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Shi D, Huang H, Zhang Y, Qian Z, Du J, Huang L, Yan X, Lin S. The roles of non-coding RNAs in male reproductive development and abiotic stress responses during this unique process in flowering plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 341:111995. [PMID: 38266717 DOI: 10.1016/j.plantsci.2024.111995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
Successful male reproductive development is the guarantee for sexual reproduction of flowering plants. Male reproductive development is a complicated and multi-stage process that integrates physiological processes and adaptation and tolerance to a myriad of environmental stresses. This well-coordinated process is governed by genetic and epigenetic machineries. Non-coding RNAs (ncRNAs) play pleiotropic roles in the plant growth and development. The identification, characterization and functional analysis of ncRNAs and their target genes have opened a new avenue for comprehensively revealing the regulatory network of male reproductive development and its response to environmental stresses in plants. This review briefly addresses the types, origin, biogenesis and mechanisms of ncRNAs in plants, highlights important updates on the roles of ncRNAs in regulating male reproductive development and emphasizes the contribution of ncRNAs, especially miRNAs and lncRNAs, in responses to abiotic stresses during this unique process in flowering plants.
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Affiliation(s)
- Dexi Shi
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Huiting Huang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Yuting Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Zhihao Qian
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Jiao Du
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xiufeng Yan
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China.
| | - Sue Lin
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China.
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Naim D, Ahsan A, Imtiaj A, Mollah NH. Genome-wide identification and in silico characterization of major RNAi gene families in date palm (Phoenix dactylifera). BMC Genom Data 2024; 25:31. [PMID: 38491426 PMCID: PMC10943882 DOI: 10.1186/s12863-024-01217-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Dates contain various minerals that are essential for good health. The major RNA interference (RNAi) gene families play a vital role in plant growth and development by controlling the expression of protein-coding genes against different biotic and abiotic stresses. However, these gene families for date palm are not yet studied. Therefore, this study has explored major RNAi genes and their characteristics in date palm. RESULTS We have identified 4 PdDCLs, 7 PdAGOs, and 3 PdRDRs as RNAi proteins from the date palm genome by using AtRNAi genes as query sequences in BLASTp search. Domain analysis of predicted RNAi genes has revealed the Helicase_C, Dicer_dimer, PAZ, RNase III, and Piwi domains that are associated with the gene silencing mechanisms. Most PdRNAi proteins have been found in the nucleus and cytosol associated with the gene silencing actions. The gene ontology (GO) enrichment analysis has revealed some important GO terms including RNA interference, dsRNA fragmentation, and ribonuclease_III activity that are related to the protein-coding gene silencing mechanisms. Gene regulatory network (GRN) analysis has identified PAZ and SNF2 as the transcriptional regulators of PdRNAi genes. Top-ranked 10 microRNAs including Pda-miR156b, Pda-miR396a, Pda-miR166a, Pda-miR167d, and Pda-miR529a have been identified as the key post-transcriptional regulators of PdRNAi genes that are associated with different biotic/abiotic stresses. The cis-acting regulatory element analysis of PdRNAi genes has detected some vital cis-acting elements including ABRE, MBS, MYB, MYC, Box-4, G-box, I-box, and STRE that are linked with different abiotic stresses. CONCLUSION The results of this study might be valuable resources for the improvement of different characteristics in date palm by further studies in wet-lab.
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Affiliation(s)
- Darun Naim
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, 6205, Rajshahi, Bangladesh
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, 6205, Rajshahi, Bangladesh
| | - Asif Ahsan
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, 6205, Rajshahi, Bangladesh
| | - Ahmed Imtiaj
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, 6205, Rajshahi, Bangladesh
| | - Nurul Haque Mollah
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, 6205, Rajshahi, Bangladesh.
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Escolà G, González-Miguel VM, Campo S, Catala-Forner M, Domingo C, Marqués L, San Segundo B. Development and Genome-Wide Analysis of a Blast-Resistant japonica Rice Variety. PLANTS (BASEL, SWITZERLAND) 2023; 12:3536. [PMID: 37896000 PMCID: PMC10667994 DOI: 10.3390/plants12203536] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 10/06/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023]
Abstract
Rice is one of the most important crops in the world, and its production is severely affected by the rice blast disease caused by the fungus Magnaporthe oryzae. Several major blast resistance genes and QTLs associated with blast resistance have been described and mostly identified in indica rice varieties. In this work, we report the obtention of a blast-resistant rice breeding line derived from crosses between the resistant indica variety CT13432 and the japonica elite cultivar JSendra (highly susceptible to blast). The breeding line, named COPSEMAR9, was found to exhibit resistance to leaf blast and panicle blast, as demonstrated by disease assays under controlled and field conditions. Furthermore, a high-quality genome sequence of the blast-resistant breeding line was obtained using a strategy that combines short-read sequencing (Illumina sequencing) and long-read sequencing (Pacbio sequencing). The use of a whole-genome approach allowed the fine mapping of DNA regions of indica and japonica origin present in the COPSEMAR9 genome and the identification of parental gene regions potentially contributing to blast resistance in the breeding line. Rice blast resistance genes (including Pi33 derived from the resistant parent) and defense-related genes in the genome of COPSEMAR9 were identified. Whole-genome analyses also revealed the presence of microRNAs (miRNAs) with a known function in the rice response to M. oryzae infection in COPSEMAR9, which might also contribute to its phenotype of blast resistance. From this study, the genomic information and analysis methods provide valuable knowledge that will be useful in breeding programs for blast resistance in japonica rice cultivars.
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Affiliation(s)
- Glòria Escolà
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), C/de la Vall Moronta, CRAG Building, 08193 Barcelona, Spain; (G.E.); (V.M.G.-M.); (S.C.)
| | - Víctor M. González-Miguel
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), C/de la Vall Moronta, CRAG Building, 08193 Barcelona, Spain; (G.E.); (V.M.G.-M.); (S.C.)
| | - Sonia Campo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), C/de la Vall Moronta, CRAG Building, 08193 Barcelona, Spain; (G.E.); (V.M.G.-M.); (S.C.)
| | - Mar Catala-Forner
- Institute of Agrifood Research and Technology (IRTA), Field Crops, Ctra. Balada km. 1, 43870 Tarragona, Spain;
| | - Concha Domingo
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Departamento del Arroz and Centro de Genómica. Ctra Moncada-Náquera km 10.7, 46113 Moncada, Spain;
| | - Luis Marqués
- Cooperativa de Productores de Semillas de Arroz, S.C.L. (COPSEMAR) Avda del Mar 1, 46410 Sueca, Spain;
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), C/de la Vall Moronta, CRAG Building, 08193 Barcelona, Spain; (G.E.); (V.M.G.-M.); (S.C.)
- Consejo Superior de Investigaciones Científicas (CSIC), 08193 Barcelona, Spain
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Zhang X, Du M, Yang Z, Wang Z, Lim KJ. Biogenesis, Mode of Action and the Interactions of Plant Non-Coding RNAs. Int J Mol Sci 2023; 24:10664. [PMID: 37445841 DOI: 10.3390/ijms241310664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 06/23/2023] [Accepted: 06/24/2023] [Indexed: 07/15/2023] Open
Abstract
The central dogma of genetics, which outlines the flow of genetic information from DNA to RNA to protein, has long been the guiding principle in molecular biology. In fact, more than three-quarters of the RNAs produced by transcription of the plant genome are not translated into proteins, and these RNAs directly serve as non-coding RNAs in the regulation of plant life activities at the molecular level. The breakthroughs in high-throughput transcriptome sequencing technology and the establishment and improvement of non-coding RNA experiments have now led to the discovery and confirmation of the biogenesis, mechanisms, and synergistic effects of non-coding RNAs. These non-coding RNAs are now predicted to play important roles in the regulation of gene expression and responses to stress and evolution. In this review, we focus on the synthesis, and mechanisms of non-coding RNAs, and we discuss their impact on gene regulation in plants.
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Affiliation(s)
- Xin Zhang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Mingjun Du
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Zhengfu Yang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Zhengjia Wang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Kean-Jin Lim
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
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Bélanger S, Zhan J, Meyers BC. Phylogenetic analyses of seven protein families refine the evolution of small RNA pathways in green plants. PLANT PHYSIOLOGY 2023; 192:1183-1203. [PMID: 36869858 PMCID: PMC10231463 DOI: 10.1093/plphys/kiad141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 06/01/2023]
Abstract
Several protein families participate in the biogenesis and function of small RNAs (sRNAs) in plants. Those with primary roles include Dicer-like (DCL), RNA-dependent RNA polymerase (RDR), and Argonaute (AGO) proteins. Protein families such as double-stranded RNA-binding (DRB), SERRATE (SE), and SUPPRESSION OF SILENCING 3 (SGS3) act as partners of DCL or RDR proteins. Here, we present curated annotations and phylogenetic analyses of seven sRNA pathway protein families performed on 196 species in the Viridiplantae (aka green plants) lineage. Our results suggest that the RDR3 proteins emerged earlier than RDR1/2/6. RDR6 is found in filamentous green algae and all land plants, suggesting that the evolution of RDR6 proteins coincides with the evolution of phased small interfering RNAs (siRNAs). We traced the origin of the 24-nt reproductive phased siRNA-associated DCL5 protein back to the American sweet flag (Acorus americanus), the earliest diverged, extant monocot species. Our analyses of AGOs identified multiple duplication events of AGO genes that were lost, retained, or further duplicated in subgroups, indicating that the evolution of AGOs is complex in monocots. The results also refine the evolution of several clades of AGO proteins, such as AGO4, AGO6, AGO17, and AGO18. Analyses of nuclear localization signal sequences and catalytic triads of AGO proteins shed light on the regulatory roles of diverse AGOs. Collectively, this work generates a curated and evolutionarily coherent annotation for gene families involved in plant sRNA biogenesis/function and provides insights into the evolution of major sRNA pathways.
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Affiliation(s)
| | - Junpeng Zhan
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
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Li Y, Ma E, Yang K, Zhao B, Li Y, Wan P. Genome-wide analysis of key gene families in RNA silencing and their responses to biotic and drought stresses in adzuki bean. BMC Genomics 2023; 24:195. [PMID: 37046231 PMCID: PMC10091639 DOI: 10.1186/s12864-023-09274-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/25/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND In plants, RNA silencing is an important conserved mechanism to regulate gene expression and combat against abiotic and biotic stresses. Dicer-like (DCL) and Argonaute (AGO) proteins and RNA-dependent RNA polymerase (RDR) are the core elements involved in gene silencing and their gene families have been explored in many plants. However, these genes and their responses to stresses have not yet been well characterized in adzuki bean. RESULTS A total of 11 AGO, 7 DCL and 6 RDR proteins were identified, and phylogenetic analyses of these proteins showed that they clustered into six, four and four clades respectively. The expression patterns of these genes in susceptible or resistant adzuki bean cultivars challenged with drought, bean common mosaic virus and Podosphaera xanthii infections were further validated by quantitative RT-PCR. The different responses of these proteins under abiotic and biotic stresses indicated their specialized regulatory mechanisms. CONCLUSIONS In this study, 24 genes of the DCL, AGO and RDR gene families in adzuki bean were identified, and the sequence characterization, structure of the encoded proteins, evolutionary relationship with orthologues in other legumes and gene expression patterns under drought and biotic stresses were primarily explored, which enriched our understanding of these genes in adzuki bean. Our findings provide a foundation for the comparative genomic analyses of RNA silencing elements in legume plants and further new insights into the functional complexity of RNA silencing in the response to various stresses in adzuki bean.
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Affiliation(s)
- Yongqiang Li
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture Rural Affairs, College of Biological Science and Resources Environment, Beijing University of Agriculture, HuilongguanBeinonglu 7, Changping District, Beijing, 102206, China.
| | - Enze Ma
- Beijing Key Laboratory of New Technology in Agricultural Application, College of Plant Science and Technology, Beijing University of Agriculture, HuilongguanBeinonglu 7, Changping District, Beijing, 102206, China
| | - Kai Yang
- Beijing Key Laboratory of New Technology in Agricultural Application, College of Plant Science and Technology, Beijing University of Agriculture, HuilongguanBeinonglu 7, Changping District, Beijing, 102206, China
| | - Bo Zhao
- Beijing Key Laboratory of New Technology in Agricultural Application, College of Plant Science and Technology, Beijing University of Agriculture, HuilongguanBeinonglu 7, Changping District, Beijing, 102206, China
| | - Yisong Li
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture Rural Affairs, College of Biological Science and Resources Environment, Beijing University of Agriculture, HuilongguanBeinonglu 7, Changping District, Beijing, 102206, China
| | - Ping Wan
- Beijing Key Laboratory of New Technology in Agricultural Application, College of Plant Science and Technology, Beijing University of Agriculture, HuilongguanBeinonglu 7, Changping District, Beijing, 102206, China.
