1
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Buhagiar AF, Kleaveland B. To kill a microRNA: emerging concepts in target-directed microRNA degradation. Nucleic Acids Res 2024; 52:1558-1574. [PMID: 38224449 PMCID: PMC10899785 DOI: 10.1093/nar/gkae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/21/2023] [Accepted: 01/02/2024] [Indexed: 01/16/2024] Open
Abstract
MicroRNAs (miRNAs) guide Argonaute (AGO) proteins to bind mRNA targets. Although most targets are destabilized by miRNA-AGO binding, some targets induce degradation of the miRNA instead. These special targets are also referred to as trigger RNAs. All triggers identified thus far have binding sites with greater complementarity to the miRNA than typical target sites. Target-directed miRNA degradation (TDMD) occurs when trigger RNAs bind the miRNA-AGO complex and recruit the ZSWIM8 E3 ubiquitin ligase, leading to AGO ubiquitination and proteolysis and subsequent miRNA destruction. More than 100 different miRNAs are regulated by ZSWIM8 in bilaterian animals, and hundreds of trigger RNAs have been predicted computationally. Disruption of individual trigger RNAs or ZSWIM8 has uncovered important developmental and physiologic roles for TDMD across a variety of model organisms and cell types. In this review, we highlight recent progress in understanding the mechanistic basis and functions of TDMD, describe common features of trigger RNAs, outline best practices for validating trigger RNAs, and discuss outstanding questions in the field.
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Affiliation(s)
- Amber F Buhagiar
- Department of Pathology and Lab Medicine, Weill Cornell Medicine, New York, NY10065, USA
| | - Benjamin Kleaveland
- Department of Pathology and Lab Medicine, Weill Cornell Medicine, New York, NY10065, USA
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2
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Rieu P, Arnoux-Courseaux M, Tichtinsky G, Parcy F. Thinking outside the F-box: how UFO controls angiosperm development. THE NEW PHYTOLOGIST 2023; 240:945-959. [PMID: 37664990 DOI: 10.1111/nph.19234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/19/2023] [Indexed: 09/05/2023]
Abstract
The formation of inflorescences and flowers is essential for the successful reproduction of angiosperms. In the past few decades, genetic studies have identified the LEAFY transcription factor and the UNUSUAL FLORAL ORGANS (UFO) F-box protein as two major regulators of flower development in a broad range of angiosperm species. Recent research has revealed that UFO acts as a transcriptional cofactor, redirecting the LEAFY floral regulator to novel cis-elements. In this review, we summarize the various roles of UFO across species, analyze past results in light of new discoveries and highlight the key questions that remain to be solved.
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Affiliation(s)
- Philippe Rieu
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 ave des martyrs, F-38054, Grenoble, France
| | - Moïra Arnoux-Courseaux
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 ave des martyrs, F-38054, Grenoble, France
| | - Gabrielle Tichtinsky
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 ave des martyrs, F-38054, Grenoble, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 ave des martyrs, F-38054, Grenoble, France
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3
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Othman SMIS, Mustaffa AF, Che-Othman MH, Samad AFA, Goh HH, Zainal Z, Ismail I. Overview of Repressive miRNA Regulation by Short Tandem Target Mimic (STTM): Applications and Impact on Plant Biology. PLANTS (BASEL, SWITZERLAND) 2023; 12:669. [PMID: 36771753 PMCID: PMC9918958 DOI: 10.3390/plants12030669] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The application of miRNA mimic technology for silencing mature miRNA began in 2007. This technique originated from the discovery of the INDUCED BY PHOSPHATE STARVATION 1 (IPS1) gene, which was found to be a competitive mimic that prevents the cleavage of the targeted mRNA by miRNA inhibition at the post-transcriptional level. To date, various studies have been conducted to understand the molecular mimic mechanism and to improve the efficiency of this technology. As a result, several mimic tools have been developed: target mimicry (TM), short tandem target mimic (STTM), and molecular sponges (SPs). STTM is the most-developed tool due to its stability and effectiveness in decoying miRNA. This review discusses the application of STTM technology on the loss-of-function studies of miRNA and members from diverse plant species. A modified STTM approach for studying the function of miRNA with spatial-temporal expression under the control of specific promoters is further explored. STTM technology will enhance our understanding of the miRNA activity in plant-tissue-specific development and stress responses for applications in improving plant traits via miRNA regulation.
