Mol Sci 2015; 16:13259-86. [PMID: 26068454 PMCID: PMC4490494 DOI: 10.3390/ijms160613259] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 06/03/2015] [Indexed: 12/13/2022] Open
Abstract
Small noncoding RNAs perform multiple regulatory functions in cells, and their exogenous mimics are widely used in research and experimental therapies to interfere with target gene expression. MicroRNAs (miRNAs) are the most thoroughly investigated representatives of the small RNA family, which includes short interfering RNAs (siRNAs), PIWI-associated RNA (piRNAs), and others. Numerous methods have been adopted for the detection and characterization of small RNAs, which is challenging due to their short length and low level of expression. These include molecular biology methods such as real-time RT-PCR, northern blotting, hybridization to microarrays, cloning and sequencing, as well as single cell miRNA detection by microscopy with in situ hybridization (ISH). In this review, we focus on the ISH method, including its fluorescent version (FISH), and we present recent methodological advances that facilitated its successful adaptation for small RNA detection. We discuss relevant technical aspects as well as the advantages and limitations of ISH. We also refer to numerous applications of small RNA ISH in basic research and molecular diagnostics.
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Affiliation(s)
- Martyna O Urbanek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland.
| | - Anna U Nawrocka
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland.
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland.
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Lam P, Zhao L, Eveleigh N, Yu Y, Chen X, Kunst L. The exosome and trans-acting small interfering RNAs regulate cuticular wax biosynthesis during Arabidopsis inflorescence stem development. PLANT PHYSIOLOGY 2015; 167:323-36. [PMID: 25502190 PMCID: PMC4326755 DOI: 10.1104/pp.114.252825] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 12/10/2014] [Indexed: 05/18/2023]
Abstract
The primary aerial surfaces of land plants are covered with a cuticle, a protective layer composed of the cutin polyester matrix and cuticular waxes. Previously, we discovered a unique mechanism of regulating cuticular wax biosynthesis during Arabidopsis (Arabidopsis thaliana) stem elongation that involves ECERIFERUM7 (CER7), a core subunit of the exosome. Because loss-of-function mutations in CER7 result in reduced expression of the wax biosynthetic gene CER3, we proposed that CER7 is involved in degrading a messenger RNA encoding a CER3 repressor. To identify this putative repressor, we performed a cer7 suppressor screen that resulted in the isolation of the posttranscriptional gene-silencing components RNA-DEPENDENT RNA POLYMERASE1 and SUPPRESSOR OF GENE SILENCING3, indicating that small RNAs regulate CER3 expression. To establish the identity of the effector RNA species and determine whether these RNAs control CER3 transcript levels directly, we cloned additional genes identified in our suppressor screen and performed next-generation sequencing of small RNA populations that differentially accumulate in the cer7 mutant in comparison with the wild type. Our results demonstrate that the trans-acting small interfering RNA class of small RNAs are the effector molecules involved in direct silencing of CER3 and that the expression of five additional genes (EARLY RESPONSE TO DEHYDRATION14, AUXIN RESISTANT1, a translation initiation factor SUI1 family protein, and two genes of unknown function) is controlled by both CER7 and trans-acting small interfering RNAs.