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Lohani N, Golicz AA, Allu AD, Bhalla PL, Singh MB. Genome-wide analysis reveals the crucial role of lncRNAs in regulating the expression of genes controlling pollen development. PLANT CELL REPORTS 2023; 42:337-354. [PMID: 36653661 DOI: 10.1007/s00299-022-02960-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
The genomic location and stage-specific expression pattern of many long non-coding RNAs reveal their critical role in regulating protein-coding genes crucial in pollen developmental progression and male germ line specification. Long non-coding RNAs (lncRNAs) are transcripts longer than 200 bp with no apparent protein-coding potential. Multiple investigations have revealed high expression of lncRNAs in plant reproductive organs in a cell and tissue-specific manner. However, their potential role as essential regulators of molecular processes involved in sexual reproduction remains largely unexplored. We have used developing field mustard (Brassica rapa) pollen as a model system for investigating the potential role of lncRNAs in reproductive development. Reference-based transcriptome assembly performed to update the existing genome annotation identified novel expressed protein-coding genes and long non-coding RNAs (lncRNAs), including 4347 long intergenic non-coding RNAs (lincRNAs, 1058 expressed) and 2,045 lncRNAs overlapping protein-coding genes on the opposite strand (lncNATs, 780 expressed). The analysis of expression profiles reveals that lncRNAs are significant and stage-specific contributors to the gene expression profile of developing pollen. Gene co-expression networks accompanied by genome location analysis identified 38 cis-acting lincRNA, 31 cis-acting lncNAT, 7 trans-acting lincRNA and 14 trans-acting lncNAT to be substantially co-expressed with target protein-coding genes involved in biological processes regulating pollen development and male lineage specification. These findings provide a foundation for future research aiming at developing strategies to employ lncRNAs as regulatory tools for gene expression control during reproductive development.
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Affiliation(s)
- Neeta Lohani
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
- School of Science, Western Sydney University, Richmond, Australia
| | - Agnieszka A Golicz
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Gießen, Gießen, Germany
| | - Annapurna D Allu
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia.
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Spotting the Targets of the Apospory Controller TGS1 in Paspalum notatum. PLANTS 2022; 11:plants11151929. [PMID: 35893633 PMCID: PMC9332697 DOI: 10.3390/plants11151929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/27/2022] [Accepted: 06/30/2022] [Indexed: 11/17/2022]
Abstract
Sexuality and apomixis are interconnected plant reproductive routes possibly behaving as polyphenic traits under the influence of the environment. In the subtropical grass Paspalum notatum, one of the controllers of apospory, a main component of gametophytic apomixis reproduction, is TRIMETHYLGUANOSINE SYNTHASE 1 (TGS1), a multifunctional gene previously associated with RNA cleavage regulation (including mRNA splicing as well as rRNA and miRNA processing), transcriptional modulation and the establishment of heterochromatin. In particular, the downregulation of TGS1 induces a sexuality decline and the emergence of aposporous-like embryo sacs. The present work was aimed at identifying TGS1 target RNAs expressed during reproductive development of Paspalum notatum. First, we mined available RNA databases originated from spikelets of sexual and apomictic plants, which naturally display a contrasting TGS1 representation, to identify differentially expressed mRNA splice variants and miRNAs. Then, the role of TGS1 in the generation of these particular molecules was investigated in antisense tgs1 sexual lines. We found that CHLOROPHYLL A-B BINDING PROTEIN 1B-21 (LHC Ib-21, a component of the chloroplast light harvesting complex), QUI-GON JINN (QGJ, encoding a MAP3K previously associated with apomixis) and miR2275 (a meiotic 24-nt phasi-RNAs producer) are directly or indirectly targeted by TGS1. Our results point to a coordinated control exercised by signal transduction and siRNA machineries to induce the transition from sexuality to apomixis.
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Yang Z, Hui S, Lv Y, Zhang M, Chen D, Tian J, Zhang H, Liu H, Cao J, Xie W, Wu C, Wang S, Yuan M. miR395-regulated sulfate metabolism exploits pathogen sensitivity to sulfate to boost immunity in rice. MOLECULAR PLANT 2022; 15:671-688. [PMID: 34968734 DOI: 10.1016/j.molp.2021.12.013] [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: 08/09/2021] [Revised: 11/30/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
MicroRNAs (miRNAs) play important roles in plant physiological activities. However, their roles and molecular mechanisms in boosting plant immunity, especially through the modulation of macronutrient metabolism in response to pathogens, are largely unknown. Here, we report that an evolutionarily conserved miRNA, miR395, promotes resistance to Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc), two destructive bacterial pathogens, by regulating sulfate accumulation and distribution in rice. Specifically, miR395 targets and suppresses the expression of the ATP sulfurylase gene OsAPS1, which functions in sulfate assimilation, and two sulfate transporter genes, OsSULTR2;1 and OsSULTR2;2, which function in sulfate translocation, to promote sulfate accumulation, resulting in broad-spectrum resistance to bacterial pathogens in miR395-overexpressing plants. Genetic analysis revealed that miR395-triggered resistance is involved in both pathogen-associated molecular pattern-triggered immunity and R gene-mediated resistance. Moreover, we found that accumulated sulfate but not S-metabolites inhibits proliferation of pathogenic bacteria, revealing a sulfate-mediated antibacterial defense mechanism that differs from sulfur-induced resistance. Furthermore, compared with other bacteria, Xoo and Xoc, which lack the sulfate transporter CysZ, are sensitive to high levels of extracellular sulfate. Accordingly, miR395-regulated sulfate accumulation impaired the virulence of Xoo and Xoc by decreasing extracellular polysaccharide production and biofilm formation. Taken together, these results suggest that rice miR395 modulates sulfate metabolism to exploit pathogen sensitivity to sulfate and thereby promotes broad-spectrum resistance.
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Affiliation(s)
- Zeyu Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Shugang Hui
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Lv
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Miaojing Zhang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Dan Chen
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingjing Tian
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Haitao Zhang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongbo Liu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianbo Cao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenya Xie
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Changyin Wu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Shiping Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
| | - Meng Yuan
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
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Kalem MC, Panepinto JC. Long Non-Coding RNAs in Cryptococcus neoformans: Insights Into Fungal Pathogenesis. Front Cell Infect Microbiol 2022; 12:858317. [PMID: 35372111 PMCID: PMC8968117 DOI: 10.3389/fcimb.2022.858317] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/18/2022] [Indexed: 12/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are highly expressed and can modulate multiple cellular processes including transcription, splicing, translation, and many diverse signaling events. LncRNAs can act as sponges for miRNAs, RNA and DNA binding proteins, functioning as competitive endogenous RNAs. The contribution of lncRNAs to microbial pathogenesis is largely neglected in eukaryotic pathogens despite the abundance of RNA sequencing datasets encompassing conditions of stress, gene deletions and conditions that mimic the host environment. The human fungal pathogen Cryptococcus neoformans encodes 6975 (84%) protein-coding and 1359 (16%) non-protein-coding RNAs, of which 1182 (14.2%) are lncRNAs defined by a threshold of greater than 200 nucleotides in length. Here, we discuss the current state of knowledge in C. neoformans lncRNA biology. Utilizing existing RNA seq datasets, we examine trends in lncRNA expression and discuss potential implications for pathogenesis.
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Affiliation(s)
- Murat C. Kalem
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York (SUNY), University at Buffalo, Buffalo, NY, United States
| | - John C. Panepinto
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York (SUNY), University at Buffalo, Buffalo, NY, United States
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11
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Small RNAs Participate in Plant-Virus Interaction and Their Application in Plant Viral Defense. Int J Mol Sci 2022; 23:ijms23020696. [PMID: 35054880 PMCID: PMC8775341 DOI: 10.3390/ijms23020696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/30/2021] [Accepted: 01/05/2022] [Indexed: 02/06/2023] Open
Abstract
Small RNAs are significant regulators of gene expression, which play multiple roles in plant development, growth, reproductive and stress response. It is generally believed that the regulation of plants’ endogenous genes by small RNAs has evolved from a cellular defense mechanism for RNA viruses and transposons. Most small RNAs have well-established roles in the defense response, such as viral response. During viral infection, plant endogenous small RNAs can direct virus resistance by regulating the gene expression in the host defense pathway, while the small RNAs derived from viruses are the core of the conserved and effective RNAi resistance mechanism. As a counter strategy, viruses evolve suppressors of the RNAi pathway to disrupt host plant silencing against viruses. Currently, several studies have been published elucidating the mechanisms by which small RNAs regulate viral defense in different crops. This paper reviews the distinct pathways of small RNAs biogenesis and the molecular mechanisms of small RNAs mediating antiviral immunity in plants, as well as summarizes the coping strategies used by viruses to override this immune response. Finally, we discuss the current development state of the new applications in virus defense based on small RNA silencing.
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Reshetnyak G, Jacobs JM, Auguy F, Sciallano C, Claude L, Medina C, Perez-Quintero AL, Comte A, Thomas E, Bogdanove A, Koebnik R, Szurek B, Dievart A, Brugidou C, Lacombe S, Cunnac S. An atypical class of non-coding small RNAs is produced in rice leaves upon bacterial infection. Sci Rep 2021; 11:24141. [PMID: 34921170 PMCID: PMC8683429 DOI: 10.1038/s41598-021-03391-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/29/2021] [Indexed: 01/18/2023] Open
Abstract
Non-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth, development and stress responses. Early insights into plant sRNAs established a role in antiviral defense and they are now extensively studied across plant-microbe interactions. Here, sRNA sequencing discovered a class of sRNA in rice (Oryza sativa) specifically associated with foliar diseases caused by Xanthomonas oryzae bacteria. Xanthomonas-induced small RNAs (xisRNAs) loci were distinctively upregulated in response to diverse virulent strains at an early stage of infection producing a single duplex of 20-22 nt sRNAs. xisRNAs production was dependent on the Type III secretion system, a major bacterial virulence factor for host colonization. xisRNA loci overlap with annotated transcripts sequences, with about half of them encoding protein kinase domain proteins. A number of the corresponding rice cis-genes have documented functions in immune signaling and xisRNA loci predominantly coincide with the coding sequence of a conserved kinase motif. xisRNAs exhibit features of small interfering RNAs and their biosynthesis depend on canonical components OsDCL1 and OsHEN1. xisRNA induction possibly mediates post-transcriptional gene silencing but they do not broadly suppress cis-genes expression on the basis of mRNA-seq data. Overall, our results identify a group of unusual sRNAs with a potential role in plant-microbe interactions.
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Affiliation(s)
- Ganna Reshetnyak
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Jonathan M Jacobs
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43201, USA
- Infectious Disease Institute, The Ohio State University, Columbus, OH, 43201, USA
| | - Florence Auguy
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Coline Sciallano
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Lisa Claude
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Clemence Medina
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Alvaro L Perez-Quintero
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Aurore Comte
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Emilie Thomas
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Adam Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Ralf Koebnik
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Boris Szurek
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Anne Dievart
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398, Montpellier, France
- CIRAD, UMR AGAP Institut, 34398, Montpellier, France
| | - Christophe Brugidou
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Severine Lacombe
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Sebastien Cunnac
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France.
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Campo S, Sánchez‐Sanuy F, Camargo‐Ramírez R, Gómez‐Ariza J, Baldrich P, Campos‐Soriano L, Soto‐Suárez M, San Segundo B. A novel Transposable element-derived microRNA participates in plant immunity to rice blast disease. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1798-1811. [PMID: 33780108 PMCID: PMC8428829 DOI: 10.1111/pbi.13592] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 02/15/2021] [Accepted: 03/02/2021] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that direct post-transcriptional gene silencing in plant development and stress responses through cleavage or translational repression of target mRNAs. Here, we report the identification and functional characterization of a new member of the miR812 family in rice (named as miR812w) involved in disease resistance. miR812w is present in cultivated Oryza species, both japonica and indica subspecies, and wild rice species within the Oryza genus, but not in dicotyledonous species. miR812w is a 24nt-long that requires DCL3 for its biogenesis and is loaded into AGO4 proteins. Whereas overexpression of miR812w increased resistance to infection by the rice blast fungus Magnaporthe oryzae, CRISPR/Cas9-mediated MIR812w editing enhances disease susceptibility, supporting that miR812w plays a role in blast resistance. We show that miR812w derives from the Stowaway type of rice MITEs (Miniature Inverted-Repeat Transposable Elements). Moreover, miR812w directs DNA methylation in trans at target genes that have integrated a Stowaway MITE copy into their 3' or 5' untranslated region (ACO3, CIPK10, LRR genes), as well as in cis at the MIR812w locus. The target genes of miR812 were found to be hypo-methylated around the miR812 recognition site, their expression being up-regulated in transgene-free CRISPR/Cas9-edited miR812 plants. These findings further support that, in addition to post-transcriptional regulation of gene expression, miRNAs can exert their regulatory function at the transcriptional level. This relationship between miR812w and Stowaway MITEs integrated into multiple coding genes might eventually create a network for miR812w-mediated regulation of gene expression with implications in rice immunity.
