1
|
Domínguez-Figueroa J, Gómez-Rojas A, Escobar C. Functional studies of plant transcription factors and their relevance in the plant root-knot nematode interaction. FRONTIERS IN PLANT SCIENCE 2024; 15:1370532. [PMID: 38784063 PMCID: PMC11113014 DOI: 10.3389/fpls.2024.1370532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 04/10/2024] [Indexed: 05/25/2024]
Abstract
Root-knot nematodes are polyphagous parasitic nematodes that cause severe losses in the agriculture worldwide. They enter the root in the elongation zone and subtly migrate to the root meristem where they reach the vascular cylinder and establish a feeding site called gall. Inside the galls they induce a group of transfer cells that serve to nurture them along their parasitic stage, the giant cells. Galls and giant cells develop through a process of post-embryogenic organogenesis that involves manipulating different genetic regulatory networks within the cells, some of them through hijacking some molecular transducers of established plant developmental processes, such as lateral root formation or root regeneration. Galls/giant cells formation involves different mechanisms orchestrated by the nematode´s effectors that generate diverse plant responses in different plant tissues, some of them include sophisticated mechanisms to overcome plant defenses. Yet, the plant-nematode interaction is normally accompanied to dramatic transcriptomic changes within the galls and giant cells. It is therefore expected a key regulatory role of plant-transcription factors, coordinating both, the new organogenesis process induced by the RKNs and the plant response against the nematode. Knowing the role of plant-transcription factors participating in this process becomes essential for a clear understanding of the plant-RKNs interaction and provides an opportunity for the future development and design of directed control strategies. In this review, we present the existing knowledge of the TFs with a functional role in the plant-RKN interaction through a comprehensive analysis of current scientific literature and available transcriptomic data.
Collapse
Affiliation(s)
- Jose Domínguez-Figueroa
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
- Centro de Biotecnologia y Genomica de Plantas (CBGP), Universidad Politecnica de Madrid and Instituto de Investigacion y Tecnologia Agraria y Alimentaria-Consejo Superior de investigaciones Cientificas (UPM-INIA/CSIC), Madrid, Spain
| | - Almudena Gómez-Rojas
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
| | - Carolina Escobar
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
| |
Collapse
|
2
|
Kang L, Li C, Qin A, Liu Z, Li X, Zeng L, Yu H, Wang Y, Song J, Chen R. Identification and Expression Analysis of the Nucleotidyl Transferase Protein (NTP) Family in Soybean ( Glycine max) under Various Abiotic Stresses. Int J Mol Sci 2024; 25:1115. [PMID: 38256188 PMCID: PMC10816777 DOI: 10.3390/ijms25021115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/16/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Nucleotidyl transferases (NTPs) are common transferases in eukaryotes and play a crucial role in nucleotide modifications at the 3' end of RNA. In plants, NTPs can regulate RNA stability by influencing 3' end modifications, which in turn affect plant growth, development, stress responses, and disease resistance. Although the functions of NTP family members have been extensively studied in Arabidopsis, rice, and maize, there is limited knowledge about NTP genes in soybeans. In this study, we identified 16 members of the NTP family in soybeans, including two subfamilies (G1 and G2) with distinct secondary structures, conserved motifs, and domain distributions at the protein level. Evolutionary analysis of genes in the NTP family across multiple species and gene collinearity analysis revealed a relatively conserved evolutionary pattern. Analysis of the tertiary structure of the proteins showed that NTPs have three conserved aspartic acids that bind together to form a possible active site. Tissue-specific expression analysis indicated that some NTP genes exhibit tissue-specific expression, likely due to their specific functions. Stress expression analysis showed significant differences in the expression levels of NTP genes under high salt, drought, and cold stress. Additionally, RNA-seq analysis of soybean plants subjected to salt and drought stress further confirmed the association of soybean NTP genes with abiotic stress responses. Subcellular localization experiments revealed that GmNTP2 and GmNTP14, which likely have similar functions to HESO1 and URT1, are located in the nucleus. These research findings provide a foundation for further investigations into the functions of NTP family genes in soybeans.
Collapse
Affiliation(s)
- Liqing Kang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Changgen Li
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Aokang Qin
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Zehui Liu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Xuanyue Li
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Liming Zeng
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Hongyang Yu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Yihua Wang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Jianbo Song
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Rongrong Chen
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| |
Collapse
|
3
|
Fan K, Wang Z, Sze CC, Niu Y, Wong FL, Li MW, Lam HM. MicroRNA 4407 modulates nodulation in soybean by repressing a root-specific ISOPENTENYLTRANSFERASE (GmIPT3). THE NEW PHYTOLOGIST 2023; 240:1034-1051. [PMID: 37653681 DOI: 10.1111/nph.19222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/28/2023] [Indexed: 09/02/2023]
Abstract
MicroRNAs (miRNAs) are important regulators of plant biological processes, including soybean nodulation. One miRNA, miR4407, was identified in soybean roots and nodules. However, the function of miR4407 in soybean is still unknown. MiR4407, unique to soybean, positively regulates lateral root emergence and root structures and represses a root-specific ISOPENTENYLTRANSFERASE (GmIPT3). By altering the expression of miR4407 and GmIPT3, we investigated the role of miR4407 in lateral root and nodule development. Both miR4407 and GmIPT3 are expressed in the inner root cortex and nodule primordia. Upon rhizobial inoculation, miR4407 was downregulated while GmIPT3 was upregulated. Overexpressing miR4407 reduced the number of nodules in transgenic soybean hairy roots while overexpressing the wild-type GmIPT3 or a miR4407-resistant GmIPT3 mutant (mGmIPT3) significantly increased the nodule number. The mechanism of miR4407 and GmIPT3 functions was also linked to autoregulation of nodulation (AON), where miR4407 overexpression repressed miR172c and activated its target, GmNNC1, turning on AON. Exogenous CK mimicked the effects of GmIPT3 overexpression on miR172c, supporting the notion that GmIPT3 regulates nodulation by enhancing root-derived CK. Overall, our data revealed a new miRNA-mediated regulatory mechanism of nodulation in soybean. MiR4407 showed a dual role in lateral root and nodule development.
Collapse
Affiliation(s)
- Kejing Fan
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Zhili Wang
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ching-Ching Sze
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yongchao Niu
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Fuk-Ling Wong
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Man-Wah Li
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| |
Collapse
|
4
|
Hazra S, Moulick D, Mukherjee A, Sahib S, Chowardhara B, Majumdar A, Upadhyay MK, Yadav P, Roy P, Santra SC, Mandal S, Nandy S, Dey A. Evaluation of efficacy of non-coding RNA in abiotic stress management of field crops: Current status and future prospective. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:107940. [PMID: 37738864 DOI: 10.1016/j.plaphy.2023.107940] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/23/2023] [Accepted: 08/04/2023] [Indexed: 09/24/2023]
Abstract
Abiotic stresses are responsible for the major losses in crop yield all over the world. Stresses generate harmful ROS which can impair cellular processes in plants. Therefore, plants have evolved antioxidant systems in defence against the stress-induced damages. The frequency of occurrence of abiotic stressors has increased several-fold due to the climate change experienced in recent times and projected for the future. This had particularly aggravated the risk of yield losses and threatened global food security. Non-coding RNAs are the part of eukaryotic genome that does not code for any proteins. However, they have been recently found to have a crucial role in the responses of plants to both abiotic and biotic stresses. There are different types of ncRNAs, for example, miRNAs and lncRNAs, which have the potential to regulate the expression of stress-related genes at the levels of transcription, post-transcription, and translation of proteins. The lncRNAs are also able to impart their epigenetic effects on the target genes through the alteration of the status of histone modification and organization of the chromatins. The current review attempts to deliver a comprehensive account of the role of ncRNAs in the regulation of plants' abiotic stress responses through ROS homeostasis. The potential applications ncRNAs in amelioration of abiotic stresses in field crops also have been evaluated.
Collapse
Affiliation(s)
- Swati Hazra
- Sharda School of Agricultural Sciences, Sharda University, Greater Noida, Uttar Pradesh 201310, India.
| | - Debojyoti Moulick
- Department of Environmental Science, University of Kalyani, Nadia, West Bengal 741235, India.
| | | | - Synudeen Sahib
- S. S. Cottage, Njarackal, P.O.: Perinad, Kollam, 691601, Kerala, India.
| | - Bhaben Chowardhara
- Department of Botany, Faculty of Science and Technology, Arunachal University of Studies, Arunachal Pradesh 792103, India.
| | - Arnab Majumdar
- Department of Earth Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, West Bengal 741246, India.
| | - Munish Kumar Upadhyay
- Department of Civil Engineering, Indian Institute of Technology Kanpur, Uttar Pradesh 208016, India.
| | - Poonam Yadav
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India.
| | - Priyabrata Roy
- Department of Molecular Biology and Biotechnology, University of Kalyani, West Bengal 741235, India.
| | - Subhas Chandra Santra
- Department of Environmental Science, University of Kalyani, Nadia, West Bengal 741235, India.
| | - Sayanti Mandal
- Department of Biotechnology, Dr. D. Y. Patil Arts, Commerce & Science College (affiliated to Savitribai Phule Pune University), Sant Tukaram Nagar, Pimpri, Pune, Maharashtra-411018, India.
| | - Samapika Nandy
- School of Pharmacy, Graphic Era Hill University, Bell Road, Clement Town, Dehradun, 248002, Uttarakhand, India; Department of Botany, Vedanta College, 33A Shiv Krishna Daw Lane, Kolkata-700054, India.
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, West Bengal 700073, India.
| |
Collapse
|
5
|
Nasrollahi V, Allam G, Kohalmi SE, Hannoufa A. MsSPL9 Modulates Nodulation under Nitrate Sufficiency Condition in Medicago sativa. Int J Mol Sci 2023; 24:ijms24119615. [PMID: 37298564 DOI: 10.3390/ijms24119615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
Nodulation in Leguminous spp. is induced by common environmental cues, such as low nitrogen availability conditions, in the presence of the specific Rhizobium spp. in the rhizosphere. Medicago sativa (alfalfa) is an important nitrogen-fixing forage crop that is widely cultivated around the world and relied upon as a staple source of forage in livestock feed. Although alfalfa's relationship with these bacteria is one of the most efficient between rhizobia and legume plants, breeding for nitrogen-related traits in this crop has received little attention. In this report, we investigate the role of Squamosa-Promoter Binding Protein-Like 9 (SPL9), a target of miR156, in nodulation in alfalfa. Transgenic alfalfa plants with SPL9-silenced (SPL9-RNAi) and overexpressed (35S::SPL9) were compared to wild-type (WT) alfalfa for phenotypic changes in nodulation in the presence and absence of nitrogen. Phenotypic analyses showed that silencing of MsSPL9 in alfalfa caused an increase in the number of nodules. Moreover, the characterization of phenotypic and molecular parameters revealed that MsSPL9 regulates nodulation under a high concentration of nitrate (10 mM KNO3) by regulating the transcription levels of the nitrate-responsive genes Nitrate Reductase1 (NR1), NR2, Nitrate transporter 2.5 (NRT2.5), and a shoot-controlled autoregulation of nodulation (AON) gene, Super numeric nodules (SUNN). While MsSPL9-overexpressing transgenic plants have dramatically increased transcript levels of SUNN, NR1, NR2, and NRT2.5, reducing MsSPL9 caused downregulation of these genes and displayed a nitrogen-starved phenotype, as downregulation of the MsSPL9 transcript levels caused a nitrate-tolerant nodulation phenotype. Taken together, our results suggest that MsSPL9 regulates nodulation in alfalfa in response to nitrate.