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Affiliation(s)
- Patricia Lam
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 (P.L., L.Z., N.E., L.K.); andDepartment of Botany and Plant Sciences, Institute of Integrative Genome Biology (Y.Y., X.C.), and Howard Hughes Medical Institute (X.C.), University of California, Riverside, California 92521
| | - Lifang Zhao
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 (P.L., L.Z., N.E., L.K.); andDepartment of Botany and Plant Sciences, Institute of Integrative Genome Biology (Y.Y., X.C.), and Howard Hughes Medical Institute (X.C.), University of California, Riverside, California 92521
| | - Nathan Eveleigh
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 (P.L., L.Z., N.E., L.K.); andDepartment of Botany and Plant Sciences, Institute of Integrative Genome Biology (Y.Y., X.C.), and Howard Hughes Medical Institute (X.C.), University of California, Riverside, California 92521
| | - Yu Yu
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 (P.L., L.Z., N.E., L.K.); andDepartment of Botany and Plant Sciences, Institute of Integrative Genome Biology (Y.Y., X.C.), and Howard Hughes Medical Institute (X.C.), University of California, Riverside, California 92521
| | - Xuemei Chen
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 (P.L., L.Z., N.E., L.K.); andDepartment of Botany and Plant Sciences, Institute of Integrative Genome Biology (Y.Y., X.C.), and Howard Hughes Medical Institute (X.C.), University of California, Riverside, California 92521
| | - Ljerka Kunst
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 (P.L., L.Z., N.E., L.K.); andDepartment of Botany and Plant Sciences, Institute of Integrative Genome Biology (Y.Y., X.C.), and Howard Hughes Medical Institute (X.C.), University of California, Riverside, California 92521
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Tatematsu K, Toyokura K, Okada K. Requirement of MIR165A primary transcript sequence for its activity pattern in Arabidopsis leaf primordia. PLANT SIGNALING & BEHAVIOR 2015; 10:e1055432. [PMID: 26177565 PMCID: PMC4623492 DOI: 10.1080/15592324.2015.1055432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 05/22/2015] [Indexed: 05/27/2023]
Abstract
miRNAs might move cell to cell and act as mobile signals in plant development, while the regulatory mechanisms of miRNA cell-to-cell movement are still unclear. Recently, in Arabidopsis leaf primordia, we revealed that miR165 from the MIR165A gene, which is expressed in the abaxial epidermal cells of leaf primordia, acts non-cell-autonomously in inner cells on the abaxial side. We proposed that not only mature miR165 sequence but also the MIR165A primary transcript sequence are required for the confinement of miR165 activity to the abaxial side of leaf primordia. The deletion analysis of the MIR165A genomic fragment showed that with a lack of the 3' region of MIR165A its activity is not confined in leaf primordia, suggesting that the full-length primary transcript of MIR165A is important for the regulatory mechanism of miRNA activity confinement in leaf primordia. It has been reported that the MIR165A transcript is predicted to be translated into the short poly peptide, proposing that the MIR165A transcript may be exported to the cytoplasm. Considering these matters, we propose a hypothesis for the confinement of miR165 activity to the abaxial side in leaf primordia dependent on the MIR165A primary transcript.
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Affiliation(s)
| | | | - Kiyotaka Okada
- Department of Agriculture; Ryukoku University; Otsu, Japan
- National Institute of Natural Science; Tokyo, Japan
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Dotto MC, Petsch KA, Aukerman MJ, Beatty M, Hammell M, Timmermans MCP. Genome-wide analysis of leafbladeless1-regulated and phased small RNAs underscores the importance of the TAS3 ta-siRNA pathway to maize development. PLoS Genet 2014; 10:e1004826. [PMID: 25503246 PMCID: PMC4263373 DOI: 10.1371/journal.pgen.1004826] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 10/15/2014] [Indexed: 01/05/2023] Open
Abstract
Maize leafbladeless1 (lbl1) encodes a key component in the trans-acting short-interfering RNA (ta-siRNA) biogenesis pathway. Correlated with a great diversity in ta-siRNAs and the targets they regulate, the phenotypes conditioned by mutants perturbing this small RNA pathway vary extensively across species. Mutations in lbl1 result in severe developmental defects, giving rise to plants with radial, abaxialized leaves. To investigate the basis for this phenotype, we compared the small RNA content between wild-type and lbl1 seedling apices. We show that LBL1 affects the accumulation of small RNAs in all major classes, and reveal unexpected crosstalk between ta-siRNA biogenesis and other small RNA pathways regulating transposons. Interestingly, in contrast to data from other plant species, we found no evidence for the existence of phased siRNAs generated via the one-hit model. Our analysis identified nine TAS loci, all belonging