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Maple R, Zhu P, Hepworth J, Wang JW, Dean C. Flowering time: From physiology, through genetics to mechanism. PLANT PHYSIOLOGY 2024; 195:190-212. [PMID: 38417841 PMCID: PMC11060688 DOI: 10.1093/plphys/kiae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/12/2024] [Accepted: 02/12/2024] [Indexed: 03/01/2024]
Abstract
Plant species have evolved different requirements for environmental/endogenous cues to induce flowering. Originally, these varying requirements were thought to reflect the action of different molecular mechanisms. Thinking changed when genetic and molecular analysis in Arabidopsis thaliana revealed that a network of environmental and endogenous signaling input pathways converge to regulate a common set of "floral pathway integrators." Variation in the predominance of the different input pathways within a network can generate the diversity of requirements observed in different species. Many genes identified by flowering time mutants were found to encode general developmental and gene regulators, with their targets having a specific flowering function. Studies of natural variation in flowering were more successful at identifying genes acting as nodes in the network central to adaptation and domestication. Attention has now turned to mechanistic dissection of flowering time gene function and how that has changed during adaptation. This will inform breeding strategies for climate-proof crops and help define which genes act as critical flowering nodes in many other species.
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Affiliation(s)
- Robert Maple
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Pan Zhu
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jo Hepworth
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
- New Cornerstone Science Laboratory, Shanghai 200032, China
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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2
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Schnabel EL, Chavan SA, Gao Y, Poehlman WL, Feltus FA, Frugoli JA. A Medicago truncatula Autoregulation of Nodulation Mutant Transcriptome Analysis Reveals Disruption of the SUNN Pathway Causes Constitutive Expression Changes in Some Genes, but Overall Response to Rhizobia Resembles Wild-Type, Including Induction of TML1 and TML2. Curr Issues Mol Biol 2023; 45:4612-4631. [PMID: 37367042 DOI: 10.3390/cimb45060293] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
Nodule number regulation in legumes is controlled by a feedback loop that integrates nutrient and rhizobia symbiont status signals to regulate nodule development. Signals from the roots are perceived by shoot receptors, including a CLV1-like receptor-like kinase known as SUNN in Medicago truncatula. In the absence of functional SUNN, the autoregulation feedback loop is disrupted, resulting in hypernodulation. To elucidate early autoregulation mechanisms disrupted in SUNN mutants, we searched for genes with altered expression in the loss-of-function sunn-4 mutant and included the rdn1-2 autoregulation mutant for comparison. We identified constitutively altered expression of small groups of genes in sunn-4 roots and in sunn-4 shoots. All genes with verified roles in nodulation that were induced in wild-type roots during the establishment of nodules were also induced in sunn-4, including autoregulation genes TML2 and TML1. Only an isoflavone-7-O-methyltransferase gene was induced in response to rhizobia in wild-type roots but not induced in sunn-4. In shoot tissues of wild-type, eight rhizobia-responsive genes were identified, including a MYB family transcription factor gene that remained at a baseline level in sunn-4; three genes were induced by rhizobia in shoots of sunn-4 but not wild-type. We cataloged the temporal induction profiles of many small secreted peptide (MtSSP) genes in nodulating root tissues, encompassing members of twenty-four peptide families, including the CLE and IRON MAN families. The discovery that expression of TML2 in roots, a key factor in inhibiting nodulation in response to autoregulation signals, is also triggered in sunn-4 in the section of roots analyzed, suggests that the mechanism of TML regulation of nodulation in M. truncatula may be more complex than published models.
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Affiliation(s)
- Elise L Schnabel
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | | | - Yueyao Gao
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | | | - Frank Alex Feltus
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
- Biomedical Data Science and Informatics Program, Clemson University, Clemson, SC 29634, USA
- Clemson Center for Human Genetics, Clemson University, Greenwood, SC 29636, USA
| | - Julia A Frugoli
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
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3
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Valmas MI, Sexauer M, Markmann K, Tsikou D. Plants Recruit Peptides and Micro RNAs to Regulate Nutrient Acquisition from Soil and Symbiosis. PLANTS (BASEL, SWITZERLAND) 2023; 12:187. [PMID: 36616316 PMCID: PMC9824779 DOI: 10.3390/plants12010187] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 12/24/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
Plants engage in symbiotic relationships with soil microorganisms to overcome nutrient limitations in their environment. Among the best studied endosymbiotic interactions in plants are those with arbuscular mycorrhizal (AM) fungi and N-fixing bacteria called rhizobia. The mechanisms regulating plant nutrient homeostasis and acquisition involve small mobile molecules such as peptides and micro RNAs (miRNAs). A large number of CLE (CLAVATA3/EMBRYO SURROUNDING REGION-RELATED) and CEP (C-TERMINALLY ENCODED PEPTIDE) peptide hormones as well as certain miRNAs have been reported to differentially respond to the availability of essential nutrients such as nitrogen (N) and phosphorus (P). Interestingly, a partially overlapping pool of these molecules is involved in plant responses to root colonization by rhizobia and AM fungi, as well as mineral nutrition. The crosstalk between root endosymbiosis and nutrient availability has been subject of intense investigations, and new insights in locally or systemically mobile molecules in nutrient- as well as symbiosis-related signaling continue to arise. Focusing on the key roles of peptides and miRNAs, we review the mechanisms that shape plant responses to nutrient limitation and regulate the establishment of symbiotic associations with beneficial soil microorganisms.
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Affiliation(s)
- Marios I. Valmas
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Moritz Sexauer
- Julius-von-Sachs-Institute for Biosciences, Würzburg University, Julius-von-Sachs-Platz 3, 97082 Würzburg, Germany
| | - Katharina Markmann
- Julius-von-Sachs-Institute for Biosciences, Würzburg University, Julius-von-Sachs-Platz 3, 97082 Würzburg, Germany
| | - Daniela Tsikou
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
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4
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Nasrollahi V, Yuan ZC, Lu QSM, McDowell T, Kohalmi SE, Hannoufa A. Deciphering the role of SPL12 and AGL6 from a genetic module that functions in nodulation and root regeneration in Medicago sativa. PLANT MOLECULAR BIOLOGY 2022; 110:511-529. [PMID: 35976552 PMCID: PMC9684250 DOI: 10.1007/s11103-022-01303-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/17/2022] [Indexed: 05/11/2023]
Abstract
Our results show that SPL12 plays a crucial role in regulating nodule development in Medicago sativa L. (alfalfa), and that AGL6 is targeted and downregulated by SPL12. Root architecture in plants is critical because of its role in controlling nutrient cycling, water use efficiency and response to biotic and abiotic stress factors. The small RNA, microRNA156 (miR156), is highly conserved in plants, where it functions by silencing a group of SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors. We previously showed that transgenic Medicago sativa (alfalfa) plants overexpressing miR156 display increased nodulation, improved nitrogen fixation and enhanced root regenerative capacity during vegetative propagation. In alfalfa, transcripts of eleven SPLs, including SPL12, are targeted for cleavage by miR156. In this study, we characterized the role of SPL12 in root architecture and nodulation by investigating the transcriptomic and phenotypic changes associated with altered transcript levels of SPL12, and by determining SPL12 regulatory targets using SPL12-silencing and -overexpressing alfalfa plants. Phenotypic analyses showed that silencing of SPL12 in alfalfa caused an increase in root regeneration, nodulation, and nitrogen fixation. In addition, AGL6 which encodes AGAMOUS-like MADS box transcription factor, was identified as being directly targeted for silencing by SPL12, based on Next Generation Sequencing-mediated transcriptome analysis and chromatin immunoprecipitation assays. Taken together, our results suggest that SPL12 and AGL6 form a genetic module that regulates root development and nodulation in alfalfa.
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Affiliation(s)
- Vida Nasrollahi
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON, N6A 3K7, Canada
| | - Ze-Chun Yuan
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Qing Shi Mimmie Lu
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Tim McDowell
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Susanne E Kohalmi
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON, N6A 3K7, Canada
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada.
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON, N6A 3K7, Canada.
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5
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Sun Y, Fu M, Wang L, Bai Y, Fang X, Wang Q, He Y, Zeng H. OsSPLs Regulate Male Fertility in Response to Different Temperatures by Flavonoid Biosynthesis and Tapetum PCD in PTGMS Rice. Int J Mol Sci 2022; 23:ijms23073744. [PMID: 35409103 PMCID: PMC8998824 DOI: 10.3390/ijms23073744] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/21/2022] [Accepted: 03/28/2022] [Indexed: 01/19/2023] Open
Abstract
Photoperiod and thermo-sensitive genic male sterile (PTGMS) rice is an important resource for two line hybrid rice production. The SQUAMOSA–promoter binding, such as the (SPL) gene family, encode the plant specific transcription factors that regulate development and defense responses in plants. However, the reports about SPLs participating in male fertility regulation are limited. Here, we identified 19 OsSPL family members and investigated their involvement in the fertility regulation of the PTGMS rice lines, PA2364S and PA2864S, with different fertility transition temperatures. The results demonstrated that OsSPL2, OsSPL4, OsSPL16 and OsSPL17 affect male fertility in response to temperature changes through the MiR156-SPL module. WGCNA (weighted gene co-expression network analysis) revealed that CHI and APX1 were co-expressed with OsSPL17. Targeted metabolite and flavonoid biosynthetic gene expression analysis revealed that OsSPL17 regulates the expression of flavonoid biosynthesis genes CHI, and the up regulation of flavanones (eriodictvol and naringenin) and flavones (apigenin and luteolin) content contributed to plant fertility. Meanwhile, OsSPL17 negatively regulates APX1 to affect APX (ascorbate peroxidase) activity, thereby regulating ROS (reactive oxygen species) content in the tapetum, controlling the PCD (programmed cell death) process and regulating male fertility in rice. Overall, this report highlights the potential role of OsSPL for the regulation of male fertility in rice and provides a new insight for the further understanding of fertility molecular mechanisms in PTGMS rice.
