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Ferraz R, Coimbra S, Correia S, Canhoto J. RNA methyltransferases in plants: Breakthroughs in function and evolution. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:449-460. [PMID: 36502609 DOI: 10.1016/j.plaphy.2022.12.001] [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: 09/08/2022] [Revised: 11/28/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Each day it is becoming increasingly difficult not to notice the completely new, fast growing, extremely intricate and challenging world of epitranscriptomics as the understanding of RNA methylation is expanding at a hasty rate. Writers (methyltransferases), erasers (demethylases) and readers (RNA-binding proteins) are responsible for adding, removing and recognising methyl groups on RNA, respectively. Several methyltransferases identified in plants are now being investigated and recent studies have shown a connection between RNA-methyltransferases (RNA-MTases) and stress and development processes. However, compared to their animal and bacteria counterparts, the understanding of RNA methyltransferases is still incipient, particularly those located in organelles. Comparative and systematic analyses allowed the tracing of the evolution of these enzymes suggesting the existence of several methyltransferases yet to be characterised. This review outlines the functions of plant nuclear and organellar RNA-MTases in plant development and stress responses and the comparative and evolutionary discoveries made on RNA-MTases across kingdoms.
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Affiliation(s)
- Ricardo Ferraz
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra 3000-456, Portugal; LAQV Requimte, Sustainable Chemistry, University of Porto, Porto, Portugal.
| | - Sílvia Coimbra
- University of Porto, Faculty of Sciences, Portugal; LAQV Requimte, Sustainable Chemistry, University of Porto, Porto, Portugal.
| | - Sandra Correia
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra 3000-456, Portugal.
| | - Jorge Canhoto
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra 3000-456, Portugal.
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2
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Yuan Z, Pan J, Chen C, Tang Y, Zhang H, Guo J, Yang X, Chen L, Li C, Zhao K, Wang Q, Yang B, Sun C, Deng X, Wang P. DRB2 Modulates Leaf Rolling by Regulating Accumulation of MicroRNAs Related to Leaf Development in Rice. Int J Mol Sci 2022; 23:ijms231911147. [PMID: 36232465 PMCID: PMC9570175 DOI: 10.3390/ijms231911147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/28/2022] Open
Abstract
As an important agronomic trait in rice (Oryza sativa), moderate leaf rolling helps to maintain the erectness of leaves and minimize shadowing between leaves, leading to improved photosynthetic efficiency and grain yield. However, the molecular mechanisms underlying rice leaf rolling still need to be elucidated. Here, we isolated a rice mutant, rl89, showing adaxially rolled leaf phenotype due to decreased number and size of bulliform cells. We confirmed that the rl89 phenotypes were caused by a single nucleotide substitution in OsDRB2 (LOC_Os10g33970) gene encoding DOUBLE-STRANDED RNA-BINDING2. This gene was constitutively expressed, and its encoded protein was localized to both nucleus and cytoplasm. Yeast two-hybrid assay showed that OsDRB2 could interact with DICER-LIKE1 (DCL1) and OsDRB1-2 respectively. qRT-PCR analysis of 29 related genes suggested that defects of the OsDRB2-miR166-OsHBs pathway could play an important role in formation of the rolled leaf phenotype of rl89, in which OsDRB2 mutation reduced miR166 accumulation, resulting in elevated expressions of the class III homeodomain-leucine zipper genes (such as OsHB1, 3 and 5) involved in leaf polarity and/or morphology development. Moreover, OsDRB2 mutation also reduced accumulation of miR160, miR319, miR390, and miR396, which could cause the abnormal leaf development in rl89 by regulating expressions of their target genes related to leaf development.
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Affiliation(s)
- Zhaodi Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Jihong Pan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Congping Chen
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yulin Tang
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongshan Zhang
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Jia Guo
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaorong Yang
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Longfei Chen
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Chunyan Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Ke Zhao
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Qian Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Bin Yang
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Changhui Sun
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaojian Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (X.D.); (P.W.)
| | - Pingrong Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (X.D.); (P.W.)
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3
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Ma J, Li C, Gao P, Qiu Y, Zong M, Zhang H, Wang J. Melon shoot organization 1, encoding an AGRONAUTE7 protein, plays a crucial role in plant development. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2875-2890. [PMID: 35802144 DOI: 10.1007/s00122-022-04156-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
A melon gene MSO1 located on chromosome 10 by map-based cloning strategy, which encodes an ARGONAUTE 7 protein, is responsible for the development of shoot organization. Plant endogenous small RNAs (sRNAs) are involved in various plant developmental processes. In Arabidopsis, sRNAs combined with ARGONAUTE (AGO) proteins are incorporated into the RNA-induced silencing complex (RISC), which functions in RNA silencing or biogenesis of trans-acting siRNAs (ta-siRNAs). However, their roles in melon (Cucumis melo L.) are still unclear. Here, the melon shoot organization 1 (mso1) mutant was identified and shown to exhibit pleiotropic phenotypes in leaf morphology and plant architecture. Positional cloning of MSO1 revealed that it encodes a homologue of Arabidopsis AGO7/ZIPPY, which is required for the production of ta-siRNAs. The AG-to-C mutation in the second exon of MSO1 caused a frameshift mutation and significantly reduced its expression. Ectopic expression of MSO1 rescued the Arabidopsis ago7 phenotype. RNA-seq analysis showed that several genes involved in transcriptional regulation and plant hormones were significantly altered in mso1 compared to WT. A total of 304 and 231 miRNAs were identified in mso1 and WT by sRNA sequencing, respectively, and among them, 42 known and ten novel miRNAs were differentially expressed. cme-miR390a significantly accumulated, and the expression levels of the two ta-siRNAs were almost completely abolished in mso1. Correspondingly, their targets, the ARF3 and ARF4 genes, showed dramatically upregulated expression, indicating that the miR390-TAS3-ARF pathway has conserved roles in melon. These findings will help us better understand the molecular mechanisms of MSO1 in plant development in melon.
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Affiliation(s)
- Jian Ma
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Congcong Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Peng Gao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Yanhong Qiu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Mei Zong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Huijun Zhang
- School of Life Science, Huaibei Normal University, Huaibei, 235000, Anhui, China.
| | - Jianshe Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
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4
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Zhao JH, Guo HS. RNA silencing: From discovery and elucidation to application and perspectives. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:476-498. [PMID: 34964265 DOI: 10.1111/jipb.13213] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/26/2021] [Indexed: 06/14/2023]
Abstract
RNA silencing (or RNA interference, RNAi) is a conserved mechanism for regulating gene expression in eukaryotes. The discovery of natural trans-kingdom RNAi indicated that small RNAs act as signaling molecules and enable communication between organisms in different kingdoms. The phenomenon and potential mechanisms of trans-kingdom RNAi are among the most exciting research topics. To better understand trans-kingdom RNAi, we review the history of the discovery and elucidation of RNAi mechanisms. Based on canonical RNAi mechanisms, we summarize the major points of divergence around RNAi pathways in the main eukaryotes' kingdoms, including plants, animals, and fungi. We review the representative incidents associated with the mechanisms and applications of trans-kingdom RNAi in crop protection, and discuss the critical factors that should be considered to develop successful trans-kingdom RNAi-based crop protection strategies.
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Affiliation(s)
- Jian-Hua Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049, China
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5
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Borna RS, Murchie EH, Pyke KA, Roberts JA, Gonzalez‐Carranza ZH. The rice EP3 and OsFBK1 E3 ligases alter plant architecture and flower development, and affect transcript accumulation of microRNA pathway genes and their targets. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:297-309. [PMID: 34543503 PMCID: PMC8753360 DOI: 10.1111/pbi.13710] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/13/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
ERECTA PANICLE 3 (EP3) and ORYZA SATIVA F-BOX KELCH 1 (OsFBK1) proteins share 57% and 54% sequence identity with the Arabidopsis F-box protein HAWAIIAN SKIRT (HWS). Previously we showed that EP3 is a functional orthologue of HWS. Here we demonstrate that OsFBK1 is another functional orthologue of HWS and show the complexity of interaction between EP3 and OsFBK1 genes at different developmental stages of the plant. qRT-PCR expression analyses and studies of EP3-GFP and OsFBK1-RFP promoter reporter lines demonstrate that although EP3 and OsFBK1 expression can be detected in the same tissues some cells exclusively express EP3 or OsFBK1 whilst others co-express both genes. Loss, reduction or gain-of-function lines for EP3 and OsFBK1, show that EP3 and OsFBK1 affect plant architecture, organ size, floral organ number and size, floral morphology, pollen viability, grain size and weight. We have identified the putative orthologue genes of the rice microRNA pathway for ORYZA SATIVA DAWDLE (OsDDL) and ORYZA SATIVA SERRATE (OsSE), and demonstrated that EP3 and OsFBK1 affect their transcript levels as well as those of CROWN ROOT DEFECT 1/ORYZA SATIVA Exportin-5 HASTY (CRD1/OsHST), ORYZA SATIVA DICER-LIKE 1 (OsDCL) and ORYZA SATIVA WEAVY LEAF1 (OsWAF1). We show that EP3 affects OsPri-MIR164, OsNAM1 and OsNAC1 transcript levels. OsNAC1 transcripts are modified by OsFBK1, suggesting two independent regulatory pathways, one via EP3 and OsMIR164 and the other via OsFBK1. Our data propose that EP3 and OsFBK1 conjointly play similar roles in rice to how HWS does in Arabidopsis.