to the conserved TAS3 family. Information from RNA deep sequencing and PARE analyses identified the tasiR-ARFs as the major functional ta-siRNAs in the maize vegetative apex where they regulate expression of AUXIN RESPONSE FACTOR3 (ARF3) homologs. Plants expressing a tasiR-ARF insensitive arf3a transgene recapitulate the phenotype of lbl1, providing direct evidence that deregulation of ARF3 transcription factors underlies the developmental defects of maize ta-siRNA biogenesis mutants. The phenotypes of Arabidopsis and Medicago ta-siRNA mutants, while strikingly different, likewise result from misexpression of the tasiR-ARF target ARF3. Our data indicate that diversity in TAS pathways and their targets cannot fully account for the phenotypic differences conditioned by ta-siRNA biogenesis mutants across plant species. Instead, we propose that divergence in the gene networks downstream of the ARF3 transcription factors or the spatiotemporal pattern during leaf development in which these proteins act constitute key factors underlying the distinct contributions of the ta-siRNA pathway to development in maize, Arabidopsis, and possibly other plant species as well. Mutations in maize leafbladeless1 (lbl1) that disrupt ta-siRNA biogenesis give rise to plants with thread-like leaves that have lost top/bottom polarity. We used genomic approaches to identify lbl1-dependent small RNAs and their targets to determine the basis for these polarity defects. This revealed substantial diversity in small RNA pathways across plant species and identified unexpected roles for LBL1 in the regulation of repetitive elements within the maize genome. We further show that only ta-siRNA loci belonging to the TAS3 family function in the maize vegetative apex. The TAS3-derived tasiR-ARFs are the main ta-siRNA active in the apex, and misregulation of their ARF3 targets emerges as the basis for the lbl1 leaf polarity defects. Supporting this, we show that plants expressing arf3a transcripts insensitive to tasiR-ARF-directed cleavage recapitulate the phenotypes observed in lbl1. The TAS3 ta-siRNA pathway, including the regulation of ARF3 genes, is conserved throughout land plant evolution, yet the phenotypes of plants defective for ta-siRNA biogenesis are strikingly different. Our data leads us to propose that divergence in the processes regulated by the ARF3 transcription factors or the spatiotemporal pattern during development in which these proteins act, underlies the diverse developmental contributions of this small RNA pathway across plants.
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Affiliation(s)
- Marcela C. Dotto
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Katherine A. Petsch
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Milo J. Aukerman
- DuPont Crop Genetics, Wilmington, Delaware, United States of America
| | - Mary Beatty
- Pioneer-DuPont, Johnston, Iowa, United States of America
| | - Molly Hammell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Marja C. P. Timmermans
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- * E-mail:
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40
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Bustos-Sanmamed P, Hudik E, Laffont C, Reynes C, Sallet E, Wen J, Mysore KS, Camproux AC, Hartmann C, Gouzy J, Frugier F, Crespi M, Lelandais-Brière C. A Medicago truncatula rdr6 allele impairs transgene silencing and endogenous phased siRNA production but not development. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:1308-1318. [PMID: 25060922 DOI: 10.1111/pbi.12230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 06/02/2014] [Accepted: 06/12/2014] [Indexed: 06/03/2023]
Abstract
RNA-dependent RNA polymerase 6 (RDR6) and suppressor of gene silencing 3 (SGS3) act together in post-transcriptional transgene silencing mediated by small interfering RNAs (siRNAs) and in biogenesis of various endogenous siRNAs including the tasiARFs, known regulators of auxin responses and plant development. Legumes, the third major crop family worldwide, has been widely improved through transgenic approaches. Here, we isolated rdr6 and sgs3 mutants in the model legume Medicago truncatula. Two sgs3 and one rdr6 alleles led to strong developmental defects and impaired biogenesis of tasiARFs. In contrast, the rdr6.1 homozygous plants produced sufficient amounts of tasiARFs to ensure proper development. High throughput sequencing of small RNAs from this specific mutant identified 354 potential MtRDR6 substrates, for which siRNA production was significantly reduced in the mutant. Among them, we found a large variety of novel phased loci corresponding to protein-encoding genes or transposable elements. Interestingly, measurement of GFP expression revealed that post-transcriptional transgene silencing was reduced in rdr6.1 roots. Hence, this novel mis-sense mutation, affecting a highly conserved amino acid residue in plant RDR6s, may be an interesting tool both to analyse endogenous pha-siRNA functions and to improve transgene expression, at least in legume species.