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Affiliation(s)
- Sonia Campo
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
| | - Ferran Sánchez‐Sanuy
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
| | - Rosany Camargo‐Ramírez
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
| | - Jorge Gómez‐Ariza
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
| | - Patricia Baldrich
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
- Present address:
Donald Danforth Plant Science Center975 N Warson RoadSt. LouisMO63132USA
| | - Lidia Campos‐Soriano
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
| | - Mauricio Soto‐Suárez
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
- Present address:
Corporación Colombiana de Investigación Agropecuaria. AGROSAVIAKm 14 vía Mosquera‐BogotáMosquera250047Colombia
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
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Chen Y, Zitello E, Guo R, Deng Y. The function of LncRNAs and their role in the prediction, diagnosis, and prognosis of lung cancer. Clin Transl Med 2021; 11:e367. [PMID: 33931980 PMCID: PMC8021541 DOI: 10.1002/ctm2.367] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/22/2021] [Accepted: 03/05/2021] [Indexed: 12/24/2022] Open
Abstract
Lung cancer remains a major threat to human health. Low dose CT scan (LDCT) has become the main method of early screening for lung cancer due to the low sensitivity of chest X-ray. However, LDCT not only has a high false positive rate, but also entails risks of overdiagnosis and cumulative radiation exposure. In addition, cumulative radiation by LDCT screening and subsequent follow-up can increase the risk of lung cancer. Many studies have shown that long noncoding RNAs (lncRNAs) remain stable in blood, and profiling of blood has the advantages of being noninvasive, readily accessible and inexpensive. Serum or plasma assay of lncRNAs in blood can be used as a novel detection method to assist LDCT while improving the accuracy of early lung cancer screening. LncRNAs can participate in the regulation of various biological processes. A large number of researches have reported that lncRNAs are key regulators involved in the progression of human cancers through multiple action models. Especially, some lncRNAs can affect various hallmarks of lung cancer. In addition to their diagnostic value, lncRNAs also possess promising potential in other clinical applications toward lung cancer. LncRNAs can be used as predictive markers for chemosensitivity, radiosensitivity, and sensitivity to epidermal growth factor receptor (EGFR)-targeted therapy, and as well markers of prognosis. Different lncRNAs have been implicated to regulate chemosensitivity, radiosensitivity, and sensitivity to EGFR-targeted therapy through diverse mechanisms. Although many challenges need to be addressed in the future, lncRNAs have bright prospects as an adjunct to radiographic methods in the clinical management of lung cancer.
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Affiliation(s)
- Yu Chen
- Department of Quantitative Health SciencesJohn A. Burns School of Medicine, University of Hawaii at ManoaHonoluluHawaiiUSA
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human ResourcesUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Emory Zitello
- Department of Quantitative Health SciencesJohn A. Burns School of Medicine, University of Hawaii at ManoaHonoluluHawaiiUSA
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human ResourcesUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Rui Guo
- School of Public HealthGuangxi Medical UniversityNanningChina
| | - Youping Deng
- Department of Quantitative Health SciencesJohn A. Burns School of Medicine, University of Hawaii at ManoaHonoluluHawaiiUSA
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15
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Zhang M, Ma X, Wang C, Li Q, Meyers BC, Springer NM, Walbot V. CHH DNA methylation increases at 24-PHAS loci depend on 24-nt phased small interfering RNAs in maize meiotic anthers. THE NEW PHYTOLOGIST 2021; 229:2984-2997. [PMID: 33135165 DOI: 10.1111/nph.17060] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/14/2020] [Indexed: 05/23/2023]
Abstract
Plant phased small interfering RNAs (phasiRNAs) contribute to robust male fertility; however, specific functions remain undefined. In maize (Zea mays), male sterile23 (ms23), necessary for both 24-nt phasiRNA precursor (24-PHAS) loci and Dicer-like5 (Dcl5) expression, and dcl5-1 mutants unable to slice PHAS transcripts lack nearly all 24-nt phasiRNAs. Based on sequence capture bisulfite-sequencing, we find that CHH DNA methylation of most 24-PHAS loci is increased in meiotic anthers of control plants but not in the ms23 and dcl5 mutants. Because dcl5-1 anthers express PHAS precursors, we conclude that the 24-nt phasiRNAs, rather than just activation of PHAS transcription, are required for targeting increased CHH methylation at these loci. Although PHAS precursors are processed into multiple 24-nt phasiRNA products, there is substantial differential product accumulation. Abundant 24-nt phasiRNA positions corresponded to high CHH methylation within individual loci, reinforcing the conclusion that 24-nt phasiRNAs contribute to increased CHH methylation in cis.
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Affiliation(s)
- Mei Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - Xuxu Ma
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - Chunyu Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Li
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
- Division of Plant Sciences, University of Missouri-Columbia, 52 Agriculture Lab, Columbia, MO, 65211, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | - Virginia Walbot
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
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16
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Dukowic-Schulze S, van der Linde K. Oxygen, secreted proteins and small RNAs: mobile elements that govern anther development. PLANT REPRODUCTION 2021; 34:1-19. [PMID: 33492519 PMCID: PMC7902584 DOI: 10.1007/s00497-020-00401-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/24/2020] [Indexed: 05/24/2023]
Abstract
Correct anther development is essential for male fertility and subsequently agricultural yield. Defects in anther development range from the early stage of stamen formation until the late stage of tapetum degeneration. In particular, the specification of the four distinct somatic layers and the inner sporogenous cells need perfect orchestration relying on precise cell-cell communication. Up to now, several signals, which coordinate the anther´s developmental program, have been identified. Among the known signals are phytohormones, environmental conditions sensed via glutaredoxins, several receptor-like kinases triggered by ligands like MAC1, and small RNAs such as miRNAs and the monocot-prevalent reproductive phasiRNAs. Rather than giving a full review on anther development, here we discuss anther development with an emphasis on mobile elements like ROS/oxygen, secreted proteins and small RNAs (only briefly touching on phytohormones), how they might act and interact, and what the future of this research area might reveal.
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Affiliation(s)
- Stefanie Dukowic-Schulze
- Department of Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany.
| | - Karina van der Linde
- Department of Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany.
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17
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Bélanger S, Baldrich P, Lemay M, Marchand S, Esteves P, Meyers BC, Belzile F. The commitment of barley microspores into embryogenesis correlates with miRNA-directed regulation of members of the SPL, GRF and HD-ZIPIII transcription factor families. PLANT DIRECT 2020; 4:e00289. [PMID: 36406053 PMCID: PMC9671080 DOI: 10.1002/pld3.289] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/26/2020] [Accepted: 10/19/2020] [Indexed: 05/19/2023]
Abstract
Microspore embryogenesis is a model for developmental plasticity and cell fate decisions. To investigate the role of miRNAs in this development, we sequenced sRNAs and the degradome of barley microspores collected prior to (day 0) and after (days 2 and 5) the application of a stress treatment known to induce embryogenesis. Microspores isolated at these timepoints were uniform in both appearance and in their complements of sRNAs. We detected 68 miRNAs in microspores. The abundance of 51 of these miRNAs differed significantly during microspore development. One group of miRNAs was induced when the stress treatment was applied, prior to being repressed when microspores transitioned to embryogenesis. Another group of miRNAs were up-regulated in day-2 microspores and their abundance remained stable or increased in day-5 microspores, a timepoint at which the first clear indications of the transition toward embryogenesis were visible. Collectively, these miRNAs might play a role in the modulation of the stress response, the repression of gametic development, and/or the gain of embryogenic potential. A degradome analysis allowed us to validate the role of miRNAs in regulating 41 specific transcripts. We showed that the transition of microspores toward the embryogenesis pathway involves miRNA-directed regulation of members of the ARF, SPL, GRF, and HD-ZIPIII transcription factor families. We noted that 41.5% of these targets were shared between day-2 and day-5 microspores while 26.8% were unique to day-5 microspores. The former set may act to disrupt transcripts involved in pollen development while the latter set may drive the commitment to embryogenesis.
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Affiliation(s)
- Sébastien Bélanger
- Département de phytologie and Institut de biologie intégrative et des systèmesUniversité LavalQuébec CityQuébecCanada
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | | | - Marc‐André Lemay
- Département de phytologie and Institut de biologie intégrative et des systèmesUniversité LavalQuébec CityQuébecCanada
| | - Suzanne Marchand
- Département de phytologie and Institut de biologie intégrative et des systèmesUniversité LavalQuébec CityQuébecCanada
| | - Patricio Esteves
- Département de phytologie and Institut de biologie intégrative et des systèmesUniversité LavalQuébec CityQuébecCanada
| | - Blake C. Meyers
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
| | - François Belzile
- Département de phytologie and Institut de biologie intégrative et des systèmesUniversité LavalQuébec CityQuébecCanada
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18
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Yao W, Li Y, Xie W, Wang L. Features of sRNA biogenesis in rice revealed by genetic dissection of sRNA expression level. Comput Struct Biotechnol J 2020; 18:3207-3216. [PMID: 33209208 PMCID: PMC7649420 DOI: 10.1016/j.csbj.2020.10.012] [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: 06/23/2020] [Revised: 09/24/2020] [Accepted: 10/11/2020] [Indexed: 01/25/2023] Open
Abstract
We previously conducted a QTL analysis of small RNA (sRNA) abundance in flag leaves of an immortalized rice F2 (IMF2) population by aligning sRNA reads to the reference genome to quantify the expression levels of sRNAs. However, this approach missed about half of the sRNAs as only 50% of all sRNA reads could be uniquely aligned to the reference genome. Here, we quantified the expression levels of sRNAs and sRNA clusters without the use of a reference genome. QTL analysis of the expression levels of sRNAs and sRNA clusters confirmed the feasibility of this approach. sRNAs and sRNA clusters with identified QTLs were then aligned to the high-quality parental genomes of the IMF2 population to resolve the identified QTLs into local vs. distant regulation mode. We were able to detect new QTL hotspots by considering sRNAs aligned to multiple positions of the parental genomes and sRNAs unaligned to the parental genomes. We found that several local-QTL hotspots were caused by sequence variations in long inverted repeats, which probably function as precursors of sRNAs, between the two parental genomes. The expression levels of these sRNAs were significantly associated with the presence/absence of the long inverted repeats in the IMF2 population. Moreover, we found that the variations in whole-genome sRNA species composition among different IMF2s were attributed to sRNA biogenesis genes including OsDCL2b and OsRDR2. Our results highlight that genetic dissection of sRNA expression is a promising approach to disclose new components functioning in sRNA biogenesis and new mechanisms of sRNA biogenesis.
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Affiliation(s)
- Wen Yao
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China.,National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Lu Y, Zhou DX, Zhao Y. Understanding epigenomics based on the rice model. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1345-1363. [PMID: 31897514 DOI: 10.1007/s00122-019-03518-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/18/2019] [Indexed: 05/26/2023]
Abstract
The purpose of this paper provides a comprehensive overview of the recent researches on rice epigenomics, including DNA methylation, histone modifications, noncoding RNAs, and three-dimensional genomics. The challenges and perspectives for future research in rice are discussed. Rice as a model plant for epigenomic studies has much progressed current understanding of epigenetics in plants. Recent results on rice epigenome profiling and three-dimensional chromatin structure studies reveal specific features and implication in gene regulation during rice plant development and adaptation to environmental changes. Results on rice chromatin regulator functions shed light on mechanisms of establishment, recognition, and resetting of epigenomic information in plants. Cloning of several rice epialleles associated with important agronomic traits highlights importance of epigenomic variation in rice plant growth, fitness, and yield. In this review, we summarize and analyze recent advances in rice epigenomics and discuss challenges and directions for future research in the field.