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Affiliation(s)
- Rita S. Borna
- Plant and Crop Sciences DivisionSchool of BiosciencesUniversity of NottinghamNottinghamUK
- Present address:
Department of BotanyUniversity of DhakaDhaka1000Bangladesh
| | - Erik H. Murchie
- Plant and Crop Sciences DivisionSchool of BiosciencesUniversity of NottinghamNottinghamUK
| | - Kevin A. Pyke
- Plant and Crop Sciences DivisionSchool of BiosciencesUniversity of NottinghamNottinghamUK
| | - Jeremy A. Roberts
- Plant and Crop Sciences DivisionSchool of BiosciencesUniversity of NottinghamNottinghamUK
- Present address:
Faculty of Science and EngineeringSchool of Biological & Marine SciencesUniversity of PlymouthDevonUK
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6
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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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7
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Loss of Function of OsARG Resulted in Pepper-Shaped Husk in Indica Rice. Life (Basel) 2021; 11:life11060523. [PMID: 34205108 PMCID: PMC8227114 DOI: 10.3390/life11060523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 12/02/2022] Open
Abstract
Grain shape is one of the most important and complex traits determining the grain yield in rice. In this study, we discovered two rice mutants with defective shape spikelets, designated as psh1-1/2 (pepper-shaped husk 1-1/2), which were both isolated from the tissue-culture-regenerated plants of indica cultivar Minghui 86. The two mutants showed the same mutant phenotypes, containing pepper-shaped spikelets; shorter, smaller and compact panicles; very low seed-setting rate; high percentage of split grains; and lower grain width. Genetic analysis indicated that the mutant phenotypes were controlled by a recessive gene. Gene mapping indicated that the target gene PSH1 was located on the short arm of chromosome 4. Sequencing analysis revealed that the two mutants each had a different nonsense mutation in OsARG, confirming that the target gene is OsARG. Compared with the previously reported OsARG mutant nglf-1, psh1-1/2 possessed some distinct mutant phenotypes, probably because of the influence of different genetic background, suggesting that OsARG may function differently under different genetic backgrounds.
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8
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Jerome Jeyakumar JM, Ali A, Wang WM, Thiruvengadam M. Characterizing the Role of the miR156-SPL Network in Plant Development and Stress Response. PLANTS 2020; 9:plants9091206. [PMID: 32942558 PMCID: PMC7570127 DOI: 10.3390/plants9091206] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/27/2020] [Accepted: 09/11/2020] [Indexed: 01/22/2023]
Abstract
MicroRNA (miRNA) is a short, single-stranded, non-coding RNA found in eukaryotic cells that can regulate the expression of many genes at the post-transcriptional level. Among various plant miRNAs with diverse functions, miR156 plays a key role in biological processes, including developmental regulation, immune response, metabolic regulation, and abiotic stress. MiRNAs have become the regulatory center for plant growth and development. MicroRNA156 (miR156) is a highly conserved and emerging tool for the improvement of plant traits, including crop productivity and stress tolerance. Fine-tuning of squamosa promoter biding-like (SPL) gene expression might be a useful strategy for crop improvement. Here, we studied the regulation of the miR156 module and its interaction with SPL factors to understand the developmental transition of various plant species. Furthermore, this review provides a strong background for plant biotechnology and is an important source of information for further molecular breeding to optimize farming productivity.
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Affiliation(s)
- John Martin Jerome Jeyakumar
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China; (J.M.J.J.); (A.A.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Institute of Rice Research, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China
| | - Asif Ali
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China; (J.M.J.J.); (A.A.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Institute of Rice Research, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China
| | - Wen-Ming Wang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China; (J.M.J.J.); (A.A.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Institute of Rice Research, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China
- Correspondence:
| | - Muthu Thiruvengadam
- Department of Applied Bioscience, College of Life and Environmental Sciences, Konkuk University, Seoul 05029, Korea;
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9
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Fard EM, Moradi S, Salekdeh NN, Bakhshi B, Ghaffari MR, Zeinalabedini M, Salekdeh GH. Plant isomiRs: origins, biogenesis, and biological functions. Genomics 2020; 112:3382-3395. [DOI: 10.1016/j.ygeno.2020.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/22/2020] [Accepted: 06/10/2020] [Indexed: 12/14/2022]
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10
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Atighi MR, Verstraeten B, De Meyer T, Kyndt T. Genome-wide DNA hypomethylation shapes nematode pattern-triggered immunity in plants. THE NEW PHYTOLOGIST 2020; 227:545-558. [PMID: 32162327 PMCID: PMC7317725 DOI: 10.1111/nph.16532] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 02/26/2020] [Indexed: 05/22/2023]
Abstract
A role for DNA hypomethylation has recently been suggested in the interaction between bacteria and plants; it is unclear whether this phenomenon reflects a conserved response. Treatment of plants of monocot rice and dicot tomato with nematode-associated molecular patterns from different nematode species or bacterial pathogen-associated molecular pattern flg22 revealed global DNA hypomethylation. A similar hypomethylation response was observed during early gall induction by Meloidogyne graminicola in rice. Evidence for the causal impact of hypomethylation on immunity was revealed by a significantly reduced plant susceptibility upon treatment with DNA methylation inhibitor 5-azacytidine. Whole-genome bisulphite sequencing of young galls revealed massive hypomethylation in the CHH context, while not for CG or CHG nucleotide contexts. Further, CHH hypomethylated regions were predominantly associated with gene promoter regions, which was not correlated with activated gene expression at the same time point but, rather, was correlated with a delayed transcriptional gene activation. Finally, the relevance of CHH hypomethylation in plant defence was confirmed in rice mutants of the RNA-directed DNA methylation pathway and DECREASED DNA METHYLATION 1. We demonstrated that DNA hypomethylation is associated with reduced susceptibility in rice towards root-parasitic nematodes and is likely to be part of the basal pattern-triggered immunity response in plants.
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Affiliation(s)
| | | | - Tim De Meyer
- Department of Data Analysis & Mathematical ModellingGhent UniversityB‐9000GhentBelgium
| | - Tina Kyndt
- Department of BiotechnologyGhent UniversityB‐9000GhentBelgium
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11
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Zhu J, Li Y, Lin J, Wu Y, Guo H, Shao Y, Wang F, Wang X, Mo X, Zheng S, Yu H, Mao C. CRD1, an Xpo1 domain protein, regulates miRNA accumulation and crown root development in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:328-342. [PMID: 31257621 DOI: 10.1111/tpj.14445] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 06/09/2023]
Abstract
Crown root (CR) is the main component of the fibrous root system in cereal crops, but the molecular mechanism underlying CR development is still unclear. Here, we isolated the crown root defect 1 (crd1) mutant from ethyl methane sulfonate-mutated mutant library, which significantly inhibited CR development. The CRD1 was identified through genome resequencing and complementation analysis, which encodes an Xpo1 domain protein: the rice ortholog of Arabidopsis HASTY (HST) and human exportin-5 (XPO5). CRD1 is ubiquitously expressed, with the highest expression levels in the CR primordium at the stem base. CRD1 is a nucleocytoplasmic protein. The crd1 mutant contains significantly reduced miRNA levels in the cytoplasm and nucleus, suggesting that CRD1 is essential for maintaining normal miRNA levels in plant cells. The altered CR phenotype of crd1 was simulated by target mimicry of miR156, suggesting that this defect is due to the disruption of miR156 regulatory pathways. Our analysis of CRD1, the HST ortholog identified in monocots, expands our understanding of the molecular mechanisms underlying miRNA level and CR development.
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Affiliation(s)
- Jianshu Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jian Lin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yunrong Wu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Huaxing Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yanlin Shao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Fei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaofei Wang
- School of Agriculture and Food Sciences, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Xiaorong Mo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shaojian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hao Yu
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543, Singapore
| | - Chuanzao Mao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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12
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Li Y, Yang Y, Liu Y, Li D, Zhao Y, Li Z, Liu Y, Jiang D, Li J, Zhou H, Chen J, Zhuang C, Liu Z. Overexpression of OsAGO1b Induces Adaxially Rolled Leaves by Affecting Leaf Abaxial Sclerenchymatous Cell Development in Rice. RICE (NEW YORK, N.Y.) 2019; 12:60. [PMID: 31396773 PMCID: PMC6687834 DOI: 10.1186/s12284-019-0323-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 08/02/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND ARGONAUTE 1 (AGO1) proteins can recruit small RNAs to regulate gene expression, involving several growth and development processes in Arabidopsis. Rice genome contains four AGO1 genes, OsAGO1a to OsAGO1d. However, the regulatory functions to rice growth and development of each AGO1 gene are still unknown. RESULTS We obtained overexpression and RNAi transgenic lines of each OsAGO1 gene. However, only up- and down-regulation of OsAGO1b caused multiple abnormal phenotypic changes in rice, indicating that OsAGO1b is the key player in rice growth and organ development compared with other three OsAGO1s. qRT-PCR assays showed that OsAGO1b was almost unanimously expressed in leaves at different developmental stages, and strongly expressed in spikelets at S1 to S3 stages. OsAGO1b is a typical AGO protein, and co-localized in both the nucleus and cytoplasm simultaneously. Overexpression of OsAGO1b caused adaxially rolled leaves and a series of abnormal phenotypes, such as the reduced tiller number and plant height. Knockdown lines of OsAGO1b showed almost normal leaves, but the seed setting percentage was significantly reduced accompanied by the disturbed anther patterning and reduced pollen fertility. Further anatomical observation revealed that OsAGO1b overexpression plants showed the partially defective development of sclerenchymatous cells on the abaxial side of leaves. In situ hybridization showed OsAGO1b mRNA was uniformly accumulated in P1 to P3 primordia without polarity property, suggesting OsAGO1b did not regulate the adaxial-abaxial polarity development directly. The expression levels of several genes related to leaf polarity development and vascular bundle differentiation were observably changed. Notably, the accumulation of miR166 and TAS3-siRNA was decreased, and their targeted OSHBs and OsARFs were significantly up-regulated. The mRNA distribution patterns of OSHB3 and OsARF4 in leaves remained almost unchanged between ZH11 and OsAGO1b overexpression lines, but their expression levels were enhanced at the regions of vascular bundles and sclerenchymatous cell differentiation. CONCLUSIONS In summary, we demonstrated OsAGO1b is the leading player among four OsAGO1s in rice growth and development. We propose that OsAGO1b may regulate the abaxial sclerenchymatous cell differentiation by affecting the expression of OSHBs in rice.