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Affiliation(s)
- Syed Muhammad Iqbal Syed Othman
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Arif Faisal Mustaffa
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - M. Hafiz Che-Othman
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Abdul Fatah A. Samad
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai, Johor Bahru 81310, Johor, Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Zamri Zainal
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Ismanizan Ismail
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
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4
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Han J, Mendell JT. MicroRNA turnover: a tale of tailing, trimming, and targets. Trends Biochem Sci 2023; 48:26-39. [PMID: 35811249 PMCID: PMC9789169 DOI: 10.1016/j.tibs.2022.06.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/06/2022] [Accepted: 06/13/2022] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) post-transcriptionally repress gene expression by guiding Argonaute (AGO) proteins to target mRNAs. While much is known about the regulation of miRNA biogenesis, miRNA degradation pathways are comparatively poorly understood. Although miRNAs generally exhibit slow turnover, they can be rapidly degraded through regulated mechanisms that act in a context- or sequence-specific manner. Recent work has revealed a particularly important role for specialized target interactions in controlling rates of miRNA degradation. Engagement of these targets is associated with the addition and removal of nucleotides from the 3' ends of miRNAs, a process known as tailing and trimming. Here we review these mechanisms of miRNA modification and turnover, highlighting the contexts in which they impact miRNA stability and discussing important questions that remain unanswered.
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Affiliation(s)
- Jaeil Han
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Joshua T Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA.
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5
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Li H, You C, Yoshikawa M, Yang X, Gu H, Li C, Cui J, Chen X, Ye N, Zhang J, Wang G. A spontaneous thermo-sensitive female sterility mutation in rice enables fully mechanized hybrid breeding. Cell Res 2022; 32:931-945. [PMID: 36068348 PMCID: PMC9525692 DOI: 10.1038/s41422-022-00711-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 08/08/2022] [Indexed: 11/08/2022] Open
Abstract
Male sterility enables hybrid crop breeding to increase yields and has been extensively studied. But thermo-sensitive female sterility, which is an ideal property that may enable full mechanization in hybrid rice breeding, has rarely been investigated due to the absence of such germplasm. Here we identify the spontaneous thermo-sensitive female sterility 1 (tfs1) mutation that confers complete sterility under regular/high temperature and partial fertility under low temperature as a point mutation in ARGONAUTE7 (AGO7). AGO7 associates with miR390 to form an RNA-Induced Silencing Complex (RISC), which triggers the biogenesis of small interfering RNAs (siRNAs) from TRANS-ACTING3 (TAS3) loci by recruiting SUPPRESSOR OF GENE SILENCING (SGS3) and RNA-DEPENDENT RNA POLYMERASE6 (RDR6) to TAS3 transcripts. These siRNAs are known as tasiR-ARFs as they act in trans to repress auxin response factor genes. The mutant TFS1 (mTFS1) protein is compromised in its ability to load the miR390/miR390* duplex and eject miR390* during RISC formation. Furthermore, tasiR-ARF levels are reduced in tfs1 due to the deficiency in RDR6 but not SGS3 recruitment by mTFS1 RISC under regular/high temperature, while low temperature partially restores mTFS1 function in RDR6 recruitment and tasiR-ARF biogenesis. A miR390 mutant also exhibits female sterility, suggesting that female fertility is controlled by the miR390-AGO7 module. Notably, the tfs1 allele introduced into various elite rice cultivars endows thermo-sensitive female sterility. Moreover, field trials confirm the utility of tfs1 as a restorer line in fully mechanized hybrid rice breeding.
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Affiliation(s)
- Haoxuan Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agriculture, Hunan Agricultural University, Changsha, Hunan, China
| | - Chenjiang You
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Manabu Yoshikawa
- Division of Plant and Microbial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai Tsukuba, Ibaraki, Japan
| | - Xiaoyu Yang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, China
| | - Haiyong Gu
- The Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Chuanguo Li
- The Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Jie Cui
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA.
| | - Nenghui Ye
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agriculture, Hunan Agricultural University, Changsha, Hunan, China.
