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López-Márquez D, Del-Espino Á, Ruiz-Albert J, Bejarano ER, Brodersen P, Beuzón CR. Regulation of plant immunity via small RNA-mediated control of NLR expression. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6052-6068. [PMID: 37449766 PMCID: PMC10575705 DOI: 10.1093/jxb/erad268] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Plants use different receptors to detect potential pathogens: membrane-anchored pattern recognition receptors (PRRs) activated upon perception of pathogen-associated molecular patterns (PAMPs) that elicit pattern-triggered immunity (PTI); and intracellular nucleotide-binding leucine-rich repeat proteins (NLRs) activated by detection of pathogen-derived effectors, activating effector-triggered immunity (ETI). The interconnections between PTI and ETI responses have been increasingly reported. Elevated NLR levels may cause autoimmunity, with symptoms ranging from fitness cost to developmental arrest, sometimes combined with run-away cell death, making accurate control of NLR dosage key for plant survival. Small RNA-mediated gene regulation has emerged as a major mechanism of control of NLR dosage. Twenty-two nucleotide miRNAs with the unique ability to trigger secondary siRNA production from target transcripts are particularly prevalent in NLR regulation. They enhance repression of the primary NLR target, but also bring about repression of NLRs only complementary to secondary siRNAs. We summarize current knowledge on miRNAs and siRNAs in the regulation of NLR expression with an emphasis on 22 nt miRNAs and propose that miRNA and siRNA regulation of NLR levels provides additional links between PTI and NLR defense pathways to increase plant responsiveness against a broad spectrum of pathogens and control an efficient deployment of defenses.
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Affiliation(s)
- Diego López-Márquez
- Department of Biology, University of Copenhagen, Copenhagen N, DK-2200, Denmark
| | - Ángel Del-Espino
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Javier Ruiz-Albert
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Peter Brodersen
- Department of Biology, University of Copenhagen, Copenhagen N, DK-2200, Denmark
| | - Carmen R Beuzón
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
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2
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Mittal M, Dhingra A, Dawar P, Payton P, Rock CD. The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea). THE PLANT GENOME 2023; 16:e20350. [PMID: 37351954 DOI: 10.1002/tpg2.20350] [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: 10/17/2022] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 06/24/2023]
Abstract
MicroRNAs (miRNAs) are 21-24 nt small RNAs (sRNAs) that negatively regulate protein-coding genes and/or trigger phased small-interfering RNA (phasiRNA) production. Two thousand nine hundred miRNA families, of which ∼40 are deeply conserved, have been identified in ∼80 different plant species genomes. miRNA functions in response to abiotic stresses is less understood than their roles in development. Only seven peanut MIRNA families are documented in miRBase, yet a reference genome assembly is now published and over 480 plant-like MIRNA loci were predicted in the diploid peanut progenitor Arachis duranensis genome. We explored by computational analysis of a leaf sRNA library and publicly available sRNA, degradome, and transcriptome datasets the miRNA and phasiRNA space associated with drought and heat stresses in peanut. We characterized 33 novel candidate and 33 ancient conserved families of MIRNAs and present degradome evidence for their cleavage activities on mRNA targets, including several noncanonical targets and novel phasiRNA-producing noncoding and mRNA loci with validated novel targets such as miR1509 targeting serine/threonine-protein phosphatase7 and miRc20 and ahy-miR3514 targeting penta-tricopeptide repeats (PPRs), in contradistinction to other claims of miR1509/173/7122 superfamily miRNAs indirectly targeting PPRs via TAS-like noncoding RNA loci. We characterized the inverse correlations of significantly differentially expressed drought- and heat-regulated miRNAs, assayed by sRNA blots or transcriptome datasets, with target mRNA expressions in the same datasets. Meta-analysis of an expression atlas and over representation of miRNA target genes in co-expression networks suggest that miRNAs have functions in unique aspects of peanut gynophore development. Genome-wide MIRNA annotation of the published allopolyploid peanut genome can facilitate molecular breeding of value-added traits.
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Affiliation(s)
- Meenakshi Mittal
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Anuradha Dhingra
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Pranav Dawar
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Paxton Payton
- USDA-ARS Plant Stress and Germplasm Lab, Lubbock, Texas, USA
| | - Christopher D Rock
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
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3
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Pei LL, Zhang LL, Liu X, Jiang J. Role of microRNA miR171 in plant development. PeerJ 2023; 11:e15632. [PMID: 37456878 PMCID: PMC10340099 DOI: 10.7717/peerj.15632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 06/02/2023] [Indexed: 07/18/2023] Open
Abstract
MicroRNAs (miRNAs) are endogenous non-coding small RNA with 19-24 nucleotides (nts) in length, which play an essential role in regulating gene expression at the post-transcriptional level. As one of the first miRNAs found in plants, miR171 is a typical class of conserved miRNAs. The miR171 sequences among different species are highly similar, and the vast majority of them have both "GAGCCG" and "CAAUAU" fragments. In addition to being involved in plant growth and development, hormone signaling and stress response, miR171 also plays multiple and important roles in plants through interactions with microbe and other small-RNAs. The miRNA functions by regulating the expression of target genes. Most of miR171's target genes are in the GRAS gene family, but also include some NSP, miRNAs, lncRNAs, and other genes. This review is intended to summarize recent updates on miR171 regarding its function in plant life and hopefully provide new ideas for understanding miR171 function and regulatory mechanisms.
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Affiliation(s)
- Ling Ling Pei
- College of Horticulture, Shenyang Agricultural University, Shenyang, Shenhe District, China
| | - Ling Ling Zhang
- College of Horticulture, Shenyang Agriculture University, Shenyang, Shenhe District, China
| | - Xin Liu
- Horticulture Department, Shenyang Agricultural University, Shenyang, Shenhe District, China
| | - Jing Jiang
- Horticulture Department, Shenyang Agricultural University, Shenyang, Shenhe District, China
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4
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Wu P, Lu C, Wang B, Zhang F, Shi L, Xu Y, Chen A, Si H, Su J, Wu J. Cotton RSG2 Mediates Plant Resistance against Verticillium dahliae by miR482b Regulation. BIOLOGY 2023; 12:898. [PMID: 37508331 PMCID: PMC10376429 DOI: 10.3390/biology12070898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/16/2023] [Accepted: 06/16/2023] [Indexed: 07/30/2023]
Abstract
Cotton Verticillium wilt, mainly caused by Verticillium dahliae, has a serious impact on the yield and quality of cotton fiber. Many microRNAs (miRNAs) have been identified to participate in plant resistance to V. dahliae infection, but the exploration of miRNA's function mechanism in plant defense is needed. Here, we demonstrate that the ghr-miR482b-GhRSG2 module mediates cotton plant resistance to V. dahliae infection. Based on the mRNA degradation data and GUS fusion experiments, ghr-miR482b directedly bonds to GhRSG2 mRNA to lead to its degradation. The knockdown and overexpression of ghr-miR482b through virus-induced gene silencing strategies enhanced (decreased by 0.39-fold in disease index compared with the control) and weakened (increased by 0.46-fold) the plant resistance to V. dahliae, respectively. In addition, silencing GhRSG2 significantly increased (increased by 0.93-fold in disease index) the plant sensitivity to V. dahliae compared with the control plants treated with empty vector. The expression levels of two SA-related disease genes, GhPR1 and GhPR2, significantly decreased in GhRSG2-silenced plants by 0.71 and 0.67 times, respectively, and in ghr-miR482b-overexpressed (OX) plants by 0.59 and 0.75 times, respectively, compared with the control, whereas the expression levels of GhPR1 and GhPR2 were significantly increased by 1.21 and 2.59 times, respectively, in ghr-miR482b knockdown (KD) plants. In sum, the ghr-miR482b-GhRSG2 module participates in the regulation of plant defense against V. dahliae by inducing the expression of PR1 and PR2 genes.
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Affiliation(s)
- Pan Wu
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Chengzhe Lu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bingting Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Feiyan Zhang
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Linfang Shi
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yunjiao Xu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Aimin Chen
- The Key Laboratory for the Creation of Cotton Varieties in the Northwest, Ministry of Agriculture and Rural Affairs, Changji 831100, China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Junji Su
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Jiahe Wu
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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5
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Nguyen CX, Dohnalkova A, Hancock CN, Kirk KR, Stacey G, Stacey MG. Critical role for uricase and xanthine dehydrogenase in soybean nitrogen fixation and nodule development. THE PLANT GENOME 2023; 16:e20171. [PMID: 34904377 DOI: 10.1002/tpg2.20172] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 09/22/2021] [Indexed: 06/14/2023]
Abstract
De novo purine biosynthesis is required for the incorporation of fixed nitrogen in ureide exporting nodules, as formed on soybean [Glycine max (L.) Merr.] roots. However, in many cases, the enzymes involved in this pathway have been deduced strictly from genome annotations with little direct genetic evidence, such as mutant studies, to confirm their biochemical function or importance to nodule development. While efforts to develop large mutant collections of soybean are underway, research on this plant is still hampered by the inability to obtain mutations in any specific gene of interest. Using a forward genetic approach, as well as CRISPR/Cas9 gene editing via Agrobacterium rhizogenes-mediated hairy root transformation, we identified and characterized the role of GmUOX (Uricase) and GmXDH (Xanthine Dehydrogenase) in nitrogen fixation and nodule development in soybean. The gmuox knockout soybean mutants displayed nitrogen deficiency chlorosis and early nodule senescence, as exemplified by the reduced nitrogenase (acetylene reduction) activity in nodules, the internal greenish-white internal appearance of nodules, and diminished leghemoglobin production. In addition, gmuox1 nodules showed collapsed infected cells with degraded cytoplasm, aggregated bacteroids with no discernable symbiosome membranes, and increased formation of poly-β-hydroxybutyrate granules. Similarly, knockout gmxdh mutant nodules, generated with the CRISPR/Cas9 system, also exhibited early nodule senescence. These genetic studies confirm the critical role of the de novo purine metabolisms pathway not only in the incorporation of fixed nitrogen but also in the successful development of a functional, nitrogen-fixing nodule. Furthermore, these studies demonstrate the great utility of the CRISPR/Cas9 system for studying root-associated gene traits when coupled with hairy root transformation.
