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Sun M, Xiao X, Khan KS, Lyu J, Yu J. Characterization and functions of Myeloblastosis (MYB) transcription factors in cucurbit crops. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 348:112235. [PMID: 39186952 DOI: 10.1016/j.plantsci.2024.112235] [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: 05/03/2024] [Revised: 07/15/2024] [Accepted: 08/18/2024] [Indexed: 08/28/2024]
Abstract
Myeloblastosis (MYB) is one of the largest family of transcription factors (TFs) in plants. It plays a key role in plant life activities, such as metabolic regulation, stress resistant, as well as helpful for plant growth and development. In China, cucurbit is an important and nutrients rich vegetable crop, which have high medicinal and socio-economic values. In this review, we discussed the structure and characterization of MYB TFs and how do regulate flower development, fruit maturity, fruit quality, and flavonoid biosynthesis. Furthermore, we highlight the effect and contribution of MYB TFs in the regulation of biotic and abiotic stress resistance. This comprehensive review will provide a new reference for the more effective application of MYB TF in quality control, stress resistance research and molecular breeding of cucurbit crops.
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Affiliation(s)
- Mingming Sun
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Xuemei Xiao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, PR China; State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, PR China.
| | - Khuram Shehzad Khan
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, PR China; College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Jian Lyu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, PR China; State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Jihua Yu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, PR China; State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, PR China.
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2
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Li S, Zhao Z, Lu Q, Li M, Dai X, Shan M, Liu Z, Bai MY, Xiang F. miR394 modulates brassinosteroid signaling to regulate hypocotyl elongation in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:645-657. [PMID: 38761364 DOI: 10.1111/tpj.16806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 04/13/2024] [Accepted: 04/30/2024] [Indexed: 05/20/2024]
Abstract
The interplay between microRNAs (miRNAs) and phytohormones allows plants to integrate multiple internal and external signals to optimize their survival of different environmental conditions. Here, we report that miR394 and its target gene LEAF CURLING RESPONSIVENESS (LCR), which are transcriptionally responsive to BR, participate in BR signaling to regulate hypocotyl elongation in Arabidopsis thaliana. Phenotypic analysis of various transgenic and mutant lines revealed that miR394 negatively regulates BR signaling during hypocotyl elongation, whereas LCR positively regulates this process. Genetically, miR394 functions upstream of BRASSINOSTEROID INSENSITIVE2 (BIN2), BRASSINAZOLEs RESISTANT1 (BZR1), and BRI1-EMS-SUPPRESSOR1 (BES1), but interacts with BRASSINOSTEROID INSENSITIVE1 (BRI1) and BRI1 SUPRESSOR PROTEIN (BSU1). RNA-sequencing analysis suggested that miR394 inhibits BR signaling through BIN2, as miR394 regulates a significant number of genes in common with BIN2. Additionally, miR394 increases the accumulation of BIN2 but decreases the accumulation of BZR1 and BES1, which are phosphorylated by BIN2. MiR394 also represses the transcription of PACLOBUTRAZOL RESISTANCE1/5/6 and EXPANSIN8, key genes that regulate hypocotyl elongation and are targets of BZR1/BES1. These findings reveal a new role for a miRNA in BR signaling in Arabidopsis.
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Affiliation(s)
- Shuo Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, People's Republic of China
| | - Zhongjuan Zhao
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, People's Republic of China
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute of Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250013, China
| | - Qing Lu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, People's Republic of China
| | - Mingru Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, People's Republic of China
| | - Xuehuan Dai
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, People's Republic of China
| | - Mengqi Shan
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, People's Republic of China
| | - Zhenhua Liu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, People's Republic of China
| | - Ming-Yi Bai
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, People's Republic of China
| | - Fengning Xiang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, People's Republic of China
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Zhou H, Jiang M, Li J, Xu Y, Li C, Lu S. Genome-Wide Identification and Functional Analysis of Salvia miltiorrhiza MicroRNAs Reveal the Negative Regulatory Role of Smi-miR159a in Phenolic Acid Biosynthesis. Int J Mol Sci 2024; 25:5148. [PMID: 38791194 PMCID: PMC11121111 DOI: 10.3390/ijms25105148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
MicroRNAs (miRNAs) are a group of endogenous small non-coding RNAs in plants. They play critical functions in various biological processes during plant growth and development. Salvia miltiorrhiza is a well-known traditional Chinese medicinal plant with significant medicinal, economic, and academic values. In order to elucidate the role of miRNAs in S. miltiorrhiza, six small RNA libraries from mature roots, young roots, stems, mature leaves, young leaves and flowers of S. miltiorrhiza and one degradome library from mixed tissues were constructed. A total of 184 miRNA precursors, generating 137 known and 49 novel miRNAs, were genome-widely identified. The identified miRNAs were predicted to play diversified regulatory roles in plants through regulating 891 genes. qRT-PCR and 5' RLM-RACE assays validated the negative regulatory role of smi-miR159a in SmMYB62, SmMYB78, and SmMYB80. To elucidate the function of smi-miR159a in bioactive compound biosynthesis, smi-miR159a transgenic hairy roots were generated and analyzed. The results showed that overexpression of smi-miR159a caused a significant decrease in rosmarinic acid and salvianolic acid B contents. qRT-PCR analysis showed that the targets of smi-miR159a, including SmMYB62, SmMYB78, and SmMYB80, were significantly down-regulated, accompanied by the down-regulation of SmPAL1, SmC4H1, Sm4CL1, SmTAT1, SmTAT3, SmHPPR1, SmRAS, and SmCYP98A14 genes involved in phenolic acid biosynthesis. It suggests that smi-miR159a is a significant negative regulator of phenolic acid biosynthesis in S. miltiorrhiza.