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
| | - Guanqun Wang
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
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Varshney V, Majee M. Emerging roles of the ubiquitin-proteasome pathway in enhancing crop yield by optimizing seed agronomic traits. PLANT CELL REPORTS 2022; 41:1805-1826. [PMID: 35678849 DOI: 10.1007/s00299-022-02884-9] [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: 11/18/2021] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Ubiquitin-proteasome pathway has the potential to modulate crop productivity by influencing agronomic traits. Being sessile, the plant often uses the ubiquitin-proteasome pathway to maintain the stability of different regulatory proteins to survive in an ever-changing environment. The ubiquitin system influences plant reproduction, growth, development, responses to the environment, and processes that control critical agronomic traits. E3 ligases are the major players in this pathway, and they are responsible for recognizing and tagging the targets/substrates. Plants have a variety of E3 ubiquitin ligases, whose functions have been studied extensively, ranging from plant growth to defense strategies. Here we summarize three agronomic traits influenced by ubiquitination: seed size and weight, seed germination, and accessory plant agronomic traits particularly panicle architecture, tillering in rice, and tassels branch number in maize. This review article highlights some recent progress on how the ubiquitin system influences the stability/modification of proteins that determine seed agronomic properties like size, weight, germination and filling, and ultimately agricultural productivity and quality. Further research into the molecular basis of the aforementioned processes might lead to the identification of genes that could be modified or selected for crop development. Likewise, we also propose advances and future perspectives in this regard.
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Affiliation(s)
- Vishal Varshney
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Majee
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Zhang L, Xiang Y, Chen S, Shi M, Jiang X, He Z, Gao S. Mechanisms of MicroRNA Biogenesis and Stability Control in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:844149. [PMID: 35350301 PMCID: PMC8957957 DOI: 10.3389/fpls.2022.844149] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
MicroRNAs (miRNAs), a class of endogenous, non-coding RNAs, which is 20-24 nucleotide long, regulate the expression of its target genes post-transcriptionally and play critical roles in plant normal growth, development, and biotic and abiotic stresses. In cells, miRNA biogenesis and stability control are important in regulating intracellular miRNA abundance. In addition, research on these two aspects has achieved fruitful results. In this review, we focus on the recent research progress in our understanding of miRNA biogenesis and their stability control in plants.
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Affiliation(s)
- Lu Zhang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Yu Xiang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Shengbo Chen
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Min Shi
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Xianda Jiang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Zhuoli He
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Shuai Gao
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
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8
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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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Nagata T, Lombardo F, Ezura H. Complementation of the tomato HWS gene with its Arabidopsis counterpart demonstrates conservation of the gene function between both species. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:387-390. [PMID: 34782827 PMCID: PMC8562581 DOI: 10.5511/plantbiotechnology.21.0729a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
The HAWAIIAN SKIRT (HWS) gene was originally described in Arabidopsis for the characteristic fusion of sepals in the mutant. A tomato line mutated in the putative ortholog gene was isolated in a previous study. The tomato hws-1 mutant showed facultative parthenocarpy and produced fruits with elevated Brix, revealing the gene as a hopeful resource for crop improvement. To confirm the orthology relationship between the Arabidopsis and tomato HWS genes, the hws-1 mutant was complemented with either the tomato wild-type genomic fragment or the Arabidopsis sequence of the gene. In both complementation experiments, defective phenotypes of hws-1 are rescued, albeit to different extents. Recovery of these phenotypes, which include parthenocarpic fruit production, increased Brix, loss of leaflet serration, alteration of bud and petal shape, firmly establishes SlHWS as an ortholog of the originally described HWS in Arabidopsis. This work indicates that the function of HWS is likely to be conserved in a wide range of plant species.