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Affiliation(s)
- Cuong X Nguyen
- Division of Plant Sciences, Univ. of Missouri, Columbia, MO, 65211, USA
| | - Alice Dohnalkova
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - C Nathan Hancock
- Dep. of Biology & Geology, Univ. of South Carolina, Aiken, SC, 29801, USA
| | - Kendall R Kirk
- Edisto Research & Education Center, Clemson Univ., Blackville, SC, 29817, USA
| | - Gary Stacey
- Division of Plant Sciences, Univ. of Missouri, Columbia, MO, 65211, USA
- Division of Biochemistry, Univ. of Missouri, Columbia, MO, 65211, USA
| | - Minviluz G Stacey
- Division of Plant Sciences, Univ. of Missouri, Columbia, MO, 65211, USA
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6
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Zhu C, Yuan T, Yang K, Liu Y, Li Y, Gao Z. Identification and characterization of CircRNA-associated CeRNA networks in moso bamboo under nitrogen stress. BMC PLANT BIOLOGY 2023; 23:142. [PMID: 36918810 PMCID: PMC10012455 DOI: 10.1186/s12870-023-04155-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Nitrogen is a macronutrient element for plant growth and development. Circular RNAs (circRNAs) serve as pivotal regulators for the coordination between nutrient supply and plant demand. Moso bamboo (Phyllostachys edulis) is an excellent plant with fast growth, and the mechanism of the circRNA-target module in response to nitrogen remains unclear. RESULTS Deep small RNA sequencing results of moso bamboo seedlings under different concentrations of KNO3 (N0 = 0 mM, N6 = 6 mM, N18 = 18 mM) were used to identify circRNAs. A total of 549 circRNAs were obtained, of which 309 were generated from corresponding parental coding genes including 66 new ones. A total of 536 circRNA-parent genes were unevenly distributed in 24 scaffolds and were associated with root growth and development. Furthermore, 52 differentially expressed circRNAs (DECs) were obtained, including 24, 33 and 15 DECs from three comparisons of N0 vs. N6, N0 vs. N18 and N6 vs. N18, respectively. Based on integrative analyses of the identified DECs, differentially expressed mRNAs (DEGs), and miRNAs (DEMs), a competitive endogenous RNA (ceRNA) network was constructed, including five DECs, eight DEMs and 32 DEGs. A regulatory module of PeSca_6:12,316,320|12,372,905-novel_miR156-PH02Gene35622 was further verified by qPCR and dual-luciferase reporter assays. CONCLUSION The results indicated that circRNAs could participate in multiple biological processes as miRNA sponges, including organ nitrogen compound biosynthesis and metabolic process regulation in moso bamboo. Our results provide valuable information for further study of circRNAs in moso bamboo under fluctuating nitrogen conditions.
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Affiliation(s)
- Chenglei Zhu
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102, China
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo &, Rattan Science and Technology, Beijing, 100102, China
| | - Tingting Yuan
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102, China
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo &, Rattan Science and Technology, Beijing, 100102, China
| | - Kebin Yang
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102, China
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo &, Rattan Science and Technology, Beijing, 100102, China
| | - Yan Liu
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102, China
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo &, Rattan Science and Technology, Beijing, 100102, China
| | - Ying Li
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102, China
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo &, Rattan Science and Technology, Beijing, 100102, China
| | - Zhimin Gao
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102, China.
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo &, Rattan Science and Technology, Beijing, 100102, China.
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7
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Kajla M, Roy A, Singh IK, Singh A. Regulation of the regulators: Transcription factors controlling biosynthesis of plant secondary metabolites during biotic stresses and their regulation by miRNAs. FRONTIERS IN PLANT SCIENCE 2023; 14:1126567. [PMID: 36938003 PMCID: PMC10017880 DOI: 10.3389/fpls.2023.1126567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Biotic stresses threaten to destabilize global food security and cause major losses to crop yield worldwide. In response to pest and pathogen attacks, plants trigger many adaptive cellular, morphological, physiological, and metabolic changes. One of the crucial stress-induced adaptive responses is the synthesis and accumulation of plant secondary metabolites (PSMs). PSMs mitigate the adverse effects of stress by maintaining the normal physiological and metabolic functioning of the plants, thereby providing stress tolerance. This differential production of PSMs is tightly orchestrated by master regulatory elements, Transcription factors (TFs) express differentially or undergo transcriptional and translational modifications during stress conditions and influence the production of PSMs. Amongst others, microRNAs, a class of small, non-coding RNA molecules that regulate gene expression post-transcriptionally, also play a vital role in controlling the expression of many such TFs. The present review summarizes the role of stress-inducible TFs in synthesizing and accumulating secondary metabolites and also highlights how miRNAs fine-tune the differential expression of various stress-responsive transcription factors during biotic stress.
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Affiliation(s)
- Mohini Kajla
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Amit Roy
- Excellent Team for Mitigation (ETM), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Indrakant K. Singh
- Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- Jagdish Chandra Bose Center for Plant Genomics, Hansraj College, University of Delhi, Delhi, India
- Delhi School of Climate Change and Sustainability, Institution of Eminence, Maharishi Karnad Bhawan, University of Delhi, Delhi, India
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8
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Sánchez-Correa MDS, Isidra-Arellano MC, Pozas-Rodríguez EA, Reyero-Saavedra MDR, Morales-Salazar A, del Castillo SMLC, Sanchez-Flores A, Jiménez-Jacinto V, Reyes JL, Formey D, Valdés-López O. Argonaute5 and its associated small RNAs modulate the transcriptional response during the rhizobia- Phaseolus vulgaris symbiosis. FRONTIERS IN PLANT SCIENCE 2022; 13:1034419. [PMID: 36466235 PMCID: PMC9714512 DOI: 10.3389/fpls.2022.1034419] [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: 09/01/2022] [Accepted: 10/19/2022] [Indexed: 06/17/2023]
Abstract
Both plant- and rhizobia-derived small RNAs play an essential role in regulating the root nodule symbiosis in legumes. Small RNAs, in association with Argonaute proteins, tune the expression of genes participating in nodule development and rhizobial infection. However, the role of Argonaute proteins in this symbiosis has been overlooked. In this study, we provide transcriptional evidence showing that Argonaute5 (AGO5) is a determinant genetic component in the root nodule symbiosis in Phaseolus vulgaris. A spatio-temporal transcriptional analysis revealed that the promoter of PvAGO5 is active in lateral root primordia, root hairs from rhizobia-inoculated roots, nodule primordia, and mature nodules. Transcriptional analysis by RNA sequencing revealed that gene silencing of PvAGO5 affected the expression of genes involved in the biosynthesis of the cell wall and phytohormones participating in the rhizobial infection process and nodule development. PvAGO5 immunoprecipitation coupled to small RNA sequencing revealed the small RNAs bound to PvAGO5 during the root nodule symbiosis. Identification of small RNAs associated to PvAGO5 revealed miRNAs previously known to participate in this symbiotic process, further supporting a role for AGO5 in this process. Overall, the data presented shed light on the roles that PvAGO5 plays during the root nodule symbiosis in P. vulgaris.
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Affiliation(s)
- María del Socorro Sánchez-Correa
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Estado de México, Mexico
| | - Mariel C. Isidra-Arellano
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Estado de México, Mexico
| | - Eithan A. Pozas-Rodríguez
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Estado de México, Mexico
| | - María del Rocío Reyero-Saavedra
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Estado de México, Mexico
| | - Alfredo Morales-Salazar
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Estado de México, Mexico
| | | | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Verónica Jiménez-Jacinto
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Jose L. Reyes
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Damien Formey
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Oswaldo Valdés-López
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Estado de México, Mexico
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9
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Santos-Medellín C, Edwards J, Nguyen B, Sundaresan V. Acquisition of a complex root microbiome reshapes the transcriptomes of rice plants. THE NEW PHYTOLOGIST 2022; 235:2008-2021. [PMID: 35590484 DOI: 10.1111/nph.18261] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Soil microorganisms can colonize plant roots and assemble in communities engaged in symbiotic relationships with their host. Though the compositional dynamics of root-associated microbiomes have been extensively studied, the host transcriptional response to these communities is poorly understood. Here, we developed an experimental system by which rice plants grown under axenic conditions can acquire a defined endosphere microbiome. Using this setup, we performed a cross-sectional characterization of plant transcriptomes in the presence or absence of a complex microbial community. To account for compositional variation, plants were inoculated with soil-derived microbiomes harvested from three distinct agricultural sites. Soil microbiomes triggered a major shift in the transcriptional profiles of rice plants that included the downregulation of one-third to one-fourth of the families of leucine-rich repeat receptor-like kinases and nucleotide-binding leucine-rich repeat receptors expressed in roots. Though the expression of several genes was consistent across all soil sources, a large fraction of this response was differentially impacted by soil type. These results demonstrate the role of root microbiomes in sculpting the transcriptomes of host plants and highlight the potential involvement of the two main receptor families of the plant immune system in the recruitment and maintenance of an endosphere microbiome.
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Affiliation(s)
| | - Joseph Edwards
- Department of Plant Biology, University of California, Davis, Davis, CA, 95616, USA
| | - Bao Nguyen
- Department of Plant Biology, University of California, Davis, Davis, CA, 95616, USA
| | - Venkatesan Sundaresan
- Department of Plant Biology, University of California, Davis, Davis, CA, 95616, USA
- Department of Plant Sciences, University of California, Davis, Davis, CA, 95616, USA
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10
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Baldrich P, Bélanger S, Kong S, Pokhrel S, Tamim S, Teng C, Schiebout C, Gurazada SGR, Gupta P, Patel P, Razifard H, Nakano M, Dusia A, Meyers BC, Frank MH. The evolutionary history of small RNAs in Solanaceae. PLANT PHYSIOLOGY 2022; 189:644-665. [PMID: 35642548 PMCID: PMC9157080 DOI: 10.1093/plphys/kiac089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/07/2022] [Indexed: 06/01/2023]
Abstract
The Solanaceae or "nightshade" family is an economically important group with remarkable diversity. To gain a better understanding of how the unique biology of the Solanaceae relates to the family's small RNA (sRNA) genomic landscape, we downloaded over 255 publicly available sRNA data sets that comprise over 2.6 billion reads of sequence data. We applied a suite of computational tools to predict and annotate two major sRNA classes: (1) microRNAs (miRNAs), typically 20- to 22-nucleotide (nt) RNAs generated from a hairpin precursor and functioning in gene silencing and (2) short interfering RNAs (siRNAs), including 24-nt heterochromatic siRNAs typically functioning to repress repetitive regions of the genome via RNA-directed DNA methylation, as well as secondary phased siRNAs and trans-acting siRNAs generated via miRNA-directed cleavage of a polymerase II-derived RNA precursor. Our analyses described thousands of sRNA loci, including poorly understood clusters of 22-nt siRNAs that accumulate during viral infection. The birth, death, expansion, and contraction of these sRNA loci are dynamic evolutionary processes that characterize the Solanaceae family. These analyses indicate that individuals within the same genus share similar sRNA landscapes, whereas comparisons between distinct genera within the Solanaceae reveal relatively few commonalities.
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Affiliation(s)
- Patricia Baldrich
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | | | - Shuyao Kong
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Suresh Pokhrel
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri 65211, USA
| | - Saleh Tamim
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA
| | - Chong Teng
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | | | - Sai Guna Ranjan Gurazada
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA
- Corteva Agriscience, Wilmington, Delaware 19805, USA
| | - Pallavi Gupta
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Institute for Data Science & Informatics, University of Missouri, Columbia, Missouri 65211, USA
| | - Parth Patel
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA
| | - Hamid Razifard
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Mayumi Nakano
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Ayush Dusia
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri 65211, USA
| | - Margaret H Frank
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
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11
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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.