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Affiliation(s)
- Youhan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
- Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223 China
| | - Yiqi Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
| | - Ye Liu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223 China
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026 China
| | - Dexia Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
| | - Yahuan Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
| | - Zhijie Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
| | - Ying Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
| | - Dagang Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
| | - Jing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
| | - Hai Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
| | - Jianghua Chen
- Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223 China
| | - Chuxiong Zhuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
| | - Zhenlan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, 510642 China
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13
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Navalikhina A, Antonyuk M, Pasichnyk T, Ternovska T. Identification of Oryza sativa’s Awn Development Regulatory Gene Orthologs in Triticinae Accessions. CYTOL GENET+ 2019. [DOI: 10.3103/s0095452719040091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Wang J, Zhang Q, Wang Y, Huang J, Luo N, Wei S, Jin J. Analysing the rice young panicle transcriptome reveals the gene regulatory network controlled by TRIANGULAR HULL1. RICE (NEW YORK, N.Y.) 2019; 12:6. [PMID: 30725309 PMCID: PMC6890884 DOI: 10.1186/s12284-019-0265-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 01/30/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND TRIANGULAR HULL1 (TH1), a member of the rice ALOG gene family, has been characterized as a rice lemma/palea-related gene. To understand the gene regulatory network that controlled by TH1, we analyzed the transcriptome from a TH1 knock out (KO) line, which was generated by CRISPR/Cas9. Our study may shed some light on the molecular mechanism of lemma/palea development. RESULTS We obtained 20 T0 th1-C transgenic plants by CRISPR/Cas9. Among the 20 plants, there were eight bi-allelic mutations, five homozygous mutations, three heterozygous mutations, and four Non-KO plants. By comparing with the wild type and the heterozygous knock out (KO) line, the homozygous KO lines showed defects in lemma/palea development as well as in grain filling. Further more, we studied the gene regulatory network that controlled by TH1 by comparing the transcriptome of a homozygous TH1 KO line with its Non-KO line as a control. A total of 622 genes were identified as differentially expressed genes (DEGs), of which 297 genes were significantly up-regulated while 325 genes were down-regulated. One hundred thirty eight of the DEGs were assigned to the 59 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. Among these annotated DEGs, 15 genes were related to plant hormone signal transduction, eight genes were related to starch and sucrose metabolism. These were the two largest groups of DEGs according to the KEGG pathway analysis. CONCLUSIONS Our results indicated that hormone related genes and starch/sucrose metabolism related genes might act as downstream targets of TH1; they might be responsible for lemma/palea development and grain filling respectively.
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Affiliation(s)
- Jun Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, People's Republic of China
- College of Life Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China
| | - Qiang Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, People's Republic of China
- College of Life Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China
| | - Yi Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, People's Republic of China
- College of Forestry, Guangxi University, Nanning, 530004, People's Republic of China
| | - Jing Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, People's Republic of China
- College of Life Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China
| | - Nengjie Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, People's Republic of China
- College of Life Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China
| | - Shengbo Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, People's Republic of China
- College of Life Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China
| | - Jian Jin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, People's Republic of China.
- College of Life Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China.
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15
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Cui X, Zhang Z, Wang Y, Wu J, Han X, Gu X, Lu T. TWI1 regulates cell-to-cell movement of OSH15 to control leaf cell fate. THE NEW PHYTOLOGIST 2019; 221:326-340. [PMID: 30151833 DOI: 10.1111/nph.15390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/01/2018] [Indexed: 06/08/2023]
Abstract
Cell pattern formation in plant leaves has attracted much attention from both plant biologists and breeders. However, in rice, the molecular mechanism remains unclear. Here, we describe the isolation and functional characterization of TWISTED-LEAF1 (TWI1), a critical gene involved in the development of the mestome sheath, vascular bundle sheath, interveinal mesophyll and sclerenchyma in rice leaves. Mutant twi1 plants have twisted leaves which might be caused by the compromised development and disordered patterning of bundle sheath, sclerenchyma and interveinal mesophyll cells. Expression of TWI1 can functionally rescue these mutant phenotypes. TWI1 encodes a transcription factor binding protein that interacts with OSH15, a class I KNOTTED1-like homeobox (KNOX) transcription factor. The cell-to-cell trafficking of OSH15 is restricted through its interaction with TWI1. Knockout or knockdown of OSH15 in twi1 rescues the twisted leaf phenotype. These studies reveal a key factor controlling cell pattern formation in rice leaves.
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Affiliation(s)
- Xuean Cui
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiguo Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yanwei Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jinxia Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiao Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tiegang Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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16
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Yao W, Li G, Yu Y, Ouyang Y. funRiceGenes dataset for comprehensive understanding and application of rice functional genes. Gigascience 2018; 7:1-9. [PMID: 29220485 PMCID: PMC5765555 DOI: 10.1093/gigascience/gix119] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 11/22/2017] [Indexed: 12/26/2022] Open
Abstract
Background As a main staple food, rice is also a model plant for functional genomic studies of monocots. Decoding of every DNA element of the rice genome is essential for genetic improvement to address increasing food demands. The past 15 years have witnessed extraordinary advances in rice functional genomics. Systematic characterization and proper deposition of every rice gene are vital for both functional studies and crop genetic improvement. Findings We built a comprehensive and accurate dataset of ∼2800 functionally characterized rice genes and ∼5000 members of different gene families by integrating data from available databases and reviewing every publication on rice functional genomic studies. The dataset accounts for 19.2% of the 39 045 annotated protein-coding rice genes, which provides the most exhaustive archive for investigating the functions of rice genes. We also constructed 214 gene interaction networks based on 1841 connections between 1310 genes. The largest network with 762 genes indicated that pleiotropic genes linked different biological pathways. Increasing degree of conservation of the flowering pathway was observed among more closely related plants, implying substantial value of rice genes for future dissection of flowering regulation in other crops. All data are deposited in the funRiceGenes database (https://funricegenes.github.io/). Functionality for advanced search and continuous updating of the database are provided by a Shiny application (http://funricegenes.ncpgr.cn/). Conclusions The funRiceGenes dataset would enable further exploring of the crosslink between gene functions and natural variations in rice, which can also facilitate breeding design to improve target agronomic traits of rice.
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Affiliation(s)
- Wen Yao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Guangwei Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiming Yu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
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17
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de Almeida C, Scheer H, Gobert A, Fileccia V, Martinelli F, Zuber H, Gagliardi D. RNA uridylation and decay in plants. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0163. [PMID: 30397100 DOI: 10.1098/rstb.2018.0163] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2018] [Indexed: 12/13/2022] Open
Abstract
RNA uridylation consists of the untemplated addition of uridines at the 3' extremity of an RNA molecule. RNA uridylation is catalysed by terminal uridylyltransferases (TUTases), which form a subgroup of the terminal nucleotidyltransferase family, to which poly(A) polymerases also belong. The key role of RNA uridylation is to regulate RNA degradation in a variety of eukaryotes, including fission yeast, plants and animals. In plants, RNA uridylation has been mostly studied in two model species, the green algae Chlamydomonas reinhardtii and the flowering plant Arabidopsis thaliana Plant TUTases target a variety of RNA substrates, differing in size and function. These RNA substrates include microRNAs (miRNAs), small interfering silencing RNAs (siRNAs), ribosomal RNAs (rRNAs), messenger RNAs (mRNAs) and mRNA fragments generated during post-transcriptional gene silencing. Viral RNAs can also get uridylated during plant infection. We describe here the evolutionary history of plant TUTases and we summarize the diverse molecular functions of uridylation during RNA degradation processes in plants. We also outline key points of future research.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
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Affiliation(s)
- Caroline de Almeida
- Institut de biologie moléculaire des plantes (IBMP), Centre national de la recherche scientifique (CNRS), Université de Strasbourg, 12 rue Zimmer, 67000 Strasbourg, France
| | - Hélène Scheer
- Institut de biologie moléculaire des plantes (IBMP), Centre national de la recherche scientifique (CNRS), Université de Strasbourg, 12 rue Zimmer, 67000 Strasbourg, France
| | - Anthony Gobert
- Institut de biologie moléculaire des plantes (IBMP), Centre national de la recherche scientifique (CNRS), Université de Strasbourg, 12 rue Zimmer, 67000 Strasbourg, France
| | - Veronica Fileccia
- Dipartimento di Scienze Agrarie Alimentari Forestali, Università degli Studi di Palermo, viale delle scienze ed. 4, Palermo 90128, Italy
| | - Federico Martinelli
- Dipartimento di Scienze Agrarie Alimentari Forestali, Università degli Studi di Palermo, viale delle scienze ed. 4, Palermo 90128, Italy
| | - Hélène Zuber
- Institut de biologie moléculaire des plantes (IBMP), Centre national de la recherche scientifique (CNRS), Université de Strasbourg, 12 rue Zimmer, 67000 Strasbourg, France
| | - Dominique Gagliardi
- Institut de biologie moléculaire des plantes (IBMP), Centre national de la recherche scientifique (CNRS), Université de Strasbourg, 12 rue Zimmer, 67000 Strasbourg, France
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18
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Ahmed MB, Santos KCGD, Sanchez IB, Petre B, Lorrain C, Plourde MB, Duplessis S, Desgagné-Penix I, Germain H. A rust fungal effector binds plant DNA and modulates transcription. Sci Rep 2018; 8:14718. [PMID: 30283062 PMCID: PMC6170375 DOI: 10.1038/s41598-018-32825-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/21/2018] [Indexed: 02/08/2023] Open
Abstract
The basidiomycete Melampsora larici-populina causes poplar rust disease by invading leaf tissues and secreting effector proteins through specialized infection structures known as haustoria. The mechanisms by which rust effectors promote pathogen virulence are poorly understood. The present study characterized Mlp124478, a candidate effector of M. larici-populina. We used the models Arabidopsis thaliana and Nicotiana benthamiana to investigate the function of Mlp124478 in plant cells. We established that Mlp124478 accumulates in the nucleus and nucleolus, however its nucleolar accumulation is not required to promote growth of the oomycete pathogen Hyaloperonospora arabidopsidis. Stable constitutive expression of Mlp124478 in A. thaliana repressed the expression of genes involved in immune responses, and also altered leaf morphology by increasing the waviness of rosette leaves. Chip-PCR experiments showed that Mlp124478 associats'e with the TGA1a-binding DNA sequence. Our results suggest that Mlp124478 exerts a virulence activity and binds the TGA1a promoter to suppress genes induced in response to pathogen infection.