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Affiliation(s)
- Toshifumi Nagata
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Fabien Lombardo
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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10
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Lombardo F, Gramazio P, Ezura H. Increase in Phloem Area in the Tomato hawaiian skirt Mutant Is Associated with Enhanced Sugar Transport. Genes (Basel) 2021; 12:genes12060932. [PMID: 34207298 PMCID: PMC8234570 DOI: 10.3390/genes12060932] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 11/29/2022] Open
Abstract
The HAWAIIAN SKIRT (HWS) gene has been described in Arabidopsis, rice, tomato and poplar where it seems to perform distinct functions with relatively little overlap. In tomato, alteration of the gene function confers facultative parthenocarpy, thought to be a consequence of changes in the microRNA metabolism. In the rice mutant, improvement in panicle architecture is associated with an increase in grain yield. Knowing that hws tomato fruits show a higher Brix level, it was suspected that vascular bundles might also be altered in this species, in a similar fashion to the rice phenotype. The pedicel structure of the hws-1 line was therefore examined under the microscope and sugar concentrations from phloem exudate were determined in an enzymatic assay. A distinct increase in the phloem area was observed as well as a higher sugar content in mutant phloem exudates, which is hypothesized to contribute to the high Brix level in the mutant fruits. Furthermore, the described phenotype in this study bridges the gap between Arabidopsis and rice phenotypes, suggesting that the modulation of the microRNA metabolism by HWS influences traits of agricultural interest across several species.
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Affiliation(s)
- Fabien Lombardo
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan;
- Correspondence:
| | - Pietro Gramazio
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan;
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan;
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba 305-8572, Japan;
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11
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Chen M, Fan W, Ji F, Hua H, Liu J, Yan M, Ma Q, Fan J, Wang Q, Zhang S, Liu G, Sun Z, Tian C, Zhao F, Zheng J, Zhang Q, Chen J, Qiu J, Wei X, Chen Z, Zhang P, Pei D, Yang J, Huang X. Genome-wide identification of agronomically important genes in outcrossing crops using OutcrossSeq. MOLECULAR PLANT 2021; 14:556-570. [PMID: 33429094 DOI: 10.1016/j.molp.2021.01.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/07/2020] [Accepted: 01/06/2021] [Indexed: 05/27/2023]
Abstract
Many important crops (e.g., tuber, root, and tree crops) are cross-pollinating. For these crops, no inbred lines are available for genetic study and breeding because they are self-incompatible, clonally propagated, or have a long generation time, making the identification of agronomically important genes difficult, particularly in crops with a complex autopolyploid genome. In this study, we developed a method, OutcrossSeq, for mapping agronomically important loci in outcrossing crops based on whole-genome low-coverage resequencing of a large genetic population, and designed three computation algorithms in OutcrossSeq for different types of outcrossing populations. We applied OutcrossSeq to a tuberous root crop (sweet potato, autopolyploid), a tree crop (walnut tree, highly heterozygous diploid), and hybrid crops (double-cross populations) to generate high-density genotype maps for the outcrossing populations, which enable precise identification of genomic loci underlying important agronomic traits. Candidate causative genes at these loci were detected based on functional clues. Taken together, our results indicate that OutcrossSeq is a robust and powerful method for identifying agronomically important genes in heterozygous species, including polyploids, in a cost-efficient way. The OutcrossSeq software and its instruction manual are available for downloading at www.xhhuanglab.cn/tool/OutcrossSeq.html.
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Affiliation(s)
- Mengjiao Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Weijuan Fan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Feiyang Ji
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Hua Hua
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jie Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Mengxiao Yan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Qingguo Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Jiongjiong Fan
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Qin Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Shufeng Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Guiling Liu
- Tai'an Academy of Agricultural Sciences, Tai'an 271000, Shandong, China
| | - Zhe Sun
- Tai'an Academy of Agricultural Sciences, Tai'an 271000, Shandong, China
| | - Changgeng Tian
- Tai'an Academy of Agricultural Sciences, Tai'an 271000, Shandong, China
| | - Fengling Zhao
- Tai'an Academy of Agricultural Sciences, Tai'an 271000, Shandong, China
| | - Jianli Zheng
- Tai'an Academy of Agricultural Sciences, Tai'an 271000, Shandong, China
| | - Qi Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jiaxin Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xin Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Ziru Chen
- National Genomics Data Center, Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Peng Zhang
- CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
| | - Dong Pei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China.