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Affiliation(s)
- Yue Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Institute of Plant Science of Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University Paris-Saclay, 91405, Orsay, France
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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20
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Das S, Swetha C, Pachamuthu K, Nair A, Shivaprasad PV. Loss of function of Oryza sativa Argonaute 18 induces male sterility and reduction in phased small RNAs. PLANT REPRODUCTION 2020; 33:59-73. [PMID: 32157461 DOI: 10.1007/s00497-020-00386-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/03/2020] [Indexed: 05/14/2023]
Abstract
In this manuscript, we show that Oryza sativa indica Argonaute protein AGO18 is required for male gametophyte development likely to through a small RNA-mediated mechanism. Monocots have evolved unique gene silencing pathways due to the presence of unique members of Dicer-like and Argonaute (AGO) family members. Among the monocot AGO homologs, AGO18 occupies a unique position. Previous reports have implicated this protein in viral resistance as well as in gametogenesis, likely through its competition with AGO1 clade members for micro(mi)RNAs and other small (s)RNAs. Although expression of rice AGO18 in specific stages of male gametogenesis has been documented, its major functions in plant development remain poorly understood. Here, we show that Oryza sativa indica AGO18 is involved in male gametophyte development. Knockdown (KD) of AGO18 in transgenic rice lines resulted in stunted plants that are male sterile, whereas their carpels were functional. Transcriptome analysis revealed downregulation of several pollen development-associated genes in KD lines. sRNA sequencing in vegetative and reproductive tissues of KD lines indicated reduction of miRNAs and phased secondary sRNAs implicated in male gametophyte development. Our results indicate a distinct role for rice AGO18 in male fertility.
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Affiliation(s)
- Soumita Das
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Chenna Swetha
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Kannan Pachamuthu
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Ashwin Nair
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - P V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India.
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21
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Debladis E, Lee TF, Huang YJ, Lu JH, Mathioni SM, Carpentier MC, Llauro C, Pierron D, Mieulet D, Guiderdoni E, Chen PY, Meyers BC, Panaud O, Lasserre E. Construction and characterization of a knock-down RNA interference line of OsNRPD1 in rice ( Oryza sativa ssp japonica cv Nipponbare). Philos Trans R Soc Lond B Biol Sci 2020; 375:20190338. [PMID: 32075556 DOI: 10.1098/rstb.2019.0338] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In plants, RNA-directed DNA methylation (RdDM) is a silencing mechanism relying on the production of 24-nt small interfering RNAs (siRNAs) by RNA POLYMERASE IV (Pol IV) to trigger methylation and inactivation of transposable elements (TEs). We present the construction and characterization of osnrpd1, a knock-down RNA interference line of OsNRPD1 gene that encodes the largest subunit of Pol IV in rice (Oryza sativa ssp japonica cv Nipponbare). We show that osnrpd1 displays a lower accumulation of OsNRPD1 transcripts, associated with an overall reduction of 24-nt siRNAs and DNA methylation level in all three contexts, CG, CHG and CHH. We uncovered new insertions of known active TEs, the LTR retrotransposons Tos17 and Lullaby and the long interspersed nuclear element-type retrotransposon Karma. However, we did not observe any clear developmental phenotype, contrary to what was expected for a mutant severely affected in RdDM. In addition, despite the presence of many putatively functional TEs in the rice genome, we found no evidence of in planta global reactivation of transposition. This knock-down of OsNRPD1 likely led to a weakly affected line, with no effect on development and a limited effect on transposition. We discuss the possibility that a knock-out mutation of OsNRPD1 would cause sterility in rice. This article is part of a discussion meeting issue 'Crossroads between transposons and gene regulation'.
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Affiliation(s)
- Emilie Debladis
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France.,Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France
| | - Tzuu-Fen Lee
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - Yan-Jiun Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Jui-Hsien Lu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | | | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France.,Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France
| | - Christel Llauro
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France.,Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France
| | - Davy Pierron
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France.,Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France
| | | | | | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA.,Division of Plant Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France.,Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France.,Institut Universitaire de France, Paris, France
| | - Eric Lasserre
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France.,Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France
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22
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De La Torre AR, Piot A, Liu B, Wilhite B, Weiss M, Porth I. Functional and morphological evolution in gymnosperms: A portrait of implicated gene families. Evol Appl 2020; 13:210-227. [PMID: 31892953 PMCID: PMC6935586 DOI: 10.1111/eva.12839] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/25/2019] [Accepted: 07/02/2019] [Indexed: 12/12/2022] Open
Abstract
Gymnosperms diverged from their sister plant clade of flowering plants 300 Mya. Morphological and functional divergence between the two major seed plant clades involved significant changes in their reproductive biology, water-conducting systems, secondary metabolism, stress defense mechanisms, and small RNA-mediated epigenetic silencing. The relatively recent sequencing of several gymnosperm genomes and the development of new genomic resources have enabled whole-genome comparisons within gymnosperms, and between angiosperms and gymnosperms. In this paper, we aim to understand how genes and gene families have contributed to the major functional and morphological differences in gymnosperms, and how this information can be used for applied breeding and biotechnology. In addition, we have analyzed the angiosperm versus gymnosperm evolution of the pleiotropic drug resistance (PDR) gene family with a wide range of functionalities in plants' interaction with their environment including defense mechanisms. Some of the genes reviewed here are newly studied members of gene families that hold potential for biotechnological applications related to commercial and pharmacological value. Some members of conifer gene families can also be exploited for their potential in phytoremediation applications.
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Affiliation(s)
| | - Anthony Piot
- Department of Wood and Forest SciencesLaval UniversityQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Laval UniversityQuebec CityQuebecCanada
- Centre for Forest Research (CEF)Laval UniversityQuebec CityQuebecCanada
| | - Bobin Liu
- School of ForestryNorthern Arizona UniversityFlagstaffAZUSA
- College of ForestryFujian Agricultural and Forestry UniversityFuzhouFujianChina
| | | | - Matthew Weiss
- School of ForestryNorthern Arizona UniversityFlagstaffAZUSA
| | - Ilga Porth
- Department of Wood and Forest SciencesLaval UniversityQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Laval UniversityQuebec CityQuebecCanada
- Centre for Forest Research (CEF)Laval UniversityQuebec CityQuebecCanada
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23
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Peng Y, Zhang Y, Gui Y, An D, Liu J, Xu X, Li Q, Wang J, Wang W, Shi C, Fan L, Lu B, Deng Y, Teng S, He Z. Elimination of a Retrotransposon for Quenching Genome Instability in Modern Rice. MOLECULAR PLANT 2019; 12:1395-1407. [PMID: 31228579 DOI: 10.1016/j.molp.2019.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 06/05/2019] [Accepted: 06/09/2019] [Indexed: 05/26/2023]
Abstract
Transposable elements (TEs) constitute the most abundant portions of plant genomes and can dramatically shape host genomes during plant evolution. They also play important roles in crop domestication. However, whether TEs themselves are also selected during crop domestication has remained unknown. Here, we identify an active long terminal repeat (LTR) retrotransposon, HUO, as a potential target of selection during rice domestication and breeding. HUO is a low-copy-number LTR retrotransposon, and is active under natural growth conditions and transmitted through male gametogenesis, preferentially inserting into genomic regions capable of transcription. HUO exists in all wild rice accessions and about half of the archaeological rice grains (1200-7000 years ago) and landraces surveyed, but is absent in almost all modern varieties, indicating its gradual elimination during rice domestication and breeding. Further analyses showed that HUO is subjected to strict gene silencing through the RNA-directed DNA methylation pathway. Our results also suggest that multiple HUO copies may trigger genomic instability through altering genome-wide DNA methylation and small RNA biogenesis and changing global gene expression, resulting in decreased disease resistance and yield, coinciding with its elimination during rice breeding. Together, our study suggests that negative selection of an active retrotransposon might be important for genome stability during crop domestication and breeding.
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Affiliation(s)
- Yu Peng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yingying Zhang
- The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Yijie Gui
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Dong An
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Junzhong Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xun Xu
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Qun Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Junmin Wang
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wen Wang
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Chunhai Shi
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Longjiang Fan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Baorong Lu
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yiwen Deng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Sheng Teng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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24
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Sun W, Chen D, Xue Y, Zhai L, Zhang D, Cao Z, Liu L, Cheng C, Zhang Y, Zhang Z. Genome-wide identification of AGO18b-bound miRNAs and phasiRNAs in maize by cRIP-seq. BMC Genomics 2019; 20:656. [PMID: 31419938 PMCID: PMC6697968 DOI: 10.1186/s12864-019-6028-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 08/12/2019] [Indexed: 12/20/2022] Open
Abstract
Background Argonaute proteins (AGOs) are important players in the regulation of plant development by directing sRNAs to target mRNAs. In maize (Zea mays), AGO18b is a tassel-enriched and grass-specific AGO. Previous studies have shown that AGO18b is highly expressed in tassels during meiosis and negatively regulates determinacy of spikelet meristems. However, binding profile on RNAs and acting mechanisms of AGO18b remain unknown. Results In this study, we explored the binding profile of AGO18b in maize tassel by UV cross-linking RNA immunoprecipitation, followed by deep sequencing of these cDNA libraries (cRIP-seq), and systematically studied AGO18b-associated small RNAs and mRNAs by bioinformatics analysis. By globally analyzing the phased small-interfering RNA (phasiRNA) and miRNA abundance bound by AGO18b, we found AGO18b primarily binds to 21-nt phasiRNAs/miRNAs with a 5′-uridine and binds less strongly to 24-nt phasiRNAs with a 5′-adenosine in the premeiotic tassels. The abundance profile of AGO18b-associated miRNAs was different from their expression profile. Moreover, AGO18b strongly binds to miR166a-3p. We then obtained the AGO18b-bound mRNA targets of miR166a-3p by cRIP-seq, and confirmed the molecular function of AGO18b in regulating spikelet meristems. Conclusions Our results indicated that AGO18b binds to phasiRNAs with obvious 5 prime end bias under different sRNA length. MiRNAs and their target mRNAs associated with AGO18b indicated the molecular mechanisms of AGO18b as a negative regulator of inflorescence meristem and tassel development through integrating both phasiRNAs and miRNA pathways, which extended our view of sRNA regulation in flower development and provided potential methods to control pollination in the future. Electronic supplementary material The online version of this article (10.1186/s12864-019-6028-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Sun
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, People's Republic of China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Dong Chen
- Center for Genome Analysis, ABLife Inc, Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China
| | - Yaqiang Xue
- Laboratory for Genome Regulation and Human Health, ABLife Inc, Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China
| | - Lihong Zhai
- Medical College of Hubei University of Arts and Science, Xiangyang, 441053, People's Republic of China
| | - Dan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Zheng Cao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Lei Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Chao Cheng
- Center for Genome Analysis, ABLife Inc, Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China
| | - Yi Zhang
- Center for Genome Analysis, ABLife Inc, Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China. .,Laboratory for Genome Regulation and Human Health, ABLife Inc, Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China.