Collapse
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
| | - Gamalat Allam
- 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
| | - 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
| |
Collapse
|
6
|
Dash PK, Gupta P, Sreevathsa R, Pradhan SK, Sanjay TD, Mohanty MR, Roul PK, Singh NK, Rai R. Phylogenomic Analysis of micro-RNA Involved in Juvenile to Flowering-Stage Transition in Photophilic Rice and Its Sister Species. Cells 2023; 12:1370. [PMID: 37408207 DOI: 10.3390/cells12101370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 07/07/2023] Open
Abstract
Vegetative to reproductive phase transition in phototropic plants is an important developmental process and is sequentially mediated by the expression of micro-RNA MIR172. To obtain insight into the evolution, adaptation, and function of MIR172 in photophilic rice and its wild relatives, we analyzed the genescape of a 100 kb segment harboring MIR172 homologs from 11 genomes. The expression analysis of MIR172 revealed its incremental accumulation from the 2-leaf to 10-leaf stage, with maximum expression coinciding with the flag-leaf stage in rice. Nonetheless, the microsynteny analysis of MIR172s revealed collinearity within the genus Oryza, but a loss of synteny was observed in (i) MIR172A in O. barthii (AA) and O. glaberima (AA); (ii) MIR172B in O. brachyantha (FF); and (iii) MIR172C in O. punctata (BB). Phylogenetic analysis of precursor sequences/region of MIR172 revealed a distinct tri-modal clade of evolution. The genomic information generated in this investigation through comparative analysis of MIRNA, suggests mature MIR172s to have evolved in a disruptive and conservative mode amongst all Oryza species with a common origin of descent. Further, the phylogenomic delineation provided an insight into the adaptation and molecular evolution of MIR172 to changing environmental conditions (biotic and abiotic) of phototropic rice through natural selection and the opportunity to harness untapped genomic regions from rice wild relatives (RWR).
Collapse
Affiliation(s)
- Prasanta K Dash
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Payal Gupta
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Rohini Sreevathsa
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | | | | | - Mihir Ranjan Mohanty
- Department of Genetics & Plant Breeding (RRTTS, Jeypore), Odisha University of Agriculture and Technology, Bhubaneswar 751003, India
| | - Pravat K Roul
- Department of Genetics & Plant Breeding (RRTTS, Jeypore), Odisha University of Agriculture and Technology, Bhubaneswar 751003, India
| | - Nagendra K Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Rhitu Rai
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| |
Collapse
|
7
|
Saputra TI, Maryanto SD, Tanjung ZA, Utomo C, Liwang T. Identification of microRNAs involved in the Phosphate starvation response in Oil Palm (Elaeis guineensis Jacq.). Mol Biol Rep 2023:10.1007/s11033-023-08484-4. [PMID: 37171552 DOI: 10.1007/s11033-023-08484-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 04/25/2023] [Indexed: 05/13/2023]
Abstract
BACKGROUND Plant microRNA, often known as miRNA, is a novel form of gene expression regulator that is known to play a significant role in phosphate starvation. The identification of microRNAs involved in the response to phosphate starvation in oil palms is beneficial for breeding programs. METHOD The main nursery stage seedlings of two oil palm progenies were treated with three different fertiliser namely: complete fertiliser with urea, P2O5, K2O, and MgO based on the standard procedure as a control (C); fertiliser with urea, K2O, MgO without P2O5 (P0); and no fertiliser (F0) for 24 weeks. A total of six oil palm roots were subjected to RNA isolation, followed by miRNA sequencing using the Illumina HiSeq 4000 platform, and all reads were computationally analysed. RESULTS In total, 119 potential miRNAs related to 5,891 genes were identified. The P-specific miRNAs were assumed based on the miRNAs that identified without P fertilizer treatment, resulted of twenty miRNA sequences in the treatment comparison of (C vs P0) vs (C vs F0). Those 20 miRNA sequences were grouped into 9 families, namely EgmiR319; EgmiR399; EgmiR396; EgmiR172; EgmiR156; EgmiR157; miR5648; miR5645; and EgmiRNA_unidentified. Two miRNAs were selected for RT-qPCR validation, namely EgMir399 and EgMir172. Their expression pattern was similar with the RNA sequencing results and shown opposite expression pattern with their target genes, UBC E2 24 and APETALA2, respectively. CONCLUSIONS The nine micro RNA families was identified in oil palm root tissue at phosphate starvation.
Collapse
Affiliation(s)
- Tengku Imam Saputra
- Genomic and Transcriptomic Section, Department of Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia.
| | - Sigit Dwi Maryanto
- Genomic and Transcriptomic Section, Department of Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia
| | - Zulfikar Achmad Tanjung
- Bioinformatics Section, Department of Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia
| | - Condro Utomo
- Department of Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia
| | - Tony Liwang
- Division of Plant Production and Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia
| |
Collapse
|
8
|
Zhang Z, Jin S, Tian H, Wang Z, Jiang R, Liu C, Xin D, Wu X, Chen Q, Zhu R. Identifying the Soybean microRNAs Related to Phytophthora sojae Based on RNA Sequencing and Bioinformatics Analysis. Int J Mol Sci 2023; 24:ijms24108546. [PMID: 37239903 DOI: 10.3390/ijms24108546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Phytophthora root rot in soybeans is caused by a pathogen called Phytophthora sojae (P. sojae), which results in a significant decrease in soybean production within affected regions. MicroRNAs (miRNAs) are a class of small non-coding RNA molecules that play a key post-transcriptional regulatory role in eukaryotes. In this paper, the miRNAs that respond to P. sojae were analyzed from the gene level to complement the study of molecular resistance mechanisms in soybean. The study utilized high-throughput sequencing of soybean data to predict miRNAs that respond to P. sojae, analyze their specific functions, and verify regulatory relationships using qRT-PCR. The results showed that the miRNAs in soybean respond to P. sojae infection. MiRNAs can be transcribed independently, suggesting the presence of transcription factor binding sites in the promoter regions. Additionally, we performed an evolutionary analysis on conserved miRNAs that respond to P. sojae. Finally, we investigated the regulatory relationships among miRNAs, genes, and transcription factors, and identified five regulatory patterns. These findings lay the groundwork for future studies on the evolution of miRNAs responsive to P. sojae.
Collapse
Affiliation(s)
- Zhanguo Zhang
- College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
- National Research Center of Soybean Engineering and Technology, Harbin 150030, China
| | - Song Jin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Huilin Tian
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Zhihao Wang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Rui Jiang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Dawei Xin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Xiaoxia Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Rongsheng Zhu
- College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| |
Collapse
|
9
|
Fan K, Ferguson BJ, Muñoz NB, Li MW, Lam HM. Editorial: Metabolic adjustments and gene expression reprogramming for symbiotic nitrogen fixation in legume nodules, volume II. FRONTIERS IN PLANT SCIENCE 2023; 14:1141269. [PMID: 36760634 PMCID: PMC9903052 DOI: 10.3389/fpls.2023.1141269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Affiliation(s)
- Kejing Fan
- Center for Soybean Research of The State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Brett James Ferguson
- Integrative Legume Research Group, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane, QLD, Australia
| | | | - Man-Wah Li
- Center for Soybean Research of The State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hon-Ming Lam
- Center for Soybean Research of The State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| |
Collapse
|
10
|
Yun J, Wang C, Zhang F, Chen L, Sun Z, Cai Y, Luo Y, Liao J, Wang Y, Cha Y, Zhang X, Ren Y, Wu J, Hasegawa PM, Tian C, Su H, Ferguson BJ, Gresshoff PM, Hou W, Han T, Li X. A nitrogen fixing symbiosis-specific pathway required for legume flowering. SCIENCE ADVANCES 2023; 9:eade1150. [PMID: 36638166 PMCID: PMC9839322 DOI: 10.1126/sciadv.ade1150] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/09/2022] [Indexed: 05/26/2023]
Abstract
Symbiotic nitrogen fixation boosts legume growth and production in nitrogen-poor soils. It has long been assumed that fixed nitrogen increases reproductive success, but until now, the regulatory mechanism was unknown. Here, we report a symbiotic flowering pathway that couples symbiotic and nutrient signals to the flowering induction pathway in legumes. We show that the symbiotic microRNA-microRNA172c (miR172c) and fixed nitrogen systemically and synergistically convey symbiotic and nutritional cues from roots to leaves to promote soybean (Glycine max) flowering. The combinations of symbiotic miR172c and local miR172c elicited by fixed nitrogen and development in leaves activate florigen-encoding FLOWERING LOCUS T (FT) homologs (GmFT2a/5a) by repressing TARGET OF EAT1-like 4a (GmTOE4a). Thus, FTs trigger reproductive development, which allows legumes to survive and reproduce under low-nitrogen conditions.
Collapse
Affiliation(s)
- Jinxia Yun
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Can Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fengrong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Li Chen
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhengxi Sun
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yupeng Cai
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanqing Luo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Junwen Liao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yongliang Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanyan Cha
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xuehai Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ya Ren
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jun Wu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Paul M. Hasegawa
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Changfu Tian
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Soil Microbiology, and Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Huanan Su
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Brett J. Ferguson
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Peter M. Gresshoff
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Wensheng Hou
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianfu Han
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xia Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong, China
| |
Collapse
|
11
|
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.
Collapse
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.
| |
Collapse
|
12
|
Chakraborty S, Valdés-López O, Stonoha-Arther C, Ané JM. Transcription Factors Controlling the Rhizobium-Legume Symbiosis: Integrating Infection, Organogenesis and the Abiotic Environment. PLANT & CELL PHYSIOLOGY 2022; 63:1326-1343. [PMID: 35552446 DOI: 10.1093/pcp/pcac063] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Legume roots engage in a symbiotic relationship with rhizobia, leading to the development of nitrogen-fixing nodules. Nodule development is a sophisticated process and is under the tight regulation of the plant. The symbiosis initiates with a signal exchange between the two partners, followed by the development of a new organ colonized by rhizobia. Over two decades of study have shed light on the transcriptional regulation of rhizobium-legume symbiosis. A large number of transcription factors (TFs) have been implicated in one or more stages of this symbiosis. Legumes must monitor nodule development amidst a dynamic physical environment. Some environmental factors are conducive to nodulation, whereas others are stressful. The modulation of rhizobium-legume symbiosis by the abiotic environment adds another layer of complexity and is also transcriptionally regulated. Several symbiotic TFs act as integrators between symbiosis and the response to the abiotic environment. In this review, we trace the role of various TFs involved in rhizobium-legume symbiosis along its developmental route and highlight the ones that also act as communicators between this symbiosis and the response to the abiotic environment. Finally, we discuss contemporary approaches to study TF-target interactions in plants and probe their potential utility in the field of rhizobium-legume symbiosis.
Collapse
Affiliation(s)
- Sanhita Chakraborty
- Department of Bacteriology, University of Wisconsin, Microbial Sciences Building, 1550 Linden Dr, Madison, WI 53706, USA
| | - Oswaldo Valdés-López
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Estado de México 54090, México
| | - Christina Stonoha-Arther
- Department of Bacteriology, University of Wisconsin, Microbial Sciences Building, 1550 Linden Dr, Madison, WI 53706, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin, Microbial Sciences Building, 1550 Linden Dr, Madison, WI 53706, USA
- Department of Agronomy, University of Wisconsin, 1575 Linden Dr, Madison, WI 53706, USA
| |
Collapse
|
13
|
Zhang F, Yang J, Zhang N, Wu J, Si H. Roles of microRNAs in abiotic stress response and characteristics regulation of plant. FRONTIERS IN PLANT SCIENCE 2022; 13:919243. [PMID: 36092392 PMCID: PMC9459240 DOI: 10.3389/fpls.2022.919243] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/08/2022] [Indexed: 05/27/2023]
Abstract
MicroRNAs (miRNAs) are a class of non-coding endogenous small RNAs (long 20-24 nucleotides) that negatively regulate eukaryotes gene expression at post-transcriptional level via cleavage or/and translational inhibition of targeting mRNA. Based on the diverse roles of miRNA in regulating eukaryotes gene expression, research on the identification of miRNA target genes has been carried out, and a growing body of research has demonstrated that miRNAs act on target genes and are involved in various biological functions of plants. It has an important influence on plant growth and development, morphogenesis, and stress response. Recent case studies indicate that miRNA-mediated regulation pattern may improve agronomic properties and confer abiotic stress resistance of plants, so as to ensure sustainable agricultural production. In this regard, we focus on the recent updates on miRNAs and their targets involved in responding to abiotic stress including low temperature, high temperature, drought, soil salinity, and heavy metals, as well as plant-growing development. In particular, this review highlights the diverse functions of miRNAs on achieving the desirable agronomic traits in important crops. Herein, the main research strategies of miRNAs involved in abiotic stress resistance and crop traits improvement were summarized. Furthermore, the miRNA-related challenges and future perspectives of plants have been discussed. miRNA-based research lays the foundation for exploring miRNA regulatory mechanism, which aims to provide insights into a potential form of crop improvement and stress resistance breeding.