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
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12
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Cambiagno DA, Giudicatti AJ, Arce AL, Gagliardi D, Li L, Yuan W, Lundberg DS, Weigel D, Manavella PA. HASTY modulates miRNA biogenesis by linking pri-miRNA transcription and processing. MOLECULAR PLANT 2021; 14:426-439. [PMID: 33385584 DOI: 10.1016/j.molp.2020.12.019] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/29/2020] [Accepted: 12/28/2020] [Indexed: 05/23/2023]
Abstract
Post-transcriptional gene silencing mediated by microRNAs (miRNAs) modulates numerous developmental and stress response pathways. For the last two decades, HASTY (HST), the ortholog of human EXPORTIN 5, was considered to be a candidate protein that exports plant miRNAs from the nucleus to the cytoplasm. Here, we report that HST functions in the miRNA pathway independent of its cargo-exporting activity in Arabidopsis. We found that Arabidopsis mutants with impaired HST shuttling exhibit normal subcellular distribution of miRNAs. Interestingly, protein-protein interaction and microscopy assays showed that HST directly interacts with the microprocessor core component DCL1 through its N-terminal domain. Moreover, mass spectrometry analysis revealed that HST also interacts independently of its N-terminal domain with the mediator complex subunit MED37. Further experiments revealed that HST could act as a scaffold to facilitate the recruitment of DCL1 to genomic MIRNA loci by stabilizing the DCL1-MED37 complex, which in turn promotes the transcription and proper processing of primary miRNA transcripts (pri-miRNAs). Taken together, these results suggest that HST is likely associated with the formation of the miRNA biogenesis complex at MIRNA genes, promoting the transcription and processing of pri-miRNAs rather than the direct export of processed miRNAs from the nucleus.
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Affiliation(s)
- Damian A Cambiagno
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Axel J Giudicatti
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Agustin L Arce
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Delfina Gagliardi
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Lei Li
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Wei Yuan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Derek S Lundberg
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
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13
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Giudicatti AJ, Tomassi AH, Manavella PA, Arce AL. Extensive Analysis of miRNA Trimming and Tailing Indicates that AGO1 Has a Complex Role in miRNA Turnover. PLANTS 2021; 10:plants10020267. [PMID: 33573197 PMCID: PMC7911489 DOI: 10.3390/plants10020267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 12/14/2022]
Abstract
MicroRNAs are small regulatory RNAs involved in several processes in plants ranging from development and stress responses to defense against pathogens. In order to accomplish their molecular functions, miRNAs are methylated and loaded into one ARGONAUTE (AGO) protein, commonly known as AGO1, to stabilize and protect the molecule and to assemble a functional RNA-induced silencing complex (RISC). A specific machinery controls miRNA turnover to ensure the silencing release of targeted-genes in given circumstances. The trimming and tailing of miRNAs are fundamental modifications related to their turnover and, hence, to their action. In order to gain a better understanding of these modifications, we analyzed Arabidopsis thaliana small RNA sequencing data from a diversity of mutants, related to miRNA biogenesis, action, and turnover, and from different cellular fractions and immunoprecipitations. Besides confirming the effects of known players in these pathways, we found increased trimming and tailing in miRNA biogenesis mutants. More importantly, our analysis allowed us to reveal the importance of ARGONAUTE 1 (AGO1) loading, slicing activity, and cellular localization in trimming and tailing of miRNAs.
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14
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Chen J, Teotia S, Lan T, Tang G. MicroRNA Techniques: Valuable Tools for Agronomic Trait Analyses and Breeding in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:744357. [PMID: 34616418 PMCID: PMC8489592 DOI: 10.3389/fpls.2021.744357] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/16/2021] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) are a class of small noncoding RNAs that regulate gene expression at the post-transcriptional level. Extensive studies have revealed that miRNAs have critical functions in plant growth, development, and stress responses and may provide valuable genetic resources for plant breeding research. We herein reviewed the development, mechanisms, and characteristics of miRNA techniques while highlighting widely used approaches, namely, the short tandem target mimic (STTM) approach. We described STTM-based advances in plant science, especially in the model crop rice, and introduced the CRISPR-based transgene-free crop breeding. Finally, we discussed the challenges and unique opportunities related to combining STTM and CRISPR technology for crop improvement and agriculture.