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Affiliation(s)
- Md Bulbul Ahmed
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada
| | - Karen Cristine Gonçalves Dos Santos
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada
| | - Ingrid Benerice Sanchez
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada
- Department of Biotechnology and Engineering in Chemistry, Instituto Tecnológico y de Estudios Superiores de Monterrey, Campus Estado de México (ITESM CEM), Margarita Maza de Juárez, 52926, Cd, López Mateos, Mexico
| | - Benjamin Petre
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- INRA, UMR 1136 Interactions Arbres/Microorganismes, INRA/Université de Lorraine, Centre INRA Grand Est - Nancy, 54280, Champenoux, France
- Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA/Université de Lorraine, Faculté des Sciences et Technologies - Campus Aiguillettes, BP, 70239-54506, Vandoeuvre-lès-Nancy, France
| | - Cécile Lorrain
- INRA, UMR 1136 Interactions Arbres/Microorganismes, INRA/Université de Lorraine, Centre INRA Grand Est - Nancy, 54280, Champenoux, France
| | - Mélodie B Plourde
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada.
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada.
| | - Sébastien Duplessis
- INRA, UMR 1136 Interactions Arbres/Microorganismes, INRA/Université de Lorraine, Centre INRA Grand Est - Nancy, 54280, Champenoux, France
| | - Isabel Desgagné-Penix
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada
| | - Hugo Germain
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada.
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada.
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19
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Fuchs Wightman F, Giono LE, Fededa JP, de la Mata M. Target RNAs Strike Back on MicroRNAs. Front Genet 2018; 9:435. [PMID: 30333855 PMCID: PMC6175985 DOI: 10.3389/fgene.2018.00435] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/13/2018] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs are extensively studied regulatory non-coding small RNAs that silence animal genes throughout most biological processes, typically doing so by binding to partially complementary sequences within target RNAs. A plethora of studies has described detailed mechanisms for microRNA biogenesis and function, as well as their temporal and spatial regulation during development. By inducing translational repression and/or degradation of their target RNAs, microRNAs can contribute to achieve highly specific cell- or tissue-specific gene expression, while their aberrant expression can lead to disease. Yet an unresolved aspect of microRNA biology is how such small RNA molecules are themselves cleared from the cell, especially under circumstances where fast microRNA turnover or specific degradation of individual microRNAs is required. In recent years, it was unexpectedly found that binding of specific target RNAs to microRNAs with extensive complementarity can reverse the outcome, triggering degradation of the bound microRNAs. This emerging pathway, named TDMD for Target RNA-Directed MicroRNA Degradation, leads to microRNA 3'-end tailing by the addition of A/U non-templated nucleotides, trimming or shortening from the 3' end, and highly specific microRNA loss, providing a new layer of microRNA regulation. Originally described in flies and known to be triggered by viral RNAs, novel endogenous instances of TDMD have been uncovered and are now starting to be understood. Here, we review our current knowledge of this pathway and its potential role in the control and diversification of microRNA expression patterns.
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Affiliation(s)
- Federico Fuchs Wightman
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Luciana E Giono
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Juan Pablo Fededa
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Manuel de la Mata
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
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20
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Chen B, Chen J, Du Q, Zhou D, Wang L, Xie J, Li Y, Zhang D. Genetic variants in microRNA biogenesis genes as novel indicators for secondary growth in Populus. THE NEW PHYTOLOGIST 2018; 219:1263-1282. [PMID: 29916214 DOI: 10.1111/nph.15262] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/06/2018] [Indexed: 05/21/2023]
Abstract
MicroRNAs (miRNAs) function as key regulators of complex traits, but how genetic alterations in miRNA biogenesis genes (miRBGs) affect quantitative variation has not been elucidated. We conducted transcript analyses and association genetics to investigate how miRBGs, miRNA genes (MIRNAs) and their respective targets contribute to secondary growth in a natural population of 435 Populus tomentosa individuals. This analysis identified 29 843 common single-nucleotide polymorphisms (SNPs; frequency > 0.10) within 682 genes (80 miRBGs, 152 MIRNAs, and 457 miRNA targets). Single-SNP association analysis found SNPs in 234 candidate genes exhibited significant additive/dominant effects on phenotypes. Among these, specific candidates that associated with the same traits produced 791 miRBG-MIRNA-target combinations, suggesting possible genetic miRBG-MIRNA and MIRNA-target interactions, providing an important clue for the regulatory mechanisms of miRBGs. Multi-SNP association found 4672 epistatic pairs involving 578 genes that showed significant associations with traits and identified 106 miRBG-MIRNA-target combinations. Two multi-hierarchical networks were constructed based on correlations of miRBG-miRNA and miRNA-target expression to further probe the mechanisms of trait diversity underlying changes in miRBGs. Our study opens avenues for the investigation of miRNA function in perennial plants and underscored miRBGs as potentially modulating quantitative variation in traits.
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Affiliation(s)
- Beibei Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Jinhui Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Qingzhang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Daling Zhou
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Longxin Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Jianbo Xie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Ying Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Deqiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
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Singh A, Gautam V, Singh S, Sarkar Das S, Verma S, Mishra V, Mukherjee S, Sarkar AK. Plant small RNAs: advancement in the understanding of biogenesis and role in plant development. PLANTA 2018; 248:545-558. [PMID: 29968061 DOI: 10.1007/s00425-018-2927-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 04/12/2018] [Indexed: 05/07/2023]
Abstract
Present review addresses the advances made in the understanding of biogenesis of plant small RNAs and their role in plant development. We discuss the elaborate role of microRNAs (miRNAs) and trans-acting small interfering RNAs (ta-siRNAs) in various aspects of plant growth and development and highlight relevance of small RNA mobility. Small non-coding RNAs regulate various aspects of plant development. Small RNAs (sRNAs) of 21-24 nucleotide length are derived from double-stranded RNAs through the combined activity of several biogenesis and processing components. These sRNAs function by negatively regulating the expression of target genes. miRNAs and ta-siRNAs constitute two important classes of endogenous small RNAs in plants, which play important roles in plant growth and developmental processes like embryogenesis, organ formation and patterning, shoot and root growth, and reproductive development. Biogenesis of miRNAs is a multistep process which includes transcription, processing and modification, and their loading onto RNA-induced silencing complex (RISC). RISC-loaded miRNAs carry out post-transcriptional silencing of their target(s). Recent studies identified orthologues of different biogenesis components of novel and conserved small RNAs from different model plants. Although many small RNAs have been identified from diverse plant species, only a handful of them have been functionally characterized. In this review, we discuss the advances made in understanding the biogenesis, functional conservation/divergence in miRNA-mediated gene regulation, and the developmental role of small RNAs in different plant species.
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Affiliation(s)
- Archita Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Vibhav Gautam
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sharmila Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shabari Sarkar Das
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Swati Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Vishnu Mishra
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shalini Mukherjee
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ananda K Sarkar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Curtin SJ, Xiong Y, Michno J, Campbell BW, Stec AO, Čermák T, Starker C, Voytas DF, Eamens AL, Stupar RM. CRISPR/Cas9 and TALENs generate heritable mutations for genes involved in small RNA processing of Glycine max and Medicago truncatula. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1125-1137. [PMID: 29087011 PMCID: PMC5978873 DOI: 10.1111/pbi.12857] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 10/17/2017] [Accepted: 10/21/2017] [Indexed: 05/14/2023]
Abstract
Processing of double-stranded RNA precursors into small RNAs is an essential regulator of gene expression in plant development and stress response. Small RNA processing requires the combined activity of a functionally diverse group of molecular components. However, in most of the plant species, there are insufficient mutant resources to functionally characterize each encoding gene. Here, mutations in loci encoding protein machinery involved in small RNA processing in soya bean and Medicago truncatula were generated using the CRISPR/Cas9 and TAL-effector nuclease (TALEN) mutagenesis platforms. An efficient CRISPR/Cas9 reagent was used to create a bi-allelic double mutant for the two soya bean paralogous Double-stranded RNA-binding2 (GmDrb2a and GmDrb2b) genes. These mutations, along with a CRISPR/Cas9-generated mutation of the M. truncatula Hua enhancer1 (MtHen1) gene, were determined to be germ-line transmissible. Furthermore, TALENs were used to generate a mutation within the soya bean Dicer-like2 gene. CRISPR/Cas9 mutagenesis of the soya bean Dicer-like3 gene and the GmHen1a gene was observed in the T0 generation, but these mutations failed to transmit to the T1 generation. The irregular transmission of induced mutations and the corresponding transgenes was investigated by whole-genome sequencing to reveal a spectrum of non-germ-line-targeted mutations and multiple transgene insertion events. Finally, a suite of combinatorial mutant plants were generated by combining the previously reported Gmdcl1a, Gmdcl1b and Gmdcl4b mutants with the Gmdrb2ab double mutant. Altogether, this study demonstrates the synergistic use of different genome engineering platforms to generate a collection of useful mutant plant lines for future study of small RNA processing in legume crops.