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Affiliation(s)
- Pilar Bustos-Sanmamed
- CNRS, Institut des Sciences du Végétal (ISV), UPR2355, Labex SPS Saclay Plant Sciences, Gif-sur-Yvette Cedex, France
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41
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Sun X, Zhang Y, Zhu X, Korir NK, Tao R, Wang C, Fang J. Advances in identification and validation of plant microRNAs and their target genes. PHYSIOLOGIA PLANTARUM 2014; 152:203-18. [PMID: 24641625 DOI: 10.1111/ppl.12191] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 01/19/2014] [Accepted: 02/12/2014] [Indexed: 05/27/2023]
Abstract
Developments in the field of molecular biology and genetics, such as microarray, gene transfer and discovery of small regulatory RNAs, have led to significant advances in plant biotechnology. Among the small RNAs, microRNAs (miRNAs) have elicited much interest as key post-transcriptional regulators in eukaryotic gene expression. Advances in genome and transcriptome sequencing of plants have facilitated the generation of a huge wealth of sequence information that can find much use in the discovery of novel miRNAs and their target genes. In this review, we present an overview of the developments in the strategies and methods used to identify and study miRNAs, their target genes and the mechanisms by which these miRNAs interact with their target genes since the discovery of the first miRNA. The approaches discussed include both reverse and forward genetics. We observed that despite the availability of advanced methods, certain limitations ranging from the cost of materials, equipment and personnel to the availability of genome sequences for many plant species present a number of challenges for the development and utilization of modern scientific methods for the elucidation and development of miRNAs in many important plant species.
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Affiliation(s)
- Xin Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, PR China
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42
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Benkovics AH, Timmermans MCP. Developmental patterning by gradients of mobile small RNAs. Curr Opin Genet Dev 2014; 27:83-91. [PMID: 24929831 DOI: 10.1016/j.gde.2014.04.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/04/2014] [Accepted: 04/17/2014] [Indexed: 11/17/2022]
Abstract
Development of multicellular organisms depends on intercellular communication via mobile signals that provide positional information to coordinate cell fate decisions. In addition to peptide ligands, transcription factors, and hormones, plants use small RNAs as positional instructive signals. The unique patterning properties of small RNA gradients resulting from regulated mobility suggest conceptual similarities to the function of animal morphogens, and provide robustness and precision to the formation of cell fate boundaries. While common principles may underlie the formation, stability, and interpretation of both plant small RNA and animal morphogen gradients, the unique nature of small RNAs with respect to their biogenesis and target regulation imply important differences as well. In this review, we discuss the patterning properties of mobile small RNAs and highlight recent studies that have advanced our understanding of how small RNAs move, and how the graded accumulation that underlies their patterning activity could be created, maintained, and interpreted.
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Affiliation(s)
- Anna H Benkovics
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; Agricultural Biotechnology Center, Szent-Györgyi 4, H-2100 Gödöllő, Hungary
| | - Marja C P Timmermans
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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43
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Liu YX, Wang M, Wang XJ. Endogenous small RNA clusters in plants. GENOMICS PROTEOMICS & BIOINFORMATICS 2014; 12:64-71. [PMID: 24769055 PMCID: PMC4411336 DOI: 10.1016/j.gpb.2014.04.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 04/09/2014] [Accepted: 04/15/2014] [Indexed: 11/25/2022]
Abstract
In plants, small RNAs (sRNAs) usually refer to non-coding RNAs (ncRNAs) with lengths of 20–24 nucleotides. sRNAs are involved in the regulation of many essential processes related to plant development and environmental responses. sRNAs in plants are mainly grouped into microRNAs (miRNAs) and small interfering RNAs (siRNAs), and the latter can be further classified into trans-acting siRNAs (ta-siRNAs), repeat-associated siRNAs (ra-siRNAs), natural anti-sense siRNAs (nat-siRNAs), etc. Many sRNAs exhibit a clustered distribution pattern in the genome. Here, we summarize the features and functions of cluster-distributed sRNAs, aimed to not only provide a thorough picture of sRNA clusters (SRCs) in plants, but also shed light on the identification of new classes of functional sRNAs.