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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25
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Hunt M, Banerjee S, Surana P, Liu M, Fuerst G, Mathioni S, Meyers BC, Nettleton D, Wise RP. Small RNA discovery in the interaction between barley and the powdery mildew pathogen. BMC Genomics 2019; 20:610. [PMID: 31345162 PMCID: PMC6657096 DOI: 10.1186/s12864-019-5947-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/30/2019] [Indexed: 01/04/2023] Open
Abstract
Background Plants encounter pathogenic and non-pathogenic microorganisms on a nearly constant basis. Small RNAs such as siRNAs and miRNAs/milRNAs influence pathogen virulence and host defense responses. We exploited the biotrophic interaction between the powdery mildew fungus, Blumeria graminis f. sp. hordei (Bgh), and its diploid host plant, barley (Hordeum vulgare) to explore fungal and plant sRNAs expressed during Bgh infection of barley leaf epidermal cells. Results RNA was isolated from four fast-neutron immune-signaling mutants and their progenitor over a time course representing key stages of Bgh infection, including appressorium formation, penetration of epidermal cells, and development of haustorial feeding structures. The Cereal Introduction (CI) 16151 progenitor carries the resistance allele Mla6, while Bgh isolate 5874 harbors the AVRa6 avirulence effector, resulting in an incompatible interaction. Parallel Analysis of RNA Ends (PARE) was used to verify sRNAs with likely transcript targets in both barley and Bgh. Bgh sRNAs are predicted to regulate effectors, metabolic genes, and translation-related genes. Barley sRNAs are predicted to influence the accumulation of transcripts that encode auxin response factors, NAC transcription factors, homeodomain transcription factors, and several splicing factors. We also identified phasing small interfering RNAs (phasiRNAs) in barley that overlap transcripts that encode receptor-like kinases (RLKs) and nucleotide-binding, leucine-rich domain proteins (NLRs). Conclusions These data suggest that Bgh sRNAs regulate gene expression in metabolism, translation-related, and pathogen effectors. PARE-validated targets of predicted Bgh milRNAs include both EKA (effectors homologous to AVRk1 and AVRa10) and CSEP (candidate secreted effector protein) families. We also identified barley phasiRNAs and miRNAs in response to Bgh infection. These include phasiRNA loci that overlap with a significant proportion of receptor-like kinases, suggesting an additional sRNA control mechanism may be active in barley leaves as opposed to predominant R-gene phasiRNA overlap in many eudicots. In addition, we identified conserved miRNAs, novel miRNA candidates, and barley genome mapped sRNAs that have PARE validated transcript targets in barley. The miRNA target transcripts are enriched in transcription factors, signaling-related proteins, and photosynthesis-related proteins. Together these results suggest both barley and Bgh control metabolism and infection-related responses via the specific accumulation and targeting of genes via sRNAs. Electronic supplementary material The online version of this article (10.1186/s12864-019-5947-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matt Hunt
- Interdepartmental Genetics & Genomics, Iowa State University, Ames, Iowa, 50011, USA.,Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa, 50011, USA
| | - Sagnik Banerjee
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa, 50011, USA.,Interdepartmental Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, 50011, USA
| | - Priyanka Surana
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa, 50011, USA.,Interdepartmental Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, 50011, USA
| | - Meiling Liu
- Interdepartmental Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, 50011, USA.,Department of Statistics, Iowa State University, Ames, Iowa, 50011, USA
| | - Greg Fuerst
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Iowa State University, Ames, Iowa, 50011, USA
| | - Sandra Mathioni
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.,Division of Plant Sciences, University of Missouri - Columbia, 52 Agriculture Lab, Columbia, MO, 65211, USA
| | - Dan Nettleton
- Interdepartmental Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, 50011, USA.,Department of Statistics, Iowa State University, Ames, Iowa, 50011, USA
| | - Roger P Wise
- Interdepartmental Genetics & Genomics, Iowa State University, Ames, Iowa, 50011, USA. .,Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa, 50011, USA. .,Interdepartmental Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, 50011, USA. .,Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Iowa State University, Ames, Iowa, 50011, USA.
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26
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Perspectives on microRNAs and Phased Small Interfering RNAs in Maize ( Zea mays L.): Functions and Big Impact on Agronomic Traits Enhancement. PLANTS 2019; 8:plants8060170. [PMID: 31212808 PMCID: PMC6630462 DOI: 10.3390/plants8060170] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 02/05/2023]
Abstract
Small RNA (sRNA) population in plants comprises of primarily micro RNAs (miRNAs) and small interfering RNAs (siRNAs). MiRNAs play important roles in plant growth and development. The miRNA-derived secondary siRNAs are usually known as phased siRNAs, including phasiRNAs and tasiRNAs. The miRNA and phased siRNA biogenesis mechanisms are highly conserved in plants. However, their functional conservation and diversification may differ in maize. In the past two decades, lots of miRNAs and phased siRNAs have been functionally identified for curbing important maize agronomic traits, such as those related to developmental timing, plant architecture, sex determination, reproductive development, leaf morphogenesis, root development and nutrition, kernel development and tolerance to abiotic stresses. In contrast to Arabidopsis and rice, studies on maize miRNA and phased siRNA biogenesis and functions are limited, which restricts the small RNA-based fundamental and applied studies in maize. This review updates the current status of maize miRNA and phased siRNA mechanisms and provides a survey of our knowledge on miRNA and phased siRNA functions in controlling agronomic traits. Furthermore, improvement of those traits through manipulating the expression of sRNAs or their targets is discussed.
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27
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Liao PF, Ouyang JX, Zhang JJ, Yang L, Wang X, Peng XJ, Wang D, Zhu YL, Li SB. OsDCL3b affects grain yield and quality in rice. PLANT MOLECULAR BIOLOGY 2019; 99:193-204. [PMID: 30652247 DOI: 10.1007/s11103-018-0806-x] [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: 10/02/2018] [Accepted: 11/29/2018] [Indexed: 06/09/2023]
Abstract
We reported that knockdown of OsDCL3b decreased grain yield but increased grain quality in rice, which is helpful for molecular breeding in crops. Multiple DICER-LIKE (DCL) genes usually exist and show diverse biochemical and phenotypic functions in land plants. In rice, the biochemical function of OsDCL3b is known to process 24-nucleotide panicle phased small RNAs, however, its phenotypic functions are unclear. Here we reported that knockdown of OsDCL3b led to reduced pollen fertility, seed setting rate, and decreased grain yield but increased grain quality in rice. To reveal the molecular mechanism of the above phenomena, extracted RNAs from rice panicles of the wild type (WT) and OsDCL3b-RNAi line S6-1 were analyzed by deep sequencing. It showed that knockdown of OsDCL3b affected the biogenesis of both 21- and 24-nucleotide small RNAs including miRNAs and phased small RNAs. Using RNA-seq, 644 up- and 530 down-regulated mRNA genes were identified in panicles of line S6-1, and 550 and 273 differentially spliced genes with various alternative splicing (AS) events were observed in panicles of line S6-1 and WT, respectively, suggesting that OsDCL3b involved in influencing the transcript levels of mRNA genes and the AS events in rice panicles. Thus, our results show that knockdown of OsDCL3b will affect the biogenesis of small RNAs, which is involved in regulating the transcription of mRNA genes, and consequently influence the grain yield and quality in rice.
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Affiliation(s)
- Peng-Fei Liao
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Jie-Xiu Ouyang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Jian-Jun Zhang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Lan Yang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Xin Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Xiao-Jue Peng
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - You-Lin Zhu
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, 330031, China.
| | - Shao-Bo Li
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, 330031, China.
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28
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Salvador-Guirao R, Baldrich P, Tomiyama S, Hsing YI, Okada K, San Segundo B. OsDCL1a activation impairs phytoalexin biosynthesis and compromises disease resistance in rice. ANNALS OF BOTANY 2019; 123:79-93. [PMID: 30032201 PMCID: PMC6344094 DOI: 10.1093/aob/mcy141] [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: 04/08/2018] [Accepted: 06/30/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS MicroRNAs (miRNAs) are small non-coding RNAs that act as post-transcriptional regulators of gene expression via sequence-specific cleavage or translational repression of target transcripts. They are transcribed as long single-stranded RNA precursors with unique stem-loop structures that are processed by a DICER-Like (DCL) ribonuclease, typically DCL1, to produce mature miRNAs. Although a plethora of miRNAs have been found to be regulated by pathogen infection in plants, the biological function of most miRNAs remains largely unknown. Here, the contribution of OsDCL1 to rice immunity was investigated. METHODS Activation-tagged Osdcl1a (Osdcl1a-Ac) rice mutants were examined for resistance to pathogen infection. mRNA and small RNA deep sequencing, quantitative real-time PCR (RT-qPCR) and stem-loop reverse tanscripion-PCR (RT-PCR) were used to examine DCL1a-mediated alterations in the rice transcriptome. Rice diterpene phytoalexins were quantified by liquid chromatography-tandem mass spectrometry (LC-MSMS). Accumulation of O2·- was determined by nitroblue tetrazolium (NBT) staining. KEY RESULTS dcl1a-Ac mutants exhibit enhanced susceptibility to infection by fungal pathogens which was associated with a weaker induction of defence gene expression. Comparison of the mRNA and miRNA transcriptomes of dcl1a-Ac and wild-type plants revealed misregulation of genes involved in detoxification of reactive oxygen species. Consequently, dcl1a-Ac plants accumulated O2·- in their leaves and were more sensitive to methyl viologen-induced oxidative stress. Furthermore, dcl1a-Ac plants showed downregulation of diterpenoid phytoalexin biosynthetic genes, these genes also being weakly induced during pathogen infection. Upon pathogen challenge, dcl1a-Ac plants failed to accumulate major diterpenoid phytoalexins. OsDCL1a activation resulted in marked alterations in the rice miRNAome, including both upregulation and downregulation of miRNAs. CONCLUSIONS OsDCL1a activation enhances susceptibility to infection by fungal pathogens in rice. Activation of OsDCL1a represses the pathogen-inducible host defence response and negatively regulates diterpenoid phytoalexin production. These findings provide a basis to understand the molecular mechanisms through which OsDCL1a mediates rice immunity.
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Affiliation(s)
- Raquel Salvador-Guirao
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| | - Patricia Baldrich
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
- Donald Danforth Plant Science Center, St Louis, MO, USA
| | - Shiho Tomiyama
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Kazunori Okada
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
- For correspondence. E-mail
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Lee Marzano SY, Neupane A, Domier L. Transcriptional and Small RNA Responses of the White Mold Fungus Sclerotinia sclerotiorum to Infection by a Virulence-Attenuating Hypovirus. Viruses 2018; 10:E713. [PMID: 30558121 PMCID: PMC6315951 DOI: 10.3390/v10120713] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/06/2018] [Accepted: 12/10/2018] [Indexed: 12/19/2022] Open
Abstract
Mycoviruses belonging to the family Hypoviridae cause persistent infection of many different host fungi. We previously determined that the white mold fungus, Sclerotiniasclerotiorum, infected with Sclerotinia sclerotiorum hypovirus 2-L (SsHV2-L) exhibits reduced virulence, delayed/reduced sclerotial formation, and enhanced production of aerial mycelia. To gain better insight into the cellular basis for these changes, we characterized changes in mRNA and small RNA (sRNA) accumulation in S.sclerotiorum to infection by SsHV2-L. A total of 958 mRNAs and 835 sRNA-producing loci were altered after infection by SsHV2-L, among which >100 mRNAs were predicted to encode proteins involved in the metabolism and trafficking of carbohydrates and lipids. Both S. sclerotiorum endogenous and virus-derived sRNAs were predominantly 22 nt in length suggesting one dicer-like enzyme cleaves both. Novel classes of endogenous small RNAs were predicted, including phasiRNAs and tRNA-derived small RNAs. Moreover, S. sclerotiorum phasiRNAs, which were derived from noncoding RNAs and have the potential to regulate mRNA abundance in trans, showed differential accumulation due to virus infection. tRNA fragments did not accumulate differentially after hypovirus infection. Hence, in-depth analysis showed that infection of S. sclerotiorum by a hypovirulence-inducing hypovirus produced selective, large-scale reprogramming of mRNA and sRNA production.
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Affiliation(s)
- Shin-Yi Lee Marzano
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA.
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD 57006, USA.
| | - Achal Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA.
| | - Leslie Domier
- United States Department of Agriculture, Agricultural Research Service, Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA.
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Danilevicz MF, Moharana KC, Venancio TM, Franco LO, Cardoso SRS, Cardoso M, Thiebaut F, Hemerly AS, Prosdocimi F, Ferreira PCG. Copaifera langsdorffii Novel Putative Long Non-Coding RNAs: Interspecies Conservation Analysis in Adaptive Response to Different Biomes. Noncoding RNA 2018; 4:ncrna4040027. [PMID: 30297664 PMCID: PMC6316758 DOI: 10.3390/ncrna4040027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/26/2018] [Accepted: 09/28/2018] [Indexed: 12/20/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in multiple regulatory pathways and its versatile form of action has disclosed a new layer in gene regulation. LncRNAs have their expression levels modulated during plant development, and in response to stresses with tissue-specific functions. In this study, we analyzed lncRNA from leaf samples collected from the legume Copaifera langsdorffii Desf. (copaíba) present in two divergent ecosystems: Cerrado (CER; Ecological Station of Botanical Garden in Brasília, Brazil) and Atlantic Rain Forest (ARF; Rio de Janeiro, Brazil). We identified 8020 novel lncRNAs, and they were compared to seven Fabaceae genomes and transcriptomes, to which 1747 and 2194 copaíba lncRNAs were mapped, respectively, to at least one species. The secondary structures of the lncRNAs that were conserved and differentially expressed between the populations were predicted using in silico methods. A few selected lncRNA were confirmed by RT-qPCR in the samples from both biomes; Additionally, the analysis of the lncRNA sequences predicted that some might act as microRNA (miRNA) targets or decoys. The emerging studies involving lncRNAs function and conservation have shown their involvement in several types of biotic and abiotic stresses. Thus, the conservation of lncRNAs among Fabaceae species considering their rapid turnover, suggests they are likely to have been under functional conservation pressure. Our results indicate the potential involvement of lncRNAs in the adaptation of C. langsdorffii in two different biomes.