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Affiliation(s)
- Shaun J. Curtin
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMNUSA
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
- Present address:
Plant Science Research UnitAgricultural Research ServiceUnited States Department of AgricultureSt PaulMNUSA
| | - Yer Xiong
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
| | - Jean‐Michel Michno
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
- Bioinformatics and Computational Biology Graduate ProgramUniversity of MinnesotaMinneapolisMNUSA
| | | | - Adrian O. Stec
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
| | - Tomas Čermák
- Department of Genetics, Cell Biology & DevelopmentCenter for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
- Present address:
Agricultural Research ServiceInari Agriculture, Inc.CambridgeMAUSA
| | - Colby Starker
- Department of Genetics, Cell Biology & DevelopmentCenter for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Daniel F. Voytas
- Department of Genetics, Cell Biology & DevelopmentCenter for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Andrew L. Eamens
- School of Environmental and Life SciencesThe University of NewcastleCallaghanNew South WalesAustralia
| | - Robert M. Stupar
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
- Bioinformatics and Computational Biology Graduate ProgramUniversity of MinnesotaMinneapolisMNUSA
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Banerjee A, Roychoudhury A. The gymnastics of epigenomics in rice. PLANT CELL REPORTS 2018; 37:25-49. [PMID: 28866772 DOI: 10.1007/s00299-017-2192-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/01/2017] [Indexed: 05/21/2023]
Abstract
Epigenomics is represented by the high-throughput investigations of genome-wide epigenetic alterations, which ultimately dictate genomic, transcriptomic, proteomic and metabolomic dynamism. Rice has been accepted as the global staple crop. As a result, this model crop deserves significant importance in the rapidly emerging field of plant epigenomics. A large number of recently available data reveal the immense flexibility and potential of variable epigenomic landscapes. Such epigenomic impacts and variability are determined by a number of epigenetic regulators and several crucial inheritable epialleles, respectively. This article highlights the correlation of the epigenomic landscape with growth, flowering, reproduction, non-coding RNA-mediated post-transcriptional regulation, transposon mobility and even heterosis in rice. We have also discussed the drastic epigenetic alterations which are reported in rice plants grown from seeds exposed to the extraterrestrial environment. Such abiotic conditions impose stress on the plants leading to epigenomic modifications in a genotype-specific manner. Some significant bioinformatic databases and in silico approaches have also been explained in this article. These softwares provide important interfaces for comparative epigenomics. The discussion concludes with a unified goal of developing epigenome editing to promote biological hacking of the rice epigenome. Such a cutting-edge technology if properly standardized, can integrate genomics and epigenomics together with the generation of high-yielding trait in several cultivars of rice.
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Affiliation(s)
- Aditya Banerjee
- Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, 700016, West Bengal, India
| | - Aryadeep Roychoudhury
- Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, 700016, West Bengal, India.
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Yu Y, Jia T, Chen X. The 'how' and 'where' of plant microRNAs. THE NEW PHYTOLOGIST 2017; 216:1002-1017. [PMID: 29048752 PMCID: PMC6040672 DOI: 10.1111/nph.14834] [Citation(s) in RCA: 253] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 08/21/2017] [Indexed: 05/18/2023]
Abstract
Contents 1002 I. 1002 II. 1007 III. 1010 IV. 1013 1013 References 1013 SUMMARY: MicroRNAs (miRNAs) are small non-coding RNAs, of typically 20-24 nt, that regulate gene expression post-transcriptionally through sequence complementarity. Since the identification of the first miRNA, lin-4, in the nematode Caenorhabditis elegans in 1993, thousands of miRNAs have been discovered in animals and plants, and their regulatory roles in numerous biological processes have been uncovered. In plants, research efforts have established the major molecular framework of miRNA biogenesis and modes of action, and are beginning to elucidate the mechanisms of miRNA degradation. Studies have implicated restricted and surprising subcellular locations in which miRNA biogenesis or activity takes place. In this article, we summarize the current knowledge on how plant miRNAs are made and degraded, and how they repress target gene expression. We discuss not only the players involved in these processes, but also the subcellular sites in which these processes are known or implicated to take place. We hope to raise awareness that the cell biology of miRNAs holds the key to a full understanding of these enigmatic molecules.
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Affiliation(s)
- Yu Yu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Tianran Jia
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- Department of Botany and Plant Sciences, Howard Hughes Medical Institute, University of California, Riverside, CA 92521, USA
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Matsumoto H, Yasui Y, Kumamaru T, Hirano HY. Characterization of a half-pipe-like leaf1 mutant that exhibits a curled leaf phenotype. Genes Genet Syst 2017; 92:287-291. [DOI: 10.1266/ggs.17-00013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Hikari Matsumoto
- Department of Biological Sciences, School of Science, The University of Tokyo
| | - Yukiko Yasui
- Department of Biological Sciences, School of Science, The University of Tokyo
| | | | - Hiro-Yuki Hirano
- Department of Biological Sciences, School of Science, The University of Tokyo
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De Almeida C, Scheer H, Zuber H, Gagliardi D. RNA uridylation: a key posttranscriptional modification shaping the coding and noncoding transcriptome. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 9. [PMID: 28984054 DOI: 10.1002/wrna.1440] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/03/2017] [Accepted: 08/07/2017] [Indexed: 12/27/2022]
Abstract
RNA uridylation is a potent and widespread posttranscriptional regulator of gene expression. RNA uridylation has been detected in a range of eukaryotes including trypanosomes, animals, plants, and fungi, but with the noticeable exception of budding yeast. Virtually all classes of eukaryotic RNAs can be uridylated and uridylation can also tag viral RNAs. The untemplated addition of a few uridines at the 3' end of a transcript can have a decisive impact on RNA's fate. In rare instances, uridylation is an intrinsic step in the maturation of noncoding RNAs like for the U6 spliceosomal RNA or mitochondrial guide RNAs in trypanosomes. Uridylation can also switch specific miRNA precursors from a degradative to a processing mode. This switch depends on the number of uridines added which is regulated by the cellular context. Yet, the typical consequence of uridylation on mature noncoding RNAs or their precursors is to accelerate decay. Importantly, mRNAs are also tagged by uridylation. In fact, the advent of novel high throughput sequencing protocols has recently revealed the pervasiveness of mRNA uridylation, from plants to humans. As for noncoding RNAs, the main function to date for mRNA uridylation is to promote degradation. Yet, additional roles begin to be ascribed to U-tailing such as the control of mRNA deadenylation, translation control and possibly storage. All these new findings illustrate that we are just beginning to appreciate the diversity of roles played by RNA uridylation and its full temporal and spatial implication in regulating gene expression. WIREs RNA 2018, 9:e1440. doi: 10.1002/wrna.1440 This article is categorized under: RNA Processing > 3' End Processing RNA Processing > RNA Editing and Modification RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms.
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Affiliation(s)
- Caroline De Almeida
- Institut de Biologie Moleculaire des Plantes (IBMP), CNRS, University of Strasbourg, Strasbourg, France
| | - Hélène Scheer
- Institut de Biologie Moleculaire des Plantes (IBMP), CNRS, University of Strasbourg, Strasbourg, France
| | - Hélène Zuber
- Institut de Biologie Moleculaire des Plantes (IBMP), CNRS, University of Strasbourg, Strasbourg, France
| | - Dominique Gagliardi
- Institut de Biologie Moleculaire des Plantes (IBMP), CNRS, University of Strasbourg, Strasbourg, France
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Feng N, Song G, Guan J, Chen K, Jia M, Huang D, Wu J, Zhang L, Kong X, Geng S, Liu J, Li A, Mao L. Transcriptome Profiling of Wheat Inflorescence Development from Spikelet Initiation to Floral Patterning Identified Stage-Specific Regulatory Genes. PLANT PHYSIOLOGY 2017; 174:1779-1794. [PMID: 28515146 PMCID: PMC5490901 DOI: 10.1104/pp.17.00310] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/13/2017] [Indexed: 05/20/2023]
Abstract
Early reproductive development in cereals is crucial for final grain number per spike and hence the yield potential of the crop. To date, however, no systematic analyses of gene expression profiles during this important process have been conducted for common wheat (Triticum aestivum). Here, we studied the transcriptome profiles at four stages of early wheat reproductive development, from spikelet initiation to floral organ differentiation. K-means clustering and stage-specific transcript identification detected dynamically expressed homeologs of important transcription regulators in spikelet and floral meristems that may be involved in spikelet initiation, floret meristem specification, and floral organ patterning, as inferred from their homologs in model plants. Small RNA transcriptome sequencing discovered key microRNAs that were differentially expressed during wheat inflorescence development alongside their target genes, suggesting that miRNA-mediated regulatory mechanisms for floral development may be conserved in cereals and Arabidopsis. Our analysis was further substantiated by the functional characterization of the ARGONAUTE1d (AGO1d) gene, which was initially expressed in stamen primordia and later in the tapetum during anther maturation. In agreement with its stage-specific expression pattern, the loss of function of the predominantly expressed B homeolog of AGO1d in a tetraploid durum wheat mutant resulted in smaller anthers with more infertile pollens than the wild type and a reduced grain number per spike. Together, our work provides a first glimpse of the gene regulatory networks in wheat inflorescence development that may be pivotal for floral and grain development, highlighting potential targets for genetic manipulation to improve future wheat yields.
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Affiliation(s)
- Nan Feng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Gaoyuan Song
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiantao Guan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kai Chen
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Meiling Jia
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dehua Huang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian 271018, China
| | - Jiajie Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian 271018, China
| | - Lichao Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuying Kong
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuaifeng Geng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | - Aili Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Long Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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30
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Samad AFA, Sajad M, Nazaruddin N, Fauzi IA, Murad AMA, Zainal Z, Ismail I. MicroRNA and Transcription Factor: Key Players in Plant Regulatory Network. FRONTIERS IN PLANT SCIENCE 2017; 8:565. [PMID: 28446918 PMCID: PMC5388764 DOI: 10.3389/fpls.2017.00565] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/29/2017] [Indexed: 05/14/2023]
Abstract
Recent achievements in plant microRNA (miRNA), a large class of small and non-coding RNAs, are very exciting. A wide array of techniques involving forward genetic, molecular cloning, bioinformatic analysis, and the latest technology, deep sequencing have greatly advanced miRNA discovery. A tiny miRNA sequence has the ability to target single/multiple mRNA targets. Most of the miRNA targets are transcription factors (TFs) which have paramount importance in regulating the plant growth and development. Various families of TFs, which have regulated a range of regulatory networks, may assist plants to grow under normal and stress environmental conditions. This present review focuses on the regulatory relationships between miRNAs and different families of TFs like; NF-Y, MYB, AP2, TCP, WRKY, NAC, GRF, and SPL. For instance NF-Y play important role during drought tolerance and flower development, MYB are involved in signal transduction and biosynthesis of secondary metabolites, AP2 regulate the floral development and nodule formation, TCP direct leaf development and growth hormones signaling. WRKY have known roles in multiple stress tolerances, NAC regulate lateral root formation, GRF are involved in root growth, flower, and seed development, and SPL regulate plant transition from juvenile to adult. We also studied the relation between miRNAs and TFs by consolidating the research findings from different plant species which will help plant scientists in understanding the mechanism of action and interaction between these regulators in the plant growth and development under normal and stress environmental conditions.