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Affiliation(s)
- Yong-Xin Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Meng Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiu-Jie Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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44
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Pandey R, Joshi G, Bhardwaj AR, Agarwal M, Katiyar-Agarwal S. A comprehensive genome-wide study on tissue-specific and abiotic stress-specific miRNAs in Triticum aestivum. PLoS One 2014; 9:e95800. [PMID: 24759739 PMCID: PMC3997425 DOI: 10.1371/journal.pone.0095800] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 03/29/2014] [Indexed: 11/18/2022] Open
Abstract
Productivity of wheat crop is largely dependent on its growth and development that, in turn, is mainly regulated by environmental conditions, including abiotic stress factors. miRNAs are key regulators of gene expression networks involved in diverse aspects of development and stress responses in plants. Using high-throughput sequencing of eight small RNA libraries prepared from diverse abiotic stresses and tissues, we identified 47 known miRNAs belonging to 20 families, 49 true novel and 1030 candidate novel miRNAs. Digital gene expression analysis revealed that 257 miRNAs exhibited tissue-specific expression and 74 were associated with abiotic stresses. Putative target genes were predicted for miRNAs identified in this study and their grouping into functional categories indicated that the putative targets were involved in diverse biological processes. RLM-RACE of predicted targets of three known miRNAs (miR156, miR160 and miR164) confirmed their mRNA cleavage, thus indicating their regulation at post-transcriptional level by the corresponding miRNAs. Mapping of the sequenced data onto the wheat progenitors and closely related monocots revealed a large number of evolutionary conserved miRNAs. Additional expression profiling of some of these miRNAs in other abiotic stresses underline their involvement in multiple stresses. Our findings provide valuable resource for an improved understanding of the role of miRNAs in stress tolerance as well as plant development.
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Affiliation(s)
- Ritu Pandey
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Gopal Joshi
- Department of Botany, University of Delhi, Delhi, India
| | | | - Manu Agarwal
- Department of Botany, University of Delhi, Delhi, India
- * E-mail: (SK-A); (MA)
| | - Surekha Katiyar-Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
- * E-mail: (SK-A); (MA)
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45
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Kim YJ, Maizel A, Chen X. Traffic into silence: endomembranes and post-transcriptional RNA silencing. EMBO J 2014; 33:968-80. [PMID: 24668229 PMCID: PMC4193931 DOI: 10.1002/embj.201387262] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
microRNAs (miRNAs) and small interfering RNAs (siRNAs) are small RNAs that repress gene expression at the post-transcriptional level in plants and animals. Small RNAs guide Argonaute-containing RNA-induced silencing complexes to target RNAs in a sequence-specific manner, resulting in mRNA deadenylation followed by exonucleolytic decay, mRNA endonucleolytic cleavage, or translational inhibition. Although our knowledge of small RNA biogenesis, turnover, and mechanisms of action has dramatically expanded in the past decade, the subcellular location of small RNA-mediated RNA silencing still needs to be defined. In contrast to the prevalent presumption that RNA silencing occurs in the cytosol, emerging evidence reveals connections between the endomembrane system and small RNA activities in plants and animals. Here, we summarize the work that uncovered this link between small RNAs and endomembrane compartments and present an overview of the involvement of the endomembrane system in various aspects of RNA silencing. We propose that the endomembrane system is an integral component of RNA silencing that has been long overlooked and predict that a marriage between cell biology and RNA biology holds the key to a full understanding of post-transcriptional gene regulation by small RNAs.
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Affiliation(s)
- Yun Ju Kim
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology University of California, Riverside, CA, USA
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46
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Haudry A, Platts AE, Vello E, Hoen DR, Leclercq M, Williamson RJ, Forczek E, Joly-Lopez Z, Steffen JG, Hazzouri KM, Dewar K, Stinchcombe JR, Schoen DJ, Wang X, Schmutz J, Town CD, Edger PP, Pires JC, Schumaker KS, Jarvis DE, Mandáková T, Lysak MA, van den Bergh E, Schranz ME, Harrison PM, Moses AM, Bureau TE, Wright SI, Blanchette M. An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet 2013; 45:891-8. [PMID: 23817568 DOI: 10.1038/ng.2684] [Citation(s) in RCA: 211] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Accepted: 06/04/2013] [Indexed: 12/17/2022]
Abstract
Despite the central importance of noncoding DNA to gene regulation and evolution, understanding of the extent of selection on plant noncoding DNA remains limited compared to that of other organisms. Here we report sequencing of genomes from three Brassicaceae species (Leavenworthia alabamica, Sisymbrium irio and Aethionema arabicum) and their joint analysis with six previously sequenced crucifer genomes. Conservation across orthologous bases suggests that at least 17% of the Arabidopsis thaliana genome is under selection, with nearly one-quarter of the sequence under selection lying outside of coding regions. Much of this sequence can be localized to approximately 90,000 conserved noncoding sequences (CNSs) that show evidence of transcriptional and post-transcriptional regulation. Population genomics analyses of two crucifer species, A. thaliana and Capsella grandiflora, confirm that most of the identified CNSs are evolving under medium to strong purifying selection. Overall, these CNSs highlight both similarities and several key differences between the regulatory DNA of plants and other species.