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Affiliation(s)
| | | | | | | | | | | | - Ying He
- Correspondence: (Y.H.); (H.Z.)
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6
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Yun J, Sun Z, Jiang Q, Wang Y, Wang C, Luo Y, Zhang F, Li X. The miR156b-GmSPL9d module modulates nodulation by targeting multiple core nodulation genes in soybean. THE NEW PHYTOLOGIST 2022; 233:1881-1899. [PMID: 34862970 PMCID: PMC9303946 DOI: 10.1111/nph.17899] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 11/27/2021] [Indexed: 05/25/2023]
Abstract
Symbiotic nodulation is initiated in the roots of legumes in response to low nitrogen and rhizobial signal molecules and is dynamically regulated by a complex regulatory network that coordinates rhizobial infection and nodule organogenesis. It has been shown that the miR156-SPL module mediates nodulation in legumes; however, conclusive evidence of how this module exerts its function during nodulation remains elusive. Here, we report that the miR156b-GmSPL9d module regulates symbiotic nodulation by targeting multiple key regulatory genes in the nodulation signalling pathway of soybean. miR156 family members are differentially expressed during nodulation, and miR156b negatively regulates nodulation by mainly targeting soybean SQUAMOSA promoter-binding protein-like 9d (GmSPL9d), a positive regulator of soybean nodulation. GmSPL9d directly binds to the miR172c promoter and activates its expression, suggesting a conserved role of GmSPL9d. Furthermore, GmSPL9d was coexpressed with the soybean nodulation marker genes nodule inception a (GmNINa) and GmENOD40-1 during nodule formation and development. Intriguingly, GmSPL9d can bind to the promoters of GmNINa and GmENOD40-1 and regulate their expression. Our data demonstrate that the miR156b-GmSPL9d module acts as an upstream master regulator of soybean nodulation, which coordinates multiple marker genes involved in soybean nodulation.
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Affiliation(s)
- Jinxia Yun
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Zhengxi Sun
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Collaborative Innovation of Modern Crops and Food Crops in JiangsuCollege of AgricultureYangzhou UniversityYangzhou225009China
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetic and Developmental BiologyChinese Academy of SciencesBeijing100101China
| | - Qiong Jiang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetic and Developmental BiologyChinese Academy of SciencesBeijing100101China
| | - Youning Wang
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Can Wang
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Yuanqing Luo
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Fengrong Zhang
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Xia Li
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
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7
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Lebedeva M, Azarakhsh M, Sadikova D, Lutova L. At the Root of Nodule Organogenesis: Conserved Regulatory Pathways Recruited by Rhizobia. PLANTS (BASEL, SWITZERLAND) 2021; 10:2654. [PMID: 34961125 PMCID: PMC8705049 DOI: 10.3390/plants10122654] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 05/13/2023]
Abstract
The interaction between legume plants and soil bacteria rhizobia results in the formation of new organs on the plant roots, symbiotic nodules, where rhizobia fix atmospheric nitrogen. Symbiotic nodules represent a perfect model to trace how the pre-existing regulatory pathways have been recruited and modified to control the development of evolutionary "new" organs. In particular, genes involved in the early stages of lateral root development have been co-opted to regulate nodule development. Other regulatory pathways, including the players of the KNOX-cytokinin module, the homologues of the miR172-AP2 module, and the players of the systemic response to nutrient availability, have also been recruited to a unique regulatory program effectively governing symbiotic nodule development. The role of the NIN transcription factor in the recruitment of such regulatory modules to nodulation is discussed in more details.
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Affiliation(s)
- Maria Lebedeva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, 199034 Saint Petersburg, Russia; (D.S.); (L.L.)
- Center for Genetic Technologies, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 Saint Petersburg, Russia
| | - Mahboobeh Azarakhsh
- Cell and Molecular Biology Department, Kosar University of Bojnord, 9415615458 Bojnord, Iran;
| | - Darina Sadikova
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, 199034 Saint Petersburg, Russia; (D.S.); (L.L.)
- Center for Genetic Technologies, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 Saint Petersburg, Russia
| | - Lyudmila Lutova
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, 199034 Saint Petersburg, Russia; (D.S.); (L.L.)
- Center for Genetic Technologies, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 Saint Petersburg, Russia
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8
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Zhou Q, Shi J, Li Z, Zhang S, Zhang S, Zhang J, Bao M, Liu G. miR156/157 Targets SPLs to Regulate Flowering Transition, Plant Architecture and Flower Organ Size in Petunia. PLANT & CELL PHYSIOLOGY 2021; 62:839-857. [PMID: 33768247 DOI: 10.1093/pcp/pcab041] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/19/2021] [Indexed: 05/15/2023]
Abstract
miR156/157 plays multiple pivotal roles during plant growth and development. In this study, we identified 11 miR156- and 5 miR157-encoding loci from the genome of Petunia axillaris and Petunia inflata, designated as PaMIR0156/157s and PiMIR0156/157s, respectively. Real-time quantitative reverse transcription PCR (qRT-PCR) analysis indicated that PhmiR156/157 was expressed predominantly in cotyledons, germinating seeds, flower buds, young fruits and seedlings. PhmiR156/157 levels declined in shoot apical buds and leaves of petunia before flowering as the plant ages; moreover, the temporal expression patterns of most miR156/157-targeted PhSPLs were complementary to that of PhmiR156/157. Ectopic expression of PhMIR0157a in Arabidopsis and petunia resulted in delayed flowering, dwarf plant stature, increased branches and reduced organ size. However, PhMIR0156f-overexpressing Arabidopsis and petunia plants showed only delayed flowering. In addition, downregulation of PhmiR156/157 level by overexpressing STTM156/157 led to taller plants with less branches, longer internodes and precocious flowering. qRT-PCR analysis indicated that PhmiR156/157 modulates these traits mainly by downregulating their PhSPL targets and subsequently decreasing the expression of flowering regulatory genes. Our results demonstrate that the PhmiR156/157-PhSPL module has conserved but also divergent functions in growth and development, which will help us decipher the genetic basis for the improvement of flower transition, plant architecture and organ development in petunia.
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Affiliation(s)
- Qin Zhou
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiewei Shi
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhineng Li
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education; College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Sisi Zhang
- Wuhan Institute of Landscape Architecture, Peace Avenue No. 1240, Wuhan 430081, China
| | - Shuting Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiaqi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Guofeng Liu
- Department of Botany, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, China
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9
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Chand Jha U, Nayyar H, Mantri N, Siddique KHM. Non-Coding RNAs in Legumes: Their Emerging Roles in Regulating Biotic/Abiotic Stress Responses and Plant Growth and Development. Cells 2021; 10:cells10071674. [PMID: 34359842 PMCID: PMC8306516 DOI: 10.3390/cells10071674] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 12/28/2022] Open
Abstract
Noncoding RNAs, including microRNAs (miRNAs), small interference RNAs (siRNAs), circular RNA (circRNA), and long noncoding RNAs (lncRNAs), control gene expression at the transcription, post-transcription, and translation levels. Apart from protein-coding genes, accumulating evidence supports ncRNAs playing a critical role in shaping plant growth and development and biotic and abiotic stress responses in various species, including legume crops. Noncoding RNAs (ncRNAs) interact with DNA, RNA, and proteins, modulating their target genes. However, the regulatory mechanisms controlling these cellular processes are not well understood. Here, we discuss the features of various ncRNAs, including their emerging role in contributing to biotic/abiotic stress response and plant growth and development, in addition to the molecular mechanisms involved, focusing on legume crops. Unravelling the underlying molecular mechanisms and functional implications of ncRNAs will enhance our understanding of the coordinated regulation of plant defences against various biotic and abiotic stresses and for key growth and development processes to better design various legume crops for global food security.
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MESH Headings
- Fabaceae/genetics
- Fabaceae/growth & development
- Fabaceae/metabolism
- Food Security
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Plant
- Humans
- MicroRNAs/classification
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Organ Specificity
- Protein Biosynthesis
- RNA, Circular/classification
- RNA, Circular/genetics
- RNA, Circular/metabolism
- RNA, Long Noncoding/classification
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Plant/classification
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Small Interfering/classification
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Species Specificity
- Stress, Physiological/genetics
- Transcription, Genetic
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Affiliation(s)
- Uday Chand Jha
- ICAR—Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
- Correspondence: (U.C.J.); (K.H.M.S.)
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh 160014, India;
| | - Nitin Mantri
- School of Science, RMIT University, Melbourne 3083, Australia;
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth 6001, Australia
- Correspondence: (U.C.J.); (K.H.M.S.)
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10
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Tiwari M, Pandey V, Singh B, Bhatia S. Dynamics of miRNA mediated regulation of legume symbiosis. PLANT, CELL & ENVIRONMENT 2021; 44:1279-1291. [PMID: 33347631 DOI: 10.1111/pce.13983] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 12/06/2020] [Accepted: 12/08/2020] [Indexed: 05/19/2023]
Abstract
Symbiotic nitrogen fixation in legume nodules is important in soils with low nitrogen availability. The initiation and sustainability of symbiosis require cellular reprogramming that involves the miRNA-mediated inhibition or activation of specific nodulation genes. The high-throughput sequencing of small RNA libraries has identified miRNAs and their targets, which are the major players in the post-transcriptional gene regulation (PTGS) of the different stages of legume-rhizobia symbiosis ranging from bacterial colonization and organogenesis to symbiotic nitrogen fixation. Here, we present an overview of information obtained from the miRNA libraries from nodulating tissues that have been sequenced to date. The functional analysis of miRNAs has revealed roles in phytohormone homeostasis and spatio-temporal regulation, as well as the mobility of miRNAs and their functions in shoot to root signalling that affects diverse functions, including bacterial entry, meristem division and differentiation, nitrogen fixation and senescence. Furthermore, small RNA fragments of rhizobial origin repress complementary plant mRNAs. We also consider the roles of miRNAs in determinate or indeterminate nodules. Taken together, this overview confirms that miRNAs are master regulators of the legume-rhizobia symbiosis.