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Affiliation(s)
- Abdul F. A. Samad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
| | - Muhammad Sajad
- Department of Plant Breeding and Genetics, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur, PunjabPakistan
- Centre of Plant Biotechnology, Institute of Systems Biology, National University of Malaysia, SelangorMalaysia
| | - Nazaruddin Nazaruddin
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Syiah Kuala University, Darussalam, Banda AcehIndonesia
| | - Izzat A. Fauzi
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
| | - Abdul M. A. Murad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
| | - Zamri Zainal
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
- Centre of Plant Biotechnology, Institute of Systems Biology, National University of Malaysia, SelangorMalaysia
| | - Ismanizan Ismail
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
- Centre of Plant Biotechnology, Institute of Systems Biology, National University of Malaysia, SelangorMalaysia
- *Correspondence: Ismanizan Ismail,
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Majumdar R, Rajasekaran K, Cary JW. RNA Interference (RNAi) as a Potential Tool for Control of Mycotoxin Contamination in Crop Plants: Concepts and Considerations. FRONTIERS IN PLANT SCIENCE 2017; 8:200. [PMID: 28261252 PMCID: PMC5306134 DOI: 10.3389/fpls.2017.00200] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 02/02/2017] [Indexed: 05/20/2023]
Abstract
Mycotoxin contamination in food and feed crops is a major concern worldwide. Fungal pathogens of the genera Aspergillus. Fusarium, and Penicillium are a major threat to food and feed crops due to production of mycotoxins such as aflatoxins, 4-deoxynivalenol, patulin, and numerous other toxic secondary metabolites that substantially reduce the value of the crop. While host resistance genes are frequently used to introgress disease resistance into elite germplasm, either through traditional breeding or transgenic approaches, such resistance is often compromised by the evolving pathogen over time. RNAi-based host-induced gene silencing of key genes required by the pathogen for optimal growth, virulence and/or toxin production, can serve as an alternative, pre-harvest approach for disease control. RNAi represents a robust and efficient tool that can be used in a highly targeted, tissue specific manner to combat mycotoxigenic fungi infecting crop plants. Successful transgenic RNAi implementation depends on several factors including (1) designing vectors to produce double-stranded RNAs (dsRNAs) that will generate small interfering RNA (siRNA) species for optimal gene silencing and reduced potential for off-target effects; (2) availability of ample target siRNAs at the infection site; (3) efficient uptake of siRNAs by the fungus; (4) siRNA half-life and (5) amplification of the silencing effect. This review provides a critical and comprehensive evaluation of the published literature on the use of RNAi-based approaches to control mycotoxin contamination in crop plants. It also examines experimental strategies used to better understand the mode of action of RNAi with the aim of eliminating mycotoxin contamination, thereby improving food and feed safety.
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Łabno A, Tomecki R, Dziembowski A. Cytoplasmic RNA decay pathways - Enzymes and mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:3125-3147. [PMID: 27713097 DOI: 10.1016/j.bbamcr.2016.09.023] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/29/2016] [Accepted: 09/30/2016] [Indexed: 12/14/2022]
Abstract
RNA decay plays a crucial role in post-transcriptional regulation of gene expression. Work conducted over the last decades has defined the major mRNA decay pathways, as well as enzymes and their cofactors responsible for these processes. In contrast, our knowledge of the mechanisms of degradation of non-protein coding RNA species is more fragmentary. This review is focused on the cytoplasmic pathways of mRNA and ncRNA degradation in eukaryotes. The major 3' to 5' and 5' to 3' mRNA decay pathways are described with emphasis on the mechanisms of their activation by the deprotection of RNA ends. More recently discovered 3'-end modifications such as uridylation, and their relevance to cytoplasmic mRNA decay in various model organisms, are also discussed. Finally, we provide up-to-date findings concerning various pathways of non-coding RNA decay in the cytoplasm.
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Affiliation(s)
- Anna Łabno
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Rafał Tomecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland.
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland.
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Huang J, Li Z, Zhao D. Deregulation of the OsmiR160 Target Gene OsARF18 Causes Growth and Developmental Defects with an Alteration of Auxin Signaling in Rice. Sci Rep 2016; 6:29938. [PMID: 27444058 PMCID: PMC4956771 DOI: 10.1038/srep29938] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 06/27/2016] [Indexed: 01/08/2023] Open
Abstract
MicroRNAs (miRNAs) control gene expression as key negative regulators at the post-transcriptional level. MiR160 plays a pivotal role in Arabidopsis growth and development through repressing expression of its target AUXIN RESPONSE FACTOR (ARF) genes; however, the function of miR160 in monocots remains elusive. In this study, we found that the mature rice miR160 (OsmiR160) was mainly derived from OsMIR160a and OsMIR160b genes. Among four potential OsmiR160 target OsARF genes, the OsARF18 transcript was cleaved at the OsmiR160 target site. Rice transgenic plants (named mOsARF18) expressing an OsmiR160-resistant version of OsARF18 exhibited pleiotropic defects in growth and development, including dwarf stature, rolled leaves, and small seeds. mOsARF18 leaves were abnormal in bulliform cell differentiation and epidermal cell division. Starch accumulation in mOsARF18 seeds was also reduced. Moreover, auxin induced expression of OsMIR160a, OsMIR160b, and OsARF18, whereas expression of OsMIR160a and OsMIR160b as well as genes involved in auxin signaling was altered in mOsARF18 plants. Our results show that negative regulation of OsARF18 expression by OsmiR160 is critical for rice growth and development via affecting auxin signaling, which will advance future studies on the molecular mechanism by which miR160 fine-tunes auxin signaling in plants.
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Affiliation(s)
- Jian Huang
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Zhiyong Li
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Dazhong Zhao
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
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35
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Sanei M, Chen X. Mechanisms of microRNA turnover. CURRENT OPINION IN PLANT BIOLOGY 2015; 27:199-206. [PMID: 26342825 PMCID: PMC4618239 DOI: 10.1016/j.pbi.2015.07.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 07/14/2015] [Accepted: 07/17/2015] [Indexed: 05/20/2023]
Abstract
MicroRNAs (miRNAs) are 20-24 nucleotide (nt) RNAs that regulate gene expression by guiding Argonaute (AGO) proteins to specific target RNAs to cause their degradation or translational repression. The abundance of miRNAs is strictly controlled at the transcriptional or post-transcriptional levels. miRNA turnover is presumably a necessary means to regulate miRNA levels in response to physiological, developmental, and environmental changes. miRNA 3' end methylation, 3' end nucleotide addition, AGO and complementary target transcripts are known or probable processes/factors that affect miRNA stability and turnover. Here we discuss the mechanisms that control miRNA turnover in plants and, where applicable, make references to similarities and differences in these mechanisms between plants and animals.
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Affiliation(s)
- Maryam Sanei
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, United States
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, United States; Howard Hughes Medical Institute, University of California, Riverside, CA, United States.
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36
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Philip A, Ferro VA, Tate RJ. Determination of the potential bioavailability of plant microRNAs using a simulated human digestion process. Mol Nutr Food Res 2015; 59:1962-72. [PMID: 26147655 DOI: 10.1002/mnfr.201500137] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 05/12/2015] [Accepted: 06/15/2015] [Indexed: 11/09/2022]
Abstract
SCOPE The "dietary xenomiR hypothesis" proposes that microRNAs (miRNAs) in foodstuffs survive transit through the mammalian gastrointestinal tract and pass into cells intact to affect gene regulation. However, debate continues as to whether dietary intake poses a feasible route for such exogenous gene regulators. Understanding on miRNA levels during pretreatments of human diet is essential to test their bioavailability during digestion. This study makes the novel first use of an in vitro method to eliminate the inherent complexities and variability of in vivo approaches used to test this hypothesis. METHODS AND RESULTS Plant miRNA levels in soybean and rice were measured during storage, processing, cooking, and early digestion using real-time PCR. We have demonstrated for the first time that storage, processing, and cooking does not abolish the plant miRNAs present in the foodstuffs. In addition, utilizing a simulated human digestion system revealed significant plant miRNA bioavailability after early stage digestion for 75 min. Attenuation of plant messenger RNA and synthetic miRNA was observed under these conditions. CONCLUSION Even after an extensive pretreatment, plant-derived miRNA, delivered by typical dietary ingestion, has a robustness that could make them bioavailable for uptake during early digestion. The potential benefit of these regulatory molecules in pharma nutrition could be explored further.
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Affiliation(s)
- Anna Philip
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, Glasgow, UK
| | - Valerie A Ferro
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, Glasgow, UK
| | - Rothwelle J Tate
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, Glasgow, UK
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37
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Ren G, Chen X, Yu B. Small RNAs meet their targets: when methylation defends miRNAs from uridylation. RNA Biol 2015; 11:1099-104. [PMID: 25483033 DOI: 10.4161/rna.36243] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Small RNAs are incorporated into Argonaute protein-containing complexes to guide the silencing of target RNAs in both animals and plants. The abundance of endogenous small RNAs is precisely controlled at multiple levels including transcription, processing and Argonaute loading. In addition to these processes, 3' end modification of small RNAs, the topic of a research area that has rapidly evolved over the last several years, adds another layer of regulation of their abundance, diversity and function. Here, we review our recent understanding of small RNA 3' end methylation and tailing.