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Affiliation(s)
- Monica F Danilevicz
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil.
| | - Kanhu C Moharana
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro 28013-602, Brazil.
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro 28013-602, Brazil.
| | - Luciana O Franco
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Diretoria de Pesquisa Científica, Rio de Janeiro 22460-030, Brazil.
| | - Sérgio R S Cardoso
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Diretoria de Pesquisa Científica, Rio de Janeiro 22460-030, Brazil.
| | - Mônica Cardoso
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Diretoria de Pesquisa Científica, Rio de Janeiro 22460-030, Brazil.
| | - Flávia Thiebaut
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil.
| | - Adriana S Hemerly
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil.
| | - Francisco Prosdocimi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil.
| | - Paulo C G Ferreira
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil.
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Bao D, Ganbaatar O, Cui X, Yu R, Bao W, Falk BW, Wuriyanghan H. Down-regulation of genes coding for core RNAi components and disease resistance proteins via corresponding microRNAs might be correlated with successful Soybean mosaic virus infection in soybean. MOLECULAR PLANT PATHOLOGY 2018; 19:948-960. [PMID: 28695996 PMCID: PMC6638018 DOI: 10.1111/mpp.12581] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 06/30/2017] [Accepted: 07/06/2017] [Indexed: 05/20/2023]
Abstract
Plants protect themselves from virus infections by several different defence mechanisms. RNA interference (RNAi) is one prominent antiviral mechanism, which requires the participation of AGO (Argonaute) and Dicer/DCL (Dicer-like) proteins. Effector-triggered immunity (ETI) is an antiviral mechanism mediated by resistance (R) genes, most of which encode nucleotide-binding site-leucine-rich repeat (NBS-LRR) family proteins. MicroRNAs (miRNAs) play important regulatory roles in plants, including the regulation of host defences. Soybean mosaic virus (SMV) is the most common virus in soybean and, in this work, we identified dozens of SMV-responsive miRNAs by microarray analysis in an SMV-susceptible soybean line. Amongst the up-regulated miRNAs, miR168a, miR403a, miR162b and miR1515a predictively regulate the expression of AGO1, AGO2, DCL1 and DCL2, respectively, and miR1507a, miR1507c and miR482a putatively regulate the expression of several NBS-LRR family disease resistance genes. The regulation of target gene expression by these seven miRNAs was validated by both transient expression assays and RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) experiments. Transcript levels for AGO1, DCL1, DCL2 and five NBS-LRR family genes were repressed at different time points after SMV infection, whereas the corresponding miRNA levels were up-regulated at these same time points. Furthermore, inhibition of miR1507a, miR1507c, miR482a, miR168a and miR1515a by short tandem target mimic (STTM) technology compromised SMV infection efficiency in soybean. Our results imply that SMV can counteract soybean defence responses by the down-regulation of several RNAi pathway genes and NBS-LRR family resistance genes via the induction of the accumulation of their corresponding miRNA levels.
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Affiliation(s)
- Duran Bao
- School of Life Sciences, University of Inner MongoliaHohhotInner Mongolia 010021, China
| | - Oyunchuluun Ganbaatar
- School of Life Sciences, University of Inner MongoliaHohhotInner Mongolia 010021, China
| | - Xiuqi Cui
- School of Life Sciences, University of Inner MongoliaHohhotInner Mongolia 010021, China
| | - Ruonan Yu
- School of Life Sciences, University of Inner MongoliaHohhotInner Mongolia 010021, China
| | - Wenhua Bao
- School of Life Sciences, University of Inner MongoliaHohhotInner Mongolia 010021, China
| | - Bryce W. Falk
- Department of Plant PathologyUniversity of California DavisDavisCA 95616USA
| | - Hada Wuriyanghan
- School of Life Sciences, University of Inner MongoliaHohhotInner Mongolia 010021, China
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Kaashyap M, Ford R, Bohra A, Kuvalekar A, Mantri N. Improving Salt Tolerance of Chickpea Using Modern Genomics Tools and Molecular Breeding. Curr Genomics 2017; 18:557-567. [PMID: 29204084 PMCID: PMC5684649 DOI: 10.2174/1389202918666170705155252] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 11/28/2016] [Accepted: 12/15/2016] [Indexed: 11/22/2022] Open
Abstract
INTRODUCTION The high protein value, essential minerals, dietary fibre and notable ability to fix atmospheric nitrogen make chickpea a highly remunerative crop, particularly in low-input food production systems. Of the variety of constraints challenging chickpea productivity worldwide, salinity remains of prime concern owing to the intrinsic sensitivity of the crop. In view of the projected expansion of chickpea into arable and salt-stressed land by 2050, increasing attention is being placed on improving the salt tolerance of this crop. Considerable effort is currently underway to address salinity stress and substantial breeding progress is being made despite the seemingly highly-complex and environment-dependent nature of the tolerance trait. CONCLUSION This review aims to provide a holistic view of recent advances in breeding chickpea for salt tolerance. Initially, we focus on the identification of novel genetic resources for salt tolerance via extensive germplasm screening. We then expand on the use of genome-wide and cost-effective techniques to gain new insights into the genetic control of salt tolerance, including the responsive genes/QTL(s), gene(s) networks/cross talk and intricate signalling cascades.
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Affiliation(s)
- Mayank Kaashyap
- School of Science, RMIT University, Melbourne, 3000, Victoria, Australia
| | - Rebecca Ford
- Environmental Futures Research Institute, School of Natural Sciences, Griffith University, Queensland 4111, Australia
| | - Abhishek Bohra
- Crop Improvement Division, Indian Institute of Pulses Research, Kanpur, India
| | - Aniket Kuvalekar
- Interactive Research School for Health Affairs, Bharati Vidyapeeth University, Pune-Satara Road, Pune, Maharashtra, 411043, India
| | - Nitin Mantri
- School of Science, RMIT University, Melbourne, 3000, Victoria, Australia
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Wang W, Shi T, Ni X, Xu Y, Qu S, Gao Z. The role of miR319a and its target gene TCP4 in the regulation of pistil development in Prunus mume. Genome 2017; 61:43-48. [PMID: 29035682 DOI: 10.1139/gen-2017-0118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The microRNAs (miRNAs) comprise a broad class of non-coding small endogenous RNAs that are associated with many biological processes through the regulation of target genes, such as leaf morphogenesis and polarity, biotic and abiotic stress responses, and root and flower development. We identified a miRNA that affects flower development, miR319a, in Prunus mume. The Pm-miR319a target, Pm-TCP4, was validated by 5'RACE. The higher expression of Pm-TCP4 in imperfect flowers showed that Pm-TCP4 might promote pistil abortion. Further experiments showed that Pm-miR319a negatively regulates the expression of Pm-TCP4 mRNAs and affected pistil development. Sixteen downstream genes of Pm-TCP4 related to flower development were predicted. Previous studies have shown that they have an impact on the development of pistils. In this study it was established that Pm-miR319a indirectly regulates the development of pistils by regulating its target gene Pm-TCP4.
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Affiliation(s)
- Wanxu Wang
- a College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China.,b Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement
| | - Ting Shi
- a College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Xiaopeng Ni
- a College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Yanshuai Xu
- a College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Shenchun Qu
- a College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Zhihong Gao
- a College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
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Liu D, Mewalal R, Hu R, Tuskan GA, Yang X. New technologies accelerate the exploration of non-coding RNAs in horticultural plants. HORTICULTURE RESEARCH 2017; 4:17031. [PMID: 28698797 PMCID: PMC5496985 DOI: 10.1038/hortres.2017.31] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 05/06/2023]
Abstract
Non-coding RNAs (ncRNAs), that is, RNAs not translated into proteins, are crucial regulators of a variety of biological processes in plants. While protein-encoding genes have been relatively well-annotated in sequenced genomes, accounting for a small portion of the genome space in plants, the universe of plant ncRNAs is rapidly expanding. Recent advances in experimental and computational technologies have generated a great momentum for discovery and functional characterization of ncRNAs. Here we summarize the classification and known biological functions of plant ncRNAs, review the application of next-generation sequencing (NGS) technology and ribosome profiling technology to ncRNA discovery in horticultural plants and discuss the application of new technologies, especially the new genome-editing tool clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems, to functional characterization of plant ncRNAs.
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Affiliation(s)
- Degao Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Ritesh Mewalal
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Rongbin Hu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
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Komiya R. Biogenesis of diverse plant phasiRNAs involves an miRNA-trigger and Dicer-processing. JOURNAL OF PLANT RESEARCH 2017; 130:17-23. [PMID: 27900550 PMCID: PMC5219027 DOI: 10.1007/s10265-016-0878-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/08/2016] [Indexed: 05/18/2023]
Abstract
It has been almost 30 years since RNA interference (RNAi) was shown to silence genes via double-stranded RNAs (dsRNAs) in Caenorhabditis elegans (Fire et al. 1998). 20-30-nucleotide (nt) small non-coding RNAs are a key element of the RNAi machinery. Recently, phased small interfering RNAs (phasiRNAs), small RNAs that are generated from a long RNA precursor at intervals of 21 to 26-nt, have been identified in plants and animals. In Drosophila, phasiRNAs are generated by the endonuclease, Zucchini (Zuc), in germlines. These phasiRNAs, known as one of PIWI-interacting RNAs (piRNAs), mainly repress transposable elements. Similarly, reproduction-specific phasiRNAs have been identified in the family Poaceae, although DICER LIKE (DCL) protein-dependent phasiRNA biogenesis in rice is distinct from piRNA biogenesis in animals. In plants, phasiRNA biogenesis is initiated when 22-nt microRNAs (miRNAs) cleave single-stranded target RNAs. Subsequently, RNA-dependent RNA polymerase (RDR) forms dsRNAs from the cleaved RNAs, and dsRNAs are further processed by DCLs into 21 to 24-nt phasiRNAs. Finally, the phasiRNAs are loaded to ARGONAUTE (AGO) proteins to induce RNA-silencing. There are diverse types of phasiRNA precursors and the miRNAs that trigger the biogenesis. Their expression patterns also differ among plant species, suggesting that species-specific combinations of these triggers dictate the spatio-temporal pattern of phasiRNA biogenesis during development, or in response to environmental stimuli.
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Affiliation(s)
- Reina Komiya
- Science and Technology Group, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Kunigami-gun, Okinawa, 904-0495, Japan.
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Baldrich P, San Segundo B. MicroRNAs in Rice Innate Immunity. RICE (NEW YORK, N.Y.) 2016; 9:6. [PMID: 26897721 PMCID: PMC4761359 DOI: 10.1186/s12284-016-0078-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/12/2016] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are short regulatory non-coding RNAs that guide gene silencing in most eukaryotes. They regulate gene expression by triggering sequence-specific cleavage or translational repression of target transcripts. Plant miRNAs are known to play important roles in a wide range of developmental processes. Increasing evidence also supports that the modulation of miRNA levels plays an important role in reprogramming plant responses to abiotic stress (drought, cold, salinity and nutrient deficiency) and biotic stress (antibacterial resistance). Most of these studies were carried out in the model plant Arabidopsis thaliana. During the last years, the adoption of high-throughput sequencing technologies has significantly contributed to uncover multiple miRNAs while allowing miRNA profiling in plants. However, although a plethora of rice miRNAs have been shown to be regulated by pathogen infection, the biological function remains largely unknown for most of them. In this review, we summarize our current understanding on the contribution of miRNAs to rice immunity and discuss their potential applications in rice biotechnology. A better understanding of the miRNA species controlling rice immunity may lead to practical biotechnological applications leading to the development of appropriate strategies for rice protection.