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Affiliation(s)
- Jiwei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Sachin Teotia
- Department of Biotechnology, Sharda University, Greater Noida, India
| | - Ting Lan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
- *Correspondence: Ting Lan,
| | - Guiliang Tang
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI, United States
- Guiliang Tang,
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15
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Abd-Hamid NA, Ahmad-Fauzi MI, Zainal Z, Ismail I. Diverse and dynamic roles of F-box proteins in plant biology. PLANTA 2020; 251:68. [PMID: 32072251 DOI: 10.1007/s00425-020-03356-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 02/05/2020] [Indexed: 05/23/2023]
Abstract
The SCF complex is a widely studied multi-subunit ring E3 ubiquitin ligase that tags targeted proteins with ubiquitin for protein degradation by the ubiquitin 26S-proteasome system (UPS). The UPS is an important system that generally keeps cellular events tightly regulated by purging misfolded or damaged proteins and selectively degrading important regulatory proteins. The specificity of this post-translational regulation is controlled by F-box proteins (FBPs) via selective recognition of a protein-protein interaction motif at the C-terminal domain. Hence, FBPs are pivotal proteins in determining the plant response in multiple scenarios. It is not surprising that the FBP family is one of the largest protein families in the plant kingdom. In this review, the roles of FBPs, specifically in plants, are compiled to provide insights into their involvement in secondary metabolites, plant stresses, phytohormone signalling, plant developmental processes and miRNA biogenesis.
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Affiliation(s)
- Nur-Athirah Abd-Hamid
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Muhammad-Izzat Ahmad-Fauzi
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Zamri Zainal
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ismanizan Ismail
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
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16
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Mei J, Jiang N, Ren G. The F-box protein HAWAIIAN SKIRT is required for mimicry target-induced microRNA degradation in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:1121-1127. [PMID: 30565372 DOI: 10.1111/jipb.12761] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 12/10/2018] [Indexed: 05/02/2023]
Abstract
Mimicry target-directed microRNA degradation is widespread and highly conserved among eukaryotes. However, little is known about its mechanism of action. In this letter, by using STTM160 (target mimic of miR160) as a reporter, we show that dysfunction of HAWAIIAN SKIRT (HWS) suppresses the pleiotropic phenotype of STTM160. Small RNA sequencing and Northern blot analyses suggested that HWS only affects a subset of microRNAs. Intriguingly, we identified a stable coexistence of miR160/miR399 and their mimicry targets within the AGO1 complex when HWS is compromised, pointing to a possible role of HWS in the clearance of RNA-induced silencing complexes associated with mimicry target.
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Affiliation(s)
- Jun Mei
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ning Jiang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Laboratory of Population & Quantitative Genetics, Institute of Genetics and Biostatistics, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Guodong Ren
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
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17
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Li J, Chen C, Wei J, Pan Y, Su C, Zhang X. SpPKE1, a Multiple Stress-Responsive Gene Confers Salt Tolerance in Tomato and Tobacco. Int J Mol Sci 2019; 20:E2478. [PMID: 31137458 PMCID: PMC6566969 DOI: 10.3390/ijms20102478] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/15/2019] [Accepted: 05/17/2019] [Indexed: 01/25/2023] Open
Abstract
Understanding the mechanism of abiotic-tolerance and producing germplasm of abiotic tolerance are important in plant research. Wild species often show more tolerance of environmental stress factors than their cultivated counterparts. Genes from wild species show potential abilities to improve abiotic resistance in cultivated species. Here, a tomato proline-, lysine-, and glutamic-rich type gene SpPKE1 was isolated from abiotic-resistant species (Solanum pennellii LA0716) for over-expression in tomato and tobacco for salt tolerance. The protein encoded by SpPKE1 was predominantly localized in the cytoplasm in tobacco. SpPKE1 and SlPKE1 (from cultivated species S. lycopersicum cv. M82) shared 89.7% similarity in amino acid sequences and their transcripts abundance in flowers and fruits was reduced by the imposition of drought or oxidative stress and the exogenous supply of abscisic acid. The DNA of the PKE1 promoter was highly methylated in fruit and leaf, and the methylation of the coding sequence in leaf was significantly higher than that in fruit at different development stages. The over-expression of SpPKE1 under the control of a CaMV (Cauliflower Mosaic Virus) 35S promoter in transgenic tomato and tobacco plants enhanced their tolerance to salt stress. PKE1 was downregulated by abiotic stresses but enhanced the plant's salt stress tolerance. Therefore, this gene may be involved in post-transcriptional regulation and may be an important candidate for molecular breeding of salt-tolerant plants.