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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
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12
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Ku YS, Cheung MY, Cheng SS, Nadeem MA, Chung G, Lam HM. Using the Knowledge of Post-transcriptional Regulations to Guide Gene Selections for Molecular Breeding in Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:867731. [PMID: 35432392 PMCID: PMC9009170 DOI: 10.3389/fpls.2022.867731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
The omics approaches allow the scientific community to successfully identify genomic regions associated with traits of interest for marker-assisted breeding. Agronomic traits such as seed color, yield, growth habit, and stress tolerance have been the targets for soybean molecular breeding. Genes governing these traits often undergo post-transcriptional modifications, which should be taken into consideration when choosing elite genes for molecular breeding. Post-transcriptional regulations of genes include transcript regulations, protein modifications, and even the regulation of the translational machinery. Transcript regulations involve elements such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) for the maintenance of transcript stability or regulation of translation efficiency. Protein modifications involve molecular modifications of target proteins and the alterations of their interacting partners. Regulations of the translational machinery include those on translation factors and the ribosomal protein complex. Post-transcriptional regulations usually involve a set of genes instead of a single gene. Such a property may facilitate molecular breeding. In this review, we will discuss the post-transcriptional modifications of genes related to favorable agronomic traits such as stress tolerance, growth, and nutrient uptake, using examples from soybean as well as other crops. The examples from other crops may guide the selection of genes for marker-assisted breeding in soybean.
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Affiliation(s)
- Yee-Shan Ku
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ming-Yan Cheung
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Sau-Shan Cheng
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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13
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Amoanimaa-Dede H, Su C, Yeboah A, Zhou H, Zheng D, Zhu H. Growth regulators promote soybean productivity: a review. PeerJ 2022; 10:e12556. [PMID: 35265396 PMCID: PMC8900611 DOI: 10.7717/peerj.12556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 11/05/2021] [Indexed: 01/06/2023] Open
Abstract
Soybean [Glycine max (L.) Merrill] is a predominant edible plant and a major supply of plant protein worldwide. Global demand for soybean keeps increasing as its seeds provide essential proteins, oil, and nutraceuticals. In a quest to meet heightened demands for soybean, it has become essential to introduce agro-technical methods that promote adaptability to complex environments, improve soybean resistance to abiotic stress , and increase productivity. Plant growth regulators are mainly exploited to achieve this due to their crucial roles in plant growth and development. Increasing research suggests the influence of plant growth regulators on soybean growth and development, yield, quality, and abiotic stress responses. In an attempt to expatiate on the topic, current knowledge, and possible applications of plant growth regulators that improve growth and yield have been reviewed and discussed. Notably, the application of plant growth regulators in their appropriate concentrations at suitable growth periods relieves abiotic stress thereby increasing the yield and yield components of soybean. Moreover, the regulation effects of different growth regulators on the morphology, physiology, and yield quality of soybean are discoursed in detail.
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Affiliation(s)
- Hanna Amoanimaa-Dede
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong Province, China
| | - Chuntao Su
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong Province, China
| | - Akwasi Yeboah
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong Province, China
| | - Hang Zhou
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong Province, China
| | - Dianfeng Zheng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong Province, China
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong Province, China
| | - Hongbo Zhu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong Province, China
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14
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Zhang Y, Waseem M, Zeng Z, Xu J, Chen C, Liu Y, Zhai J, Xia R. MicroRNA482/2118, a miRNA superfamily essential for both disease resistance and plant development. THE NEW PHYTOLOGIST 2022; 233:2047-2057. [PMID: 34761409 DOI: 10.1111/nph.17853] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 11/07/2021] [Indexed: 05/17/2023]
Abstract
MicroRNAs (miRNAs) are a class of 21-24 nucleotides (nt) noncoding small RNAs ubiquitously distributed across the plant kingdom. miR482/2118, one of the conserved miRNA superfamilies originating from gymnosperms, has divergent main functions in core-angiosperms. It mainly regulates NUCLEOTIDE BINDING SITE-LEUCINE-RICH REPEAT (NBS-LRR) genes in eudicots, functioning as an essential component in plant disease resistance; in contrast, it predominantly targets numerous long noncoding RNAs (lncRNAs) in monocot grasses, which are vital for plant reproduction. Usually, miR482/2118 is 22-nt in length, which can trigger the production of phased small interfering RNAs (phasiRNAs) after directed cleavage. PhasiRNAs instigated from target genes of miR482/2118 enhance their roles in corresponding biological processes by cis-regulation on cognate genes and expands their function to other pathways via trans activity on different genes. This review summarizes the origin, biogenesis, conservation, and evolutionary characteristics of the miR482/2118 superfamily and delineates its diverse functions in disease resistance, plant development, stress responses, etc.
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Affiliation(s)
- Yanqing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
| | - Muhammad Waseem
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
| | - Zaohai Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
| | - Jing Xu
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
| | - Chengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
| | - Yuanlong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
| | - Jixian Zhai
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
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15
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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: 57] [Impact Index Per Article: 28.5] [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.
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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
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16
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Šečić E, Kogel KH, Ladera-Carmona MJ. Biotic stress-associated microRNA families in plants. JOURNAL OF PLANT PHYSIOLOGY 2021; 263:153451. [PMID: 34119743 DOI: 10.1016/j.jplph.2021.153451] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 06/12/2023]
Abstract
Plants and animals utilize various regulatory mechanisms for control of gene expression during development in different tissues and cell types. About 30 years ago, a new mechanism of gene regulation, termed RNA interference (RNAi), was discovered and proved revolutionary for the mechanistic understanding of gene regulation. Noncoding RNAs, including short, 21-24 nucleotide (nt) long microRNAs (miRNAs), endogenously-generated from MIR genes, are key components of RNAi processes, by post-transcriptionally controlling transcripts with antisense complementarity through either translational repression or mRNA degradation. Since their discovery, important roles in regulation of ontogenetic development, cell differentiation, proliferation, and apoptosis in eukaryotes have been elucidated. In plants, miRNAs are known regulatory elements of basic endogenous functions and responses to the environmental stimuli. While the role of miRNAs in regulation of nutrient uptake, circadian clock and general response to abiotic stress is already well understood, a comprehensive understanding of their immune-regulatory roles in response to various biotic stress factors has not yet been achieved. This review summarizes the current understanding of the function of miRNAs and their targets in plants during interaction with microbial pathogens and symbionts. Additionally, we provide a consensus conclusion regarding the typical induction or repression response of conserved miRNA families to pathogenic and beneficial fungi, bacteria, and oomycetes, as well as an outlook of agronomic application of miRNAs in plants. Further investigation of plant miRNAs responsive to microbes, aided with novel sequencing and bioinformatics approaches for discovery and prediction in non-model organisms holds great potential for development of new forms of plant protection.
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Affiliation(s)
- Ena Šečić
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26, D-35392, Giessen, Germany.
| | - Karl-Heinz Kogel
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26, D-35392, Giessen, Germany.
| | - Maria Jose Ladera-Carmona
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26, D-35392, Giessen, Germany.
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17
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Cataloguing the small RNA content of honey using next generation sequencing. FOOD CHEMISTRY. MOLECULAR SCIENCES 2021; 2:100014. [PMID: 35415639 PMCID: PMC8991712 DOI: 10.1016/j.fochms.2021.100014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/09/2021] [Accepted: 02/12/2021] [Indexed: 12/02/2022]
Abstract
Plant miRNAs are present in Australian polyfloral and Leptospermum scoparium honey. Sequencing shows that honey contains a diverse range of small, non-coding RNAs. Honey RNA comes from different phylogenies including invertebrates and prokaryotes. Unique small RNA profiles can provide insight into honey production conditions.
Honey adulteration is a problem that effects the global honey industry and specifically, has been discovered in the Australian market. Common methods of adulteration include dilution with sugar syrup substitutes and the mislabelling of the floral and geographic origin(s) of honey. Current authentication tools rely on the molecular variability between different honeys, identifying unique chemical profiles and/or DNA signatures characteristic of a particular honey. Honey is known to contain plant miRNAs derived from its floral source. To explore the composition and variability of honey RNA molecules, this is the first study to catalogue the small RNA content of Australian polyfloral table honey and New Zealand Leptospermum scoparium honey using next generation sequencing. The data shows that in addition to miRNAs, honey contains a variety of small non-coding RNAs including tRNA-derived fragments. Moreover, the honey small RNAs are derived from a range of phylogenetic sources, including from plant, invertebrate, and prokaryotic species. The data indicates that different honeys contain unique small RNA profiles, which suggests a novel avenue in developing molecular-based honey authentication tools.
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18
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Chand Jha U, Nayyar H, Mantri N, Siddique KHM. Non-Coding RNAs in Legumes: Their Emerging Roles in Regulating Biotic/Abiotic Stress Responses and Plant Growth and Development. Cells 2021; 10:cells10071674. [PMID: 34359842 PMCID: PMC8306516 DOI: 10.3390/cells10071674] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 12/28/2022] Open
Abstract
Noncoding RNAs, including microRNAs (miRNAs), small interference RNAs (siRNAs), circular RNA (circRNA), and long noncoding RNAs (lncRNAs), control gene expression at the transcription, post-transcription, and translation levels. Apart from protein-coding genes, accumulating evidence supports ncRNAs playing a critical role in shaping plant growth and development and biotic and abiotic stress responses in various species, including legume crops. Noncoding RNAs (ncRNAs) interact with DNA, RNA, and proteins, modulating their target genes. However, the regulatory mechanisms controlling these cellular processes are not well understood. Here, we discuss the features of various ncRNAs, including their emerging role in contributing to biotic/abiotic stress response and plant growth and development, in addition to the molecular mechanisms involved, focusing on legume crops. Unravelling the underlying molecular mechanisms and functional implications of ncRNAs will enhance our understanding of the coordinated regulation of plant defences against various biotic and abiotic stresses and for key growth and development processes to better design various legume crops for global food security.
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MESH Headings
- Fabaceae/genetics
- Fabaceae/growth & development
- Fabaceae/metabolism
- Food Security
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Plant
- Humans
- MicroRNAs/classification
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Organ Specificity
- Protein Biosynthesis
- RNA, Circular/classification
- RNA, Circular/genetics
- RNA, Circular/metabolism
- RNA, Long Noncoding/classification
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Plant/classification
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Small Interfering/classification
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Species Specificity
- Stress, Physiological/genetics
- Transcription, Genetic
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Affiliation(s)
- Uday Chand Jha
- ICAR—Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
- Correspondence: (U.C.J.); (K.H.M.S.)
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh 160014, India;
| | - Nitin Mantri
- School of Science, RMIT University, Melbourne 3083, Australia;
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth 6001, Australia
- Correspondence: (U.C.J.); (K.H.M.S.)
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19
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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.
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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
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20
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Tiwari M, Pandey V, Singh B, Bhatia S. Dynamics of miRNA mediated regulation of legume symbiosis. PLANT, CELL & ENVIRONMENT 2021; 44:1279-1291. [PMID: 33347631 DOI: 10.1111/pce.13983] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 12/06/2020] [Accepted: 12/08/2020] [Indexed: 05/19/2023]
Abstract
Symbiotic nitrogen fixation in legume nodules is important in soils with low nitrogen availability. The initiation and sustainability of symbiosis require cellular reprogramming that involves the miRNA-mediated inhibition or activation of specific nodulation genes. The high-throughput sequencing of small RNA libraries has identified miRNAs and their targets, which are the major players in the post-transcriptional gene regulation (PTGS) of the different stages of legume-rhizobia symbiosis ranging from bacterial colonization and organogenesis to symbiotic nitrogen fixation. Here, we present an overview of information obtained from the miRNA libraries from nodulating tissues that have been sequenced to date. The functional analysis of miRNAs has revealed roles in phytohormone homeostasis and spatio-temporal regulation, as well as the mobility of miRNAs and their functions in shoot to root signalling that affects diverse functions, including bacterial entry, meristem division and differentiation, nitrogen fixation and senescence. Furthermore, small RNA fragments of rhizobial origin repress complementary plant mRNAs. We also consider the roles of miRNAs in determinate or indeterminate nodules. Taken together, this overview confirms that miRNAs are master regulators of the legume-rhizobia symbiosis.