Collapse
Affiliation(s)
- Feiyan Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
- State Key Laboratory of Plant Genomics/Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jiangwei Yang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ning Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiahe Wu
- State Key Laboratory of Plant Genomics/Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| |
Collapse
|
14
|
Uncovering a Phenomenon of Active Hormone Transcriptional Regulation during Early Somatic Embryogenesis in Medicago sativa. Int J Mol Sci 2022; 23:ijms23158633. [PMID: 35955760 PMCID: PMC9368939 DOI: 10.3390/ijms23158633] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/30/2022] [Accepted: 08/01/2022] [Indexed: 12/04/2022] Open
Abstract
Somatic embryogenesis (SE) is a developmental process in which somatic cells undergo dedifferentiation to become plant stem cells, and redifferentiation to become a whole embryo. SE is a prerequisite for molecular breeding and is an excellent platform to study cell development in the majority of plant species. However, the molecular mechanism involved in M. sativa somatic embryonic induction, embryonic and maturation is unclear. This study was designed to examine the differentially expressed genes (DEGs) and miRNA roles during somatic embryonic induction, embryonic and maturation. The cut cotyledon (ICE), non-embryogenic callus (NEC), embryogenic callus (EC) and cotyledon embryo (CE) were selected for transcriptome and small RNA sequencing. The results showed that 17,251 DEGs, and 177 known and 110 novel miRNAs families were involved in embryonic induction (ICE to NEC), embryonic (NEC to EC), and maturation (EC to CE). Expression patterns and functional classification analysis showed several novel genes and miRNAs involved in SE. Moreover, embryonic induction is an active process of molecular regulation, and hormonal signal transduction related to pathways involved in the whole SE. Finally, a miRNA–target interaction network was proposed during M. sativa SE. This study provides novel perspectives to comprehend the molecular mechanisms in M. sativa SE.
Collapse
|
15
|
Yu L, Huang T, Qi X, Yu J, Wu T, Luo Z, Zhou L, Li Y. Genome-Wide Analysis of Long Non-coding RNAs Involved in Nodule Senescence in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2022; 13:917840. [PMID: 35707611 PMCID: PMC9189404 DOI: 10.3389/fpls.2022.917840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
Plant long non-coding RNAs (lncRNAs) are widely accepted to play crucial roles during diverse biological processes. In recent years, thousands of lncRNAs related to the establishment of symbiosis, root nodule organogenesis and nodule development have been identified in legumes. However, lncRNAs involved in nodule senescence have not been reported. In this study, senescence-related lncRNAs were investigated in Medicago truncatula nodules by high-throughput strand-specific RNA-seq. A total of 4576 lncRNAs and 126 differentially expressed lncRNAs (DElncRNAs) were identified. We found that more than 60% lncRNAs were associated with transposable elements, especially TIR/Mutator and Helitron DNA transposons families. In addition, 49 DElncRNAs were predicted to be the targets of micro RNAs. Functional analysis showed that the largest sub-set of differently expressed target genes of DElncRNAs were associated with the membrane component. Of these, nearly half genes were related to material transport, suggesting that an important function of DElncRNAs during nodule senescence is the regulation of substance transport across membranes. Our findings will be helpful for understanding the functions of lncRNAs in nodule senescence and provide candidate lncRNAs for further research.
Collapse
|
16
|
Wang D, Dong W, Murray J, Wang E. Innovation and appropriation in mycorrhizal and rhizobial Symbioses. THE PLANT CELL 2022; 34:1573-1599. [PMID: 35157080 PMCID: PMC9048890 DOI: 10.1093/plcell/koac039] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/21/2022] [Indexed: 05/20/2023]
Abstract
Most land plants benefit from endosymbiotic interactions with mycorrhizal fungi, including legumes and some nonlegumes that also interact with endosymbiotic nitrogen (N)-fixing bacteria to form nodules. In addition to these helpful interactions, plants are continuously exposed to would-be pathogenic microbes: discriminating between friends and foes is a major determinant of plant survival. Recent breakthroughs have revealed how some key signals from pathogens and symbionts are distinguished. Once this checkpoint has been passed and a compatible symbiont is recognized, the plant coordinates the sequential development of two types of specialized structures in the host. The first serves to mediate infection, and the second, which appears later, serves as sophisticated intracellular nutrient exchange interfaces. The overlap in both the signaling pathways and downstream infection components of these symbioses reflects their evolutionary relatedness and the common requirements of these two interactions. However, the different outputs of the symbioses, phosphate uptake versus N fixation, require fundamentally different components and physical environments and necessitated the recruitment of different master regulators, NODULE INCEPTION-LIKE PROTEINS, and PHOSPHATE STARVATION RESPONSES, for nodulation and mycorrhization, respectively.
Collapse
Affiliation(s)
- Dapeng Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wentao Dong
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | | | - Ertao Wang
- Authors for correspondence: (E.W) and (J.M.)
| |
Collapse
|
17
|
Ding C, Shen T, Ran N, Zhang H, Pan H, Su X, Xu M. Integrated Degradome and Srna Sequencing Revealed miRNA-mRNA Regulatory Networks between the Phloem and Developing Xylem of Poplar. Int J Mol Sci 2022; 23:ijms23094537. [PMID: 35562928 PMCID: PMC9100975 DOI: 10.3390/ijms23094537] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/27/2022] [Accepted: 04/14/2022] [Indexed: 02/04/2023] Open
Abstract
Lignin and cellulose are the most abundant natural organic polymers in nature. MiRNAs are a class of regulatory RNAs discovered in mammals, plants, viruses, and bacteria. Studies have shown that miRNAs play a role in lignin and cellulose biosynthesis by targeting key enzymes. However, the specific miRNAs functioning in the phloem and developing xylem of Populus deltoides are still unknown. In this study, a total of 134 miRNAs were identified via high-throughput small RNA sequencing, including 132 known and two novel miRNAs, six of which were only expressed in the phloem. A total of 58 differentially expressed miRNAs (DEmiRNAs) were identified between the developing xylem and the phloem. Among these miRNAs, 21 were significantly upregulated in the developing xylem in contrast to the phloem and 37 were significantly downregulated. A total of 2431 target genes of 134 miRNAs were obtained via high-throughput degradome sequencing. Most target genes of these miRNAs were transcription factors, including AP2, ARF, bHLH, bZIP, GRAS, GRF, MYB, NAC, TCP, and WRKY genes. Furthermore, 13 and nine miRNAs were involved in lignin and cellulose biosynthesis, respectively, and we validated the miRNAs via qRT-PCR. Our study explores these miRNAs and their regulatory networks in the phloem and developing xylem of P.deltoides and provides new insight into wood formation.
Collapse
Affiliation(s)
- Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China;
| | - Tengfei Shen
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (T.S.); (N.R.); (H.Z.); (H.P.)
| | - Na Ran
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (T.S.); (N.R.); (H.Z.); (H.P.)
| | - Heng Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (T.S.); (N.R.); (H.Z.); (H.P.)
| | - Huixin Pan
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (T.S.); (N.R.); (H.Z.); (H.P.)
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China;
- Correspondence: (X.S.); (M.X.); Tel.: +86-136-4130-7199 (X.S.); +86-150-9430-7586 (M.X.)
| | - Meng Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (T.S.); (N.R.); (H.Z.); (H.P.)
- Correspondence: (X.S.); (M.X.); Tel.: +86-136-4130-7199 (X.S.); +86-150-9430-7586 (M.X.)
| |
Collapse
|
18
|
Chang H, Zhang H, Zhang T, Su L, Qin QM, Li G, Li X, Wang L, Zhao T, Zhao E, Zhao H, Liu Y, Stacey G, Xu D. A Multi-Level Iterative Bi-Clustering Method for Discovering miRNA Co-regulation Network of Abiotic Stress Tolerance in Soybeans. FRONTIERS IN PLANT SCIENCE 2022; 13:860791. [PMID: 35463453 PMCID: PMC9021755 DOI: 10.3389/fpls.2022.860791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
Although growing evidence shows that microRNA (miRNA) regulates plant growth and development, miRNA regulatory networks in plants are not well understood. Current experimental studies cannot characterize miRNA regulatory networks on a large scale. This information gap provides an excellent opportunity to employ computational methods for global analysis and generate valuable models and hypotheses. To address this opportunity, we collected miRNA-target interactions (MTIs) and used MTIs from Arabidopsis thaliana and Medicago truncatula to predict homologous MTIs in soybeans, resulting in 80,235 soybean MTIs in total. A multi-level iterative bi-clustering method was developed to identify 483 soybean miRNA-target regulatory modules (MTRMs). Furthermore, we collected soybean miRNA expression data and corresponding gene expression data in response to abiotic stresses. By clustering these data, 37 MTRMs related to abiotic stresses were identified, including stress-specific MTRMs and shared MTRMs. These MTRMs have gene ontology (GO) enrichment in resistance response, iron transport, positive growth regulation, etc. Our study predicts soybean MTRMs and miRNA-GO networks under different stresses, and provides miRNA targeting hypotheses for experimental analyses. The method can be applied to other biological processes and other plants to elucidate miRNA co-regulation mechanisms.
Collapse
Affiliation(s)
- Haowu Chang
- Key Laboratory of Symbol Computation and Knowledge Engineering, College of Computer Science and Technology, Ministry of Education, Jilin University, Jilin, China
- Department of Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Hao Zhang
- Key Laboratory of Symbol Computation and Knowledge Engineering, College of Computer Science and Technology, Ministry of Education, Jilin University, Jilin, China
- Department of Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Tianyue Zhang
- Key Laboratory of Symbol Computation and Knowledge Engineering, College of Computer Science and Technology, Ministry of Education, Jilin University, Jilin, China
| | - Lingtao Su
- Department of Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- College of Computer Science and Engineering, Shandong University of Science and Technology, Qingdao, China
| | - Qing-Ming Qin
- College of Plant Sciences and Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Jilin, China
| | - Guihua Li
- College of Plant Sciences and Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Jilin, China
| | - Xueqing Li
- Key Laboratory of Symbol Computation and Knowledge Engineering, College of Computer Science and Technology, Ministry of Education, Jilin University, Jilin, China
| | - Li Wang
- Key Laboratory of Symbol Computation and Knowledge Engineering, College of Computer Science and Technology, Ministry of Education, Jilin University, Jilin, China
| | - Tianheng Zhao
- Key Laboratory of Symbol Computation and Knowledge Engineering, College of Computer Science and Technology, Ministry of Education, Jilin University, Jilin, China
| | - Enshuang Zhao
- Key Laboratory of Symbol Computation and Knowledge Engineering, College of Computer Science and Technology, Ministry of Education, Jilin University, Jilin, China
| | - Hengyi Zhao
- Key Laboratory of Symbol Computation and Knowledge Engineering, College of Computer Science and Technology, Ministry of Education, Jilin University, Jilin, China
| | - Yuanning Liu
- Key Laboratory of Symbol Computation and Knowledge Engineering, College of Computer Science and Technology, Ministry of Education, Jilin University, Jilin, China
- Department of Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Gary Stacey
- Division of Plant Sciences and Technology, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Dong Xu
- Department of Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Zhang M, Liu S, Wang Z, Yuan Y, Zhang Z, Liang Q, Yang X, Duan Z, Liu Y, Kong F, Liu B, Ren B, Tian Z. Progress in soybean functional genomics over the past decade. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:256-282. [PMID: 34388296 PMCID: PMC8753368 DOI: 10.1111/pbi.13682] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 05/24/2023]
Abstract
Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.