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Affiliation(s)
- Annabelle Haudry
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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47
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Ortiz-Morea FA, Vicentini R, Silva GF, Silva EM, Carrer H, Rodrigues AP, Nogueira FT. Global analysis of the sugarcane microtranscriptome reveals a unique composition of small RNAs associated with axillary bud outgrowth. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:2307-20. [PMID: 23564956 PMCID: PMC3654421 DOI: 10.1093/jxb/ert089] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Axillary bud outgrowth determines shoot architecture and is under the control of endogenous hormones and a fine-tuned gene-expression network, which probably includes small RNAs (sRNAs). Although it is well known that sRNAs act broadly in plant development, our understanding about their roles in vegetative bud outgrowth remains limited. Moreover, the expression profiles of microRNAs (miRNAs) and their targets within axillary buds are largely unknown. Here, we employed sRNA next-generation sequencing as well as computational and gene-expression analysis to identify and quantify sRNAs and their targets in vegetative axillary buds of the biofuel crop sugarcane (Saccharum spp.). Computational analysis allowed the identification of 26 conserved miRNA families and two putative novel miRNAs, as well as a number of trans-acting small interfering RNAs. sRNAs associated with transposable elements and protein-encoding genes were similarly represented in both inactive and developing bud libraries. Conversely, sequencing and quantitative reverse transcription-PCR results revealed that specific miRNAs were differentially expressed in developing buds, and some correlated negatively with the expression of their targets at specific stages of axillary bud development. For instance, the expression patterns of miR159 and its target GAMYB suggested that they may play roles in regulating abscisic acid-signalling pathways during sugarcane bud outgrowth. Our work reveals, for the first time, differences in the composition and expression profiles of diverse sRNAs and targets between inactive and developing vegetative buds that, together with the endogenous balance of specific hormones, may be important in regulating axillary bud outgrowth.
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Affiliation(s)
- Fausto A. Ortiz-Morea
- Centro de Biotecnologia Agricola (CEBTEC), Escola Superior de Agricultura ‘Luiz de Queiroz’, (ESALQ)/USP, Piracicaba, SP, Brazil
- Laboratory of Molecular Genetics of Plant Development, Department of Genetics, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr.,17 s/n. CEP 18618–970 Botucatu, SP, Brazil
- These authors contributed equally to this work
| | - Renato Vicentini
- Centro de Biologia Molecular e Engenharia Genetica (CBMEG), Universidade Estadual de Campinas, Campinas, SP, Brazil
- These authors contributed equally to this work
| | - Geraldo F.F. Silva
- Centro de Biotecnologia Agricola (CEBTEC), Escola Superior de Agricultura ‘Luiz de Queiroz’, (ESALQ)/USP, Piracicaba, SP, Brazil
- Laboratory of Molecular Genetics of Plant Development, Department of Genetics, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr.,17 s/n. CEP 18618–970 Botucatu, SP, Brazil
| | - Eder M. Silva
- Laboratory of Molecular Genetics of Plant Development, Department of Genetics, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr.,17 s/n. CEP 18618–970 Botucatu, SP, Brazil
| | - Helaine Carrer
- Centro de Biotecnologia Agricola (CEBTEC), Escola Superior de Agricultura ‘Luiz de Queiroz’, (ESALQ)/USP, Piracicaba, SP, Brazil
| | - Ana P. Rodrigues
- Laboratory of Molecular Genetics of Plant Development, Department of Genetics, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr.,17 s/n. CEP 18618–970 Botucatu, SP, Brazil
| | - Fabio T.S. Nogueira
- Centro de Biotecnologia Agricola (CEBTEC), Escola Superior de Agricultura ‘Luiz de Queiroz’, (ESALQ)/USP, Piracicaba, SP, Brazil
- Laboratory of Molecular Genetics of Plant Development, Department of Genetics, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr.,17 s/n. CEP 18618–970 Botucatu, SP, Brazil
- To whom correspondence should be addressed.