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Affiliation(s)
- Manish Tiwari
- Legume Genomics Laboratory, National Institute of Plant Genome Research, New Delhi, India
| | - Vimal Pandey
- Legume Genomics Laboratory, National Institute of Plant Genome Research, New Delhi, India
| | - Baljinder Singh
- Legume Genomics Laboratory, National Institute of Plant Genome Research, New Delhi, India
| | - Sabhyata Bhatia
- Legume Genomics Laboratory, National Institute of Plant Genome Research, New Delhi, India
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21
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Smita S, Robben M, Deuja A, Accerbi M, Green PJ, Subramanian S, Fennell A. Integrative Analysis of Gene Expression and miRNAs Reveal Biological Pathways Associated with Bud Paradormancy and Endodormancy in Grapevine. PLANTS (BASEL, SWITZERLAND) 2021; 10:669. [PMID: 33807184 PMCID: PMC8067045 DOI: 10.3390/plants10040669] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 11/16/2022]
Abstract
Transition of grapevine buds from paradormancy to endodormancy is coordinated by changes in gene expression, phytohormones, transcription factors, and other molecular regulators, but the mechanisms involved in transcriptional and post-transcriptional regulation of dormancy stages are not well delineated. To identify potential regulatory targets, an integrative analysis of differential gene expression profiles and their inverse relationships with miRNA abundance was performed in paradormant (long day (LD) 15 h) or endodormant (short day (SD), 13 h) Vitis riparia buds. There were 400 up- and 936 downregulated differentially expressed genes in SD relative to LD budsGene set and gene ontology enrichment analysis indicated that hormone signaling and cell cycling genes were downregulated in SD relative to LD buds. miRNA abundance and inverse expression analyses of miRNA target genes indicated increased abundance of miRNAs that negatively regulate genes involved with cell cycle and meristem development in endodormant buds and miRNAs targeting starch metabolism related genes in paradormant buds. Analysis of interactions between abundant miRNAs and transcription factors identified a network with coinciding regulation of cell cycle and epigenetic regulation related genes in SD buds. This network provides evidence for cross regulation occurring between miRNA and transcription factors both upstream and downstream of MYB3R1.
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Affiliation(s)
- Shuchi Smita
- Edgar McFadden BioStress Laboratory, Agronomy, Horticulture, and Plant Science Department, BioSNTR, South Dakota State University, Brookings, SD 57007, USA; (S.S.); (M.R.); (A.D.); (S.S.)
| | - Michael Robben
- Edgar McFadden BioStress Laboratory, Agronomy, Horticulture, and Plant Science Department, BioSNTR, South Dakota State University, Brookings, SD 57007, USA; (S.S.); (M.R.); (A.D.); (S.S.)
| | - Anup Deuja
- Edgar McFadden BioStress Laboratory, Agronomy, Horticulture, and Plant Science Department, BioSNTR, South Dakota State University, Brookings, SD 57007, USA; (S.S.); (M.R.); (A.D.); (S.S.)
| | - Monica Accerbi
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19713, USA; (M.A.); (P.J.G.)
| | - Pamela J. Green
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19713, USA; (M.A.); (P.J.G.)
| | - Senthil Subramanian
- Edgar McFadden BioStress Laboratory, Agronomy, Horticulture, and Plant Science Department, BioSNTR, South Dakota State University, Brookings, SD 57007, USA; (S.S.); (M.R.); (A.D.); (S.S.)
| | - Anne Fennell
- Edgar McFadden BioStress Laboratory, Agronomy, Horticulture, and Plant Science Department, BioSNTR, South Dakota State University, Brookings, SD 57007, USA; (S.S.); (M.R.); (A.D.); (S.S.)
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22
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Joshi S, Kaur K, Khare T, Srivastava AK, Suprasanna P, Kumar V. Genome-wide identification, characterization and transcriptional profiling of NHX-type (Na +/H +) antiporters under salinity stress in soybean. 3 Biotech 2021; 11:16. [PMID: 33442515 DOI: 10.1007/s13205-020-02555-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/12/2020] [Indexed: 11/25/2022] Open
Abstract
This study was aimed at the genome-wide identification, a comprehensive in silico characterization of NHX genes from soybean (Glycine max L.) and their tissue-specific expression under varied levels (0-200 mM NaCl) of salinity stress. A total of nine putative NHX genes were identified from soybean. The phylogenetic analysis confirmed a total of five sub-groups and GmNHXs were distributed in three of them. Bioinformatics analyses confirmed all GmNHXs as ion transporters in nature, and all were localized on the vacuolar membrane. Several cis-acting regulatory elements involved in hormonal signal-responsiveness and abiotic stress including salinity responses were identified in the promoter regions of GmNHXs. Amiloride, which is a known Na+/H+ exchanger activity inhibitor, binding motifs were observed in all the GmNHXs. Furthermore, the identified GmNHXs were predicted-targets of 75 different miRNA candidates. To gain an insight into the functional divergence of GmNHX transporters, qRT-PCR based gene expression analysis was done in control and salt-treated root, stem and leaf tissues of two contrasting Indian soybean varieties MAUS-47 (tolerant) and Gujosoya-2 (sensitive). The gene up-regulation was tissue-specific and varied amongst the soybean varieties, with higher induction in tolerant variety. Maximum induction was observed in GmNHX2 in root tissues of MAUS-47 at 200 mM NaCl stress. Overall, identified GmNHXs may be explored further as potential gene candidates for soybean improvement.
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Affiliation(s)
- Shrushti Joshi
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Ganeshkhind, Pune, 411016 India
| | - Kawaljeet Kaur
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Ganeshkhind, Pune, 411016 India
| | - Tushar Khare
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Ganeshkhind, Pune, 411016 India
- Department of Environmental Science, Savitribai Phule Pune University, Pune, 411007 India
| | - Ashish Kumar Srivastava
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
- Homi Bhabha National Institute, Mumbai, 400094 India
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
- Homi Bhabha National Institute, Mumbai, 400094 India
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Ganeshkhind, Pune, 411016 India
- Department of Environmental Science, Savitribai Phule Pune University, Pune, 411007 India
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23
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Cadavid IC, da Fonseca GC, Margis R. HDAC inhibitor affects soybean miRNA482bd expression under salt and osmotic stress. JOURNAL OF PLANT PHYSIOLOGY 2020; 253:153261. [PMID: 32947244 DOI: 10.1016/j.jplph.2020.153261] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 08/07/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding molecules that modulate gene expression through targeting mRNA by specific-sequence cleavage, translation inhibition, or transcriptional regulation. miRNAs are key molecules in regulatory networks in abiotic stresses such as salt stress and water deficit in plants. Throughout the world, soybean is a critical crop, the production of which is affected by environmental stress conditions. In this study, RNA-Seq libraries from leaves of soybean under salt treatment were analyzed. 17 miRNAs and 31 putative target genes were identified with inverse differential expression patterns, indicating miRNA-target interaction. The differential expression of six miRNAs, including miR482bd-5p, and their potential targets, were confirmed by RT-qPCR. The miR482bd-5p expression was repressed, while its potential HEC1 and BAK1 targets were increased. Polyethylene glycol experiment was used to simulate drought stress, and miR482bd-5p, HEC1, and BAK1 presented a similar expression pattern, as found in salt stress. Histone modifications occur in response to abiotic stress, where histone deacetylases (HDACs) can lead to gene repression and silencing. The miR482bd-5p epigenetic regulation by histone deacetylation was evaluated by using the SAHA-HDAC inhibitor. The miR482bd-5p was up-regulated, and HEC1 was down-regulated under SAHA-salt treatment. It suggests an epigenetic regulation, where the miRNA gene is repressed by HDAC under salt stress, reducing its transcription, with an associated increase in the HEC1 target expression.
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Affiliation(s)
- Isabel Cristina Cadavid
- Programa de Pós-graduação em Biologia Celular e Molecular (PPGBCM), Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Rogerio Margis
- Programa de Pós-graduação em Biologia Celular e Molecular (PPGBCM), Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Departamento de Biofisica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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24
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Niyikiza D, Piya S, Routray P, Miao L, Kim WS, Burch-Smith T, Gill T, Sams C, Arelli PR, Pantalone V, Krishnan HB, Hewezi T. Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1744-1766. [PMID: 32491251 DOI: 10.1111/tpj.14861] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/19/2020] [Accepted: 05/20/2020] [Indexed: 06/11/2023]
Abstract
Soybean nodulation is a highly controlled process that involves complex gene regulation at both transcriptional and post-transcriptional levels. In the present study, we profiled gene expression changes, alternative splicing events, and DNA methylation patterns during nodule formation, development, and senescence. The transcriptome data uncovered key transcription patterns of nodule development that included 9669 core genes and 7302 stage-specific genes. Alternative splicing analysis uncovered a total of 2323 genes that undergo alternative splicing events in at least one nodule developmental stage, with activation of exon skipping and repression of intron retention being the most common splicing events in nodules compared to roots. Approximately 40% of the differentially spliced genes were also differentially expressed at the same nodule developmental stage, implying a substantial association between gene expression and alternative splicing. Genome-wide-DNA methylation analysis revealed dynamic changes in nodule methylomes that were specific to each nodule stage, occurred in a sequence-specific manner, and impacted the expression of 1864 genes. An attractive hypothesis raised by our data is that increased DNA methylation may contribute to the efficiency of alternative splicing. Together, our results provide intriguing insights into the associations between gene expression, alternative splicing, and DNA methylation that may shape transcriptome complexity and proteome specificity in developing soybean nodules.
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Affiliation(s)
- Daniel Niyikiza
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Pratyush Routray
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Long Miao
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Won-Seok Kim
- Plant Science Division, University of Missouri, Columbia, MI, 65211, USA
| | - Tessa Burch-Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996-0840, USA
| | - Tom Gill
- Smith Center for International Sustainable Agriculture, University of Tennessee, Knoxville, TN, 37996, USA
| | - Carl Sams
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | | | - Vince Pantalone
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Hari B Krishnan
- Plant Science Division, University of Missouri, Columbia, MI, 65211, USA
- Plant Genetics Research, USDA-Agricultural Research Service, Columbia, MI, 65211, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
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25
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Križnik M, Baebler Š, Gruden K. Roles of small RNAs in the establishment of tolerant interaction between plants and viruses. Curr Opin Virol 2020; 42:25-31. [PMID: 32480352 DOI: 10.1016/j.coviro.2020.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 02/06/2023]
Abstract
In a tolerant plant-virus interaction, viral multiplication is sustained without substantial effects on plant growth or reproduction. Such interactions are, in natural environments, frequent and sometimes even beneficial for both interactors. Here we compiled evidence showing that small RNAs modulate plant immune responses and growth, hence adjusting its physiology to enable a tolerant interaction. Importantly, the role of small RNAs in tolerant interactions resembles that required for establishment of a mutualistic symbiosis. Tolerance can become a sustainable strategy for breeding for virus resistance as selection pressure for emergence of more aggressive strains is low. Understanding the processes underlying establishment of tolerance is, therefore, important for the development of future crops.