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Affiliation(s)
- Manish Tiwari
- Legume Genomics Laboratory, National Institute of Plant Genome Research, New Delhi, India
| | - Vimal Pandey
- Legume Genomics Laboratory, National Institute of Plant Genome Research, New Delhi, India
| | - Baljinder Singh
- Legume Genomics Laboratory, National Institute of Plant Genome Research, New Delhi, India
| | - Sabhyata Bhatia
- Legume Genomics Laboratory, National Institute of Plant Genome Research, New Delhi, India
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11
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Mallet J, Laufs P, Leduc N, Le Gourrierec J. Photocontrol of Axillary Bud Outgrowth by MicroRNAs: Current State-of-the-Art and Novel Perspectives Gained From the Rosebush Model. FRONTIERS IN PLANT SCIENCE 2021; 12:770363. [PMID: 35173747 PMCID: PMC8841825 DOI: 10.3389/fpls.2021.770363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/13/2021] [Indexed: 05/05/2023]
Abstract
Shoot branching is highly dependent on environmental factors. While many species show some light dependence for branching, the rosebush shows a strict requirement for light to allow branching, making this species an excellent model to further understand how light impinges on branching. Here, in the first part, we provide a review of the current understanding of how light may modulate the complex regulatory network of endogenous factors like hormones (SL, IAA, CK, GA, and ABA), nutrients (sugar and nitrogen), and ROS to control branching. We review the regulatory contribution of microRNAs (miRNAs) to branching in different species, highlighting the action of such evolutionarily conserved factors. We underline some possible pathways by which light may modulate miRNA-dependent regulation of branching. In the second part, we exploit the strict light dependence of rosebush for branching to identify putative miRNAs that could contribute to the photocontrol of branching. For this, we first performed a profiling of the miRNAs expressed in early light-induced rosebush buds and next tested whether they were predicted to target recognized regulators of branching. Thus, we identified seven miRNAs (miR156, miR159, miR164, miR166, miR399, miR477, and miR8175) that could target nine genes (CKX1/6, EXPA3, MAX4, CYCD3;1, SUSY, 6PFK, APX1, and RBOHB1). Because these genes are affecting branching through different hormonal or metabolic pathways and because expression of some of these genes is photoregulated, our bioinformatic analysis suggests that miRNAs may trigger a rearrangement of the regulatory network to modulate branching in response to light environment.
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Affiliation(s)
- Julie Mallet
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Patrick Laufs
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Nathalie Leduc
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - José Le Gourrierec
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
- *Correspondence: José Le Gourrierec,
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12
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Wu Z, Huang W, Qin E, Liu S, Liu H, Grennan AK, Liu H, Qin R. Comprehensive Identification and Expression Profiling of Circular RNAs During Nodule Development in Phaseolus vulgaris. FRONTIERS IN PLANT SCIENCE 2020; 11:587185. [PMID: 33193538 PMCID: PMC7655914 DOI: 10.3389/fpls.2020.587185] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 10/05/2020] [Indexed: 05/03/2023]
Abstract
Symbiotic nitrogen fixation by legume nodules provides an abundant nitrogen source for plants, and understanding this process is key for developing green agriculture. Circular RNA (circRNA), a type of endogenous RNA produced by reverse splicing of mRNA precursors, plays important regulatory roles in plants at the transcriptional and post-transcriptional levels. However, the relationship between circRNAs and legume-rhizobium is unknown. Here, we performed comprehensive identification and expression profiling of circRNAs during nodulation in common bean (Phaseolus vulgaris) compared to uninoculated roots of corresponding ages by constructing circRNA-seq and mRNA-seq libraries. We identified 8,842 high-confident circRNAs, 3,448 of which were specifically produced during symbiosis, with the highest number at the nitrogen-fixing stage. Significantly, more circRNAs were derived from exons than from intergenic regions or introns in all samples. The lengths and GC contents of the circRNAs were similar in roots and nodules. However, circRNAs showed specific spatiotemporal expression patterns during nodule and root development. GO and other functional annotation of parental genes of differentially expressed circRNAs indicated their potential involvement in different biological processes. The expression of major circRNAs during symbiosis is independent of parental genes' expression to a certain degree, while expression of the remaining minor circRNAs showed positive correlation to parental genes. Functional annotation of the targeted mRNAs in the circRNA-miRNA-mRNA network showed that circRNAs may be involved in transmembrane transport and positive regulation of kinase activity during nodulation and nitrogen fixation as miRNA sponges. Our comprehensive analysis of the expression profile of circRNAs and their potential functions suggests that circRNAs may function as new post-transcriptional regulators in legume-rhizobium symbiosis.
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Affiliation(s)
- Zhihua Wu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
- Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Wen Huang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
- Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Erdai Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
- Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Shuo Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
- Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Huan Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
- Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Aleel K. Grennan
- Biology Department, Worcester State University, Worcester, MA, United States
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
- Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
- Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
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13
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Waheed S, Zeng L. The Critical Role of miRNAs in Regulation of Flowering Time and Flower Development. Genes (Basel) 2020; 11:genes11030319. [PMID: 32192095 PMCID: PMC7140873 DOI: 10.3390/genes11030319] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 03/02/2020] [Accepted: 03/13/2020] [Indexed: 12/14/2022] Open
Abstract
Flowering is an important biological process for plants that ensures reproductive success. The onset of flowering needs to be coordinated with an appropriate time of year, which requires tight control of gene expression acting in concert to form a regulatory network. MicroRNAs (miRNAs) are non-coding RNAs known as master modulators of gene expression at the post-transcriptional level. Many different miRNA families are involved in flowering-related processes such as the induction of floral competence, floral patterning, and the development of floral organs. This review highlights the diverse roles of miRNAs in controlling the flowering process and flower development, in combination with potential biotechnological applications for miRNAs implicated in flower regulation.
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Affiliation(s)
- Saquib Waheed
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 35002, China;
- Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lihui Zeng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 35002, China;
- Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: or
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14
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Zhang L, Ding H, Jiang H, Wang H, Chen K, Duan J, Feng S, Wu G. Regulation of cadmium tolerance and accumulation by miR156 in Arabidopsis. CHEMOSPHERE 2020; 242:125168. [PMID: 31678850 DOI: 10.1016/j.chemosphere.2019.125168] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 10/18/2019] [Accepted: 10/20/2019] [Indexed: 05/28/2023]
Abstract
Plants have evolved effective strategies to cope with heavy metals Cd toxicity, but the regulatory mechanism underlying Cd tolerance and accumulation are still poorly understood. miR156 has been shown to be the master regulator of development and stress response in plants. However, whether miR156 is also involved in plant Cd stress response remains unknown. Here, we show that plants overexpressing miR156 (miR156OE) accumulated significantly less Cd in the shoot, and conferred enhanced tolerance to Cd stress. Plants with a knocked-down level of miR156 (MIM156) were sensitive to Cd stress, and accumulated significantly higher Cd. Under Cd stress, miR156OE had significantly longer primary root length, higher biomass and chlorophyll content, increased activities of antioxidative enzymes and lower levels of endogenous reactive oxygen species (ROS), while MIM156 had the opposite phenotype. To investigate the underlying mechanism of miR156-mediated Cd stress response in Arabidopsis, we profiled the expression of several Cd transporter genes. The expression of Cd uptake transporter of AtZIP1、AtZIP2 and vacuole segregated transporter AtABCC1 was significantly elevated in miR156OE, whereas it was significantly reduced in MIM156. MIM156 also led to an elevated level of AtHMA4 responsible for transporting Cd from the root to the shoot. Our results indicate that miR156 acts as a positive regulator of plant tolerance to Cd stress by modulating ROS levels and Cd uptake/transport genes expression. Therefore, our study adds a new layer of regulatory mechanism for Cd transport and tolerance in plants, and provides a perspective to regulate Cd transport artificially by modulating plant vegetative growth and development using miR156.
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Affiliation(s)
- Lu Zhang
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Zhejiang Agriculture and Forestry University, Hangzhou, China.
| | - Han Ding
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Zhejiang Agriculture and Forestry University, Hangzhou, China.
| | - Hailing Jiang
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Zhejiang Agriculture and Forestry University, Hangzhou, China.
| | - Huasen Wang
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Zhejiang Agriculture and Forestry University, Hangzhou, China.
| | - Kexin Chen
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Zhejiang Agriculture and Forestry University, Hangzhou, China.
| | - Jinju Duan
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Zhejiang Agriculture and Forestry University, Hangzhou, China; Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China.
| | - Shengjun Feng
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Zhejiang Agriculture and Forestry University, Hangzhou, China.
| | - Gang Wu
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Zhejiang Agriculture and Forestry University, Hangzhou, China.