Collapse
Affiliation(s)
- Min Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Zhao Wang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yaqin Yuan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhifang Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qianjin Liang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xia Yang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zongbiao Duan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Baohui Liu
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Bo Ren
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| |
Collapse
|
21
|
Ding T, Tomes S, Gleave AP, Zhang H, Dare AP, Plunkett B, Espley RV, Luo Z, Zhang R, Allan AC, Zhou Z, Wang H, Wu M, Dong H, Liu C, Liu J, Yan Z, Yao JL. microRNA172 targets APETALA2 to regulate flavonoid biosynthesis in apple (Malus domestica). HORTICULTURE RESEARCH 2022; 9:uhab007. [PMID: 35039839 PMCID: PMC8846330 DOI: 10.1093/hr/uhab007] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 01/18/2022] [Accepted: 10/02/2021] [Indexed: 05/24/2023]
Abstract
MicroRNA172 (miR172) plays a role in regulating a diverse range of plant developmental processes, including flowering, fruit development and nodulation. However, its role in regulating flavonoid biosynthesis is unclear. In this study, we show that transgenic apple plants over-expressing miR172 show a reduction in red coloration and anthocyanin accumulation in various tissue types. This reduction was consistent with decreased expression of APETALA2 homolog MdAP2_1a (a miR172 target gene), MdMYB10, and targets of MdMYB10, as demonstrated by both RNA-seq and qRT-PCR analyses. The positive role of MdAP2_1a in regulating anthocyanin biosynthesis was supported by the enhanced petal anthocyanin accumulation in transgenic tobacco plants overexpressing MdAP2_1a, and by the reduction in anthocyanin accumulation in apple and cherry fruits transfected with an MdAP2_1a virus-induced-gene-silencing construct. We demonstrated that MdAP2_1a could bind directly to the promoter and protein sequences of MdMYB10 in yeast and tobacco, and enhance MdMYB10 promotor activity. In Arabidopsis, over-expression of miR172 reduced flavonoid (including anthocyanins and flavonols) concentration and RNA transcript abundance of flavonoid genes in plantlets cultured on medium containing 7% sucrose. The anthocyanin content and RNA abundance of anthocyanin genes could be partially restored by using a synonymous mutant of MdAP2_1a, which had lost the miR172 target sequences at mRNA level, but not restored by using a WT MdAP2_1a. These results indicate that miR172 inhibits flavonoid biosynthesis through suppressing the expression of an AP2 transcription factor that positively regulates MdMYB10.
Collapse
Affiliation(s)
- Tiyu Ding
- Zhengzhou Fruit Research Institute, Chinese Academy of
Agricultural Sciences, 32 Gangwan Road, Zhengzhou 450009, China
| | - Sumathi Tomes
- The New Zealand Institute for Plant & Food Research
Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Andrew P Gleave
- The New Zealand Institute for Plant & Food Research
Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Hengtao Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of
Agricultural Sciences, 32 Gangwan Road, Zhengzhou 450009, China
| | - Andrew P Dare
- The New Zealand Institute for Plant & Food Research
Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Blue Plunkett
- The New Zealand Institute for Plant & Food Research
Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Richard V Espley
- The New Zealand Institute for Plant & Food Research
Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Zhiwei Luo
- The New Zealand Institute for Plant & Food Research
Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Ruiping Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of
Agricultural Sciences, 32 Gangwan Road, Zhengzhou 450009, China
| | - Andrew C Allan
- The New Zealand Institute for Plant & Food Research
Limited, Private Bag 92169, Auckland 1142, New Zealand
- School of Biological Sciences, University of
Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Zhe Zhou
- Zhengzhou Fruit Research Institute, Chinese Academy of
Agricultural Sciences, 32 Gangwan Road, Zhengzhou 450009, China
| | - Huan Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of
Agricultural Sciences, 32 Gangwan Road, Zhengzhou 450009, China
| | - Mengmeng Wu
- Zhengzhou Fruit Research Institute, Chinese Academy of
Agricultural Sciences, 32 Gangwan Road, Zhengzhou 450009, China
| | - Haiqing Dong
- Zhengzhou Fruit Research Institute, Chinese Academy of
Agricultural Sciences, 32 Gangwan Road, Zhengzhou 450009, China
| | - Chonghuai Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of
Agricultural Sciences, 32 Gangwan Road, Zhengzhou 450009, China
| | - Jihong Liu
- College of Horticulture and Forestry Sciences, Huazhong
Agricultural University, 1 Shizishan Street Wuhan 430070, China
| | - Zhenli Yan
- Zhengzhou Fruit Research Institute, Chinese Academy of
Agricultural Sciences, 32 Gangwan Road, Zhengzhou 450009, China
| | - Jia-Long Yao
- Zhengzhou Fruit Research Institute, Chinese Academy of
Agricultural Sciences, 32 Gangwan Road, Zhengzhou 450009, China
- The New Zealand Institute for Plant & Food Research
Limited, Private Bag 92169, Auckland 1142, New Zealand
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
The Regulation of Plant Vegetative Phase Transition and Rejuvenation: miRNAs, a Key Regulator. EPIGENOMES 2021; 5:epigenomes5040024. [PMID: 34968248 PMCID: PMC8715473 DOI: 10.3390/epigenomes5040024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 01/13/2023] Open
Abstract
In contrast to animals, adult organs in plants are not formed during embryogenesis but generated from meristematic cells as plants advance through development. Plant development involves a succession of different phenotypic stages and the transition between these stages is termed phase transition. Phase transitions need to be tightly regulated and coordinated to ensure they occur under optimal seasonal, environmental conditions. Polycarpic perennials transition through vegetative stages and the mature, reproductive stage many times during their lifecycles and, in both perennial and annual species, environmental factors and culturing methods can reverse the otherwise unidirectional vector of plant development. Epigenetic factors regulating gene expression in response to internal cues and external (environmental) stimuli influencing the plant’s phenotype and development have been shown to control phase transitions. How developmental and environmental cues interact to epigenetically alter gene expression and influence these transitions is not well understood, and understanding this interaction is important considering the current climate change scenarios, since epigenetic maladaptation could have catastrophic consequences for perennial plants in natural and agricultural ecosystems. Here, we review studies focusing on the epigenetic regulators of the vegetative phase change and highlight how these mechanisms might act in exogenously induced plant rejuvenation and regrowth following stress.
Collapse
|
24
|
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.
Collapse
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
Collapse
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.)
| |
Collapse
|
25
|
Fan K, Wong-Bajracharya J, Lin X, Ni M, Ku YS, Li MW, Tian CF, Chan TF, Lam HM. Differentially expressed microRNAs that target functional genes in mature soybean nodules. THE PLANT GENOME 2021; 14:e20103. [PMID: 33973410 DOI: 10.1002/tpg2.20103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
MicroRNAs (miRNAs) are important regulators of biological functions in plants. To find out what roles miRNAs play in regulating symbiotic nitrogen fixation (SNF) in soybean [Glycine max (L.) Merr.], we identified high-confidence differentially expressed (DE) miRNAs from uninoculated roots (UR), rhizobium-inoculated roots (IR), and nodules (NODs) of soybean by robust small RNA sequencing (sRNA-seq). Based on their predicted target messenger RNAs (mRNAs), the expression profiles of some of these DE miRNAs could be linked to nodule functions. In particular, several miRNAs associated with nutrient transportation genes were differentially expressed in IRs and mature NODs. MiR399b, specifically, was highly induced in IRs and NODs, as well as by inorganic phosphate (Pi) starvation. In composite soybean plants overexpressing miR399b, PHOSPHATE2 (PHO2), a known target of miR399b that inhibits the activities of high-affinity Pi transporters, was strongly repressed. In addition, the overexpression of miR399b in the roots of transgenic composite plants significantly improved whole-plant Pi and ureide concentrations and the overall growth in terms of leaf node numbers and whole-plant dry weight. Our findings suggest that the induction of miR399b in NODs could enhance nitrogen fixation and soybean growth, possibly via improving Pi uptake to achieve a better Pi-nitrogen balance to promote SNF in nodules.
Collapse
Affiliation(s)
- Kejing Fan
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Johanna Wong-Bajracharya
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Xiao Lin
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Meng Ni
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Yee-Shan Ku
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Man-Wah Li
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Chang Fu Tian
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ting-Fung Chan
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Hon-Ming Lam
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| |
Collapse
|
26
|
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.
Collapse
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
| |
Collapse
|
27
|
Oladzad A, González A, Macchiavelli R, de Jensen CE, Beaver J, Porch T, McClean P. Genetic Factors Associated With Nodulation and Nitrogen Derived From Atmosphere in a Middle American Common Bean Panel. FRONTIERS IN PLANT SCIENCE 2020; 11:576078. [PMID: 33384700 PMCID: PMC7769817 DOI: 10.3389/fpls.2020.576078] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
Among grain legume crops, common beans (Phaseolus vulgaris L.) are considered to have poor biological nitrogen (N2) fixation (BNF) capabilities although variation in N2 fixing capabilities exists within the species. The availability of genetic panel varying in BNF capacity and a large-scale single nucleotide polymorphism (SNP) data set for common bean provided an opportunity to discover genetic factors associated with N2 fixation among genotypes in the Middle American gene pool. Using nodulation and percentage of N2-derived from atmosphere (%NDFA) data collected from field trials, at least 11 genotypes with higher levels of BNF capacity were identified. Genome-wide association studies (GWASs) detected both major and minor effects that control these traits. A major nodulation interval at Pv06:28.0-28.27 Mbp was discovered. In this interval, the peak SNP was located within a small GTPase that positively regulates cellular polarity and growth of root hair tips. Located 20 kb upstream of this peak SNP is an auxin-responsive factor AUX/indole acetic auxin (IAA)-related gene involved in auxin transportation during root nodulation. For %NDFA, nitrate (NO3 -) transporters, NRT1:2 and NRT1.7 (Pv02:8.64), squamosa promoter binding transcriptome factor (Pv08:28.42), and multi-antimicrobial extrusion protein (MATE) efflux family protein (Pv06:10.91) were identified as candidate genes. Three additional QTLs were identified on chromosomes Pv03:5.24, Pv09:25.89, and Pv11: 32.89 Mbp. These key candidate genes from both traits were integrated with previous results on N2 fixation to describe a BNF pathway.
Collapse
Affiliation(s)
- Atena Oladzad
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Abiezer González
- Department of Agroenvironmental Sciences, University of Puerto Rico, Mayagüez, Puerto Rico
| | - Raul Macchiavelli
- Department of Agroenvironmental Sciences, University of Puerto Rico, Mayagüez, Puerto Rico
| | | | - James Beaver
- Department of Agroenvironmental Sciences, University of Puerto Rico, Mayagüez, Puerto Rico
| | - Tim Porch
- USDA-ARS, Tropical Agriculture Research Station, Mayagüez, Puerto Rico
| | - Phillip McClean
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| |
Collapse
|
28
|
Ahmed S, Rashid MAR, Zafar SA, Azhar MT, Waqas M, Uzair M, Rana IA, Azeem F, Chung G, Ali Z, Atif RM. Genome-wide investigation and expression analysis of APETALA-2 transcription factor subfamily reveals its evolution, expansion and regulatory role in abiotic stress responses in Indica Rice (Oryza sativa L. ssp. indica). Genomics 2020; 113:1029-1043. [PMID: 33157261 DOI: 10.1016/j.ygeno.2020.10.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/08/2020] [Accepted: 10/30/2020] [Indexed: 12/18/2022]
Abstract
Rice is an important cereal crop that serves as staple food for more than half of the world population. Abiotic stresses resulting from changing climatic conditions are continuously threating its yield and production. Genes in APETALA-2 (AP2) family encode transcriptional regulators implicated during regulation of developmental processes and abiotic stress responses but their identification and characterization in indica rice was still missing. In this context, twenty-six genes distributed among eleven chromosomes in Indica rice encoding AP2 transcription-factor subfamily were identified and their diverse haplotypes were studied. Phylogenetic analysis of OsAP2 TF family-members grouped them into three clades indicating conservation of clades among cereals. Segmental duplications were observed to be principal route of evolution, supporting the higher positive selection-pressure, which were estimated to be originated about 10.57 to 56.72 million years ago (MYA). Conserved domain analysis and intron-exon distribution pattern of identified OsAP2s revealed their exclusive distribution among the specific clades of the phylogenetic tree. Moreover, the members of osa-miR172 family were also identified potentially targeting four OsAP2 genes. The real-time quantitative expression profiling of OsAP2s under heat stress conditions in contrasting indica rice genotypes revealed the differential expression pattern of OsAP2s (6 genes up-regulated and 4 genes down-regulated) in stress- and genotype-dependent manner. These findings unveiled the evolutionary pathways of AP2-TF in rice, and can help the functional characterization under developmental and stress responses.