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Affiliation(s)
- Maja Križnik
- National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Špela Baebler
- National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Kristina Gruden
- National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia.
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26
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Glazinska P, Kulasek M, Glinkowski W, Wysocka M, Kosiński JG. LuluDB-The Database Created Based on Small RNA, Transcriptome, and Degradome Sequencing Shows the Wide Landscape of Non-coding and Coding RNA in Yellow Lupine ( Lupinus luteus L.) Flowers and Pods. Front Genet 2020; 11:455. [PMID: 32499815 PMCID: PMC7242762 DOI: 10.3389/fgene.2020.00455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/14/2020] [Indexed: 11/13/2022] Open
Abstract
Yellow lupine (Lupinus luteus L.) belongs to a legume family that benefits from symbiosis with nitrogen-fixing bacteria. Its seeds are rich in protein, which makes it a valuable food source for animals and humans. Yellow lupine is also the model plant for basic research on nodulation or abscission of organs. Nevertheless, the knowledge about the molecular regulatory mechanisms of its generative development is still incomplete. The RNA-Seq technique is becoming more prominent in high-throughput identification and expression profiling of both coding and non-coding RNA sequences. However, the huge amount of data generated with this method may discourage other scientific groups from making full use of them. To overcome this inconvenience, we have created a database containing analysis-ready information about non-coding and coding L. luteus RNA sequences (LuluDB). LuluDB was created on the basis of RNA-Seq analysis of small RNA, transcriptome, and degradome libraries obtained from yellow lupine cv. Taper flowers, pod walls, and seeds in various stages of development, flower pedicels, and pods undergoing abscission or maintained on the plant. It contains sequences of miRNAs and phased siRNAs identified in L. luteus, information about their expression in individual samples, and their target sequences. LuluDB also contains identified lncRNAs and protein-coding RNA sequences with their organ expression and annotations to widely used databases like GO, KEGG, NCBI, Rfam, Pfam, etc. The database also provides sequence homology search by BLAST using, e.g., an unknown sequence as a query. To present the full capabilities offered by our database, we performed a case study concerning transcripts annotated as DCL 1–4 (DICER LIKE 1–4) homologs involved in small non-coding RNA biogenesis and identified miRNAs that most likely regulate DCL1 and DCL2 expression in yellow lupine. LuluDB is available at http://luluseqdb.umk.pl/basic/web/index.php.
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Affiliation(s)
- Paulina Glazinska
- Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Torun, Poland.,Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland
| | - Milena Kulasek
- Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Torun, Poland.,Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland
| | - Wojciech Glinkowski
- Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Torun, Poland.,Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland
| | - Marta Wysocka
- Department of Computational Biology, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Jan Grzegorz Kosiński
- Department of Computational Biology, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
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27
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Zhao C, Li T, Zhao Y, Zhang B, Li A, Zhao S, Hou L, Xia H, Fan S, Qiu J, Li P, Zhang Y, Guo B, Wang X. Integrated small RNA and mRNA expression profiles reveal miRNAs and their target genes in response to Aspergillus flavus growth in peanut seeds. BMC PLANT BIOLOGY 2020; 20:215. [PMID: 32404101 PMCID: PMC7222326 DOI: 10.1186/s12870-020-02426-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 04/30/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND MicroRNAs are important gene expression regulators in plants immune system. Aspergillus flavus is the most common causal agents of aflatoxin contamination in peanuts, but information on the function of miRNA in peanut-A. flavus interaction is lacking. In this study, the resistant cultivar (GT-C20) and susceptible cultivar (Tifrunner) were used to investigate regulatory roles of miRNAs in response to A. flavus growth. RESULTS A total of 30 miRNAs, 447 genes and 21 potential miRNA/mRNA pairs were differentially expressed significantly when treated with A. flavus. A total of 62 miRNAs, 451 genes and 44 potential miRNA/mRNA pairs exhibited differential expression profiles between two peanut varieties. Gene Ontology (GO) analysis showed that metabolic-process related GO terms were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses further supported the GO results, in which many enriched pathways were related with biosynthesis and metabolism, such as biosynthesis of secondary metabolites and metabolic pathways. Correlation analysis of small RNA, transcriptome and degradome indicated that miR156/SPL pairs might regulate the accumulation of flavonoids in resistant and susceptible genotypes. The miR482/2118 family might regulate NBS-LRR gene which had the higher expression level in resistant genotype. These results provided useful information for further understanding the roles of miR156/157/SPL and miR482/2118/NBS-LRR pairs. CONCLUSIONS Integration analysis of the transcriptome, miRNAome and degradome of resistant and susceptible peanut varieties were performed in this study. The knowledge gained will help to understand the roles of miRNAs of peanut in response to A. flavus.
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Affiliation(s)
- Chuanzhi Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
- College of Life Sciences, Shandong Normal University, Jinan, 250014 PR China
| | - Tingting Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
- Rizhao Experimental High School od Shandong, Rizhao, 276826 PR China
| | - Yuhan Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
- College of Life Sciences, Shandong Normal University, Jinan, 250014 PR China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC USA
| | - Aiqin Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Shuzhen Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Lei Hou
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Han Xia
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Shoujin Fan
- College of Life Sciences, Shandong Normal University, Jinan, 250014 PR China
| | - Jingjing Qiu
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
- College of Life Sciences, Shandong Normal University, Jinan, 250014 PR China
| | - Pengcheng Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Ye Zhang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Baozhu Guo
- Crop Protection and Management Research Unit, USDA-Agricultural Research Service, Tifton, GA 31793 USA
- Department of Plant Pathology, University of Georgia, Tifton, GA USA
| | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
- College of Life Sciences, Shandong Normal University, Jinan, 250014 PR China
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28
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Sós‐Hegedűs A, Domonkos Á, Tóth T, Gyula P, Kaló P, Szittya G. Suppression of NB-LRR genes by miRNAs promotes nitrogen-fixing nodule development in Medicago truncatula. PLANT, CELL & ENVIRONMENT 2020; 43:1117-1129. [PMID: 31834628 PMCID: PMC7317971 DOI: 10.1111/pce.13698] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/26/2019] [Accepted: 12/04/2019] [Indexed: 05/29/2023]
Abstract
Plant genomes contain two major classes of innate immune receptors to recognize different pathogens. The pattern recognition receptors perceive conserved pathogen-associated molecular patterns and the resistance genes with nucleotide-binding (NB) and leucine-rich repeat (LRR) domains recognize specific pathogen effectors. The precise regulation of resistance genes is important since the unregulated expression of NB-LRR genes can inhibit growth and may result in autoimmunity in the absence of pathogen infection. It was shown that a subset of miRNAs could target NB-LRR genes and act as an important regulator of plant immunity in the absence of pathogens. Plants not only interact with pathogens, but they can also establish symbiotic interactions with microbes. Nitrogen-fixing symbiotic interaction and nodule formation of legumes may also require the suppression of host defence to prevent immune responses. We found that upon symbiotic interactions, miRNAs repressing NB-LRR expression are upregulated in the developing nodules of Medicago truncatula. Furthermore, we show that the suppression of the activity of the NB-LRR genes targeted by these miRNAs is important during nodule development. Our results suggest that the downregulation of NB-LRR resistance genes in the developing nodule produces a suitable niche that facilitates bacterial colonization and the development of an N-fixing nodule.
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Affiliation(s)
- Anita Sós‐Hegedűs
- Department of Plant BiotechnologyAgricultural Biotechnology Institute, National Agricultural Research and Innovation CenterGödöllőHungary
| | - Ágota Domonkos
- Department of GeneticsAgricultural Biotechnology Institute, National Agricultural Research and Innovation CenterGödöllőHungary
| | - Tamás Tóth
- Department of Plant BiotechnologyAgricultural Biotechnology Institute, National Agricultural Research and Innovation CenterGödöllőHungary
| | - Péter Gyula
- Department of Plant BiotechnologyAgricultural Biotechnology Institute, National Agricultural Research and Innovation CenterGödöllőHungary
| | - Péter Kaló
- Department of GeneticsAgricultural Biotechnology Institute, National Agricultural Research and Innovation CenterGödöllőHungary
- Institute of Plant BiologyBiological Research CentreSzegedHungary
| | - György Szittya
- Department of Plant BiotechnologyAgricultural Biotechnology Institute, National Agricultural Research and Innovation CenterGödöllőHungary
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29
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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.
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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
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Ye W, Jiang J, Lin Y, Yeh KW, Lai Z, Xu X, Oelmüller R. Colonisation of Oncidium orchid roots by the endophyte Piriformospora indica restricts Erwinia chrysanthemi infection, stimulates accumulation of NBS-LRR resistance gene transcripts and represses their targeting micro-RNAs in leaves. BMC PLANT BIOLOGY 2019; 19:601. [PMID: 31888486 PMCID: PMC6937650 DOI: 10.1186/s12870-019-2105-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 10/28/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND Erwinia chrysanthemi (Ec) is a destructive pathogen which causes soft-rot diseases in diverse plant species including orchids. We investigated whether colonization of Oncidium roots by the endophytic fungus Piriformospora indica (Pi) restricts Ec-induced disease development in leaves, and whether this might be related to the regulation of nucleotide binding site-leucine rich repeat (NBS-LRR) Resistance (R) genes. RESULTS Root colonization of Oncidium stackings by Pi restricts progression of Ec-induced disease development in the leaves. Since Pi does not inhibit Ec growth on agar plates, we tested whether NBS-LRR R gene transcripts and the levels of their potential target miRNAs in Oncidium leaves might be regulated by Pi. Using bioinformatic tools, we first identified NBS-LRR R gene sequences from Oncidium, which are predicted to be targets of miRNAs. Among them, the expression of two R genes was repressed and the accumulation of several regulatory miRNA stimulated by Ec in the leaves of Oncidium plants. This correlated with the progression of disease development, jasmonic and salicylic acid accumulation, ethylene synthesis and H2O2 production after Ec infection of Oncidium leaves. Interestingly, root colonization by Pi restricted disease development in the leaves, and this was accompanied by higher expression levels of several defense-related R genes and lower expression level of their target miRNA. CONCLUSION Based on these data we propose that Pi controls the levels of NBS-LRR R mRNAs and their target miRNAs in leaves. This regulatory circuit correlates with the protection of Oncidium plants against Ec infection, and molecular and biochemical investigations will demonstrate in the future whether, and if so, to what extent these two observations are related to each other.