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Affiliation(s)
- Jinhua Li
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing 400715, China.
| | - Chunrui Chen
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing 400715, China.
| | - Juanjuan Wei
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing 400715, China.
| | - Yu Pan
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing 400715, China.
| | - Chenggang Su
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing 400715, China.
| | - Xingguo Zhang
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing 400715, China.
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18
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Wang J, Mei J, Ren G. Plant microRNAs: Biogenesis, Homeostasis, and Degradation. FRONTIERS IN PLANT SCIENCE 2019; 10:360. [PMID: 30972093 PMCID: PMC6445950 DOI: 10.3389/fpls.2019.00360] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 03/07/2019] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs), a class of endogenous, tiny, non-coding RNAs, are master regulators of gene expression among most eukaryotes. Intracellular miRNA abundance is regulated under multiple levels of control including transcription, processing, RNA modification, RNA-induced silencing complex (RISC) assembly, miRNA-target interaction, and turnover. In this review, we summarize our current understanding of the molecular components and mechanisms that influence miRNA biogenesis, homeostasis, and degradation in plants. We also make comparisons with findings from other organisms where necessary.
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Affiliation(s)
| | | | - Guodong Ren
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
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19
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Damayanti F, Lombardo F, Masuda JI, Shinozaki Y, Ichino T, Hoshikawa K, Okabe Y, Wang N, Fukuda N, Ariizumi T, Ezura H. Functional Disruption of the Tomato Putative Ortholog of HAWAIIAN SKIRT Results in Facultative Parthenocarpy, Reduced Fertility and Leaf Morphological Defects. FRONTIERS IN PLANT SCIENCE 2019; 10:1234. [PMID: 31681360 PMCID: PMC6801985 DOI: 10.3389/fpls.2019.01234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/05/2019] [Indexed: 05/03/2023]
Abstract
A number of plant microRNAs have been demonstrated to regulate developmental processes by integrating internal and environmental cues. Recently, the Arabidopsis thaliana F-box protein HAWAIIAN SKIRT (HWS) gene has been described for its role in miRNA biogenesis. We have isolated in a forward genetic screen a tomato (Solanum lycopersicum) line mutated in the putative ortholog of HWS. We show that the tomato hws-1 mutant exhibits reduction in leaflet serration, leaflet fusion, some degree of floral organ fusion, and alteration in miRNA levels, similarly to the original A. thaliana hws-1 mutant. We also describe novel phenotypes for hws such as facultative parthenocarpy, reduction in fertility and flowering delay. In slhws-1, the parthenocarpy trait is influenced by temperature, with higher parthenocarpy rate in warmer environmental conditions. Conversely, slhws-1 is able to produce seeds when grown in cooler environment. We show that the reduction in seed production in the mutant is mainly due to a defective male function and that the levels of several miRNAs are increased, in accordance with previous HWS studies, accounting for the abnormal leaf and floral phenotypes as well as the altered flowering and fruit development processes. This is the first study of HWS in fleshy fruit plant, providing new insights in the function of this gene in fruit development.