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15
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Kouhi F, Sorkheh K, Ercisli S. MicroRNA expression patterns unveil differential expression of conserved miRNAs and target genes against abiotic stress in safflower. PLoS One 2020; 15:e0228850. [PMID: 32069300 PMCID: PMC7028267 DOI: 10.1371/journal.pone.0228850] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 01/25/2020] [Indexed: 01/08/2023] Open
Abstract
Environmental stresses influence the growth and development of plants by influencing patterns of gene expression. Different regulators control gene expression, including transcription factors (TFs) and microRNAs. MicroRNAs (miRNAs: ~21 nucleotides long) are encoded by miRNA genes transcribed by RNA polymerase II (RNP-II) and play key roles in plant development and physiology. There is little knowledge currently available on miRNAs and their function in response to environmental stresses in safflower. To obtain more information on safflower miRNAs, we initially used a comparative genomics approach and succeeded in identifying 126 miRNAs belonging to 29 conserved families, along with their target genes. In this study, we investigated the expression profiles of seven conserved miRNAs related to drought, salinity, heat, and Cd stress in the leaf and root organs using qRT-PCR, for the first time. Gene Ontology (GO) analysis found that target genes of miRNAs are often TFs such as AP2/ERF and HD-ZIP as well as NAC domain-containing proteins. Expression analyses confirmed that miRNAs can play a vital role in keeping safflower stress-tolerant. Differential expression of miR156, miR162, miR164, miR166, miR172, miR398, and miR408 regulate the expression of their respective target genes. These genes activate several pathways leading to physiological and biochemical responses to abiotic stresses. Some conserved miRNAs were regulated by abiotic stresses. Our finding provides valuable information to understand miRNAs in relation to different abiotic stresses in safflower.
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Affiliation(s)
- Farshid Kouhi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Karim Sorkheh
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
- * E-mail: (SE); , (KS)
| | - Sezai Ercisli
- Department of Horticulture, Agricultural Faculty, Ataturk University, Erzurum, Turkey
- * E-mail: (SE); , (KS)
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16
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Wang C, Wang Q, Zhu X, Cui M, Jia H, Zhang W, Tang W, Leng X, Shen W. Characterization on the conservation and diversification of miRNA156 gene family from lower to higher plant species based on phylogenetic analysis at the whole genomic level. Funct Integr Genomics 2019; 19:933-952. [PMID: 31172301 DOI: 10.1007/s10142-019-00679-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 04/06/2019] [Accepted: 04/15/2019] [Indexed: 01/18/2023]
Abstract
miRNA156 family members (miR156s) participate in regulating the transition of plant vegetative and reproductive growth, flower development, and formation of berry skin color by negatively modulating their target gene SPLs. However, the evolution and functional diversification of miR156s in plants remain elusive. Phylogenetic analysis on 310 miR156s from 51 plant species on miRBase 21.0 showed that only miR156a could be conserved in the 51 plant species, but their sequences exhibited variation; another set of miR156s, such as miR156m/n/o/p/q/r/s/t/u/v/w/x/y/z, was identified only in certain special plant species (Glycine max and Malus); also, all base variations in the sequences of 310 miR156s occurred within one miR156 seed sequence, "TGACAGAAGAGAGTGAGCAC," and the changed base sites were mainly located at the 11th and 14th bases from the 5' end of the miR156 seed sequence, in which some base variations of miR156s resulted in a difference in miR156 targeting modes; by contrast, miR156 precursor sequences are highly divergent across diverse species. Similarly, cis-regulatory motifs on the promoter sequence of MIR156s in various plants also exhibited significant discrepancy. The intragenic MIR156 genes overlapped their target SBP genes, thereby suggesting that some microRNAs (miRNAs) originate from duplication of target genes. These traits might be the reasons of the conservation and diversification of miR156 gene family. This study identified the conserved seed sequence "TGACAGAAGAGAGTGAGCAC," and the sequence variation characterization, of miR156 family evolution, also investigated the varied traits of their promoters, precursors, and mature sequences in sequence evolutions and found some miRNAs might originate from duplication of target genes. Our findings will contribute to our understanding of the functional diversification of miRNAs and the interactions of miRNA/target pairs based on the evolutionary history of miRNA genes.
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Affiliation(s)
- Chen Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Qinglian Wang
- Institute of Horticulture, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Xudong Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Menjie Cui
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haifeng Jia
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenying Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wei Tang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiangpeng Leng
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenbiao Shen
- College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China
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17
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Yin H, Hong G, Li L, Zhang X, Kong Y, Sun Z, Li J, Chen J, He Y. miR156/SPL9 Regulates Reactive Oxygen Species Accumulation and Immune Response in Arabidopsis thaliana. PHYTOPATHOLOGY 2019; 109:632-642. [PMID: 30526361 DOI: 10.1094/phyto-08-18-0306-r] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The functions of microRNA156 (miR156) and its targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factor genes in plant development have been widely investigated. However, the role of the miR156/SPLs regulatory network in plant immune systems remains obscure. Here, we found that the accumulation of reactive oxygen species (ROS) and the transcripts of basal salicylic acid (SA) signaling pathway genes were lower in Arabidopsis Pro35S:MIR156 seedlings (miR156 overexpression mutants) but higher in Pro35S:MIM156 (miR156 repression mutants) and ProSPL9:rSPL9 (SPL9 overexpression mutants) seedlings compared with wild-type Col-0 plants (WT). As a result, Pro35S:MIR156 mutants induced greater susceptibility to Pseudomonas syringae pv. tomato DC3000 following syringe infiltration than WT, while Pro35S:MIM156 and ProSPL9:rSPL9 mutants showed enhanced resistance. In addition, foliar H2O2 application resulted in activation of SA-mediated defense response and ablation of miR156-induced susceptibility to P. syringae pv. tomato DC3000 infection. Collectively, our results provide new insights into the function of the miR156/SPL network in Arabidopsis immune response by regulating ROS accumulation and activating the SA signaling pathway.
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Affiliation(s)
- Hongbiao Yin
- 1 College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China
- 2 State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China
| | - Gaojie Hong
- 2 State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China
| | - Linying Li
- 2 State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China
- 3 School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Xueying Zhang
- 2 State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China
- 4 Department of Tea Science, Zhejiang University, Hangzhou 310058, China; and
| | - Yaze Kong
- 2 State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China
- 5 College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China; and
| | - Zongtao Sun
- 2 State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China
- 6 Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Junmin Li
- 2 State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China
- 6 Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jianping Chen
- 1 College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China
- 2 State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China
- 6 Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Yuqing He
- 2 State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China
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18
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Micromanagement of Developmental and Stress-Induced Senescence: The Emerging Role of MicroRNAs. Genes (Basel) 2019; 10:genes10030210. [PMID: 30871088 PMCID: PMC6470504 DOI: 10.3390/genes10030210] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/22/2019] [Accepted: 03/06/2019] [Indexed: 01/13/2023] Open
Abstract
MicroRNAs are short (19⁻24-nucleotide-long), non-coding RNA molecules. They downregulate gene expression by triggering the cleavage or translational inhibition of complementary mRNAs. Senescence is a stage of development following growth completion and is dependent on the expression of specific genes. MicroRNAs control the gene expression responsible for plant competence to answer senescence signals. Therefore, they coordinate the juvenile-to-adult phase transition of the whole plant, the growth and senescence phase of each leaf, age-related cellular structure changes during vessel formation, and remobilization of resources occurring during senescence. MicroRNAs are also engaged in the ripening and postharvest senescence of agronomically important fruits. Moreover, the hormonal regulation of senescence requires microRNA contribution. Environmental cues, such as darkness or drought, induce senescence-like processes in which microRNAs also play regulatory roles. In this review, we discuss recent findings concerning the role of microRNAs in the senescence of various plant species.
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19
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Sun Z, Su C, Yun J, Jiang Q, Wang L, Wang Y, Cao D, Zhao F, Zhao Q, Zhang M, Zhou B, Zhang L, Kong F, Liu B, Tong Y, Li X. Genetic improvement of the shoot architecture and yield in soya bean plants via the manipulation of GmmiR156b. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:50-62. [PMID: 29729214 PMCID: PMC6330639 DOI: 10.1111/pbi.12946] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/10/2018] [Accepted: 04/28/2018] [Indexed: 05/20/2023]
Abstract
The optimization of plant architecture in order to breed high-yielding soya bean cultivars is a goal of researchers. Tall plants bearing many long branches are desired, but only modest success in reaching these goals has been achieved. MicroRNA156 (miR156)-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene modules play pivotal roles in controlling shoot architecture and other traits in crops like rice and wheat. However, the effects of miR156-SPL modules on soya bean architecture and yield, and the molecular mechanisms underlying these effects, remain largely unknown. In this study, we achieved substantial improvements in soya bean architecture and yield by overexpressing GmmiR156b. Transgenic plants produced significantly increased numbers of long branches, nodes and pods, and they exhibited an increased 100-seed weight, resulting in a 46%-63% increase in yield per plant. Intriguingly, GmmiR156b overexpression had no significant impact on plant height in a growth room or under field conditions; however, it increased stem thickness significantly. Our data indicate that GmmiR156b modulates these traits mainly via the direct cleavage of SPL transcripts. Moreover, we found that GmSPL9d is expressed in the shoot apical meristem and axillary meristems (AMs) of soya bean, and that GmSPL9d may regulate axillary bud formation and branching by physically interacting with the homeobox gene WUSCHEL (WUS), a central regulator of AM formation. Together, our results identify GmmiR156b as a promising target for the improvement of soya bean plant architecture and yields, and they reveal a new and conserved regulatory cascade involving miR156-SPL-WUS that will help researchers decipher the genetic basis of plant architecture.