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Affiliation(s)
- Wei Ye
- Sanming Academy of Agricultural Sciences, Sanming, Fujian China
| | - Jinlan Jiang
- Sanming Academy of Agricultural Sciences, Sanming, Fujian China
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Kai-Wun Yeh
- Matthias-Schleiden-Institute, Plant Physiology, Friedrich Schiller University Jena, Jena, Germany
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Xuming Xu
- Sanming Academy of Agricultural Sciences, Sanming, Fujian China
| | - Ralf Oelmüller
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
- Matthias-Schleiden-Institute, Plant Physiology, Friedrich Schiller University Jena, Jena, Germany
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Identification of miRNA, their targets and miPEPs in peanut (Arachis hypogaea L.). Comput Biol Chem 2019; 83:107100. [DOI: 10.1016/j.compbiolchem.2019.107100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 07/04/2019] [Accepted: 08/06/2019] [Indexed: 01/28/2023]
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Basso MF, Ferreira PCG, Kobayashi AK, Harmon FG, Nepomuceno AL, Molinari HBC, Grossi‐de‐Sa MF. MicroRNAs and new biotechnological tools for its modulation and improving stress tolerance in plants. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1482-1500. [PMID: 30947398 PMCID: PMC6662102 DOI: 10.1111/pbi.13116] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/22/2019] [Accepted: 03/17/2019] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) modulate the abundance and spatial-temporal accumulation of target mRNAs and indirectly regulate several plant processes. Transcriptional regulation of the genes encoding miRNAs (MIR genes) can be activated by numerous transcription factors, which themselves are regulated by other miRNAs. Fine-tuning of MIR genes or miRNAs is a powerful biotechnological strategy to improve tolerance to abiotic or biotic stresses in crops of economic importance. Current approaches for miRNA fine-tuning are based on the down- or up-regulation of MIR gene transcription and the use of genetic engineering tools to manipulate the final concentration of these miRNAs in the cytoplasm. Transgenesis, cisgenesis, intragenesis, artificial MIR genes, endogenous and artificial target mimicry, MIR genes editing using Meganucleases, ZNF proteins, TALENs and CRISPR/Cas9 or CRISPR/Cpf1, CRISPR/dCas9 or dCpf1, CRISPR13a, topical delivery of miRNAs and epigenetic memory have been successfully explored to MIR gene or miRNA modulation and improve agronomic traits in several model or crop plants. However, advantages and drawbacks of each of these new biotechnological tools (NBTs) are still not well understood. In this review, we provide a brief overview of the biogenesis and role of miRNAs in response to abiotic or biotic stresses, we present critically the main NBTs used for the manipulation of MIR genes and miRNAs, we show current efforts and findings with the MIR genes and miRNAs modulation in plants, and we summarize the advantages and drawbacks of these NBTs and provide some alternatives to overcome. Finally, challenges and future perspectives to miRNA modulating in important crops are also discussed.
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Affiliation(s)
| | | | | | - Frank G. Harmon
- Plant Gene Expression CenterUSDA‐ARSAlbanyCAUSA
- Department of Plant and Microbial BiologyUC BerkeleyBerkeleyCAUSA
| | | | | | - Maria Fatima Grossi‐de‐Sa
- Embrapa Genetic Resources and BiotechnologyBrasíliaDFBrazil
- Post‐Graduation Program in Genomic Sciences and BiotechnologyCatholic University of BrasíliaBrasíliaDFBrazil
- Post‐Graduation Program in BiotechnologyPotiguar University (UNP)NatalRNBrazil
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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.
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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
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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.
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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
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Yu L, Guo R, Jiang Y, Ye X, Yang Z, Meng Y, Shao C. Genome-wide identification and characterization of novel microRNAs in seed development of soybean. Biosci Biotechnol Biochem 2019; 83:233-242. [PMID: 30355067 DOI: 10.1080/09168451.2018.1536513] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/03/2018] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in eukaryotes. However, the information about miRNAs population and their regulatory functions involving in soybean seed development remains incomplete. Base on the Dicer-like1-mediated cleavage signals during miRNA processing could be employed for novel miRNA discovery, a genome-wide search for miRNA candidates involved in seed development was carried out. As a result, 17 novel miRNAs, 14 isoforms of miRNA (isomiRs) and 31 previously validated miRNAs were discovered. These novel miRNAs and isomiRs represented tissue-specific expression and the isomiRs showed significantly higher abundance than that of their miRNA counterparts in different tissues. After target prediction and degradome sequencing data-based validation, 13 novel miRNA-target pairs were further identified. Besides, five targets of 22-nt iso-gma-miR393h were found to be triggered to produce secondary trans-acting siRNA (ta-siRNAs). Summarily, our results could expand the repertoire of miRNAs with potentially important functions in soybean.
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Affiliation(s)
- Lan Yu
- a College of Life Sciences , Huzhou University , Huzhou P.R. China
| | - Rongkai Guo
- b Shanghai Institute of Plant Physiology and Ecology , Chinese Academy of Sciences , Shanghai China
| | - Yeqin Jiang
- a College of Life Sciences , Huzhou University , Huzhou P.R. China
| | - Xinghuo Ye
- a College of Life Sciences , Huzhou University , Huzhou P.R. China
| | - Zhihong Yang
- a College of Life Sciences , Huzhou University , Huzhou P.R. China
| | - Yijun Meng
- c College of Life and Environmental Sciences , Hangzhou Normal University , Hangzhou P.R. China
| | - Chaogang Shao
- a College of Life Sciences , Huzhou University , Huzhou P.R. China
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Liu X, Liu S, Wang R, Chen X, Fan Z, Wu B, Zhou T. Analyses of MiRNA Functions in Maize Using a Newly Developed ZMBJ-CMV-2b N81-STTM Vector. FRONTIERS IN PLANT SCIENCE 2019; 10:1277. [PMID: 31681375 PMCID: PMC6811604 DOI: 10.3389/fpls.2019.01277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/12/2019] [Indexed: 05/21/2023]
Abstract
Endogenous microRNAs (miRNAs) play pivotal roles in plant development and responses to various biotic or abiotic stresses. Up to now, more than 500 maize miRNAs have been identified. However, functions of these identified miRNAs remained largely unknown due mainly to the lack of rapid and reliable tools. We previously reported a cucumber mosaic virus strain ZMBJ (ZMBJ-CMV)-based gene silencing vector for rapid and efficient gene function studies in maize lines with agronomical importance. Because ZMBJ-CMV induces very mild disease symptoms but strong gene silencing in maize, we decided to further modify this vector to suppress miRNA expressions in maize. The newly developed ZMBJ-CMV-2bN81-STTM vector expresses a short tandem target mimic (STTM) containing two target-mimic sequences separated by a short spacer sequence. Our results showed that ZMBJ-CMV-2bN81-STTM can be used to investigate miRNA function in Nicotiana benthamiana and maize seedlings. The ZMBJ-CMV-2bN81-STTM-based downregulation of Nbe-miR165/166 or Nbe-miR159 induced specific and strong miRNA-sequestering phenotypes, and increased the expressions of their predicted target genes. For maize, the ZMBJ-CMV-2bN81-STTM based downregulation of zma-miR167 or zma-miR482 caused a decrease of lateral roots growth and a plant stunting phenotypes, respectively. In both cases, the target genes of zma-miR167- or zma-miR482 were increased significantly. Thus, we consider ZMBJ-CMV based VbMS system as a useful tool for high-throughput investigations of miRNA functions in maize.
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Affiliation(s)
- Xuedong Liu
- State Key Laboratory for Agro-Biotechnology and Key Laboratory for Pest Monitoring and Green Management-Ministry of Agriculture and Rural Affairs, Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Sijia Liu
- State Key Laboratory for Agro-Biotechnology and Key Laboratory for Pest Monitoring and Green Management-Ministry of Agriculture and Rural Affairs, Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Rong Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xi Chen
- State Key Laboratory for Agro-Biotechnology and Key Laboratory for Pest Monitoring and Green Management-Ministry of Agriculture and Rural Affairs, Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Zaifeng Fan
- State Key Laboratory for Agro-Biotechnology and Key Laboratory for Pest Monitoring and Green Management-Ministry of Agriculture and Rural Affairs, Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Boming Wu
- State Key Laboratory for Agro-Biotechnology and Key Laboratory for Pest Monitoring and Green Management-Ministry of Agriculture and Rural Affairs, Department of Plant Pathology, China Agricultural University, Beijing, China
- *Correspondence: Boming Wu, ; Tao Zhou,
| | - Tao Zhou
- State Key Laboratory for Agro-Biotechnology and Key Laboratory for Pest Monitoring and Green Management-Ministry of Agriculture and Rural Affairs, Department of Plant Pathology, China Agricultural University, Beijing, China
- *Correspondence: Boming Wu, ; Tao Zhou,
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Borrelli GM, Mazzucotelli E, Marone D, Crosatti C, Michelotti V, Valè G, Mastrangelo AM. Regulation and Evolution of NLR Genes: A Close Interconnection for Plant Immunity. Int J Mol Sci 2018; 19:E1662. [PMID: 29867062 PMCID: PMC6032283 DOI: 10.3390/ijms19061662] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/01/2018] [Accepted: 06/02/2018] [Indexed: 12/12/2022] Open
Abstract
NLR (NOD-like receptor) genes belong to one of the largest gene families in plants. Their role in plants' resistance to pathogens has been clearly described for many members of this gene family, and dysregulation or overexpression of some of these genes has been shown to induce an autoimmunity state that strongly affects plant growth and yield. For this reason, these genes have to be tightly regulated in their expression and activity, and several regulatory mechanisms are described here that tune their gene expression and protein levels. This gene family is subjected to rapid evolution, and to maintain diversity at NLRs, a plethora of genetic mechanisms have been identified as sources of variation. Interestingly, regulation of gene expression and evolution of this gene family are two strictly interconnected aspects. Indeed, some examples have been reported in which mechanisms of gene expression regulation have roles in promotion of the evolution of this gene family. Moreover, co-evolution of the NLR gene family and other gene families devoted to their control has been recently demonstrated, as in the case of miRNAs.
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Affiliation(s)
- Grazia M Borrelli
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 673, km 25.2, 71122 Foggia, Italy.
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Daniela Marone
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 673, km 25.2, 71122 Foggia, Italy.
| | - Cristina Crosatti
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Vania Michelotti
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Giampiero Valè
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, Italy.
| | - Anna M Mastrangelo
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, via Stezzano 24, 24126 Bergamo, Italy.
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Curtin SJ, Xiong Y, Michno J, Campbell BW, Stec AO, Čermák T, Starker C, Voytas DF, Eamens AL, Stupar RM. CRISPR/Cas9 and TALENs generate heritable mutations for genes involved in small RNA processing of Glycine max and Medicago truncatula. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1125-1137. [PMID: 29087011 PMCID: PMC5978873 DOI: 10.1111/pbi.12857] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 10/17/2017] [Accepted: 10/21/2017] [Indexed: 05/14/2023]
Abstract
Processing of double-stranded RNA precursors into small RNAs is an essential regulator of gene expression in plant development and stress response. Small RNA processing requires the combined activity of a functionally diverse group of molecular components. However, in most of the plant species, there are insufficient mutant resources to functionally characterize each encoding gene. Here, mutations in loci encoding protein machinery involved in small RNA processing in soya bean and Medicago truncatula were generated using the CRISPR/Cas9 and TAL-effector nuclease (TALEN) mutagenesis platforms. An efficient CRISPR/Cas9 reagent was used to create a bi-allelic double mutant for the two soya bean paralogous Double-stranded RNA-binding2 (GmDrb2a and GmDrb2b) genes. These mutations, along with a CRISPR/Cas9-generated mutation of the M. truncatula Hua enhancer1 (MtHen1) gene, were determined to be germ-line transmissible. Furthermore, TALENs were used to generate a mutation within the soya bean Dicer-like2 gene. CRISPR/Cas9 mutagenesis of the soya bean Dicer-like3 gene and the GmHen1a gene was observed in the T0 generation, but these mutations failed to transmit to the T1 generation. The irregular transmission of induced mutations and the corresponding transgenes was investigated by whole-genome sequencing to reveal a spectrum of non-germ-line-targeted mutations and multiple transgene insertion events. Finally, a suite of combinatorial mutant plants were generated by combining the previously reported Gmdcl1a, Gmdcl1b and Gmdcl4b mutants with the Gmdrb2ab double mutant. Altogether, this study demonstrates the synergistic use of different genome engineering platforms to generate a collection of useful mutant plant lines for future study of small RNA processing in legume crops.