Collapse
Affiliation(s)
- Sohaib Ahmed
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Muhammad Abdul Rehman Rashid
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center of Perennial Rice Engineering and Technology in Yunnan, School of Agriculture, Yunnan University, Kunming 650500, China; Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China; Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan.
| | - Syed Adeel Zafar
- National key facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Tehseen Azhar
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan; School of Agriculture Sciences, Zhengzhou University, Zhengzhou 450000, China.
| | - Muhammad Waqas
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Muhammad Uzair
- National key facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Iqrar Ahmad Rana
- Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad 38040, Pakistan.
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Republic of Korea.
| | - Zulfiqar Ali
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef University of Agriculture, Multan 66000, Pakistan.
| | - Rana Muhammad Atif
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan; Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture Faisalabad, Faisalabad-38040 Pakistan.
| |
Collapse
|
29
|
Jerome Jeyakumar JM, Ali A, Wang WM, Thiruvengadam M. Characterizing the Role of the miR156-SPL Network in Plant Development and Stress Response. PLANTS 2020; 9:plants9091206. [PMID: 32942558 PMCID: PMC7570127 DOI: 10.3390/plants9091206] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/27/2020] [Accepted: 09/11/2020] [Indexed: 01/22/2023]
Abstract
MicroRNA (miRNA) is a short, single-stranded, non-coding RNA found in eukaryotic cells that can regulate the expression of many genes at the post-transcriptional level. Among various plant miRNAs with diverse functions, miR156 plays a key role in biological processes, including developmental regulation, immune response, metabolic regulation, and abiotic stress. MiRNAs have become the regulatory center for plant growth and development. MicroRNA156 (miR156) is a highly conserved and emerging tool for the improvement of plant traits, including crop productivity and stress tolerance. Fine-tuning of squamosa promoter biding-like (SPL) gene expression might be a useful strategy for crop improvement. Here, we studied the regulation of the miR156 module and its interaction with SPL factors to understand the developmental transition of various plant species. Furthermore, this review provides a strong background for plant biotechnology and is an important source of information for further molecular breeding to optimize farming productivity.
Collapse
Affiliation(s)
- John Martin Jerome Jeyakumar
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China; (J.M.J.J.); (A.A.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Institute of Rice Research, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China
| | - Asif Ali
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China; (J.M.J.J.); (A.A.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Institute of Rice Research, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China
| | - Wen-Ming Wang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China; (J.M.J.J.); (A.A.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Institute of Rice Research, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China
- Correspondence:
| | - Muthu Thiruvengadam
- Department of Applied Bioscience, College of Life and Environmental Sciences, Konkuk University, Seoul 05029, Korea;
| |
Collapse
|
30
|
Chung MY, Nath UK, Vrebalov J, Gapper N, Lee JM, Lee DJ, Kim CK, Giovannoni J. Ectopic expression of miRNA172 in tomato (Solanum lycopersicum) reveals novel function in fruit development through regulation of an AP2 transcription factor. BMC PLANT BIOLOGY 2020; 20:283. [PMID: 32560687 PMCID: PMC7304166 DOI: 10.1186/s12870-020-02489-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 06/11/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are short non-coding RNAs that can influence gene expression via diverse mechanisms. Tomato is a fruit widely consumed for its flavor, culinary attributes, and high nutritional quality. Tomato fruit are climacteric and fleshy, and their ripening is regulated by endogenous and exogenous signals operating through a coordinated genetic network. Much research has been conducted on mechanisms of tomato fruit ripening, but the roles of miRNA-regulated repression/expression of specific regulatory genes are not well documented. RESULTS In this study, we demonstrate that miR172 specifically targets four SlAP2 transcription factor genes in tomato. Among them, SlAP2a was repressed by the overexpression of SlmiR172, manifesting in altered flower morphology, development and accelerated ripening. miR172 over-expression lines specifically repressed SlAP2a, enhancing ethylene biosynthesis, fruit color and additional ripening characteristics. Most previously described ripening-regulatory genes, including RIN-MADS, NR, TAGL1 and LeHB-1 were not influenced by miR172 while CNR showed altered expression. CONCLUSIONS Tomato fruit ripening is directly influenced by miR172 targeting of the APETALA2 transcription factor, SlAP2a, with minimal influence over additional known ripening-regulatory genes. miR172a-guided SlAP2a expression provides insight into another layer of genetic control of ripening and a target for modifying the quality and nutritional value of tomato and possibly other fleshy fruit crops.
Collapse
Affiliation(s)
- Mi-Young Chung
- Department of Agricultural Education, Sunchon National University, Suncheon, South Korea
| | - Ujjal Kumar Nath
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Julia Vrebalov
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Nigel Gapper
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Je Min Lee
- Department of Horticulture, Kyungpook National University, Daegu, Korea
| | - Do-Jin Lee
- Department of Agricultural Education, Sunchon National University, Suncheon, South Korea
| | - Chang Kil Kim
- Department of Horticulture, Kyungpook National University, Daegu, Korea.
| | - James Giovannoni
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA.
- US Department of Agriculture/Agriculture Research Service, Robert W. Holley Centre for Agriculture and Health, Ithaca, New York, USA.
| |
Collapse
|
31
|
Hoang NT, Tóth K, Stacey G. The role of microRNAs in the legume-Rhizobium nitrogen-fixing symbiosis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1668-1680. [PMID: 32163588 DOI: 10.1093/jxb/eraa018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/10/2020] [Indexed: 06/10/2023]
Abstract
Under nitrogen starvation, most legume plants form a nitrogen-fixing symbiosis with Rhizobium bacteria. The bacteria induce the formation of a novel organ called the nodule in which rhizobia reside as intracellular symbionts and convert atmospheric nitrogen into ammonia. During this symbiosis, miRNAs are essential for coordinating the various plant processes required for nodule formation and function. miRNAs are non-coding, endogenous RNA molecules, typically 20-24 nucleotides long, that negatively regulate the expression of their target mRNAs. Some miRNAs can move systemically within plant tissues through the vascular system, which mediates, for example, communication between the stem/leaf tissues and the roots. In this review, we summarize the growing number of miRNAs that function during legume nodulation focusing on two model legumes, Lotus japonicus and Medicago truncatula, and two important legume crops, soybean (Glycine max) and common bean (Phaseolus vulgaris). This regulation impacts a variety of physiological processes including hormone signaling and spatial regulation of gene expression. The role of mobile miRNAs in regulating legume nodule number is also highlighted.
Collapse
Affiliation(s)
- Nhung T Hoang
- C.S. Bond Life Sciences Center, Divisions of Plant Science and Biochemistry, University of Missouri-Columbia, MO, USA
| | - Katalin Tóth
- C.S. Bond Life Sciences Center, Divisions of Plant Science and Biochemistry, University of Missouri-Columbia, MO, USA
| | - Gary Stacey
- C.S. Bond Life Sciences Center, Divisions of Plant Science and Biochemistry, University of Missouri-Columbia, MO, USA
| |
Collapse
|
32
|
Liu F, Tang Y, Guo Q, Chen J. Identification and characterization of microRNAs in phloem and xylem from ramie (Boehmeria nivea). Mol Biol Rep 2019; 47:1013-1020. [PMID: 31820312 DOI: 10.1007/s11033-019-05193-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 11/12/2019] [Indexed: 11/28/2022]
Abstract
Ramie (Boehmeria nivea) is a widely cropped species in southern China due to its high economic value of natural fiber for industry. Development of phloem and xylem is key evidence for generating fiber. However, the MicroRNA (miRNA) profiles of phloem and xylem in ramie have not been reported yet. miRNA belong to a small RNA family which has been recognized as an important regulator for various biological processes. In the present study, we aimed to identify differently expressed miRNAs between phloem and xylem in adult ramie. The results showed that 137 and 122 unique conserved miRNAs were identified from phloem and xylem libraries, respectively. Meanwhile, 4 novel miRNAs were identified from ramie by miRDeep2. Of these miRNAs, 77 conserved miRNAs in ramie were differentially expressed. Among the differentially expressed miRNAs, 44 miRNAs and 33 miRNAs were up-regulated and down-regulated in phloem compared to that in xylem, respectively. The functions of differentially expressed miRNAs were associated with regulating the development and differentiation of phloem and xylem. The present study provides a glance of miRNA profiles for further understanding of miRNA role in ramie development.
Collapse
Affiliation(s)
- Fang Liu
- Department of Biotechnology and Environmental Science, Changsha University, Hongshan Road 98#, Changsha, 410003, Hunan, China
| | - Yinghong Tang
- Department of Biotechnology and Environmental Science, Changsha University, Hongshan Road 98#, Changsha, 410003, Hunan, China
| | - Qingquan Guo
- Department of Biotechnology and Environmental Science, Changsha University, Hongshan Road 98#, Changsha, 410003, Hunan, China
| | - Jianrong Chen
- Department of Biotechnology and Environmental Science, Changsha University, Hongshan Road 98#, Changsha, 410003, Hunan, China.
| |
Collapse
|
33
|
Solomon CU, Drea S. Besides and Beyond Flowering: Other roles of EuAP2 Genes in Plant Development. Genes (Basel) 2019; 10:genes10120994. [PMID: 31805740 PMCID: PMC6947164 DOI: 10.3390/genes10120994] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/27/2019] [Accepted: 11/27/2019] [Indexed: 12/18/2022] Open
Abstract
EuAP2 genes are well-known for their role in flower development, a legacy of the founding member of this subfamily of transcription factors, whose mutants lacked petals in Arabidopsis. However, studies of euAP2 genes in several species have accumulated evidence highlighting the diverse roles of euAP2 genes in other aspects of plant development. Here, we emphasize other developmental roles of euAP2 genes in various species and suggest a shift from regarding euAP2 genes as just flowering genes to consider the global role they may be playing in plant development. We hypothesize that their almost universal expression profile and pleiotropic effects of their mutation suggest their involvement in fundamental plant development processes.