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Affiliation(s)
- Guodong Ren
- a State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development; Institute of Plant Biology; School of Life Sciences; Fudan University ; Shanghai , China
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38
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Xu Q, Xing S, Zhu C, Liu W, Fan Y, Wang Q, Song Z, Yang W, Luo F, Shang F, Kang L, Chen W, Yan J, Li J, Sang T. Population transcriptomics reveals a potentially positive role of expression diversity in adaptation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:284-99. [PMID: 25251542 DOI: 10.1111/jipb.12287] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 09/19/2014] [Indexed: 05/27/2023]
Abstract
While it is widely accepted that genetic diversity determines the potential of adaptation, the role that gene expression variation plays in adaptation remains poorly known. Here we show that gene expression diversity could have played a positive role in the adaptation of Miscanthus lutarioriparius. RNA-seq was conducted for 80 individuals of the species, with half planted in the energy crop domestication site and the other half planted in the control site near native habitats. A leaf reference transcriptome consisting of 18,503 high-quality transcripts was obtained using a pipeline developed for de novo assembling with population RNA-seq data. The population structure and genetic diversity of M. lutarioriparius were estimated based on 30,609 genic single nucleotide polymorphisms. Population expression (Ep ) and expression diversity (Ed ) were defined to measure the average level and the magnitude of variation of a gene expression in the population, respectively. It was found that expression diversity increased while genetic diversity decreased after the species was transplanted from the native habitats to the harsh domestication site, especially for genes involved in abiotic stress resistance, histone methylation, and biomass synthesis under water limitation. The increased expression diversity could have enriched phenotypic variation directly subject to selections in the new environment.
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Affiliation(s)
- Qin Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
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Baranauskė S, Mickutė M, Plotnikova A, Finke A, Venclovas Č, Klimašauskas S, Vilkaitis G. Functional mapping of the plant small RNA methyltransferase: HEN1 physically interacts with HYL1 and DICER-LIKE 1 proteins. Nucleic Acids Res 2015; 43:2802-12. [PMID: 25680966 PMCID: PMC4357707 DOI: 10.1093/nar/gkv102] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Methylation of 3′-terminal nucleotides of miRNA/miRNA* is part of miRNAs biogenesis in plants but is not found in animals. In Arabidopsis thaliana this reaction is carried out by a multidomain AdoMet-dependent 2′-O-methyltransferase HEN1. Using deletion and structure-guided mutational analysis, we show that the double-stranded RNA-binding domains R1 and R2 of HEN1 make significant but uneven contributions to substrate RNA binding, and map residues in each domain responsible for this function. Using GST pull-down assays and yeast two-hybrid analysis we demonstrate direct HEN1 interactions, mediated by its FK506-binding protein-like domain and R2 domain, with the microRNA biogenesis protein HYL1. Furthermore, we find that HEN1 forms a complex with DICER-LIKE 1 (DCL1) ribonuclease, another key protein involved in miRNA biogenesis machinery. In contrast, no direct interaction is detectable between HEN1 and SERRATE. On the basis of these findings, we propose a mechanism of plant miRNA maturation which involves binding of the HEN1 methyltransferase to the DCL1•HYL1•miRNA complex excluding the SERRATE protein.
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Affiliation(s)
- Simona Baranauskė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-02241, Lithuania
| | - Milda Mickutė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-02241, Lithuania
| | - Alexandra Plotnikova
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-02241, Lithuania
| | - Andreas Finke
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Česlovas Venclovas
- Department of Bioinformatics, Institute of Biotechnology, Vilnius University, Vilnius LT-02241, Lithuania
| | - Saulius Klimašauskas
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-02241, Lithuania
| | - Giedrius Vilkaitis
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-02241, Lithuania
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Abstract
Grasses bear unique flowers lacking obvious petals and sepals in special inflorescence units, the florets and the spikelet. Despite this, grass floral organs such as stamens and lodicules (petal homologs) are specified by ABC homeotic genes encoding MADS domain transcription factors, suggesting that the ABC model of eudicot flower development is largely applicable to grass flowers. However, some modifications need to be made for the model to fit grasses well: for example, a YABBY gene plays an important role in carpel specification. In addition, a number of genes are involved in the development of the lateral organs that constitute the spikelet. In this review, we discuss recent progress in elucidating the genes required for flower and spikelet development in grasses, together with those involved in fate determination of the spikelet and flower meristems.
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Affiliation(s)
- Hiro-Yuki Hirano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan,
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Shi J, Dong A, Shen WH. Epigenetic regulation of rice flowering and reproduction. FRONTIERS IN PLANT SCIENCE 2014; 5:803. [PMID: 25674094 PMCID: PMC4309181 DOI: 10.3389/fpls.2014.00803] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 12/22/2014] [Indexed: 05/19/2023]
Abstract
Current understanding of the epigenetic regulator roles in plant growth and development has largely derived from studies in the dicotyledonous model plant Arabidopsis thaliana. Rice (Oryza sativa) is one of the most important food crops in the world and has more recently becoming a monocotyledonous model plant in functional genomics research. During the past few years, an increasing number of studies have reported the impact of DNA methylation, non-coding RNAs and histone modifications on transcription regulation, flowering time control, and reproduction in rice. Here, we review these studies to provide an updated complete view about chromatin modifiers characterized in rice and in particular on their roles in epigenetic regulation of flowering time, reproduction, and seed development.
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Affiliation(s)
- Jinlei Shi
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan UniversityShanghai, China
- CNRS, Institut de Biologie Moléculaire des Plantes, Université de StrasbourgStrasbourg, France
| | - Aiwu Dong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan UniversityShanghai, China
| | - Wen-Hui Shen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan UniversityShanghai, China
- CNRS, Institut de Biologie Moléculaire des Plantes, Université de StrasbourgStrasbourg, France
- *Correspondence: Wen-Hui Shen, CNRS, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 12 Rue du Général Zimmer, 67084 Strasbourg Cédex, France e-mail:
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Li X, Lei M, Yan Z, Wang Q, Chen A, Sun J, Luo D, Wang Y. The REL3-mediated TAS3 ta-siRNA pathway integrates auxin and ethylene signaling to regulate nodulation in Lotus japonicus. THE NEW PHYTOLOGIST 2014; 201:531-544. [PMID: 24164597 DOI: 10.1111/nph.12550] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 09/10/2013] [Indexed: 05/04/2023]
Abstract
The ta-siRNA pathway is required for lateral organ development, including leaf patterning, flower differentiation and lateral root growth. Legumes can develop novel lateral root organs--nodules--resulting from symbiotic interactions with rhizobia. However, ta-siRNA regulation in nodule formation remains unknown. To explore ta-siRNA regulation in nodule formation, we investigated the roles of REL3, a key component of TAS3 ta-siRNA biogenesis, during nodulation in Lotus japonicus. We characterized the symbiotic phenotypes of the TAS3 ta-siRNA defective rel3 mutant, and analyzed the responses of the rel3 mutant to auxin and ethylene in order to gain insight into TAS3 ta-siRNA regulation of nodulation. The rel3 mutant produced fewer pink nitrogen-fixing nodules, with substantially decreased infection frequency and nodule initiation. Moreover, the rel3 mutant was more resistant than wild-type to 1-naphthaleneacetic acid (NAA) and N-1-naphthylphthalamic acid (NPA) in root growth, and exhibited insensitivity to auxins but greater sensitivity to auxin transport inhibitors during nodulation. Furthermore, the rel3 mutant has enhanced root-specific ethylene sensitivity and altered responses to ethylene during nodulation; the low-nodulating phenotype of the rel3 mutant can be restored by ethylene synthesis inhibitor L-α-(2-aminoethoxyvinyl)-glycine (AVG) or action inhibitor Ag(+). The REL3-mediated TAS3 ta-siRNA pathway regulates nodulation by integrating ethylene and auxin signaling.
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Affiliation(s)
- Xiaolin Li
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Mingjuan Lei
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhongyuan Yan
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Qi Wang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Aimin Chen
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jie Sun
- The key Laboratory of Oasis Eco-agriculture, Agriculture College of Shihezi University, Shihezi, 832003, China
| | - Da Luo
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yanzhang Wang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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Anderson SN, Johnson CS, Jones DS, Conrad LJ, Gou X, Russell SD, Sundaresan V. Transcriptomes of isolated Oryza sativa gametes characterized by deep sequencing: evidence for distinct sex-dependent chromatin and epigenetic states before fertilization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:729-41. [PMID: 24215296 DOI: 10.1111/tpj.12336] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 09/12/2013] [Accepted: 09/19/2013] [Indexed: 05/19/2023]
Abstract
The formation of a zygote by the fusion of egg and sperm involves the two gametic transcriptomes. In flowering plants, the embryo sac embedded within the ovule contains the egg cell, whereas the pollen grain contains two sperm cells inside a supporting vegetative cell. The difficulties of collecting isolated gametes and consequent low recovery of RNA have restricted in-depth analysis of gametic transcriptomes in flowering plants. We isolated living egg cells, sperm cells and pollen vegetative cells from Oryza sativa (rice), and identified transcripts for approximately 36 000 genes by deep sequencing. The three transcriptomes are highly divergent, with about three-quarters of those genes differentially expressed in the different cell types. Distinctive expression profiles were observed for genes involved in chromatin conformation, including an unexpected expression in the sperm cell of genes associated with active chromatin. Furthermore, both the sperm cell and the pollen vegetative cell were deficient in expression of key RNAi components. Differences in gene expression were also observed for genes for hormonal signaling and cell cycle regulation. The egg cell and sperm cell transcriptomes reveal major differences in gene expression to be resolved in the zygote, including pathways affecting chromatin configuration, hormones and cell cycle. The sex-specific differences in the expression of RNAi components suggest that epigenetic silencing in the zygote might act predominantly through female-dependent pathways. More generally, this study provides a detailed gene expression landscape for flowering plant gametes, enabling the identification of specific gametic functions, and their contributions to zygote and seed development.