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Affiliation(s)
- Patricia Baldrich
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Carrer de la Vall Moronta, Edifici CRAG, Campus UAB, Bellaterra (Cerdanyola del Vallés), Barcelona, 08193 Spain
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Carrer de la Vall Moronta, Edifici CRAG, Campus UAB, Bellaterra (Cerdanyola del Vallés), Barcelona, 08193 Spain
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Ta KN, Sabot F, Adam H, Vigouroux Y, De Mita S, Ghesquière A, Do NV, Gantet P, Jouannic S. miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species. RICE (NEW YORK, N.Y.) 2016; 9:10. [PMID: 26969003 PMCID: PMC4788661 DOI: 10.1186/s12284-016-0082-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 03/06/2016] [Indexed: 05/27/2023]
Abstract
BACKGROUND Rice exhibits a wide range of panicle structures. To explain these variations, much emphasis has been placed on changes in transcriptional regulation, but no large-scale study has yet reported on changes in small RNA regulation in the various rice species. To evaluate this aspect, we performed deep sequencing and expression profiling of small RNAs from two closely related species with contrasting panicle development: the cultivated African rice Oryza glaberrima and its wild relative Oryza barthii. RESULTS Our RNA-seq analysis revealed a dramatic difference between the two species in the 21 nucleotide small RNA population, corresponding mainly to miR2118-triggered phased siRNAs. A detailed expression profiling during the panicle development of O. glaberrima and O. barthii using qRT-PCRs and in situ hybridization, confirmed a delayed expression of the phased siRNAs as well as their lncRNA precursors and regulators (miR2118 and MEL1 gene) in O. glaberrima compared to O. barthii. We provide evidence that the 21-nt phasiRNA pathway in rice is associated with male-gametogenesis but is initiated in spikelet meristems. CONCLUSION Differential expression of the miR2118-triggered 21-nt phasiRNA pathway between the two African rice species reflects differential rates of determinate fate acquisition of panicle meristems between the two species.
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Affiliation(s)
- K. N. Ta
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
- />LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong road, Hanoi, Vietnam
| | - F. Sabot
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
| | - H. Adam
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
| | - Y. Vigouroux
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
| | - S. De Mita
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
- />Present address: INRA, Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, F-54280 Champenoux, France
| | - A. Ghesquière
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
| | - N. V. Do
- />LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong road, Hanoi, Vietnam
| | - P. Gantet
- />LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong road, Hanoi, Vietnam
- />Université de Montpellier, UMR DIADE, Place Eugène Bataillon, F-34095 Montpellier, Cedex 5 France
| | - S. Jouannic
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
- />LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong road, Hanoi, Vietnam
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Fei Q, Yang L, Liang W, Zhang D, Meyers BC. Dynamic changes of small RNAs in rice spikelet development reveal specialized reproductive phasiRNA pathways. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:6037-6049. [PMID: 27702997 PMCID: PMC5100018 DOI: 10.1093/jxb/erw361] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Dissection of the genetic pathways and mechanisms by which anther development occurs in grasses is crucial for both a basic understanding of plant development and for examining traits of agronomic importance such as male sterility. In rice, MULTIPLE SPOROCYTES1 (MSP1), a leucine-rich-repeat receptor kinase, plays an important role in anther development by limiting the number of sporocytes. OsTDL1a (a TPD1-like gene in rice) encodes a small protein that acts as a cofactor of MSP1 in the same regulatory pathway. In this study, we analyzed small RNA and mRNA changes in different stages of spikelets from wild-type rice, and from msp1 and ostdl1a mutants. Analysis of the small RNA data identified miRNAs demonstrating differential abundances. miR2275 was depleted in the two rice mutants; this miRNA is specifically enriched in anthers and functions to trigger the production of 24-nt phased secondary siRNAs (phasiRNAs) from PHAS loci. We observed that the 24-nt phasiRNAs as well as their precursor PHAS mRNAs were also depleted in the two mutants. An analysis of co-expression identified three Argonaute-encoding genes (OsAGO1d, OsAGO2b, and OsAGO18) that accumulate transcripts coordinately with phasiRNAs, suggesting a functional relationship. By mRNA in situ analysis, we demonstrated a strong correlation between the spatiotemporal pattern of these OsAGO transcripts and phasiRNA accumulations.
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Affiliation(s)
- Qili Fei
- Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - Li Yang
- State Key Laboratory of Hybrid Rice, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University and University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wanqi Liang
- State Key Laboratory of Hybrid Rice, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University and University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dabing Zhang
- State Key Laboratory of Hybrid Rice, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University and University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Agriculture, Food and Wine, University of Adelaide, South Australia 5064, Australia
| | - Blake C Meyers
- Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA
- University of Missouri - Columbia, Division of Plant Sciences, 52 Agriculture Lab, Columbia, MO 65211, USA
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Yang L, Wu Y, Yu M, Mao B, Zhao B, Wang J. Genome-wide transcriptome analysis of female-sterile rice ovule shed light on its abortive mechanism. PLANTA 2016; 244:1011-1028. [PMID: 27357232 DOI: 10.1007/s00425-016-2563-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 06/23/2016] [Indexed: 05/03/2023]
Abstract
The comprehensive transcriptome analysis of rice female-sterile line and wild-type line ovule provides an important clue for exploring the regulatory network of the formation of rice fertile female gametophyte. Ovules are the female reproductive tissues of rice (Oryza sativa L.) and play a major role in sexual reproduction. To investigate the potential mechanism of rice female gametophyte fertility, we used RNA sequencing, combined with genetic subtraction, to compare the transcriptome of the ovules of a high-frequency female-sterile line (fsv1) and a rice wild-type line (Gui 99) during ovule development. Ovules were harvested at three developmental stages: ovule containing megaspore mother cell in meiosis process (stage 1), ovule containing functional megaspore in mitosis process (stage 2), and ovule containing mature female gametophyte (stage 3). Six cDNA libraries generated a total of 42.2 million high-quality clean reads that aligned with 30,204 genes. The comparison between the fsv1 and Gui 99 ovules identified a large number of differentially expressed genes (DEGs), i.e., 45, 495, and 932 DEGs at the three ovule developmental stages, respectively. From the comparison of the two rice lines, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and MapMan analyses indicated that a large number of DEGs associated with starch and sucrose metabolism, plant hormone signal transduction, protein modification and degradation, oxidative phosphorylation, and receptor kinase. These DEGs might play roles in ovule development and fertile female gametophyte formation. Many transcription factor genes and epigenetic-related genes also exhibit different expression patterns and significantly different expression levels in two rice lines during ovule development, which might provide important information regarding the abortive mechanism of the female gametophyte in rice.
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Affiliation(s)
- Liyu Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ya Wu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Meiling Yu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Bigang Mao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Bingran Zhao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China.
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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41
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Deng X, Song X, Wei L, Liu C, Cao X. Epigenetic regulation and epigenomic landscape in rice. Natl Sci Rev 2016. [DOI: 10.1093/nsr/nww042] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Abstract
Epigenetic regulation has been implicated in the control of complex agronomic traits in rice (Oryza sativa), a staple food crop and model monocot plant. Recent advances in high-throughput sequencing and the moderately complex genome of rice have made it possible to study epigenetic regulation in rice on a genome-wide scale. This review discusses recent advances in our understanding of epigenetic regulation in rice, with an emphasis on the roles of key epigenetic regulators, the epigenomic landscape, epigenetic variation, transposon repression, and plant development.
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Affiliation(s)
- Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liya Wei
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Chunyan Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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42
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Baldrich P, Hsing YIC, San Segundo B. Genome-Wide Analysis of Polycistronic MicroRNAs in Cultivated and Wild Rice. Genome Biol Evol 2016; 8:1104-14. [PMID: 27190137 PMCID: PMC4860694 DOI: 10.1093/gbe/evw062] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that direct posttranscriptional gene silencing in eukaryotes. They are frequently clustered in the genomes of animals and can be independently transcribed or simultaneously transcribed into single polycistronic transcripts. Only a few miRNA clusters have been described in plants, and most of them are generated from independent transcriptional units. Here, we used a combination of bioinformatic tools and experimental analyses to discover new polycistronic miRNAs in rice. A genome-wide analysis of clustering patterns of MIRNA loci in the rice genome was carried out using a criterion of 3 kb as the maximal distance between two miRNAs. This analysis revealed 28 loci with the ability to form the typical hairpin structure of miRNA precursors in which 2 or more mature miRNAs mapped along the same structure. RT-PCR provided evidence for the polycistronic nature of seven miRNA precursors containing homologous or nonhomologous miRNA species. Polycistronic miRNAs and candidate polycistronic miRNAs are located across different rice chromosomes, except chromosome 12, and resided in both duplicated and nonduplicated chromosomal regions. Finally, most polycistronic and candidate polycistronic miRNAs showed a pattern of conservation in the genome of rice species with an AA genome. The diversity in the organization of MIR genes that are transcribed as polycistrons suggests a versatile mechanism for the control of gene expression in different biological processes and supports additional levels of complexity in miRNA functioning in plants.
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Affiliation(s)
- Patricia Baldrich
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| | | | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
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43
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Niedojadło J, Dełeńko K, Niedojadło K. Regulation of poly(A) RNA retention in the nucleus as a survival strategy of plants during hypoxia. RNA Biol 2016; 13:531-43. [PMID: 27002417 DOI: 10.1080/15476286.2016.1166331] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Last finding indicates that post-transcriptional processes are significant in low-oxygen conditions, but their nature is poorly understood. Here, we localized poly(A) RNA and mRNA coding proteins involved and not involved with resistance to hypoxia in Lupinus luteus and Arabidopsis thaliana during submergence and after recovery of aerobic conditions. We showed a strong nuclear accumulation of poly(A) RNA and 6 of 7 studied mRNAs with a concurrent strong reduction in RNA polymerase II transcription during hypoxia. In this study, the nucleus did not accumulate mRNA of the ADH1 (alcohol dehydrogenase 1) gene, which is a core hypoxia gene. The RNA accumulation in the nucleus is among the mechanisms of post-transcriptional gene regulation that prevents translation. However re-aeration was accompanied by a strong increase in the amount of the mRNAs in the cytoplasm and a simultaneous decrease in nuclear mRNAs. This finding indicates that the nucleus is a storage site for those of mRNAs which are not involved in the response to hypoxia for use by the plants after the hypoxic stress. In this study, the highest intensity of RNA accumulation occurred in Cajal bodies (CBs); the intensity of accumulation was inversely correlated with transcription. Under hypoxia, ncb-1 mutants of Arabidopsis thaliana with a complete absence of CBs died sooner than wild type (WT), accompanied by a strong reduction in the level of poly(A) RNA in the nucleus. These results suggest that the CBs not only participate in the storage of the nuclear RNA, but they also could take part in its stabilization under low-oxygen conditions.
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Affiliation(s)
- Janusz Niedojadło
- a Department of Cell Biology, Faculty of Biology and Environment Protection , Nicolaus Copernicus University , Torun , Poland
| | - Konrad Dełeńko
- a Department of Cell Biology, Faculty of Biology and Environment Protection , Nicolaus Copernicus University , Torun , Poland
| | - Katarzyna Niedojadło
- a Department of Cell Biology, Faculty of Biology and Environment Protection , Nicolaus Copernicus University , Torun , Poland
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Zhang H, Tao Z, Hong H, Chen Z, Wu C, Li X, Xiao J, Wang S. Transposon-derived small RNA is responsible for modified function of WRKY45 locus. NATURE PLANTS 2016; 2:16016. [PMID: 27249351 DOI: 10.1038/nplants.2016.16] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 01/15/2016] [Indexed: 05/20/2023]
Abstract
Transposable elements (TEs) are an important source for generating small interfering RNAs (siRNAs) in plants and animals. Although TE-siRNA-induced silencing of TEs by RNA-directed DNA methylation (RdDM) in the maintenance of genome integrity has been intensively studied, it is unknown whether this type of silencing occurs in suppressing endogenous non-TE genes during host-pathogen interactions. Here we show that a TE-siRNA, TE-siR815, causes opposite functions for the two alleles, WRKY45-1 and WRKY45-2, of the WRKY45 transcription factor in rice resistance to Xanthomonas oryzae pv. oryzae, which causes the most devastating bacterial disease in rice worldwide. Expression of WRKY45-1, but not WRKY45-2, generated TE-siR815, which in turn repressed ST1, an important component in WRKY45-mediated resistance, by RdDM. Suppression of ST1 abolished WRKY45-mediated resistance leading to pathogen susceptibility. These results suggest that TE-siR815 contributes to the natural variation of the WRKY45 locus and TE-siR815-induced suppression of ST1 results in the negative role of WRKY45-1 but positive role of WRKY45-2 in regulating disease resistance.