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48
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Plant microRNAs and development. J Genet Genomics 2013; 40:217-30. [PMID: 23706297 DOI: 10.1016/j.jgg.2013.04.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Revised: 03/15/2013] [Accepted: 04/02/2013] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) are a class of about 20-24 nt small non-coding RNAs that can regulate their target gene expression transcriptionally and posttranscriptionally. There are an increasing number of studies describing the identification of new components and regulatory mechanisms involved in the miRNA biogenesis and effector pathway as well as new functions of miRNAs in plant development. This review mainly focuses on the components involved in this pathway, and the developmental defects associated with the corresponding mutations. Some functions of important miRNAs in plant development, together with the modes of miRNA action, are also discussed in this review to describe the recent advance in this area.
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49
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Nazim Uddin M, Kim JY. Intercellular and systemic spread of RNA and RNAi in plants. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:279-93. [PMID: 23536229 DOI: 10.1002/wrna.1160] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Plants possess dynamic networks of intercellular communication that are crucial for plant development and physiology. In plants, intercellular communication involves a combination of ligand-receptor-based apoplasmic signaling, and plasmodesmata and phloem-mediated symplasmic signaling. The intercellular trafficking of macromolecules, including RNAs and proteins, has emerged as a novel mechanism of intercellular communication in plants. Various forms of regulatory RNAs move over distinct cellular boundaries through plasmodesmata and phloem. This plant-specific, non-cell-autonomous RNA trafficking network is also involved in development, nutrient homeostasis, gene silencing, pathogen defense, and many other physiological processes. However, the mechanism underlying macromolecular trafficking in plants remains poorly understood. Current progress made in RNA trafficking research and its biological relevance to plant development will be summarized. Diverse plant regulatory mechanisms of cell-to-cell and systemic long-distance transport of RNAs, including mRNAs, viral RNAs, and small RNAs, will also be discussed.
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Affiliation(s)
- Mohammad Nazim Uddin
- Division of Applied Life Science (BK21-WCU Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, South Korea
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50
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Bertolini E, Verelst W, Horner DS, Gianfranceschi L, Piccolo V, Inzé D, Pè ME, Mica E. Addressing the role of microRNAs in reprogramming leaf growth during drought stress in Brachypodium distachyon. MOLECULAR PLANT 2013; 6:423-43. [PMID: 23264558 PMCID: PMC3603004 DOI: 10.1093/mp/sss160] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 12/15/2012] [Indexed: 05/04/2023]
Abstract
Plant responses to drought are regulated by complex genetic and epigenetic networks leading to rapid reprogramming of plant growth. miRNAs have been widely indicated as key players in the regulation of growth and development. The role of miRNAs in drought response was investigated in young leaves of Brachypodium distachyon, a drought-tolerant monocot model species. Adopting an in vivo drought assay, shown to cause a dramatic reduction in leaf size, mostly due to reduced cell expansion, small RNA libraries were produced from proliferating and expanding leaf cells. Next-generation sequencing data were analyzed using an in-house bioinformatics pipeline allowing the identification of 66 annotated miRNA genes and 122 new high confidence predictions greatly expanding the number of known Brachypodium miRNAs. In addition, we identified four TAS3 loci and a large number of siRNA-producing loci that show characteristics suggesting that they may represent young miRNA genes. Most miRNAs showed a high expression level, consistent with their involvement in early leaf development and cell identity. Proliferating and expanding leaf cells respond differently to drought treatment and differential expression analyses suggest novel evidence for an miRNA regulatory network controlling cell division in both normal and stressed conditions and demonstrate that drought triggers a genetic reprogramming of leaf growth in which miRNAs are deeply involved.
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Affiliation(s)
- Edoardo Bertolini
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Piazza Martiri della Libertà 33, 56127 Pisa, Italy
| | - Wim Verelst
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium
| | - David Stephen Horner
- Department of BioSciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Luca Gianfranceschi
- Department of BioSciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Viviana Piccolo
- Department of BioSciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium
| | - Mario Enrico Pè
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Piazza Martiri della Libertà 33, 56127 Pisa, Italy
| | - Erica Mica
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Piazza Martiri della Libertà 33, 56127 Pisa, Italy
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