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Affiliation(s)
- Zhengxi Sun
- State Key Laboratory of Agricultural MicrobiologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetic and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Chao Su
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetic and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Jinxia Yun
- State Key Laboratory of Agricultural MicrobiologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Qiong Jiang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetic and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Lixiang Wang
- State Key Laboratory of Agricultural MicrobiologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Youning Wang
- State Key Laboratory of Agricultural MicrobiologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Dong Cao
- The Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography and AgroecologyChinese Academy of SciencesHarbinChina
| | - Fang Zhao
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetic and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Qingsong Zhao
- Hebei Academy of Agriculture and Forestry SciencesShijiazhuangChina
| | - Mengchen Zhang
- Hebei Academy of Agriculture and Forestry SciencesShijiazhuangChina
| | - Bin Zhou
- Anhui Academy of Agricultural ScienceHefeiChina
| | - Lei Zhang
- Anhui Academy of Agricultural ScienceHefeiChina
| | - Fanjiang Kong
- The Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography and AgroecologyChinese Academy of SciencesHarbinChina
- School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Baohui Liu
- The Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography and AgroecologyChinese Academy of SciencesHarbinChina
- School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Yiping Tong
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetic and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Xia Li
- State Key Laboratory of Agricultural MicrobiologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
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20
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Proust H, Hartmann C, Crespi M, Lelandais-Brière C. Root Development in Medicago truncatula: Lessons from Genetics to Functional Genomics. Methods Mol Biol 2018; 1822:205-239. [PMID: 30043307 DOI: 10.1007/978-1-4939-8633-0_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This decade introduced "omics" approaches, such as genomics, transcriptomics, proteomics, and metabolomics in association with reverse and forward genetic approaches, developed earlier, to try to identify molecular pathways involved in the development or in the response to environmental conditions as well as in animals and plants. This review summarizes studies that utilized "omics" strategies to unravel the root development in the model legume Medicago truncatula and how external factors such as soil mineral status or the presence of bacteria and fungi affect root system architecture in this species. We also compare these "omics" data to the knowledges concerning the Arabidopsis thaliana root development, nowadays considered as the model of allorhiz root systems. However, unlike legumes, this species is unable to interact with soil nitrogen-fixing rhizobia and arbuscular-mycorrhizal (AM) fungi to develop novel root-derived symbiotic structures. Differences in root organization, development, and regulatory pathways between these two model species have been highlighted.
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Affiliation(s)
- Hélène Proust
- Institute of Plant Sciences Paris-Saclay, IPS2, Univ. Paris-Diderot, CNRS, INRA, Univ. Paris-Sud, Univ. Evry Val d'Essonne, Sorbonne Paris-Cité, University of Paris-Saclay, Orsay, France
| | - Caroline Hartmann
- Institute of Plant Sciences Paris-Saclay, IPS2, Univ. Paris-Diderot, CNRS, INRA, Univ. Paris-Sud, Univ. Evry Val d'Essonne, Sorbonne Paris-Cité, University of Paris-Saclay, Orsay, France
| | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay, IPS2, Univ. Paris-Diderot, CNRS, INRA, Univ. Paris-Sud, Univ. Evry Val d'Essonne, Sorbonne Paris-Cité, University of Paris-Saclay, Orsay, France
| | - Christine Lelandais-Brière
- Institute of Plant Sciences Paris-Saclay, IPS2, Univ. Paris-Diderot, CNRS, INRA, Univ. Paris-Sud, Univ. Evry Val d'Essonne, Sorbonne Paris-Cité, University of Paris-Saclay, Orsay, France.
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MsmiR156 affects global gene expression and promotes root regenerative capacity and nitrogen fixation activity in alfalfa. Transgenic Res 2017; 26:541-557. [DOI: 10.1007/s11248-017-0024-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 05/18/2017] [Indexed: 10/19/2022]
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22
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Noronha Fernandes-Brum C, Marinho Rezende P, Cherubino Ribeiro TH, Ricon de Oliveira R, Cunha de Sousa Cardoso T, Rodrigues do Amaral L, de Souza Gomes M, Chalfun-Junior A. A genome-wide analysis of the RNA-guided silencing pathway in coffee reveals insights into its regulatory mechanisms. PLoS One 2017; 12:e0176333. [PMID: 28448529 PMCID: PMC5407642 DOI: 10.1371/journal.pone.0176333] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 04/10/2017] [Indexed: 11/28/2022] Open
Abstract
microRNAs (miRNAs) are derived from self-complementary hairpin structures, while small-interfering RNAs (siRNAs) are derived from double-stranded RNA (dsRNA) or hairpin precursors. The core mechanism of sRNA production involves DICER-like (DCL) in processing the smallRNAs (sRNAs) and ARGONAUTE (AGO) as effectors of silencing, and siRNA biogenesis also involves action of RNA-Dependent RNA Polymerase (RDR), Pol IV and Pol V in biogenesis. Several other proteins interact with the core proteins to guide sRNA biogenesis, action, and turnover. We aimed to unravel the components and functions of the RNA-guided silencing pathway in a non-model plant species of worldwide economic relevance. The sRNA-guided silencing complex members have been identified in the Coffea canephora genome, and they have been characterized at the structural, functional, and evolutionary levels by computational analyses. Eleven AGO proteins, nine DCL proteins (which include a DCL1-like protein that was not previously annotated), and eight RDR proteins were identified. Another 48 proteins implicated in smallRNA (sRNA) pathways were also identified. Furthermore, we identified 235 miRNA precursors and 317 mature miRNAs from 113 MIR families, and we characterized ccp-MIR156, ccp-MIR172, and ccp-MIR390. Target prediction and gene ontology analyses of 2239 putative targets showed that significant pathways in coffee are targeted by miRNAs. We provide evidence of the expansion of the loci related to sRNA pathways, insights into the activities of these proteins by domain and catalytic site analyses, and gene expression analysis. The number of MIR loci and their targeted pathways highlight the importance of miRNAs in coffee. We identified several roles of sRNAs in C. canephora, which offers substantial insight into better understanding the transcriptional and post-transcriptional regulation of this major crop.
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Affiliation(s)
- Christiane Noronha Fernandes-Brum
- Department of Biology, Section of Plant Physiology, Laboratory of Plant Molecular Physiology (LFMP), Federal University of Lavras (UFLA), Lavras, Minas Gerais, Brazil
| | - Pâmela Marinho Rezende
- Department of Biology, Section of Plant Physiology, Laboratory of Plant Molecular Physiology (LFMP), Federal University of Lavras (UFLA), Lavras, Minas Gerais, Brazil
| | - Thales Henrique Cherubino Ribeiro
- Department of Biology, Section of Plant Physiology, Laboratory of Plant Molecular Physiology (LFMP), Federal University of Lavras (UFLA), Lavras, Minas Gerais, Brazil
| | | | - Thaís Cunha de Sousa Cardoso
- Institute of Genetics and Biochemistry (INGEB),Laboratory of Bioinformatics and Molecular Analysis (LBAM), Federal University of Uberlândia (UFU)- Campus Patos de Minas, Patos de Minas, Minas Gerais, Brasil
| | - Laurence Rodrigues do Amaral
- Institute of Genetics and Biochemistry (INGEB),Laboratory of Bioinformatics and Molecular Analysis (LBAM), Federal University of Uberlândia (UFU)- Campus Patos de Minas, Patos de Minas, Minas Gerais, Brasil
| | - Matheus de Souza Gomes
- Institute of Genetics and Biochemistry (INGEB),Laboratory of Bioinformatics and Molecular Analysis (LBAM), Federal University of Uberlândia (UFU)- Campus Patos de Minas, Patos de Minas, Minas Gerais, Brasil
| | - Antonio Chalfun-Junior
- Department of Biology, Section of Plant Physiology, Laboratory of Plant Molecular Physiology (LFMP), Federal University of Lavras (UFLA), Lavras, Minas Gerais, Brazil
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Arshad M, Gruber MY, Wall K, Hannoufa A. An Insight into microRNA156 Role in Salinity Stress Responses of Alfalfa. FRONTIERS IN PLANT SCIENCE 2017; 8:356. [PMID: 28352280 PMCID: PMC5348497 DOI: 10.3389/fpls.2017.00356] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 03/01/2017] [Indexed: 05/21/2023]
Abstract
Salinity is one of the major abiotic stresses affecting alfalfa productivity. Developing salinity tolerant alfalfa genotypes could contribute to sustainable crop production. The functions of microRNA156 (miR156) have been investigated in several plant species, but so far, no studies have been published that explore the role of miR156 in alfalfa response to salinity stress. In this work, we studied the role of miR156 in modulating commercially important traits of alfalfa under salinity stress. Our results revealed that overexpression of miR156 increased biomass, number of branches and time to complete growth stages, while it reduced plant height under control and salinity stress conditions. We observed a miR156-related reduction in neutral detergent fiber under non-stress, and acid detergent fiber under mild salinity stress conditions. In addition, enhanced total Kjeldahl nitrogen content was recorded in miR156 overexpressing genotypes under severe salinity stress. Furthermore, alfalfa genotypes overexpressing miR156 exhibited an altered ion homeostasis under salinity conditions. Under severe salinity stress, miR156 downregulated SPL transcription factor family genes, modified expression of other important transcription factors, and downstream salt stress responsive genes. Taken together, our results reveal that miR156 plays a role in mediating physiological and transcriptional responses of alfalfa to salinity stress.