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Affiliation(s)
- Haitao Zhang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Zeng Tao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Hanming Hong
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Zhihui Chen
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Changyin Wu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Shiping Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Khatabi B, Arikit S, Xia R, Winter S, Oumar D, Mongomake K, Meyers BC, Fondong VN. High-resolution identification and abundance profiling of cassava (Manihot esculenta Crantz) microRNAs. BMC Genomics 2016; 17:85. [PMID: 26822616 PMCID: PMC4730657 DOI: 10.1186/s12864-016-2391-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 01/13/2016] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Small RNAs (sRNAs) are endogenous sRNAs that play regulatory roles in plant growth, development, and biotic and abiotic stress responses. In plants, one subset of sRNAs, microRNAs (miRNAs) exhibit tissue-differential expression and regulate gene expression mainly through direct cleavage of mRNA or indirectly via production of secondary phased siRNAs (phasiRNAs) that silence cognate target transcripts in trans. RESULTS Here, we have identified cassava (Manihot esculenta Crantz) miRNAs using high resolution sequencing of sRNA libraries from leaf, stem, callus, male and female flower tissues. To analyze the data, we built a cassava genome database and, via sequence analysis and secondary structure prediction, 38 miRNAs not previously reported in cassava were identified. These new cassava miRNAs included two miRNAs not previously been reported in any plant species. The miRNAs exhibited tissue-differential accumulation as confirmed by quantitative RT-PCR and Northern blot analysis, largely reflecting levels observed in sequencing data. Some of the miRNAs identified were predicted to trigger production of secondary phased siRNAs (phasiRNAs) from 80 PHAS loci. CONCLUSIONS Cassava is a woody perennial shrub, grown principally for its starch-rich storage roots, which are rich in calories. In this study, new miRNAs were identified and their expression was validated using qRT-PCR of RNA from five different tissues. The data obtained expand the list of annotated miRNAs and provide additional new resources for cassava improvement research.
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Affiliation(s)
- Behnam Khatabi
- Department of Biological Sciences, Delaware State University, Dover, DE, 19901, USA.
| | - Siwaret Arikit
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA.
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen and Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, 73140, Thailand.
| | - Rui Xia
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA.
| | - Stephan Winter
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
| | - Doungous Oumar
- Department of Biological Sciences, Delaware State University, Dover, DE, 19901, USA.
- Ekona Research Centre, Southwest, Cameroon.
| | - Kone Mongomake
- Department of Biological Sciences, Delaware State University, Dover, DE, 19901, USA.
- Université Nangui Abrogoua, Abidjan, Côte d'Ivoire.
| | - Blake C Meyers
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA
| | - Vincent N Fondong
- Department of Biological Sciences, Delaware State University, Dover, DE, 19901, USA.
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46
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Field S, Thompson B. Analysis of the Maize dicer-like1 Mutant, fuzzy tassel, Implicates MicroRNAs in Anther Maturation and Dehiscence. PLoS One 2016; 11:e0146534. [PMID: 26745722 PMCID: PMC4706427 DOI: 10.1371/journal.pone.0146534] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/18/2015] [Indexed: 11/23/2022] Open
Abstract
Sexual reproduction in plants requires development of haploid gametophytes from somatic tissues. Pollen is the male gametophyte and develops within the stamen; defects in the somatic tissues of the stamen and in the male gametophyte itself can result in male sterility. The maize fuzzy tassel (fzt) mutant has a mutation in dicer-like1 (dcl1), which encodes a key enzyme required for microRNA (miRNA) biogenesis. Many miRNAs are reduced in fzt, and fzt mutants exhibit a broad range of developmental defects, including male sterility. To gain further insight into the roles of miRNAs in maize stamen development, we conducted a detailed analysis of the male sterility defects in fzt mutants. Early development was normal in fzt mutant anthers, however fzt anthers arrested in late stages of anther maturation and did not dehisce. A minority of locules in fzt anthers also exhibited anther wall defects. At maturity, very little pollen in fzt anthers was viable or able to germinate. Normal pollen is tricellular at maturity; pollen from fzt anthers included a mixture of unicellular, bicellular, and tricellular pollen. Pollen from normal anthers is loaded with starch before dehiscence, however pollen from fzt anthers failed to accumulate starch. Our results indicate an absolute requirement for miRNAs in the final stages of anther and pollen maturation in maize. Anther wall defects also suggest that miRNAs have key roles earlier in anther development. We discuss candidate miRNAs and pathways that might underlie fzt anther defects, and also note that male sterility in fzt resembles water deficit-induced male sterility, highlighting a possible link between development and stress responses in plants.
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Affiliation(s)
- Sterling Field
- Department of Biology, East Carolina University, Greenville, North Carolina, 27858, United States of America
| | - Beth Thompson
- Department of Biology, East Carolina University, Greenville, North Carolina, 27858, United States of America
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Dukowic-Schulze S, Sundararajan A, Ramaraj T, Kianian S, Pawlowski WP, Mudge J, Chen C. Novel Meiotic miRNAs and Indications for a Role of PhasiRNAs in Meiosis. FRONTIERS IN PLANT SCIENCE 2016; 7:762. [PMID: 27313591 PMCID: PMC4889585 DOI: 10.3389/fpls.2016.00762] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/17/2016] [Indexed: 05/03/2023]
Abstract
Small RNAs (sRNA) add additional layers to the regulation of gene expression, with siRNAs directing gene silencing at the DNA level by RdDM (RNA-directed DNA methylation), and micro RNAs (miRNAs) directing post-transcriptional regulation of specific target genes, mostly by mRNA cleavage. We used manually isolated male meiocytes from maize (Zea mays) to investigate sRNA and DNA methylation landscapes during zygotene, an early stage of meiosis during which steps of meiotic recombination and synapsis of paired homologous chromosomes take place. We discovered two novel miRNAs from meiocytes, zma-MIR11969 and zma-MIR11970, and identified putative target genes. Furthermore, we detected abundant phasiRNAs of 21 and 24 nt length. PhasiRNAs are phased small RNAs which occur in 21 or 24 nt intervals, at a few hundred loci, specifically in male reproductive tissues in grasses. So far, the function of phasiRNAs remained elusive. Data from isolated meiocytes now revealed elevated DNA methylation at phasiRNA loci, especially in the CHH context, suggesting a role for phasiRNAs in cis DNA methylation. In addition, we consider a role of these phasiRNAs in chromatin remodeling/dynamics during meiosis. However, this is not well supported yet and will need more additional data. Here, we only lay out the idea due to other relevant literature and our additional observation of a peculiar GC content pattern at phasiRNA loci. Chromatin remodeling is also indicated by the discovery that histone genes were enriched for sRNA of 22 nt length. Taken together, we gained clues that lead us to hypothesize sRNA-driven DNA methylation and possibly chromatin remodeling during male meiosis in the monocot maize which is in line with and extends previous knowledge.
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Affiliation(s)
| | | | | | - Shahryar Kianian
- Cereal Disease Laboratory, United States Department of Agriculture – Agricultural Research Service, St. PaulMN, USA
| | - Wojciech P. Pawlowski
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, IthacaNY, USA
| | - Joann Mudge
- National Center for Genome Resources, Santa FeNM, USA
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, St. PaulMN, USA
- *Correspondence: Changbin Chen,
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48
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Liu J, Zhang X, Zhang F, Hong N, Wang G, Wang A, Wang L. Identification and characterization of microRNAs from in vitro-grown pear shoots infected with Apple stem grooving virus in response to high temperature using small RNA sequencing. BMC Genomics 2015; 16:945. [PMID: 26573813 PMCID: PMC4647338 DOI: 10.1186/s12864-015-2126-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/22/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) have functions in diverse biological processes such as growth, signal transduction, disease resistance, and stress responses in plants. Thermotherapy is an effective approach for elimination of viruses from fruit trees. However, the role of miRNAs in this process remains elusive. Previously, we showed that high temperature treatment reduces the titers of Apple stem grooving virus (ASGV) from the tips of in vitro-grown Pyrus pyrifolia plants. In this study, we identified high temperature-altered pear miRNAs using the next generation sequencing technology, and futher molecularly characterized miRNA-mediated regulaton of target gene expression in the meristem tip and base tissues of in vitro-grown, ASGV-infected pear shoots under different temperatures. RESULTS Using in vitro-grown P. pyrifolia shoot meristem tips infected with ASGV, a total of 22,592,997 and 20,411,254 clean reads were obtained from Illumina high-throughput sequencing of small RNA libraries at 24 °C and 37 °C, respectively. We identified 149 conserved and 141 novel miRNAs. Seven conserved miRNAs and 77 novel miRNAs were differentially expressed at different temperatures. Target genes for differentially expressed known and novel miRNAs were predicted and functionally annotated. Gene Ontology (GO) analysis showed that high-ranking miRNA target genes were involved in metabolic processes, responses to stress, and signaling, indicating that these high temperature-responsive miRNAs have functions in diverse gene regulatory networks. Spatial expression patterns of the miRNAs and their target genes were found to be expressed in shoot tip and base tissues by qRT-PCR. In addition, high temperature reduced viral titers in the shoot meristem tip, while negatively regulated miRNA-mediated target genes related to resistance disease defense and hormone signal transduction pathway were up-regulated in the P. pyrifolia shoot tip in response to high temperature. These results suggested that miRNAs may have important functions in the high temperature-dependent decrease of ASGV titer in in vitro-grown pear shoots. CONCLUSIONS This is the first report of miRNAs differentially expressed at 24 °C and 37 °C in the meristem tip of pear shoots infected with ASGV. The results of this study provide valuable information for further exploration of the function of high temperature-altered miRNAs in suppressing viral infections in pear and other fruit trees.
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Affiliation(s)
- Juan Liu
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei, 430070, P. R. China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, P. R. China.,National Indoor Conservation Center of Virus-Free Germplasms of Fruit Crops, Wuhan, Hubei, 430070, P. R. China.,Lab of Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, 430070, P. R. China
| | - XueJiao Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, P. R. China.,Shihezi University, Shihezi City, Xinjiang Uyghur Autonomous Region, 832003, P. R. China
| | - FangPeng Zhang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei, 430070, P. R. China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, P. R. China.,National Indoor Conservation Center of Virus-Free Germplasms of Fruit Crops, Wuhan, Hubei, 430070, P. R. China.,Lab of Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, 430070, P. R. China
| | - Ni Hong
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei, 430070, P. R. China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, P. R. China.,National Indoor Conservation Center of Virus-Free Germplasms of Fruit Crops, Wuhan, Hubei, 430070, P. R. China.,Lab of Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, 430070, P. R. China
| | - GuoPing Wang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei, 430070, P. R. China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, P. R. China.,National Indoor Conservation Center of Virus-Free Germplasms of Fruit Crops, Wuhan, Hubei, 430070, P. R. China.,Lab of Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, 430070, P. R. China
| | - Aiming Wang
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, N5V 4T3, ON, Canada
| | - LiPing Wang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei, 430070, P. R. China. .,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, P. R. China. .,National Indoor Conservation Center of Virus-Free Germplasms of Fruit Crops, Wuhan, Hubei, 430070, P. R. China. .,Lab of Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, 430070, P. R. China.
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Abstract
Plant genomes encode various small RNAs that function in distinct, yet overlapping, genetic and epigenetic silencing pathways. However, the abundance and diversity of small-RNA classes varies among plant species, suggesting coevolution between environmental adaptations and gene-silencing mechanisms. Biogenesis of small RNAs in plants is well understood, but we are just beginning to uncover their intricate regulation and activity. Here, we discuss the biogenesis of plant small RNAs, such as microRNAs, secondary siRNAs and heterochromatic siRNAs, and their diverse cellular and developmental functions, including in reproductive transitions, genomic imprinting and paramutation. We also discuss the diversification of small-RNA-directed silencing pathways through the expansion of RNA-dependent RNA polymerases, DICER proteins and ARGONAUTE proteins.
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50
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Zhang H, Xia R, Meyers BC, Walbot V. Evolution, functions, and mysteries of plant ARGONAUTE proteins. CURRENT OPINION IN PLANT BIOLOGY 2015; 27:84-90. [PMID: 26190741 DOI: 10.1016/j.pbi.2015.06.011] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 06/09/2015] [Accepted: 06/15/2015] [Indexed: 05/05/2023]
Abstract
ARGONAUTE (AGO) proteins bind small RNAs (sRNAs) to form RNA-induced silencing complexes for transcriptional and post-transcriptional gene silencing. Genomes of primitive plants encode only a few AGO proteins. The Arabidopsis thaliana genome encodes ten AGO proteins, designated AGO1 to AGO10. Most early studies focused on these ten proteins and their interacting sRNAs. AGOs in other flowering plant species have duplicated and diverged from this set, presumably corresponding to new, diverged or specific functions. Among these, the grass-specific AGO18 family has been discovered and implicated as playing important roles during plant reproduction and viral defense. This review covers our current knowledge about functions and features of AGO proteins in both eudicots and monocots and compares their similarities and differences. On the basis of these features, we propose a new nomenclature for some plant AGOs.
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Affiliation(s)
- Han Zhang
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| | - Rui Xia
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716, USA
| | - Blake C Meyers
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716, USA
| | - Virginia Walbot
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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