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Affiliation(s)
- Shaun J. Curtin
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMNUSA
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
- Present address:
Plant Science Research UnitAgricultural Research ServiceUnited States Department of AgricultureSt PaulMNUSA
| | - Yer Xiong
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
| | - Jean‐Michel Michno
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
- Bioinformatics and Computational Biology Graduate ProgramUniversity of MinnesotaMinneapolisMNUSA
| | | | - Adrian O. Stec
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
| | - Tomas Čermák
- Department of Genetics, Cell Biology & DevelopmentCenter for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
- Present address:
Agricultural Research ServiceInari Agriculture, Inc.CambridgeMAUSA
| | - Colby Starker
- Department of Genetics, Cell Biology & DevelopmentCenter for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Daniel F. Voytas
- Department of Genetics, Cell Biology & DevelopmentCenter for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Andrew L. Eamens
- School of Environmental and Life SciencesThe University of NewcastleCallaghanNew South WalesAustralia
| | - Robert M. Stupar
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
- Bioinformatics and Computational Biology Graduate ProgramUniversity of MinnesotaMinneapolisMNUSA
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Lai Y, Eulgem T. Transcript-level expression control of plant NLR genes. MOLECULAR PLANT PATHOLOGY 2018; 19:1267-1281. [PMID: 28834153 PMCID: PMC6638128 DOI: 10.1111/mpp.12607] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/14/2017] [Accepted: 08/15/2017] [Indexed: 05/20/2023]
Abstract
Plant NLR genes encode sensitive immune receptors that can mediate the specific recognition of pathogen avirulence effectors and activate a strong defence response, termed effector-triggered immunity. The expression of NLRs requires strict regulation, as their ability to trigger immunity is dependent on their dose, and overexpression of NLRs results in autoimmunity and massive fitness costs. An elaborate interplay of different mechanisms controlling NLR transcript levels allows plants to maximize their defence capacity, whilst limiting negative impact on their fitness. Global suppression of NLR transcripts may be a prerequisite for the fast evolution of new NLR variants and the expansion of this gene family. Here, we summarize recent progress made towards a comprehensive understanding of NLR transcript-level expression control. Multiple mechanistic steps, including transcription as well as co-/post-transcriptional processing and transcript turn-over, contribute to balanced base levels of NLR transcripts and allow for dynamic adjustments to defence situations.
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Affiliation(s)
- Yan Lai
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome BiologyUniversity of California at RiversideRiversideCA 92521USA
- College of Life SciencesFujian Agricultural and Forestry UniversityFuzhouFujian 350002China
| | - Thomas Eulgem
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome BiologyUniversity of California at RiversideRiversideCA 92521USA
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Gai YP, Zhao HN, Zhao YN, Zhu BS, Yuan SS, Li S, Guo FY, Ji XL. MiRNA-seq-based profiles of miRNAs in mulberry phloem sap provide insight into the pathogenic mechanisms of mulberry yellow dwarf disease. Sci Rep 2018; 8:812. [PMID: 29339758 PMCID: PMC5770470 DOI: 10.1038/s41598-018-19210-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 12/20/2017] [Indexed: 11/09/2022] Open
Abstract
A wide range of miRNAs have been identified as phloem-mobile molecules that play important roles in coordinating plant development and physiology. Phytoplasmas are associated with hundreds of plant diseases, and the pathogenesis involved in the interactions between phytoplasmas and plants is still poorly understood. To analyse the molecular mechanisms of phytoplasma pathogenicity, the miRNAs profiles in mulberry phloem saps were examined in response to phytoplasma infection. A total of 86 conserved miRNAs and 19 novel miRNAs were identified, and 30 conserved miRNAs and 13 novel miRNAs were differentially expressed upon infection with phytoplasmas. The target genes of the differentially expressed miRNAs are involved in diverse signalling pathways showing the complex interactions between mulberry and phytoplasma. Interestingly, we found that mul-miR482a-5p was up-regulated in the infected phloem saps, and grafting experiments showed that it can be transported from scions to rootstock. Based on the results, the complexity and roles of the miRNAs in phloem sap and the potential molecular mechanisms of their changes were discussed. It is likely that the phytoplasma-responsive miRNAs in the phloem sap modulate multiple pathways and work cooperatively in response to phytoplasma infection, and their expression changes may be responsible for some symptoms in the infected plants.
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Affiliation(s)
- Ying-Ping Gai
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Huai-Ning Zhao
- College of Forestry, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Ya-Nan Zhao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Bing-Sen Zhu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Shuo-Shuo Yuan
- College of Forestry, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Shuo Li
- College of Forestry, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Fang-Yue Guo
- College of Forestry, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Xian-Ling Ji
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China. .,College of Forestry, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China.
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Ji HM, Zhao M, Gao Y, Cao XX, Mao HY, Zhou Y, Fan WY, Borkovich KA, Ouyang SQ, Liu P. FRG3, a Target of slmiR482e-3p, Provides Resistance against the Fungal Pathogen Fusarium oxysporum in Tomato. FRONTIERS IN PLANT SCIENCE 2018; 9:26. [PMID: 29434609 PMCID: PMC5797444 DOI: 10.3389/fpls.2018.00026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 01/08/2018] [Indexed: 05/20/2023]
Abstract
The vast majority of plant disease resistance (R) genes encode nucleotide binding site-leucine-rich repeat (NBS-LRR) proteins, which specifically determine the plant immune response and have been demonstrated to be targets of several microRNA (miRNA) families. The fungus Fusarium oxysporum f. sp. lycopersici (FOL) causes vascular wilt disease in tomato worldwide. Here, we explored a possible role for FGR3 in tomato defense against FOL. FRG3 is a predicted NBS-LRR like gene that is targeted by slmiR482e-3p, a member of slmiR482 miRNA family. Northern blot data demonstrated that all seven members of the slmiR482 family were regulated in diverse ways after infection by FOL. The ability of FRG3 to be regulated by slmiR482e-3p was confirmed at the transcript level by co-expression studies in Nicotiana benthamiana. A virus-induced gene silencing (VIGS) approach revealed that FRG3 confers resistance to the Motelle tomato cultivar. Taken together, our study has identified a novel R gene, FRG3, which is targeted by slmiR482e-3p at the transcript level, and is necessary for resistance to tomato wilt disease in planta.
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Affiliation(s)
- Hui-Min Ji
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Min Zhao
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Ying Gao
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Xin-Xin Cao
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Hui-Ying Mao
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Yi Zhou
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Wen-Yu Fan
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Katherine A. Borkovich
- Department of Plant Pathology and Microbiology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | - Shou-Qiang Ouyang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
- *Correspondence: Shou-Qiang Ouyang, Peng Liu,
| | - Peng Liu
- Testing Center, Yangzhou University, Yangzhou, China
- *Correspondence: Shou-Qiang Ouyang, Peng Liu,
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Križnik M, Petek M, Dobnik D, Ramšak Ž, Baebler Š, Pollmann S, Kreuze JF, Žel J, Gruden K. Salicylic Acid Perturbs sRNA-Gibberellin Regulatory Network in Immune Response of Potato to Potato virus Y Infection. FRONTIERS IN PLANT SCIENCE 2017; 8:2192. [PMID: 29312421 PMCID: PMC5744193 DOI: 10.3389/fpls.2017.02192] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 12/12/2017] [Indexed: 05/19/2023]
Abstract
Potato virus Y is the most economically important potato viral pathogen. We aimed at unraveling the roles of small RNAs (sRNAs) in the complex immune signaling network controlling the establishment of tolerant response of potato cv. Désirée to the virus. We constructed a sRNA regulatory network connecting sRNAs and their targets to link sRNA level responses to physiological processes. We discovered an interesting novel sRNAs-gibberellin regulatory circuit being activated as early as 3 days post inoculation (dpi) before viral multiplication can be detected. Two endogenous sRNAs, miR167 and phasiRNA931 were predicted to regulate gibberellin biosynthesis genes GA20-oxidase and GA3-oxidase. The increased expression of phasiRNA931 was also reflected in decreased levels of GA3-oxidase transcripts. Moreover, decreased concentration of gibberellin confirmed this regulation. The functional relation between lower activity of gibberellin signaling and reduced disease severity was previously confirmed in Arabidopsis-virus interaction using knockout mutants. We further showed that this regulation is salicylic acid-dependent as the response of sRNA network was attenuated in salicylic acid-depleted transgenic counterpart NahG-Désirée expressing severe disease symptoms. Besides downregulation of gibberellin signaling, regulation of immune receptor transcripts by miR6022 as well as upregulation of miR164, miR167, miR169, miR171, miR319, miR390, and miR393 in tolerant Désirée, revealed striking similarities to responses observed in mutualistic symbiotic interactions. The intertwining of different regulatory networks revealed, shows how developmental signaling, disease symptom development, and stress signaling can be balanced.
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Affiliation(s)
- Maja Križnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- JoŽef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Živa Ramšak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Špela Baebler
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Stephan Pollmann
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid UPM - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Jan F. Kreuze
- Global Program of Integrated Crop and Systems Research, International Potato Center (CIP), Lima, Peru
| | - Jana Žel
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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43
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Zhao D, Xia X, Wei M, Sun J, Meng J, Tao J. Overexpression of herbaceous peony miR156e-3p improves anthocyanin accumulation in transgenic Arabidopsis thaliana lateral branches. 3 Biotech 2017; 7:379. [PMID: 29071176 DOI: 10.1007/s13205-017-1011-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/14/2017] [Indexed: 12/19/2022] Open
Abstract
microRNAs (miRNAs) play critical regulatory roles in plant growth and development. In the present study, the function of herbaceous peony (Paeonia lactiflora Pall.) miR156e-3p in the regulation of color formation has been investigated. Firstly, P. lactiflora miR156e-3p precursor sequence (pre-miR156e-3p) was isolated. Subsequently, the overexpression vector of pre-miR156e-3p was constructed and transformed into Arabidopsis thaliana. Moreover, the medium screening, GUS staining, polymerase chain reaction (PCR) of the GUS region and real-time quantitative PCR (qRT-PCR) of miR156e-3p all confirmed that the purpose gene had been successfully transferred into Arabidopsis plants and expressed, which resulted in apparent purple lateral branches. And this change in color was caused by the improved anthocyanin accumulation. In addition, expression analysis had shown that the level of miR156e-3p transcript was increased, while transcription level of target gene squamosa promoter binding protein-like gene (SPL1), encoding SPL transcription factor that negatively regulated anthocyanin accumulation, was repressed in miR156e-3p-overexpressing transgenic plants, and its downstream gene dihydroflavonol 4-reductase gene (DFR) that was directly involved in anthocyanin biosynthesis was strongly expressed, which resulted in anthocyanin accumulation of Arabidopsis lateral branches. These findings would improve the understanding of miRNAs regulation of color formation in P. lactiflora.