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Affiliation(s)
| | | | - Ken Wall
- Agriculture and Agri-Food Canada, Swift CurrentSK, Canada
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, LondonON, Canada
- *Correspondence: Abdelali Hannoufa,
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24
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Wang Z, Wang Y, Kohalmi SE, Amyot L, Hannoufa A. SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 2 controls floral organ development and plant fertility by activating ASYMMETRIC LEAVES 2 in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2016; 92:661-674. [PMID: 27605094 DOI: 10.1007/s11103-016-0536-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 08/26/2016] [Indexed: 05/09/2023]
Abstract
A network of genes is coordinately expressed to ensure proper development of floral organs and fruits, which are essential for generating new offspring in flowering plants. In Arabidopsis thaliana, microRNA156 (miR156) plays a role in regulating the development of flowers and siliques by targeting members of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene family. Despite the important roles of the miR156/SPL network, our understanding of its downstream genes that are involved in floral organ and silique growth is still incomplete. Here, we report that the miR156/SPL2 regulatory pathway regulates pollen production, fertility rate, and the elongation of floral organs, including petals, sepals, and siliques in Arabidopsis. Transgenic plants exhibiting both overexpression of miR156 and dominant-negative alleles of SPL2 had reduced ASYMMETRIC LEAVES 2 (AS2) transcript levels in their siliques. Furthermore, their fertility phenotype was similar to that of the AS2 loss-of-function mutant. We also demonstrate that the SPL2 protein binds to the 5'UTR of the AS2 gene in vivo, indicating that AS2 is directly regulated by SPL2. Our results suggest that the miR156/SPL2 pathway affects floral organs, silique development and plant fertility, as well as directly regulates AS2 expression.
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Affiliation(s)
- Zhishuo Wang
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
- Department of Biology, University of Western Ontario, 1511 Richmond Street, London, ON, N6A 5B7, Canada
| | - Ying Wang
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
- Department of Biology, University of Western Ontario, 1511 Richmond Street, London, ON, N6A 5B7, Canada
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Susanne E Kohalmi
- Department of Biology, University of Western Ontario, 1511 Richmond Street, London, ON, N6A 5B7, Canada
| | - Lisa Amyot
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada.
- Department of Biology, University of Western Ontario, 1511 Richmond Street, London, ON, N6A 5B7, Canada.
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25
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Xu Y, Guo C, Zhou B, Li C, Wang H, Zheng B, Ding H, Zhu Z, Peragine A, Cui Y, Poethig S, Wu G. Regulation of Vegetative Phase Change by SWI2/SNF2 Chromatin Remodeling ATPase BRAHMA. PLANT PHYSIOLOGY 2016; 172:2416-2428. [PMID: 27803189 PMCID: PMC5129735 DOI: 10.1104/pp.16.01588] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 10/30/2016] [Indexed: 05/05/2023]
Abstract
Plants progress from a juvenile vegetative phase of development to an adult vegetative phase of development before they enter the reproductive phase. miR156 has been shown to be the master regulator of the juvenile-to-adult transition in plants. However, the mechanism of how miR156 is transcriptionally regulated still remains elusive. In a forward genetic screen, we identified that a mutation in the SWI2/SNF2 chromatin remodeling ATPase BRAHMA (BRM) exhibited an accelerated vegetative phase change phenotype by reducing the expression of miR156, which in turn caused a corresponding increase in the levels of SQUAMOSA PROMOTER BINDING PROTEIN LIKE genes. BRM regulates miR156 expression by directly binding to the MIR156A promoter. Mutations in BRM not only increased occupancy of the -2 and +1 nucleosomes proximal to the transcription start site at the MIR156A locus but also the levels of trimethylated histone H3 at Lys 27. The precocious phenotype of brm mutant was partially suppressed by a second mutation in SWINGER (SWN), but not by a mutation in CURLEY LEAF, both of which are key components of the Polycomb Group Repressive Complex 2 in plants. Our results indicate that BRM and SWN act antagonistically at the nucleosome level to fine-tune the temporal expression of miR156 to regulate vegetative phase change in Arabidopsis.
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Affiliation(s)
- Yunmin Xu
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Changkui Guo
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Bingying Zhou
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Chenlong Li
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Huasen Wang
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Ben Zheng
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Han Ding
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Zhujun Zhu
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Angela Peragine
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Yuhai Cui
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Scott Poethig
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Gang Wu
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.);
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
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26
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Gao R, Austin RS, Amyot L, Hannoufa A. Comparative transcriptome investigation of global gene expression changes caused by miR156 overexpression in Medicago sativa. BMC Genomics 2016; 17:658. [PMID: 27542359 PMCID: PMC4992203 DOI: 10.1186/s12864-016-3014-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 08/12/2016] [Indexed: 11/24/2022] Open
Abstract
Background Medicago sativa (alfalfa) is a low-input forage and potential bioenergy crop, and improving its yield and quality has always been a focus of the alfalfa breeding industry. Transgenic alfalfa plants overexpressing a precursor of alfalfa microRNA156 (MsmiR156) were recently generated by our group. These plants (miR156OE) showed enhanced biomass yield, reduced internodal length, increased shoot branching and trichome density, and a delay in flowering time. Transcripts of three SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) genes (MsSPL6, MsSPL12, and MsSPL13) were found to be targeted for cleavage by MsmiR156 in alfalfa. Results To further illustrate the molecular mechanisms underlying the effects of miR156 in alfalfa, two miR156OE genotypes (A11a and A17) were subjected to Next Generation RNA Sequencing with Illumina HiSeq. More than 1.11 billion clean reads were obtained from our available sequenced samples. A total of 160,472 transcripts were generated using Trinity de novo assembly and 4,985 significantly differentially expressed genes were detected in miR156OE plants A11a and A17 using the Medicago truncatula genome as reference. A total of 17 genes (including upregulated, downregulated, and unchanged) were selected for quantitative real-time PCR (qRT-PCR) validation, which showed that gene expression levels were largely consistent between qRT-PCR and RNA-Seq data. In addition to the established SPL genes MsSPL6, MsSPL12 and MsSPL13, four new SPLs; MsSPL2, MsSPL3, MsSPL4 and MsSPL9 were also down-regulated significantly in both miR156OE plants. These seven SPL genes belong to genes phylogeny clades VI, IV, VIII, V and VII, which have been reported to be targeted by miR156 in Arabidopsis thaliana. The gene ontology terms characterized electron transporter, starch synthase activity, sucrose transport, sucrose-phosphate synthase activity, chitin binding, sexual reproduction, flavonoid biosynthesis and lignin catabolism correlate well to the phenotypes of miR156OE alfalfa plants. Conclusions This is the first report of changes in global gene expression in response to miR156 overexpression in alfalfa. The discovered miR156-targeted SPL genes belonging to different clades indicate miR156 plays fundamental and multifunctional roles in regulating alfalfa plant development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3014-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ruimin Gao
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Ryan S Austin
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada.,Department of Biology, University of Western Ontario, 151 Richmond Street, London, ON, N6A 5B7, Canada
| | - Lisa Amyot
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada. .,Department of Biology, University of Western Ontario, 151 Richmond Street, London, ON, N6A 5B7, Canada.
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27
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Zhou Y, Xu Z, Duan C, Chen Y, Meng Q, Wu J, Hao Z, Wang Z, Li M, Yong H, Zhang D, Zhang S, Weng J, Li X. Dual transcriptome analysis reveals insights into the response to Rice black-streaked dwarf virus in maize. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4593-609. [PMID: 27493226 PMCID: PMC4973738 DOI: 10.1093/jxb/erw244] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Maize rough dwarf disease (MRDD) is a viral infection that results in heavy yield losses in maize worldwide, particularly in the summer maize-growing regions of China. MRDD is caused by the Rice black-streaked dwarf virus (RBSDV). In the present study, analyses of microRNAs (miRNAs), the degradome, and transcriptome sequences were used to elucidate the RBSDV-responsive pathway(s) in maize. Genomic analysis indicated that the expression of three non-conserved and 28 conserved miRNAs, representing 17 known miRNA families and 14 novel miRNAs, were significantly altered in response to RBSDV when maize was inoculated at the V3 (third leaf) stage. A total of 99 target transcripts from 48 genes of 10 known miRNAs were found to be responsive to RBSDV infection. The annotations of these target genes include a SQUAMOSA promoter binding (SPB) protein, a P450 reductase, an oxidoreductase, and a ubiquitin-related gene, among others. Characterization of the entire transcriptome suggested that a total of 28 and 1085 differentially expressed genes (DEGs) were detected at 1.5 and 3.0 d, respectively, after artificial inoculation with RBSDV. The expression patterns of cell wall- and chloroplast-related genes, and disease resistance- and stress-related genes changed significantly in response to RBSDV infection. The negatively regulated genes GRMZM2G069316 and GRMZM2G031169, which are the target genes for miR169i-p5 and miR8155, were identified as a nucleolin and a NAD(P)-binding Rossmann-fold superfamily protein in maize, respectively. The gene ontology term GO:0003824, including GRMZM2G031169 and other 51 DEGs, was designated as responsive to RBSDV.
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Affiliation(s)
- Yu Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang Province 150030, China
| | - Zhennan Xu
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang Province 150030, China
| | - Canxing Duan
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China
| | - Yanping Chen
- Jiangsu Academy of Agricultural Sciences, Zhongling Street, Xuanwu District, Nanjing, Jiangsu Province 210014, China
| | - Qingchang Meng
- Jiangsu Academy of Agricultural Sciences, Zhongling Street, Xuanwu District, Nanjing, Jiangsu Province 210014, China
| | - Jirong Wu
- Jiangsu Academy of Agricultural Sciences, Zhongling Street, Xuanwu District, Nanjing, Jiangsu Province 210014, China
| | - Zhuanfang Hao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China
| | - Zhenhua Wang
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang Province 150030, China
| | - Mingshun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China
| | - Hongjun Yong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China
| | - Degui Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China
| | - Shihuang Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China
| | - Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China
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28
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Feng S, Xu Y, Guo C, Zheng J, Zhou B, Zhang Y, Ding Y, Zhang L, Zhu Z, Wang H, Wu G. Modulation of miR156 to identify traits associated with vegetative phase change in tobacco (Nicotiana tabacum). JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1493-504. [PMID: 26763975 DOI: 10.1093/jxb/erv551] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
After germination, plants progress through juvenile and adult phases of vegetative development before entering the reproductive phase. The character and timing of these phases vary significantly between different plant species, which makes it difficult to know whether temporal variations in various vegetative traits represent the same, or different, developmental processes. miR156 has been shown to be the master regulator of vegetative development in plants. Overexpression of miR156 prolongs the juvenile phase of development, whereas knocking-down the level of miR156 promotes the adult phase of development. Therefore, artificial modulation of miR156 expression is expected to cause corresponding changes in vegetative-specific traits in different plant species, particularly in those showing no substantial difference in morphology during vegetative development. To identify specific traits associated with the juvenile-to-adult transition in tobacco, we examined the phenotype of transgenic tobacco plants with elevated or reduced levels of miR156. We found that leaf shape, the density of abaxial trichomes, the number of leaf veins, the number of stomata, the size and density of epidermal cells, patterns of epidermal cell staining, the content of chlorophyll and the rate of photosynthesis, are all affected by miR156. These newly identified miR156-regulated traits therefore can be used to distinguish between juvenile and adult phases of development in tobacco, and provide a starting point for future studies of vegetative phase change in the family Solanaceae.