Collapse
Affiliation(s)
- Charles U. Solomon
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Department of Plant Science and Biotechnology, Abia State University, PMB 2000, Uturu 441107, Nigeria
- Correspondence:
| | - Sinéad Drea
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| |
Collapse
|
34
|
Schwember AR, Schulze J, Del Pozo A, Cabeza RA. Regulation of Symbiotic Nitrogen Fixation in Legume Root Nodules. PLANTS (BASEL, SWITZERLAND) 2019; 8:E333. [PMID: 31489914 PMCID: PMC6784058 DOI: 10.3390/plants8090333] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 08/30/2019] [Accepted: 09/04/2019] [Indexed: 12/11/2022]
Abstract
In most legume nodules, the di-nitrogen (N2)-fixing rhizobia are present as organelle-like structures inside their root host cells. Many processes operate and interact within the symbiotic relationship between plants and nodules, including nitrogen (N)/carbon (C) metabolisms, oxygen flow through nodules, oxidative stress, and phosphorous (P) levels. These processes, which influence the regulation of N2 fixation and are finely tuned on a whole-plant basis, are extensively reviewed in this paper. The carbonic anhydrase (CA)-phosphoenolpyruvate carboxylase (PEPC)-malate dehydrogenase (MDH) is a key pathway inside nodules involved in this regulation, and malate seems to play a crucial role in many aspects of symbiotic N2 fixation control. How legumes specifically sense N-status and how this stimulates all of the regulatory factors are key issues for understanding N2 fixation regulation on a whole-plant basis. This must be thoroughly studied in the future since there is no unifying theory that explains all of the aspects involved in regulating N2 fixation rates to date. Finally, high-throughput functional genomics and molecular tools (i.e., miRNAs) are currently very valuable for the identification of many regulatory elements that are good candidates for accurately dissecting the particular N2 fixation control mechanisms associated with physiological responses to abiotic stresses. In combination with existing information, utilizing these abundant genetic molecular tools will enable us to identify the specific mechanisms underlying the regulation of N2 fixation.
Collapse
Affiliation(s)
- Andrés R Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 306-22, Chile.
| | - Joachim Schulze
- Department of Crop Science, Section for Plant Nutrition and Crop Physiology, Faculty of Agriculture, University of Goettingen, Carl-Sprengel-Weg 1, 37075 Goettingen, Germany.
| | - Alejandro Del Pozo
- Centro de Mejoramiento Genético y Fenómica Vegetal, Facultad de Ciencias Agrarias, Universidad de Talca, Talca 3460000, Chile.
- Departamento de Producción Agrícola, Facultad de Ciencias Agrarias, Universidad de Talca, Campus Talca, Talca 3460000, Chile.
| | - Ricardo A Cabeza
- Departamento de Producción Agrícola, Facultad de Ciencias Agrarias, Universidad de Talca, Campus Talca, Talca 3460000, Chile.
| |
Collapse
|
35
|
Ahsan MU, Hayward A, Alam M, Bandaralage JH, Topp B, Beveridge CA, Mitter N. Scion control of miRNA abundance and tree maturity in grafted avocado. BMC PLANT BIOLOGY 2019; 19:382. [PMID: 31481026 PMCID: PMC6724330 DOI: 10.1186/s12870-019-1994-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/27/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Grafting is the common propagation method for avocado and primarily benefits orchard production by reducing the time to tree productivity. It also allows use of scions and rootstocks specifically selected for improved productivity and commercial acceptance. Rootstocks in avocado may be propagated from mature tree cuttings ('mature'), or from seed ('juvenile'). While the use of mature scion material hastens early bearing/maturity and economic return, the molecular factors involved in the role of the scion and/or rootstock in early bearing/reduced juvenility of the grafted tree are still unknown. RESULTS Here, we utilized juvenility and flowering associated miRNAs; miR156 and miR172 and their putative target genes to screen pre-graft and post-graft material in different combinations from avocado. The abundance of mature miR156, miR172 and the miR156 target gene SPL4, showed a strong correlation to the maturity of the scion and rootstock material in avocado. Graft transmissibility of miR156 and miR172 has been explored in annual plants. Here, we show that the scion may be responsible for grafted tree maturity involving these factors, while the rootstock maturity does not significantly influence miRNA abundance in the scion. We also demonstrate that the presence of leaves on cutting rootstocks supports graft success and contributes towards intergraft signalling involving the carbohydrate-marker TPS1. CONCLUSION Here, we suggest that the scion largely controls the molecular 'maturity' of grafted avocado trees, however, leaves on the rootstock not only promote graft success, but can influence miRNA and mRNA abundance in the scion. This constitutes the first study on scion and rootstock contribution towards grafted tree maturity using the miR156-SPL4-miR172 regulatory module as a marker for juvenility and reproductive competence.
Collapse
Affiliation(s)
- Muhammad Umair Ahsan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland 4072 Australia
| | - Alice Hayward
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland 4072 Australia
| | - Mobashwer Alam
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland 4072 Australia
| | - Jayeni Hiti Bandaralage
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland 4072 Australia
| | - Bruce Topp
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland 4072 Australia
| | - Christine Anne Beveridge
- School of Biological Sciences, The University of Queensland, St. Lucia, Brisbane, Queensland 4072 Australia
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland 4072 Australia
| |
Collapse
|
36
|
Ahsan MU, Hayward A, Alam M, Bandaralage JH, Topp B, Beveridge CA, Mitter N. Scion control of miRNA abundance and tree maturity in grafted avocado. BMC PLANT BIOLOGY 2019; 19:382. [PMID: 31481026 DOI: 10.1186/s12870-019-1994-1995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/27/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Grafting is the common propagation method for avocado and primarily benefits orchard production by reducing the time to tree productivity. It also allows use of scions and rootstocks specifically selected for improved productivity and commercial acceptance. Rootstocks in avocado may be propagated from mature tree cuttings ('mature'), or from seed ('juvenile'). While the use of mature scion material hastens early bearing/maturity and economic return, the molecular factors involved in the role of the scion and/or rootstock in early bearing/reduced juvenility of the grafted tree are still unknown. RESULTS Here, we utilized juvenility and flowering associated miRNAs; miR156 and miR172 and their putative target genes to screen pre-graft and post-graft material in different combinations from avocado. The abundance of mature miR156, miR172 and the miR156 target gene SPL4, showed a strong correlation to the maturity of the scion and rootstock material in avocado. Graft transmissibility of miR156 and miR172 has been explored in annual plants. Here, we show that the scion may be responsible for grafted tree maturity involving these factors, while the rootstock maturity does not significantly influence miRNA abundance in the scion. We also demonstrate that the presence of leaves on cutting rootstocks supports graft success and contributes towards intergraft signalling involving the carbohydrate-marker TPS1. CONCLUSION Here, we suggest that the scion largely controls the molecular 'maturity' of grafted avocado trees, however, leaves on the rootstock not only promote graft success, but can influence miRNA and mRNA abundance in the scion. This constitutes the first study on scion and rootstock contribution towards grafted tree maturity using the miR156-SPL4-miR172 regulatory module as a marker for juvenility and reproductive competence.
Collapse
Affiliation(s)
- Muhammad Umair Ahsan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia
| | - Alice Hayward
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia
| | - Mobashwer Alam
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia
| | - Jayeni Hiti Bandaralage
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia
| | - Bruce Topp
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia
| | - Christine Anne Beveridge
- School of Biological Sciences, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia.
| |
Collapse
|
37
|
Wang L, Sun Z, Su C, Wang Y, Yan Q, Chen J, Ott T, Li X. A GmNINa-miR172c-NNC1 Regulatory Network Coordinates the Nodulation and Autoregulation of Nodulation Pathways in Soybean. MOLECULAR PLANT 2019; 12:1211-1226. [PMID: 31201867 DOI: 10.1016/j.molp.2019.06.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 06/02/2019] [Accepted: 06/04/2019] [Indexed: 05/25/2023]
Abstract
Symbiotic root nodules are root lateral organs of plants in which nitrogen-fixing bacteria (rhizobia) convert atmospheric nitrogen to ammonia. The formation and number of nodules in legumes are precisely controlled by a rhizobia-induced signal cascade and host-controlled autoregulation of nodulation (AON). However, how these pathways are integrated and their underlying mechanisms are unclear. Here, we report that microRNA172c (miR172c) activates soybean (Glycine max) Rhizobia-Induced CLE1 (GmRIC1) and GmRIC2 by removing the transcriptional repression of these genes by Nodule Number Control 1 (NNC1), leading to the activation of the AON pathway. NNC1 interacts with GmNINa, the soybean ortholog of Lotus NODULE INCEPTION (NIN), and hampers its transcriptional activation of GmRIC1 and GmRIC2. Importantly, GmNINa acts as a transcriptional activator of miR172c. Intriguingly, NNC1 can transcriptionally repress miR172c expression, adding a negative feedback loop into the NNC1 regulatory network. Moreover, GmNINa interacts with NNC1 and can relieve the NNC1-mediated repression of miR172c transcription. Thus, the GmNINa-miR172c-NNC1 network is a master switch that coordinately regulates and optimizes NF and AON signaling, supporting the balance between nodulation and AON in soybean.
Collapse
Affiliation(s)
- Lixiang Wang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, P.R. China; College of Biological Science and Engineering, Panzhihua University, No. 10 Airport Road, Eastern District, Panzhihua, Sichuan, China
| | - Zhengxi Sun
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, P.R. China
| | - Chao Su
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, P.R. China; University of Freiburg, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Yongliang Wang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, P.R. China
| | - Qiqi Yan
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, P.R. China
| | - Jiahuan Chen
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, P.R. China
| | - Thomas Ott
- University of Freiburg, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Xia Li
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, P.R. China.
| |
Collapse
|
38
|
Ye J, Han W, Fan R, Liu M, Li L, Jia X. Integration of Transcriptomes, Small RNAs, and Degradome Sequencing to Identify Putative miRNAs and Their Targets Related to Eu-Rubber Biosynthesis in Eucommia ulmoides. Genes (Basel) 2019; 10:genes10080623. [PMID: 31430866 PMCID: PMC6722833 DOI: 10.3390/genes10080623] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/10/2019] [Accepted: 08/13/2019] [Indexed: 01/24/2023] Open
Abstract
Eucommia ulmoides has attracted much attention as a valuable natural rubber (Eu-rubber) production tree. As a strategic material, Eu-rubber plays a vital role in general and defence industries. However, the study of Eu-rubber biosynthesis at a molecular level is scarce, and the regulatory network between microRNAs (miRNAs) and messenger RNAs (mRNAs) in Eu-rubber biosynthesis has not been assessed. In this study, we comprehensively analyzed the transcriptomes, small RNAs (sRNAs) and degradome to reveal the regulatory network of Eu-rubber biosynthesis in E. ulmoides. A total of 82,065 unigenes and 221 miRNAs were identified using high-throughput sequencing; 20,815 targets were predicted using psRNATarget software. Of these targets, 779 miRNA-target pairs were identified via degradome sequencing. Thirty-one miRNAs were differentially expressed; 22 targets of 34 miRNAs were annotated in the terpenoid backbone biosynthesis pathway (ko00900) based on the Kyoto Encyclopedia of Genes and Genomes (KEGG). These miRNAs were putatively related to Eu-rubber biosynthesis. A regulatory network was constructed according to the expression profiles of miRNAs and their targets. These results provide a comprehensive analysis of transcriptomics, sRNAs and degradome to reveal the Eu-rubber accumulation, and provide new insights into genetic engineering techniques which may improve the content of Eu-rubber in E. ulmoides.
Collapse
Affiliation(s)
- Jing Ye
- College of Forestry, Northwest A&F University, Shaanxi 712100, China
| | - Wenjing Han
- College of Forestry, Northwest A&F University, Shaanxi 712100, China
| | - Ruisheng Fan
- College of Forestry, Northwest A&F University, Shaanxi 712100, China
| | - Minhao Liu
- College of Forestry, Northwest A&F University, Shaanxi 712100, China
| | - Long Li
- College of Forestry, Northwest A&F University, Shaanxi 712100, China
| | - Xiaoming Jia
- College of Forestry, Northwest A&F University, Shaanxi 712100, China.
| |
Collapse
|
39
|
Ramesh SV, Govindasamy V, Rajesh MK, Sabana AA, Praveen S. Stress-responsive miRNAome of Glycine max (L.) Merrill: molecular insights and way forward. PLANTA 2019; 249:1267-1284. [PMID: 30798358 DOI: 10.1007/s00425-019-03114-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
MAIN CONCLUSION Analysis of stress-associated miRNAs of Glycine max (L.) Merrill reveals wider ramifications of small RNA-mediated (conserved and legume-specific miRNAs) gene regulatory foot prints in molecular adaptive responses. MicroRNAs (miRNAs) are indispensable components of gene regulatory mechanism of plants. Soybean is a crop of immense commercial potential grown worldwide for its edible oil and soy meal. Intensive research efforts, using the next generation sequencing and bioinformatics techniques, have led to the identification and characterization of numerous small RNAs, especially microRNAs (miRNAs), in soybean. Furthermore, studies have unequivocally demonstrated the significance of miRNAs during the developmental processes and various stresses in soybean. In this review, we summarize the current state of understanding of miRNA-based abiotic and biotic stress responses in soybean. In addition, the molecular insights gained from the stress-related soybean miRNAs have been compared to the miRNAs of other crops, especially legumes, and the core commonalities have been highlighted, though differences among them were not ignored. Nature of response of soybean-derived conserved miRNAs during various stresses was also analyzed to gain deeper insights regarding sRNAome-based defense responses. This review further provides way forward in legume small RNA transcriptomics based on the adaptive responses of soybean and other legume-derived miRNAs.