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Affiliation(s)
- Sarah N Anderson
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
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Role of the Trypanosoma brucei HEN1 family methyltransferase in small interfering RNA modification. EUKARYOTIC CELL 2013; 13:77-86. [PMID: 24186950 DOI: 10.1128/ec.00233-13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Parasitic protozoa of the flagellate order Kinetoplastida represent one of the deepest branches of the eukaryotic tree. Among this group of organisms, the mechanism of RNA interference (RNAi) has been investigated in Trypanosoma brucei and to a lesser degree in Leishmania (Viannia) spp. The pathway is triggered by long double-stranded RNA (dsRNA) and in T. brucei requires a set of five core genes, including a single Argonaute (AGO) protein, T. brucei AGO1 (TbAGO1). The five genes are conserved in Leishmania (Viannia) spp. but are absent in other major kinetoplastid species, such as Trypanosoma cruzi and Leishmania major. In T. brucei small interfering RNAs (siRNAs) are methylated at the 3' end, whereas Leishmania (Viannia) sp. siRNAs are not. Here we report that T. brucei HEN1, an ortholog of the metazoan HEN1 2'-O-methyltransferases, is required for methylation of siRNAs. Loss of TbHEN1 causes a reduction in the length of siRNAs. The shorter siRNAs in hen1(-/-) parasites are single stranded and associated with TbAGO1, and a subset carry a nontemplated uridine at the 3' end. These findings support a model wherein TbHEN1 methylates siRNA 3' ends after they are loaded into TbAGO1 and this methylation protects siRNAs from uridylation and 3' trimming. Moreover, expression of TbHEN1 in Leishmania (Viannia) panamensis did not result in siRNA 3' end methylation, further emphasizing mechanistic differences in the trypanosome and Leishmania RNAi mechanisms.
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45
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Mechanistic insights into small RNA recognition and modification by the HEN1 methyltransferase. Biochem J 2013; 453:281-90. [PMID: 23621770 DOI: 10.1042/bj20121699] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The HEN1 methyltransferase from Arabidopsis thaliana modifies the 3'-terminal nucleotides of small regulatory RNAs. Although it is one of the best characterized members of the 2'-O-methyltransferase family, many aspects of its interactions with the cofactor and substrate RNA remained unresolved. To better understand the substrate interactions and contributions of individual steps during HEN1 catalysis, we studied the binding and methylation kinetics of the enzyme using a series of unmethylated, hemimethylated and doubly methylated miRNA and siRNA substrates. The present study shows that HEN1 specifically binds double-stranded unmethylated or hemimethylated miR173/miR173* substrates with a subnanomolar affinity in a cofactor-dependent manner. Kinetic studies under single turnover and pre-steady state conditions in combination with isotope partitioning analysis showed that the binary HEN1-miRNA/miRNA* complex is catalytically competent; however, successive methylation of the two strands in a RNA duplex occurs in a non-processive (distributive) manner. We also find that the observed moderate methylation strand preference is largely exerted at the RNA-binding step and is fairly independent of the nature of the 3'-terminal nucleobase, but shows some dependency on proximal nucleotide mispairs. The results of the present study thus provide novel insights into the mechanism of RNA recognition and modification by a representative small RNA 2'-O-methyltransferase.
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46
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Rogers K, Chen X. Biogenesis, turnover, and mode of action of plant microRNAs. THE PLANT CELL 2013; 25:2383-99. [PMID: 23881412 PMCID: PMC3753372 DOI: 10.1105/tpc.113.113159] [Citation(s) in RCA: 583] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 04/25/2013] [Accepted: 07/08/2013] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are small RNAs that control gene expression through silencing of target mRNAs. Mature miRNAs are processed from primary miRNA transcripts by the endonuclease activity of the DICER-LIKE1 (DCL1) protein complex. Mechanisms exist that allow the DCL1 complex to precisely excise the miRNA from its precursor. Our understanding of miRNA biogenesis, particularly its intersection with transcription and other aspects of RNA metabolism such as splicing, is still evolving. Mature miRNAs are incorporated into an ARGONAUTE (AGO) effector complex competent for target gene silencing but are also subjected to turnover through a degradation mechanism that is beginning to be understood. The mechanisms of miRNA target silencing in plants are no longer limited to AGO-catalyzed slicing, and the contribution of translational inhibition is increasingly appreciated. Here, we review the mechanisms underlying the biogenesis, turnover, and activities of plant miRNAs.
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Affiliation(s)
- Kestrel Rogers
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
- Howard Hughes Medical Institute, University of California, Riverside, California 92521
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47
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Zhai J, Zhao Y, Simon SA, Huang S, Petsch K, Arikit S, Pillay M, Ji L, Xie M, Cao X, Yu B, Timmermans M, Yang B, Chen X, Meyers BC. Plant microRNAs display differential 3' truncation and tailing modifications that are ARGONAUTE1 dependent and conserved across species. THE PLANT CELL 2013; 25:2417-28. [PMID: 23839787 PMCID: PMC3753374 DOI: 10.1105/tpc.113.114603] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 06/06/2013] [Accepted: 06/20/2013] [Indexed: 05/18/2023]
Abstract
Plant small RNAs are 3' methylated by the methyltransferase HUA1 ENHANCER1 (HEN1). In plant hen1 mutants, 3' modifications of small RNAs, including oligo-uridylation (tailing), are associated with accelerated degradation of microRNAs (miRNAs). By sequencing small RNAs of the wild type and hen1 mutants from Arabidopsis thaliana, rice (Oryza sativa), and maize (Zea mays), we found 3' truncation prior to tailing is widespread in these mutants. Moreover, the patterns of miRNA truncation and tailing differ substantially among miRNA families but are conserved across species. The same patterns are also observable in wild-type libraries from a broad range of species, only at lower abundances. ARGONAUTE (AGO1), even with defective slicer activity, can bind these truncated and tailed variants of miRNAs. An ago1 mutation in hen1 suppressed such 3' modifications, indicating that they occur while miRNAs are in association with AGO1, either during or after RNA-induced silencing complex assembly. Our results showed AGO1-bound miRNAs are actively 3' truncated and tailed, possibly reflecting the activity of cofactors acting in conserved patterns in miRNA degradation.
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Affiliation(s)
- Jixian Zhai
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711
| | - Yuanyuan Zhao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Stacey A. Simon
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711
| | - Sheng Huang
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Katherine Petsch
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Siwaret Arikit
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711
| | - Manoj Pillay
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711
| | - Lijuan Ji
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Meng Xie
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Yu
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588
| | - Marja Timmermans
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Bing Yang
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
- Howard Hughes Medical Institute, University of California, Riverside, California 92521
| | - Blake C. Meyers
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711
- Address correspondence to
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Abstract
MicroRNAs (miRNAs) regulate the expression of most genes in animals, but we are only now beginning to understand how they are generated, assembled into functional complexes and destroyed. Various mechanisms have now been identified that regulate miRNA stability and that diversify miRNA sequences to create distinct isoforms. The production of different isoforms of individual miRNAs in specific cells and tissues may have broader implications for miRNA-mediated gene expression control. Rigorously testing the many discrepant models for how miRNAs function using quantitative biochemical measurements made in vivo and in vitro remains a major challenge for the future.
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Arikit S, Zhai J, Meyers BC. Biogenesis and function of rice small RNAs from non-coding RNA precursors. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:170-9. [PMID: 23466255 DOI: 10.1016/j.pbi.2013.01.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 01/30/2013] [Indexed: 05/20/2023]
Abstract
Non-coding RNAs, especially small RNAs, play important roles in many biological processes. Several small RNA types, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), are well-described in rice (Oryza sativa), although much remains to be learned about their function. Many small RNAs along with their targets have been characterized with deep sequencing technologies. Some special classes of these small RNAs have been found to be unique to rice or within the larger group of grasses. The functional and biological roles of numerous plants small RNAs have been described in detail, including functions as varied as the regulation of tissue development, phase transition, or abiotic and biotic stress resistance. Mutant analysis has proven useful in the genetic identification of components involved in small RNA biogenesis and also in identification of regulatory functions of small RNAs. Although many small RNAs have been identified by deep sequencing in rice, their precise regulatory functions and cell-type specificity are in many cases still unknown.
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Affiliation(s)
- Siwaret Arikit
- Department of Plant & Soil Sciences, and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
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Zhang J, Zhang S, Li S, Han S, Wu T, Li X, Qi L. A genome-wide survey of microRNA truncation and 3' nucleotide addition events in larch (Larix leptolepis). PLANTA 2013; 237:1047-56. [PMID: 23232766 DOI: 10.1007/s00425-012-1823-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 11/26/2012] [Indexed: 05/15/2023]
Abstract
MicroRNAs (miRNAs) play essential roles in numerous developmental and metabolic processes in animals and plants. Although the framework of miRNA biogenesis and function is established, the mechanism of miRNA degradation or modification remains to be investigated in plants. Mature miRNAs may be truncated or added nucleotides to generate variants. A detailed analysis of small RNA deep sequencing data sets resulted in the cloning of a large number of variants derived from larch miRNAs. Many 5'- and/or 3'-end truncated versions of miRNAs suggested that larch miRNAs might be degraded through either 5'-3' or 3'-5'. The relative abundance of variants truncated from 3'-end was higher than that of 5'-end for most miRNAs. The addition of adenine, uridine, and cytidine to the 3'-end of miRNAs was globally present, and the subtle variability in isomiR abundance might be regulated and biologically meaningful. It is the first report for cytidine addition in plant, and our examination of published small RNA deep sequencing data sets of Arabidopsis, rice, and moss suggests that cytidine addition to miRNA 3'-end exists broadly in plants. In addition, the nucleotide addition might be associated with 3'-5' miRNA degradation. Our results provide valuable information for a genome-wide survey of miRNA truncation and modification in larch or plants.
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Affiliation(s)
- Junhong Zhang
- Laboratory of Cell Biology, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China.
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