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Affiliation(s)
- Daqiu Zhao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 People's Republic of China
| | - Xing Xia
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 People's Republic of China
| | - Mengran Wei
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 People's Republic of China
| | - Jing Sun
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 People's Republic of China
| | - Jiasong Meng
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 People's Republic of China
| | - Jun Tao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 People's Republic of China
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Zogli P, Libault M. Plant response to biotic stress: Is there a common epigenetic response during plant-pathogenic and symbiotic interactions? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 263:89-93. [PMID: 28818387 DOI: 10.1016/j.plantsci.2017.07.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 07/04/2017] [Accepted: 07/07/2017] [Indexed: 05/26/2023]
Abstract
Plants constantly interact with pathogenic and symbiotic microorganisms. Recent studies have revealed several regulatory mechanisms controlling these interactions. Among them, the plant defense system is activated not only in response to pathogenic, but also in response to symbiotic microbes. Interestingly, shortly after symbiotic microbial recognition, the plant defense system is suppressed to promote plant infection by symbionts. Research studies have demonstrated the influence of the plant epigenome in modulating both pathogenic and symbiotic plant-microbe interactions, thereby influencing plant survival, adaptation and evolution of the plant response to microbial infections. It is however unclear if plant pathogenic and symbiotic responses share similar epigenomic profiles or if epigenomic changes differentially regulate plant-microbe symbiosis and pathogenesis. In this mini-review, we provide an update of the current knowledge of epigenomic control on plant immune responses and symbiosis, with a special attention being paid to knowledge gap and potential strategies to fill-in the missing links.
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Affiliation(s)
- Prince Zogli
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Marc Libault
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
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45
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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.
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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.
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46
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Tian B, Wang S, Todd TC, Johnson CD, Tang G, Trick HN. Genome-wide identification of soybean microRNA responsive to soybean cyst nematodes infection by deep sequencing. BMC Genomics 2017; 18:572. [PMID: 28768484 PMCID: PMC5541722 DOI: 10.1186/s12864-017-3963-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 07/25/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The soybean cyst nematode (SCN), Heterodera glycines, is one of the most devastating diseases limiting soybean production worldwide. It is known that small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), play important roles in regulating plant growth and development, defense against pathogens, and responses to environmental changes. RESULTS In order to understand the role of soybean miRNAs during SCN infection, we analyzed 24 small RNA libraries including three biological replicates from two soybean cultivars (SCN susceptible KS4607, and SCN HG Type 7 resistant KS4313N) that were grown under SCN-infested and -noninfested soil at two different time points (SCN feeding establishment and egg production). In total, 537 known and 70 putative novel miRNAs in soybean were identified from a total of 0.3 billion reads (average about 13.5 million reads for each sample) with the programs of Bowtie and miRDeep2 mapper. Differential expression analyses were carried out using edgeR to identify miRNAs involved in the soybean-SCN interaction. Comparative analysis of miRNA profiling indicated a total of 60 miRNAs belonging to 25 families that might be specifically related to cultivar responses to SCN. Quantitative RT-PCR validated similar miRNA interaction patterns as sequencing results. CONCLUSION These findings suggest that miRNAs are likely to play key roles in soybean response to SCN. The present work could provide a framework for miRNA functional identification and the development of novel approaches for improving soybean SCN resistance in future studies.
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Affiliation(s)
- Bin Tian
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, 4024 Throckmorton Plant Sciences Center, Manhattan, KS 66506 USA
| | - Shichen Wang
- Genomics and Bioinformatics Service, Texas A&M AgriLife, College Station, TX 77845 USA
| | - Timothy C. Todd
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, 4024 Throckmorton Plant Sciences Center, Manhattan, KS 66506 USA
| | - Charles D. Johnson
- Genomics and Bioinformatics Service, Texas A&M AgriLife, College Station, TX 77845 USA
| | - Guiliang Tang
- Department of Biological Sciences, Michigan Technological University, Dow Environmental Sciences and Engineering Building - Room 406, 1400 Townsend Drive, Houghton, MI 49931-1295 USA
| | - Harold N. Trick
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, 4024 Throckmorton Plant Sciences Center, Manhattan, KS 66506 USA
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47
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Hobecker KV, Reynoso MA, Bustos-Sanmamed P, Wen J, Mysore KS, Crespi M, Blanco FA, Zanetti ME. The MicroRNA390/TAS3 Pathway Mediates Symbiotic Nodulation and Lateral Root Growth. PLANT PHYSIOLOGY 2017; 174:2469-2486. [PMID: 28663332 PMCID: PMC5543954 DOI: 10.1104/pp.17.00464] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/24/2017] [Indexed: 05/19/2023]
Abstract
Legume roots form two types of postembryonic organs, lateral roots and symbiotic nodules. Nodule formation is the result of the interaction of legumes with rhizobia and requires the mitotic activation and differentiation of root cells as well as an independent, but coordinated, program that allows infection by rhizobia. MicroRNA390 (miR390) is an evolutionarily conserved microRNA that targets the Trans-Acting Short Interference RNA3 (TAS3) transcript. Cleavage of TAS3 by ARGONAUTE7 results in the production of trans-acting small interference RNAs, which target mRNAs encoding AUXIN RESPONSE FACTOR2 (ARF2), ARF3, and ARF4. Here, we show that activation of the miR390/TAS3 regulatory module by overexpression of miR390 in Medicago truncatula promotes lateral root growth but prevents nodule organogenesis, rhizobial infection, and the induction of two key nodulation genes, Nodulation Signaling Pathway1 (NSP1) and NSP2 Accordingly, inactivation of the miR390/TAS3 module, either by expression of a miR390 target mimicry construct or mutations in ARGONAUTE7, enhances nodulation and rhizobial infection, alters the spatial distribution of the nodules, and increases the percentage of nodules with multiple meristems. Our results revealed a key role of the miR390/TAS3 pathway in legumes as a modulator of lateral root organs, playing opposite roles in lateral root and nodule development.
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Affiliation(s)
- Karen Vanesa Hobecker
- Instituto de Biotecnología y Biología Molecular, FCE-UNLP CCT-CONICET, C.P. 1900 La Plata, Argentina
| | - Mauricio Alberto Reynoso
- Instituto de Biotecnología y Biología Molecular, FCE-UNLP CCT-CONICET, C.P. 1900 La Plata, Argentina
| | - Pilar Bustos-Sanmamed
- Institute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Universités Paris-Sud, Evry, Paris-Diderot, Université Paris-Saclay, 91405 Orsay, France
| | - Jiangqi Wen
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Kirankumar S Mysore
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Martín Crespi
- Institute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Universités Paris-Sud, Evry, Paris-Diderot, Université Paris-Saclay, 91405 Orsay, France
| | - Flavio Antonio Blanco
- Instituto de Biotecnología y Biología Molecular, FCE-UNLP CCT-CONICET, C.P. 1900 La Plata, Argentina
| | - María Eugenia Zanetti
- Instituto de Biotecnología y Biología Molecular, FCE-UNLP CCT-CONICET, C.P. 1900 La Plata, Argentina
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48
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Zhao W, Cheng Y, Zhang C, You Q, Shen X, Guo W, Jiao Y. Genome-wide identification and characterization of circular RNAs by high throughput sequencing in soybean. Sci Rep 2017; 7:5636. [PMID: 28717203 PMCID: PMC5514102 DOI: 10.1038/s41598-017-05922-9] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/06/2017] [Indexed: 12/01/2022] Open
Abstract
Circular RNAs (circRNAs) arise during pre-mRNA splicing, in which the 3' and 5' ends are linked to each other by a covalent bond. Soybean is an ancient tetraploid, which underwent two whole genome duplications. Most of soybean genes are paralogous genes with multiple copies. Although many circRNAs have been identified in animals and plants, little is known about soybean circRNAs, especially about circRNAs derived from paralogous genes. Here, we used deep sequencing technology coupled with RNase R enrichment strategy and bioinformatic approach to uncover circRNAs in soybean. A total of 5,372 circRNAs were identified, approximately 80% of which were paralogous circRNAs generated from paralogous genes. Despite high sequence homology, the paralogous genes could produce different paralogous circRNAs with different expression patterns. Two thousand and one hundred thirty four circRNAs were predicted to be 92 miRNAs target mimicry. CircRNAs and circRNA isoforms exhibited tissue-specific expression patterns in soybean. Based on the function of circRNA-host genes, the soybean circRNAs may participate in many biological processes such as developmental process, multi-organism process, and metabolic process. Our study not only provided a basis for research into the function of circRNAs in soybean but also new insights into the plant circRNA kingdom.
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Affiliation(s)
- Wei Zhao
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Science, Wuhan, China
| | - Yihui Cheng
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Science, Wuhan, China
| | - Chi Zhang
- BGI-Wuhan, Wuhan, 430075, Hubei, China
| | - Qingbo You
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Science, Wuhan, China
| | - Xinjie Shen
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Science, Wuhan, China
| | - Wei Guo
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Science, Wuhan, China
| | - Yongqing Jiao
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Science, Wuhan, China.
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49
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MsmiR156 affects global gene expression and promotes root regenerative capacity and nitrogen fixation activity in alfalfa. Transgenic Res 2017; 26:541-557. [DOI: 10.1007/s11248-017-0024-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 05/18/2017] [Indexed: 10/19/2022]
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50
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Li S, Castillo-González C, Yu B, Zhang X. The functions of plant small RNAs in development and in stress responses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:654-670. [PMID: 27943457 DOI: 10.1111/tpj.13444] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/29/2016] [Accepted: 12/06/2016] [Indexed: 05/22/2023]
Abstract
Like metazoans, plants use small regulatory RNAs (sRNAs) to direct gene expression. Several classes of sRNAs, which are distinguished by their origin and biogenesis, exist in plants. Among them, microRNAs (miRNAs) and trans-acting small interfering RNAs (ta-siRNAs) mainly inhibit gene expression at post-transcriptional levels. In the past decades, plant miRNAs and ta-siRNAs have been shown to be essential for numerous developmental processes, including growth and development of shoots, leaves, flowers, roots and seeds, among others. In addition, miRNAs and ta-siRNAs are also involved in the plant responses to abiotic and biotic stresses, such as drought, temperature, salinity, nutrient deprivation, bacteria, virus and others. This review summarizes the roles of miRNAs and ta-siRNAs in plant physiology and development.
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Affiliation(s)
- Shengjun Li
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588-0660, USA
| | - Claudia Castillo-González
- Department of Biochemistry and Biophysics & Institute of Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, 77843, USA
| | - Bin Yu
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588-0660, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics & Institute of Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, 77843, USA
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