Collapse
Affiliation(s)
- S V Ramesh
- ICAR-Indian Institute of Soybean Research (ICAR-IISR), Indore, Madhya Pradesh, 452001, India.
- ICAR-Central Plantation Crops Research Institute (ICAR-CPCRI), Kasaragod, Kerala, 671124, India.
| | - V Govindasamy
- ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, 110012, India
| | - M K Rajesh
- ICAR-Central Plantation Crops Research Institute (ICAR-CPCRI), Kasaragod, Kerala, 671124, India
| | - A A Sabana
- ICAR-Central Plantation Crops Research Institute (ICAR-CPCRI), Kasaragod, Kerala, 671124, India
| | - Shelly Praveen
- ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, 110012, India
| |
Collapse
|
40
|
Hossain MS, Hoang NT, Yan Z, Tóth K, Meyers BC, Stacey G. Characterization of the Spatial and Temporal Expression of Two Soybean miRNAs Identifies SCL6 as a Novel Regulator of Soybean Nodulation. FRONTIERS IN PLANT SCIENCE 2019; 10:475. [PMID: 31057581 PMCID: PMC6477095 DOI: 10.3389/fpls.2019.00475] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/28/2019] [Indexed: 05/13/2023]
Abstract
MicroRNAs (miRNAs) control expression of endogenous target genes through transcript cleavage or translational inhibition. Legume plants can form a specialized organ, the nodule, through interaction with nitrogen fixing soil bacteria. To understand the regulatory roles of miRNAs in the nodulation process, we functionally validated gma-miR171o and gma-miR171q and their target genes in soybean. These two miRNA sequences are identical in sequence but their miRNA genes are divergent and show unique, tissue-specific expression patterns. The expression levels of the two miRNAs are negatively correlated with that of their target genes. Ectopic expression of these miRNAs in transgenic hairy roots resulted in a significant reduction in nodule formation. Both gma-miR171o and gma-miR171q target members of the GRAS transcription factor superfamily, namely GmSCL-6 and GmNSP2. Transient interaction of miRNAs and their target genes in tobacco cells further confirmed their cleavage activity. The results suggest that gma-miR171o and gma-miR171q regulate GmSCL-6 and GmNSP2, which in turn, influence expression of the Nodule inception (NIN), Early Nodulin 40 (ENOD40), and Ethylene Response Factor Required for Nodulation (ERN) genes during the Bradyrhizobium japonicum-soybean nodulation process. Collectively, our data suggest a role for two miRNAs, gma-miR171o and gma-miR171q, in regulating the spatial and temporal aspects of soybean nodulation.
Collapse
Affiliation(s)
- Md Shakhawat Hossain
- C.S. Bond Life Science Center, Divisions of Plant Sciences and Biochemistry, University of Missouri, Columbia, MO, United States
| | - Nhung T. Hoang
- C.S. Bond Life Science Center, Divisions of Plant Sciences and Biochemistry, University of Missouri, Columbia, MO, United States
| | - Zhe Yan
- C.S. Bond Life Science Center, Divisions of Plant Sciences and Biochemistry, University of Missouri, Columbia, MO, United States
| | - Katalin Tóth
- C.S. Bond Life Science Center, Divisions of Plant Sciences and Biochemistry, University of Missouri, Columbia, MO, United States
| | - Blake C. Meyers
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Gary Stacey
- C.S. Bond Life Science Center, Divisions of Plant Sciences and Biochemistry, University of Missouri, Columbia, MO, United States
| |
Collapse
|
41
|
The miRNA-Mediated Post-Transcriptional Regulation of Maize in Response to High Temperature. Int J Mol Sci 2019; 20:ijms20071754. [PMID: 30970661 PMCID: PMC6480492 DOI: 10.3390/ijms20071754] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 01/20/2023] Open
Abstract
High temperature (HT) has recently become one of the most important abiotic stresses restricting crop production worldwide. MicroRNAs (miRNAs) are important regulators in plant development and stress responses. However, knowledge of miRNAs of maize in response to HT is limited. In this study, we simultaneously adopted miRNA sequencing and transcriptome profiling to analyze the differential expression of miRNAs and mRNAs in maize during exposure to HT stress. Our analysis revealed 61 known miRNAs belonging to 26 miRNA families and 42 novel miRNAs showing significant differential expression, with the majority being downregulated. Meanwhile, the expression of 5450 mRNAs was significantly altered in the same stressed tissues. Differentially expressed transcripts were most significantly associated with response to stress, photosynthesis, biosynthesis of secondary metabolites, and signal transduction pathways. In addition, we discovered 129 miRNA–mRNA pairs that were regulated antagonistically, and further depiction of the targeted mRNAs indicated that several transcription factors, protein kinases, and receptor-like-protein-related transmembrane transport and signaling transduction were profoundly affected. This study has identified potential key regulators of HT-stress response in maize and the subset of genes that are likely to be post-transcriptionally regulated by miRNAs under HT stress.
Collapse
|
42
|
Noon JB, Hewezi T, Baum TJ. Homeostasis in the soybean miRNA396-GRF network is essential for productive soybean cyst nematode infections. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1653-1668. [PMID: 30715445 PMCID: PMC6411377 DOI: 10.1093/jxb/erz022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 01/15/2019] [Indexed: 05/20/2023]
Abstract
Heterodera glycines, the soybean cyst nematode, penetrates soybean roots and migrates to the vascular cylinder where it forms a feeding site called the syncytium. MiRNA396 (miR396) targets growth-regulating factor (GRF) genes, and the miR396-GRF1/3 module is a master regulator of syncytium development in model cyst nematode H. schachtii infection of Arabidopsis. Here, we investigated whether this regulatory system operates similarly in soybean roots and is likewise important for H. glycines infection. We found that a network involving nine MIR396 and 23 GRF genes is important for normal development of soybean roots and that GRF function is specified in the root apical meristem by miR396. All MIR396 genes are down-regulated in the syncytium during its formation phase while, specifically, 11 different GRF genes are up-regulated. The switch to the syncytium maintenance phase coincides with up-regulation of MIR396 and down-regulation of the 11 GRF genes specifically via post-transcriptional regulation by miR396. Furthermore, interference with the miR396-GRF6/8-13/15-17/19 regulatory network, through either overexpression or knockdown experiments, does not affect the number of H. glycines juveniles that enter the vascular cylinder to initiate syncytia, but specifically inhibits efficient H. glycines development to adult females. Therefore, homeostasis in the miR396-GRF6/8-13/15-17/19 regulatory network is essential for productive H. glycines infections.
Collapse
Affiliation(s)
- Jason B Noon
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| |
Collapse
|
43
|
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.
Collapse
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
| |
Collapse
|
44
|
Pandey P, Wang M, Baldwin IT, Pandey SP, Groten K. Complex regulation of microRNAs in roots of competitively-grown isogenic Nicotiana attenuata plants with different capacities to interact with arbuscular mycorrhizal fungi. BMC Genomics 2018; 19:937. [PMID: 30558527 PMCID: PMC6296096 DOI: 10.1186/s12864-018-5338-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 11/29/2018] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Nicotiana attenuata is an ecological model plant whose 2.57 Gb genome has recently been sequenced and assembled and for which miRNAs and their genomic locations have been identified. To understand how this plant's miRNAs are reconfigured during plant-arbuscular mycorrhizal fungal (AMF) interactions and whether hostplant calcium- and calmodulin dependent protein kinase (CCaMK) expression which regulates the AMF interaction also modulates miRNAs levels and regulation, we performed a large-scale miRNA analysis of this plant-AMF interaction. RESULTS Next generation sequencing of miRNAs in roots of empty vector (EV) N. attenuata plants and an isogenic line silenced in CCaMK expression (irCCaMK) impaired in AMF-interactions grown under competitive conditions with and without AMF inoculum revealed a total of 149 unique miRNAs: 67 conserved and 82 novel ones. The majority of the miRNAs had a length of 21 nucleotides. MiRNA abundances were highly variable ranging from 400 to more than 25,000 reads per million. The miRNA profile of irCCaMK plants impaired in AMF colonization was distinct from fully AMF-functional EV plants grown in the same pot. Six conserved miRNAs were present in all conditions and accumulated differentially depending on treatment and genotype; five (miR6153, miR403a-3p, miR7122a, miR167-5p and miR482d, but not miR399a-3p) showed the highest accumulation in AMF inoculated EV plants compared to inoculated irCCaMK plants. Furthermore, the accumulation patterns of sequence variants of selected conserved miRNAs showed a very distinct pattern related to AMF colonization - one variant of miR473-5p specifically accumulated in AMF-inoculated plants. Also abundances of miR403a-3p, miR171a-3p and one of the sequence variants of miR172a-3p increased in AMF-inoculated EV compared to inoculated irCCaMK plants and to non-inoculated EV plants, while miR399a-3p was most strongly enriched in AMF inoculated irCCaMK plants grown in competition with EV. The analysis of putative targets of selected miRNAs revealed an involvement in P starvation (miR399), phytohormone signaling (Nat-R-PN59, miR172, miR393) and defense (e.g. miR482, miR8667, Nat-R-PN-47). CONCLUSIONS Our study demonstrates (1) a large-scale reprograming of miRNAs induced by AMF colonization and (2) that the impaired AMF signaling due to CCaMK silencing and the resulting reduced competitive ability of irCCaMK plants play a role in modulating signal-dependent miRNA accumulation.
Collapse
Affiliation(s)
- Priyanka Pandey
- National Institute of Biomedical Genomics, Kalyani, West Bengal India
| | - Ming Wang
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - Ian T. Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - Shree P. Pandey
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745 Jena, Germany
- Department of Biological Sciences, IISER Kolkata, Mohanpur, Nadia, West Bengal 741246 India
| | - Karin Groten
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745 Jena, Germany
| |
Collapse
|
45
|
Tang M, Bai X, Niu LJ, Chai X, Chen MS, Xu ZF. miR172 Regulates both Vegetative and Reproductive Development in the Perennial Woody Plant Jatropha curcas. PLANT & CELL PHYSIOLOGY 2018; 59:2549-2563. [PMID: 30541045 PMCID: PMC6290486 DOI: 10.1093/pcp/pcy175] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/21/2018] [Indexed: 05/04/2023]
Abstract
Jatropha curcas is a promising feedstock for biofuel production because its oil is highly suitable for processing bio-jet fuels and biodiesel. However, Jatropha exhibits a long juvenile stage in subtropical areas. miR172, a conserved small non-protein-coding RNA molecule with 21 nucleotides, regulates a wide range of developmental processes. To date, however, no studies have examined the function of miR172 in Jatropha. There are five miR172 precursors encoding two mature miR172s in Jatropha, which are expressed in all tissues, with the highest expression level in leaves, and the levels are up-regulated with age. Overexpression of JcmiR172a resulted in early flowering, abnormal flowers, and altered leaf morphology in transgenic Arabidopsis and Jatropha. The expression levels of miR172 target genes were down-regulated, and the flower identity genes were up-regulated in the JcmiR172a-overexpressing transgenic plants. Interestingly, we showed that JcmiR172 might be involved in regulation of stem vascular development through manipulating the expression of cellulose and lignin biosynthesis genes. Overexpression of JcmiR172a enhanced xylem development and reduced phloem and pith development. This study helped elucidate the functions of miR172 in perennial plants, a known age-related miRNA involved in the regulation of perennial plant phase change and organ development.