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Affiliation(s)
- Farida Damayanti
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Fabien Lombardo
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Jun-ichiro Masuda
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Yoshihito Shinozaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Japan
| | - Takuji Ichino
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto, Japan
| | - Ken Hoshikawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | - Yoshihiro Okabe
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Innovation Center, Nippon Flour Mills Co., Ltd, Atsugi, Japan
| | - Ning Wang
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Japan
| | - Naoya Fukuda
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Japan
| | - Tohru Ariizumi
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Japan
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Japan
- *Correspondence: Hiroshi Ezura,
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20
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Zhang X, Jayaweera D, Peters JL, Szecsi J, Bendahmane M, Roberts JA, González-Carranza ZH. The Arabidopsis thaliana F-box gene HAWAIIAN SKIRT is a new player in the microRNA pathway. PLoS One 2017; 12:e0189788. [PMID: 29244865 PMCID: PMC5731758 DOI: 10.1371/journal.pone.0189788] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/03/2017] [Indexed: 11/26/2022] Open
Abstract
In Arabidopsis, the F-box HAWAIIAN SKIRT (HWS) protein is important for organ growth. Loss of function of HWS exhibits pleiotropic phenotypes including sepal fusion. To dissect the HWS role, we EMS-mutagenized hws-1 seeds and screened for mutations that suppress hws-1 associated phenotypes. We identified shs-2 and shs-3 (suppressor of hws-2 and 3) mutants in which the sepal fusion phenotype of hws-1 was suppressed. shs-2 and shs-3 (renamed hst-23/hws-1 and hst-24/hws-1) carry transition mutations that result in premature terminations in the plant homolog of Exportin-5 HASTY (HST), known to be important in miRNA biogenesis, function and transport. Genetic crosses between hws-1 and mutant lines for genes in the miRNA pathway also suppress the phenotypes associated with HWS loss of function, corroborating epistatic relations between the miRNA pathway genes and HWS. In agreement with these data, accumulation of miRNA is modified in HWS loss or gain of function mutants. Our data propose HWS as a new player in the miRNA pathway, important for plant growth.
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Affiliation(s)
- Xuebin Zhang
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Dasuni Jayaweera
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Janny L. Peters
- Department of Molecular Plant Physiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Judit Szecsi
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, Lyon, France
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, Lyon, France
| | - Jeremy A. Roberts
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Zinnia H. González-Carranza
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
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21
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González-Carranza ZH, Zhang X, Peters JL, Boltz V, Szecsi J, Bendahmane M, Roberts JA. HAWAIIAN SKIRT controls size and floral organ number by modulating CUC1 and CUC2 expression. PLoS One 2017; 12:e0185106. [PMID: 28934292 PMCID: PMC5608315 DOI: 10.1371/journal.pone.0185106] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/06/2017] [Indexed: 12/02/2022] Open
Abstract
The Arabidopsis thaliana F-box gene HAWAIIAN SKIRT (HWS) affects organ growth and the timing of floral organ abscission. The loss-of-function hws-1 mutant exhibits fused sepals and increased organ size. To understand the molecular mechanisms of HWS during plant development, we mutagenized hws-1 seeds with ethylmethylsulphonate (EMS) and screened for mutations suppressing hws-1 associated phenotypes. We isolated the shs1/hws-1 (suppressor of hws-1) mutant in which hws-1 sepal fusion phenotype was suppressed. The shs1/hws-1 mutant carries a G→A nucleotide substitution in the MIR164 binding site of CUP-SHAPED COTYLEDON 1 (CUC1) mRNA. CUC1 and CUP-SHAPED COTYLEDON 2 (CUC2) transcript levels were altered in shs1, renamed cuc1-1D, and in hws-1 mutant. Genetic interaction analyses using single, double and triple mutants of cuc1-1D, cuc2-1D (a CUC2 mutant similar to cuc1-1D), and hws-1, demonstrate that HWS, CUC1 and CUC2 act together to control floral organ number. Loss of function of HWS is associated with larger petal size due to alterations in cell proliferation and mitotic growth, a role shared with the CUC1 gene.
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Affiliation(s)
- Zinnia H. González-Carranza
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Xuebin Zhang
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Janny L. Peters
- Department of Molecular Plant Physiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Veronique Boltz
- Laboratoire Reproduction et Développement des Plantes, Univesité de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Judit Szecsi
- Laboratoire Reproduction et Développement des Plantes, Univesité de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Développement des Plantes, Univesité de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Jeremy A. Roberts
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
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