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Affiliation(s)
- Shengjun Feng
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China
| | - Yunmin Xu
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China
| | - Changkui Guo
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China
| | - Jirong Zheng
- Institute of Vegetable Research, Hangzhou Academy of Agricultural Science, Hangzhou 310024, China
| | - Bingying Zhou
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China
| | - Yuting Zhang
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China
| | - Yue Ding
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China
| | - Lu Zhang
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China
| | - Zhujun Zhu
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China
| | - Huasen Wang
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China
| | - Gang Wu
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China
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Lelandais-Brière C, Moreau J, Hartmann C, Crespi M. Noncoding RNAs, Emerging Regulators in Root Endosymbioses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:170-80. [PMID: 26894282 DOI: 10.1094/mpmi-10-15-0240-fi] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Endosymbiosis interactions allow plants to grow in nutrient-deficient soil environments. The arbuscular mycorrhizal (AM) symbiosis is an ancestral interaction between land plants and fungi, whereas nitrogen-fixing symbioses are highly specific for certain plants, notably major crop legumes. The signaling pathways triggered by specific lipochitooligosaccharide molecules involved in these interactions have common components that also overlap with plant root development. These pathways include receptor-like kinases, transcription factors (TFs), and various intermediate signaling effectors, including noncoding (nc)RNAs. These latter molecules have emerged as major regulators of gene expression and small ncRNAs, composed of micro (mi)RNAs and small interfering (si)RNAs, are known to control gene expression at transcriptional (chromatin) or posttranscriptional levels. In this review, we describe exciting recent data connecting variants of conserved si/miRNAs with the regulation of TFs, such as NSP2, NFY-A1, auxin-response factors, and AP2-like proteins, known to be involved in symbiosis. The link between hormonal regulations and these si- and miRNA-TF nodes is proposed in a model in which different feedback loops or regulations controlling endosymbiosis signaling are integrated. The diversity and emerging regulatory networks of young legume miRNAs are also highlighted.
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Affiliation(s)
- Christine Lelandais-Brière
- Institute of Plant Sciences Paris-Saclay, IPS2, Univ. Paris-Diderot, CNRS, INRA, Univ. Paris-Sud, Univ. Evry, Sorbone Paris-Cité, University of Paris-Saclay, 91405 Orsay, France
| | - Jérémy Moreau
- Institute of Plant Sciences Paris-Saclay, IPS2, Univ. Paris-Diderot, CNRS, INRA, Univ. Paris-Sud, Univ. Evry, Sorbone Paris-Cité, University of Paris-Saclay, 91405 Orsay, France
| | - Caroline Hartmann
- Institute of Plant Sciences Paris-Saclay, IPS2, Univ. Paris-Diderot, CNRS, INRA, Univ. Paris-Sud, Univ. Evry, Sorbone Paris-Cité, University of Paris-Saclay, 91405 Orsay, France
| | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay, IPS2, Univ. Paris-Diderot, CNRS, INRA, Univ. Paris-Sud, Univ. Evry, Sorbone Paris-Cité, University of Paris-Saclay, 91405 Orsay, France
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30
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Li M, Li X, Zhou Z, Wu P, Fang M, Pan X, Lin Q, Luo W, Wu G, Li H. Reassessment of the Four Yield-related Genes Gn1a, DEP1, GS3, and IPA1 in Rice Using a CRISPR/Cas9 System. FRONTIERS IN PLANT SCIENCE 2016; 7:377. [PMID: 27066031 PMCID: PMC4811884 DOI: 10.3389/fpls.2016.00377] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/11/2016] [Indexed: 05/17/2023]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated (Cas) systems have been successfully used as efficient tools for genome editing in a variety of species. We used the CRISPR/Cas9 system to mutate the Gn1a (Os01g0197700), DEP1 (Os09g0441900), GS3 (Os03g0407400), and IPA1 (Os08g0509600) genes of rice cultivar Zhonghua 11, genes which have been reported to function as regulators of grain number, panicle architecture, grain size and plant architecture, respectively. Analysis of the phenotypes and frequencies of edited genes in the first generation of transformed plants (T0) showed that the CRISPR/Cas9 system was highly efficient in inducing targeted gene editing, with the desired genes being edited in 42.5% (Gn1a), 67.5% (DEP1), 57.5% (GS3), and 27.5% (IPA1) of the transformed plants. The T2 generation of the gn1a, dep1, and gs3 mutants featured enhanced grain number, dense erect panicles, and larger grain size, respectively. Furthermore, semi-dwarf, and grain with long awn, phenotypes were observed in dep1 and gs3 mutants, respectively. The ipa1 mutants showed two contrasting phenotypes, having either fewer tillers or more tillers, depending on the changes induced in the OsmiR156 target region. In addition, we found that mutants with deletions occurred more frequently than previous reports had indicated and that off-targeting had taken place in highly similar target sequences. These results proved that multiple regulators of important traits can be modified in a single cultivar by CRISPR/Cas9, and thus facilitate the dissection of complex gene regulatory networks in the same genomic background and the stacking of important traits in cultivated varieties.
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Affiliation(s)
- Meiru Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Xiaoxia Li
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, South China Normal UniversityGuangzhou, China
| | - Zejiao Zhou
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, South China Normal UniversityGuangzhou, China
| | - Pingzhi Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Maichun Fang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Xiaoping Pan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Qiupeng Lin
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, South China Normal UniversityGuangzhou, China
| | - Wanbin Luo
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, South China Normal UniversityGuangzhou, China
| | - Guojiang Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- *Correspondence: Guojiang Wu, ; Hongqing Li,
| | - Hongqing Li
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, South China Normal UniversityGuangzhou, China
- *Correspondence: Guojiang Wu, ; Hongqing Li,
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Holt DB, Gupta V, Meyer D, Abel NB, Andersen SU, Stougaard J, Markmann K. micro RNA 172 (miR172) signals epidermal infection and is expressed in cells primed for bacterial invasion in Lotus japonicus roots and nodules. THE NEW PHYTOLOGIST 2015; 208:241-56. [PMID: 25967282 DOI: 10.1111/nph.13445] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/26/2015] [Indexed: 05/13/2023]
Abstract
Legumes interact with rhizobial bacteria to form nitrogen-fixing root nodules. Host signalling following mutual recognition ensures a specific response, but is only partially understood. Focusing on the stage of epidermal infection with Mesorhizobium loti, we analysed endogenous small RNAs (sRNAs) of the model legume Lotus japonicus to investigate their involvement in host response regulation. We used Illumina sequencing to annotate the L. japonicus sRNA-ome and isolate infection-responsive sRNAs, followed by candidate-based functional characterization. Sequences from four libraries revealed 219 novel L. japonicus micro RNAs (miRNAs) from 114 newly assigned families, and 76 infection-responsive sRNAs. Unlike infection-associated coding genes such as NODULE INCEPTION (NIN), a micro RNA 172 (miR172) isoform showed strong accumulation in dependency of both Nodulation (Nod) factor and compatible rhizobia. The genetics of miR172 induction support the existence of distinct epidermal and cortical signalling events. MIR172a promoter activity followed a previously unseen pattern preceding infection thread progression in epidermal and cortical cells. Nodule-associated miR172a expression was infection-independent, representing the second of two genetically separable activity waves. The combined data provide a valuable resource for further study, and identify miR172 as an sRNA marking successful epidermal infection. We show that miR172 acts upstream of several APETALA2-type (AP2) transcription factors, and suggest that it has a role in fine-tuning AP2 levels during bacterial symbiosis.
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Affiliation(s)
- Dennis B Holt
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling (CARB), Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Vikas Gupta
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling (CARB), Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Dörte Meyer
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling (CARB), Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Nikolaj B Abel
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling (CARB), Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling (CARB), Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling (CARB), Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Katharina Markmann
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling (CARB), Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
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Discovery of microRNAs and transcript targets related to witches' broom disease in Paulownia fortunei by high-throughput sequencing and degradome approach. Mol Genet Genomics 2015; 291:181-91. [PMID: 26243687 DOI: 10.1007/s00438-015-1102-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 07/28/2015] [Indexed: 10/23/2022]
Abstract
Paulownia witches' broom (PaWB) caused by the phytoplasma is a devastating disease of Paulownia trees. It has caused heavy yield losses to Paulownia production worldwide. However, knowledge of the transcriptional and post-transcriptional regulation of gene expression by microRNAs (miRNAs), especially miRNAs responsive to PaWB disease stress, is still rudimentary. In this study, to identify miRNAs and their transcript targets that are responsive to PaWB disease stress, six sequencing libraries were constructed from healthy (PF), PaWB-infected (PFI), and PaWB-infected, 20 mg L(-1) methyl methane sulfonate-treated (PFI20) P. fortunei seedlings. As a result, 95 conserved miRNAs belonging to 18 miRNA families, as well as 122 potential novel miRNAs, were identified. Most of them were found to be a response to PaWB disease-induced stress, and the expression levels of these miRNAs were validated by quantitative real-time PCR analysis. The study simultaneously identified 109 target genes from the P. fortunei for 14 conserved miRNA families and 24 novel miRNAs by degradome sequencing. Furthermore, the functions of the miRNA targets were annotated based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis. The results presented here provide the groundwork for further analysis of miRNAs and target genes responsive to the PaWB disease stress, and could be also useful for addressing new questions to better understand the mechanisms of plant infection by phytoplasma in the future.