Collapse
Affiliation(s)
- Mingyong Tang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
| | - Xue Bai
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Long-Jian Niu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
| | - Xia Chai
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Mao-Sheng Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
| | - Zeng-Fu Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
- Corresponding author: E-mail, ; Fax, +86-691-8715070
| |
Collapse
|
46
|
Libault M. Transcriptional Reprogramming of Legume Genomes: Perspective and Challenges Associated With Single-Cell and Single Cell-Type Approaches During Nodule Development. FRONTIERS IN PLANT SCIENCE 2018; 9:1600. [PMID: 30467509 PMCID: PMC6237103 DOI: 10.3389/fpls.2018.01600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 10/17/2018] [Indexed: 05/11/2023]
Abstract
Transcriptomic approaches revealed thousands of genes differentially or specifically expressed during nodulation, a biological process resulting from the symbiosis between leguminous plant roots and rhizobia, atmospheric nitrogen-fixing symbiotic bacteria. Ultimately, nodulation will lead to the development of a new root organ, the nodule. Through functional genomic studies, plant transcriptomes have been used by scientists to reveal plant genes potentially controlling nodulation. However, it is important to acknowledge that the physiology, transcriptomic programs, and biochemical properties of the plant cells involved in nodulation are continuously regulated. They also differ between the different cell-types composing the nodules. To generate a more accurate picture of the transcriptome, epigenome, proteome, and metabolome of the cells infected by rhizobia and cells composing the nodule, there is a need to implement plant single-cell and single cell-types strategies and methods. Accessing such information would allow a better understanding of the infection of plant cells by rhizobia and will help understanding the complex interactions existing between rhizobia and the plant cells. In this mini-review, we are reporting the current knowledge on legume nodulation gained by plant scientists at the level of single cell-types, and provide perspectives on single cell/single cell-type approaches when applied to legume nodulation.
Collapse
Affiliation(s)
- Marc Libault
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Centre for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
- Center for Root and Rhizobiome Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
| |
Collapse
|
47
|
Diédhiou I, Diouf D. Transcription factors network in root endosymbiosis establishment and development. World J Microbiol Biotechnol 2018; 34:37. [PMID: 29450655 DOI: 10.1007/s11274-018-2418-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/29/2018] [Indexed: 11/29/2022]
Abstract
Root endosymbioses are mutualistic interactions between plants and the soil microorganisms (Fungus, Frankia or Rhizobium) that lead to the formation of nitrogen-fixing root nodules and/or arbuscular mycorrhiza. These interactions enable many species to survive in different marginal lands to overcome the nitrogen-and/or phosphorus deficient environment and can potentially reduce the chemical fertilizers used in agriculture which gives them an economic, social and environmental importance. The formation and the development of these structures require the mediation of specific gene products among which the transcription factors play a key role. Three of these transcription factors, viz., CYCLOPS, NSP1 and NSP2 are well conserved between actinorhizal, legume, non-legume and mycorrhizal symbioses. They interact with DELLA proteins to induce the expression of NIN in nitrogen fixing symbiosis or RAM1 in mycorrhizal symbiosis. Recently, the small non coding RNA including micro RNAs (miRNAs) have emerged as major regulators of root endosymbioses. Among them, miRNA171 targets NSP2, a TF conserved in actinorhizal, legume, non-legume and mycorrhizal symbioses. This review will also focus on the recent advances carried out on the biological function of others transcription factors during the root pre-infection/pre-contact, infection or colonization. Their role in nodule formation and AM development will also be described.
Collapse
Affiliation(s)
- Issa Diédhiou
- Laboratoire Campus de Biotecnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar-Fann, Senegal.
| | - Diaga Diouf
- Laboratoire Campus de Biotecnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar-Fann, Senegal
| |
Collapse
|
48
|
Díaz-Manzano FE, Cabrera J, Ripoll JJ, del Olmo I, Andrés MF, Silva AC, Barcala M, Sánchez M, Ruíz-Ferrer V, de Almeida-Engler J, Yanofsky MF, Piñeiro M, Jarillo JA, Fenoll C, Escobar C. A role for the gene regulatory module microRNA172/TARGET OF EARLY ACTIVATION TAGGED 1/FLOWERING LOCUS T (miRNA172/TOE1/FT) in the feeding sites induced by Meloidogyne javanica in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2018; 217:813-827. [PMID: 29105090 PMCID: PMC5922426 DOI: 10.1111/nph.14839] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 09/05/2017] [Indexed: 05/20/2023]
Abstract
Root knot nematodes (RKNs) penetrate into the root vascular cylinder, triggering morphogenetic changes to induce galls, de novo formed 'pseudo-organs' containing several giant cells (GCs). Distinctive gene repression events observed in early gall/GCs development are thought to be mediated by post-transcriptional silencing via microRNAs (miRNAs), a process that is far from being fully characterized. Arabidopsis thaliana backgrounds with altered activities based on target 35S::MIMICRY172 (MIM172), 35S::TARGET OF EARLY ACTIVATION TAGGED 1 (TOE1)-miR172-resistant (35S::TOE1R ) and mutant (flowering locus T-10 (ft-10)) lines were used for functional analysis of nematode infective and reproductive parameters. The GUS-reporter lines, MIR172A-E::GUS, treated with auxin (IAA) and an auxin-inhibitor (a-(phenyl ethyl-2-one)-indole-3-acetic acid (PEO-IAA)), together with the MIR172C AuxRE::GUS line with two mutated auxin responsive elements (AuxREs), were assayed for nematode-dependent gene expression. Arabidopsis thaliana backgrounds with altered expression of miRNA172, TOE1 or FT showed lower susceptibility to the RKNs and smaller galls and GCs. MIR172C-D::GUS showed restricted promoter activity in galls/GCs that was regulated by auxins through auxin-responsive factors. IAA induced their activity in galls while PEO-IAA treatment and mutations in AuxRe motifs abolished it. The results showed that the regulatory module miRNA172/TOE1/FT plays an important role in correct GCs and gall development, where miRNA172 is modulated by auxins.
Collapse
Affiliation(s)
- Fernando E. Díaz-Manzano
- Universidad de Castilla-La Mancha. Facultad de Ciencias Ambientales y Bioquímica, Área de Fisiología Vegetal. Avda. Carlos III, s/n, 45071 Toledo, Spain
| | - Javier Cabrera
- Universidad de Castilla-La Mancha. Facultad de Ciencias Ambientales y Bioquímica, Área de Fisiología Vegetal. Avda. Carlos III, s/n, 45071 Toledo, Spain
| | - Juan-José Ripoll
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA 92093-0116 USA
| | - Iván del Olmo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Mari Fe Andrés
- Instituto de Ciencias Agrarias (ICA, CSIC), Protección Vegetal, Calle de Serrano 115, 28006 Madrid, Spain
| | - Ana Cláudia Silva
- Universidad de Castilla-La Mancha. Facultad de Ciencias Ambientales y Bioquímica, Área de Fisiología Vegetal. Avda. Carlos III, s/n, 45071 Toledo, Spain
| | - Marta Barcala
- Universidad de Castilla-La Mancha. Facultad de Ciencias Ambientales y Bioquímica, Área de Fisiología Vegetal. Avda. Carlos III, s/n, 45071 Toledo, Spain
| | - María Sánchez
- Universidad de Castilla-La Mancha. Facultad de Ciencias Ambientales y Bioquímica, Área de Fisiología Vegetal. Avda. Carlos III, s/n, 45071 Toledo, Spain
| | - Virginia Ruíz-Ferrer
- Universidad de Castilla-La Mancha. Facultad de Ciencias Ambientales y Bioquímica, Área de Fisiología Vegetal. Avda. Carlos III, s/n, 45071 Toledo, Spain
| | - Janice de Almeida-Engler
- Institut National de la Recherche Agronomique (INRA) - University of Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900 Sophia Antipolis, France
| | - Martin F. Yanofsky
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA 92093-0116 USA
| | - Manuel Piñeiro
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Jose Antonio Jarillo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Carmen Fenoll
- Universidad de Castilla-La Mancha. Facultad de Ciencias Ambientales y Bioquímica, Área de Fisiología Vegetal. Avda. Carlos III, s/n, 45071 Toledo, Spain
| | - Carolina Escobar
- Universidad de Castilla-La Mancha. Facultad de Ciencias Ambientales y Bioquímica, Área de Fisiología Vegetal. Avda. Carlos III, s/n, 45071 Toledo, Spain
| |
Collapse
|
49
|
Sahito ZA, Wang L, Sun Z, Yan Q, Zhang X, Jiang Q, Ullah I, Tong Y, Li X. The miR172c-NNC1 module modulates root plastic development in response to salt in soybean. BMC PLANT BIOLOGY 2017; 17:229. [PMID: 29191158 PMCID: PMC5709930 DOI: 10.1186/s12870-017-1161-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 11/08/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND Plant roots are highly plastic to high salinity. However, the molecular mechanism by which root developmental plasticity is regulated remains largely unknown. Previously we reported that miR172c-NNC1 module plays a key role in soybean-rhizobial symbiosis. The fact that the miR172c promoter contains several stress-related cis elements indicates that miR172c may have a role in root response to abiotic stress. RESULTS Here we showed that miR172c is greatly induced by salt stress in soybean. Overexpression of miR172c and knockdown of miR172c activity resulted in substantially increased and reduced root sensitivity to salt stress, respectively. Furthermore, we show that the target gene NNC1 (Nodule Number Control 1) of miR172c was downregulated by salt stress. The transgenic roots overexpressing or knocking down NNC1 expression also exhibited the altered root sensitivity to salt stress. CONCLUSION The study reveals the crucial role of miR172c-NNC1 module in root stress tolerance to salt stress in soybean.
Collapse
Affiliation(s)
- Zulfiqar Ali Sahito
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, Hebei 050021 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Lixiang Wang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, Hebei 050021 People’s Republic of China
| | - Zhengxi Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Qiqi Yan
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Xingke Zhang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Qiong Jiang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, Hebei 050021 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Ihteram Ullah
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, Hebei 050021 People’s Republic of China
| | - Yiping Tong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xia Li
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| |
Collapse
|
50
|
Chien PS, Chiang CB, Wang Z, Chiou TJ. MicroRNA-mediated signaling and regulation of nutrient transport and utilization. CURRENT OPINION IN PLANT BIOLOGY 2017; 39:73-79. [PMID: 28668626 DOI: 10.1016/j.pbi.2017.06.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 06/10/2017] [Accepted: 06/12/2017] [Indexed: 05/23/2023]
Abstract
MicroRNAs (miRNAs), a group of small-RNA regulators, control diverse developmental processes and stress responses. Recent studies of nutrient-responsive miRNAs have offered novel insights into how plants regulate gene expression to coordinate endogenous demand and external availability of nutrients. Here, we review the mechanisms mediated by miRNAs to facilitate nutrient transport and utilization and show that miRNAs: first, control nutrient uptake and translocation by targeting nutrient transporters or their regulators; second, adjust nutrient metabolism by redistributing nutrients for biosynthesis of more essential compounds; and third, modulate root development and microbial symbiosis to exploit soil nutrients. We also highlight the long-distance movement of miRNAs in maintaining whole-plant nutrient homeostasis and propose several directions for future research.
Collapse
Affiliation(s)
- Pei-Shan Chien
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chih-Bin Chiang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Zhengrui Wang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Tzyy-Jen Chiou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan.
| |
Collapse
|