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Nova-Franco B, Íñiguez LP, Valdés-López O, Alvarado-Affantranger X, Leija A, Fuentes SI, Ramírez M, Paul S, Reyes JL, Girard L, Hernández G. The micro-RNA72c-APETALA2-1 node as a key regulator of the common bean-Rhizobium etli nitrogen fixation symbiosis. PLANT PHYSIOLOGY 2015; 168:273-91. [PMID: 25739700 PMCID: PMC4424015 DOI: 10.1104/pp.114.255547] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/02/2015] [Indexed: 05/18/2023]
Abstract
Micro-RNAs are recognized as important posttranscriptional regulators in plants. The relevance of micro-RNAs as regulators of the legume-rhizobia nitrogen-fixing symbiosis is emerging. The objective of this work was to functionally characterize the role of micro-RNA172 (miR172) and its conserved target APETALA2 (AP2) transcription factor in the common bean (Phaseolus vulgaris)-Rhizobium etli symbiosis. Our expression analysis revealed that mature miR172c increased upon rhizobial infection and continued increasing during nodule development, reaching its maximum in mature nodules and decaying in senescent nodules. The expression of AP2-1 target showed a negative correlation with miR172c expression. A drastic decrease in miR172c and high AP2-1 mRNA levels were observed in ineffective nodules. Phenotypic analysis of composite bean plants with transgenic roots overexpressing miR172c or a mutated AP2-1 insensitive to miR172c cleavage demonstrated the pivotal regulatory role of the miR172 node in the common bean-rhizobia symbiosis. Increased miR172 resulted in improved root growth, increased rhizobial infection, increased expression of early nodulation and autoregulation of nodulation genes, and improved nodulation and nitrogen fixation. In addition, these plants showed decreased sensitivity to nitrate inhibition of nodulation. Through transcriptome analysis, we identified 114 common bean genes that coexpressed with AP2-1 and proposed these as being targets for transcriptional activation by AP2-1. Several of these genes are related to nodule senescence, and we propose that they have to be silenced, through miR172c-induced AP2-1 cleavage, in active mature nodules. Our work sets the basis for exploring the miR172-mediated improvement of symbiotic nitrogen fixation in common bean, the most important grain legume for human consumption.
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Affiliation(s)
- Bárbara Nova-Franco
- Centro de Ciencias Genómicas (B.N.-F., L.P.I., A.L., S.I.F., M.R., S.P., L.G., G.H.), Laboratorio Nacional de Microscopía Avanzada (X.A.-A.), and Departamento de Biología Molecular de Plantas (J.L.R.), Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico; andLaboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Edo de Mexico 54090, Mexico (O.V.-L.)
| | - Luis P Íñiguez
- Centro de Ciencias Genómicas (B.N.-F., L.P.I., A.L., S.I.F., M.R., S.P., L.G., G.H.), Laboratorio Nacional de Microscopía Avanzada (X.A.-A.), and Departamento de Biología Molecular de Plantas (J.L.R.), Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico; andLaboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Edo de Mexico 54090, Mexico (O.V.-L.)
| | - Oswaldo Valdés-López
- Centro de Ciencias Genómicas (B.N.-F., L.P.I., A.L., S.I.F., M.R., S.P., L.G., G.H.), Laboratorio Nacional de Microscopía Avanzada (X.A.-A.), and Departamento de Biología Molecular de Plantas (J.L.R.), Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico; andLaboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Edo de Mexico 54090, Mexico (O.V.-L.)
| | - Xochitl Alvarado-Affantranger
- Centro de Ciencias Genómicas (B.N.-F., L.P.I., A.L., S.I.F., M.R., S.P., L.G., G.H.), Laboratorio Nacional de Microscopía Avanzada (X.A.-A.), and Departamento de Biología Molecular de Plantas (J.L.R.), Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico; andLaboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Edo de Mexico 54090, Mexico (O.V.-L.)
| | - Alfonso Leija
- Centro de Ciencias Genómicas (B.N.-F., L.P.I., A.L., S.I.F., M.R., S.P., L.G., G.H.), Laboratorio Nacional de Microscopía Avanzada (X.A.-A.), and Departamento de Biología Molecular de Plantas (J.L.R.), Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico; andLaboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Edo de Mexico 54090, Mexico (O.V.-L.)
| | - Sara I Fuentes
- Centro de Ciencias Genómicas (B.N.-F., L.P.I., A.L., S.I.F., M.R., S.P., L.G., G.H.), Laboratorio Nacional de Microscopía Avanzada (X.A.-A.), and Departamento de Biología Molecular de Plantas (J.L.R.), Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico; andLaboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Edo de Mexico 54090, Mexico (O.V.-L.)
| | - Mario Ramírez
- Centro de Ciencias Genómicas (B.N.-F., L.P.I., A.L., S.I.F., M.R., S.P., L.G., G.H.), Laboratorio Nacional de Microscopía Avanzada (X.A.-A.), and Departamento de Biología Molecular de Plantas (J.L.R.), Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico; andLaboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Edo de Mexico 54090, Mexico (O.V.-L.)
| | - Sujay Paul
- Centro de Ciencias Genómicas (B.N.-F., L.P.I., A.L., S.I.F., M.R., S.P., L.G., G.H.), Laboratorio Nacional de Microscopía Avanzada (X.A.-A.), and Departamento de Biología Molecular de Plantas (J.L.R.), Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico; andLaboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Edo de Mexico 54090, Mexico (O.V.-L.)
| | - José L Reyes
- Centro de Ciencias Genómicas (B.N.-F., L.P.I., A.L., S.I.F., M.R., S.P., L.G., G.H.), Laboratorio Nacional de Microscopía Avanzada (X.A.-A.), and Departamento de Biología Molecular de Plantas (J.L.R.), Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico; andLaboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Edo de Mexico 54090, Mexico (O.V.-L.)
| | - Lourdes Girard
- Centro de Ciencias Genómicas (B.N.-F., L.P.I., A.L., S.I.F., M.R., S.P., L.G., G.H.), Laboratorio Nacional de Microscopía Avanzada (X.A.-A.), and Departamento de Biología Molecular de Plantas (J.L.R.), Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico; andLaboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Edo de Mexico 54090, Mexico (O.V.-L.)
| | - Georgina Hernández
- Centro de Ciencias Genómicas (B.N.-F., L.P.I., A.L., S.I.F., M.R., S.P., L.G., G.H.), Laboratorio Nacional de Microscopía Avanzada (X.A.-A.), and Departamento de Biología Molecular de Plantas (J.L.R.), Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico; andLaboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Edo de Mexico 54090, Mexico (O.V.-L.)
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Kulcheski FR, Côrrea R, Gomes IA, de Lima JC, Margis R. NPK macronutrients and microRNA homeostasis. FRONTIERS IN PLANT SCIENCE 2015; 6:451. [PMID: 26136763 PMCID: PMC4468412 DOI: 10.3389/fpls.2015.00451] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 06/02/2015] [Indexed: 05/02/2023]
Abstract
Macronutrients are essential elements for plant growth and development. In natural, non-cultivated systems, the availability of macronutrients is not a limiting factor of growth, due to fast recycling mechanisms. However, their availability might be an issue in modern agricultural practices, since soil has been frequently over exploited. From a crop management perspective, the nitrogen (N), phosphorus (P), and potassium (K) are three important limiting factors and therefore frequently added as fertilizers. NPK are among the nutrients that have been reported to alter post-embryonic root developmental processes and consequently, impairs crop yield. To cope with nutrients scarcity, plants have evolved several mechanisms involved in metabolic, physiological, and developmental adaptations. In this scenario, microRNAs (miRNAs) have emerged as additional key regulators of nutrients uptake and assimilation. Some studies have demonstrated the intrinsic relation between miRNAs and their targets, and how they can modulate plants to deal with the NPK availability. In this review, we focus on miRNAs and their regulation of targets involved in NPK metabolism. In general, NPK starvation is related with miRNAs that are involved in root-architectural changes and uptake activity modulation. We further show that several miRNAs were discovered to be involved in plant-microbe symbiosis during N and P uptake, and in this way we present a global view of some studies that were conducted in the last years. The integration of current knowledge about miRNA-NPK signaling may help future studies to focus in good candidates genes for the development of important tools for plant nutritional breeding.
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Affiliation(s)
- Franceli R. Kulcheski
- Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto AlegreBrazil
| | - Régis Côrrea
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de JaneiroBrazil
| | - Igor A. Gomes
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de JaneiroBrazil
| | - Júlio C. de Lima
- Laboratório de Genética Molecular, Instituto de Ciências Biológicas, Universidade de Passo Fundo, Passo FundoBrazil
| | - Rogerio Margis
- Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto AlegreBrazil
- *Correspondence: Rogerio Margis, Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, Setor IV, Prédio 43431, Sala 213, Porto Alegre, RS, CEP, Brazil
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