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Affiliation(s)
- Hong Zhou
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (H.Z.); (M.J.); (J.L.); (Y.X.)
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China
| | - Maochang Jiang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (H.Z.); (M.J.); (J.L.); (Y.X.)
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Jiang Li
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (H.Z.); (M.J.); (J.L.); (Y.X.)
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Yayun Xu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (H.Z.); (M.J.); (J.L.); (Y.X.)
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Caili Li
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (H.Z.); (M.J.); (J.L.); (Y.X.)
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Shanfa Lu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (H.Z.); (M.J.); (J.L.); (Y.X.)
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
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Zhao M, Lei Y, Wu L, Qi H, Song Z, Xu M. The miR159a-PeMYB33 module regulates poplar adventitious rooting through the abscisic acid signal pathway. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:879-891. [PMID: 38271219 DOI: 10.1111/tpj.16643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024]
Abstract
As sessile organisms, plants experience variable environments and encounter diverse stresses during their growth and development. Adventitious rooting, orchestrated by multiple coordinated signaling pathways, represents an adaptive strategy evolved by plants to adapt to cope with changing environmental conditions. This study uncovered the role of the miR159a-PeMYB33 module in the formation of adventitious roots (ARs) synergistically with abscisic acid (ABA) signaling in poplar. Overexpression of miR159a increased the number of ARs and plant height while reducing sensitivity to ABA in transgenic plants. In contrast, inhibition of miR159a (using Short Tandem Target Mimic) or overexpression of PeMYB33 decreased the number of ARs in transgenic plants. Additionally, miR159a targets and cleaves transcripts of PeMYB33 using degradome analysis, which was further confirmed by a transient expression experiment of poplar protoplast. We show the miR159a-PeMYB33 module controls ARs development in poplar through ABA signaling. In particular, we demonstrated that miR159a promotes the expression of genes in the ABA signaling pathway. The findings from this study shed light on the intricate regulatory mechanisms governing the development of ARs in poplar plants. The miR159a-PeMYB33 module, in conjunction with ABA signaling, plays a crucial role in modulating AR formation and subsequent plant growth.
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Affiliation(s)
- Meiqi Zhao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Yijing Lei
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Ling Wu
- Jiangsu Yanjiang Institute of Agricultural Science, Nantong, Jiangsu, 226541, China
| | - Haoran Qi
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Zihe Song
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Meng Xu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
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Peng C, Xu H, Xie S, Zhong X, Chen L, He Y, Li Z, Zhou Y, Duan L. Unveiling the Regulatory Role of miRNAs in Internode Elongation: Integrated Analysis of MicroRNA and mRNA Expression Profiles across Diverse Dwarfing Treatments in Maize ( Zea mays L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7533-7545. [PMID: 38527761 DOI: 10.1021/acs.jafc.3c09507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
MicroRNAs are crucial regulators of gene expression in maize. However, the mechanisms through which miRNAs control internode elongation remain poorly understood. This study engineered varying levels of internode elongation inhibition, revealing that dwarfing treatments diminished gibberellin levels, curtailed cell longitudinal growth, and slowed the rate of internode elongation. Comprehensive transcriptome and miRNA profiling of the internode elongation zone showed gene expression changes that paralleled the extent of the internode length reduction. We identified 543 genes and 29 miRNAs with significant correlations to internode length, predominantly within families, including miR164 and miR396. By incorporating target gene expression levels, we pinpointed nine miRNA-mRNA pairs that are significantly associated with the regulation of the internode elongation. The inhibitory effects of these miRNAs on their target genes were confirmed through dual-luciferase reporter assays. Overexpression of miR164h in maize resulted in increased internode and cell length, suggesting a novel genetic avenue for manipulating plant stature. These miRNAs may also serve as precise spatiotemporal regulators for in vitro plant development.
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Affiliation(s)
- Chuanxi Peng
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Haidong Xu
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Shipeng Xie
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xingyu Zhong
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Limei Chen
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Yan He
- National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Zhaohu Li
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yuyi Zhou
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Liusheng Duan
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
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Wang Y, Zhao S, Wang S, Zhang J, Zhao Y, Ye C, Zhao Z, Li J, Shen H, Wu D. Electrochemistry detection of estrogenic effect: Regulation of de novo purine synthesis and catabolism by gibberellin and fulvestrant. Bioelectrochemistry 2024; 156:108634. [PMID: 38160510 DOI: 10.1016/j.bioelechem.2023.108634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/16/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
The estrogenic effect of plant growth regulators has been received little attention, which leads to the lack of relevant toxicity data. In this study, the estrogenic effect induced by gibberellin with ERα-dependent manner was found by E-screen and western blot methods, and the electrochemical signals of MCF-7 cells regulated by gibberellin and fulvestrant were investigated. The results showed that the electrochemical signals of MCF-7 cells were increased by gibberellin, while reduced by fulvestrant significantly, and displayed an extremely sensitive response to the effects of estrogenic effect induced by ERα agonist and antagonist. Western blot results showed that the expressions of phosphoribosyl pyrophosphate amidotransferase and hypoxanthine nucleotide dehydrogenase in de novo purine synthesis and adenine deaminase in catabolism were more effective regulated by gibberellin and fulvestrant, resulting in significant changes of the levels of guanine, hypoxanthine and xanthine in cells, and then electrochemical signals. The results provide a theoretical basis for the establishment of new electrochemical detection method of the estrogenic effect of plant regulators.
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Affiliation(s)
- Yuhang Wang
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, PR China
| | - Shuo Zhao
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, PR China
| | - Shuhong Wang
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, PR China
| | - Jing Zhang
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, PR China
| | - Yanli Zhao
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, PR China; Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi 154007, PR China
| | - Cai Ye
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, PR China; Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi 154007, PR China
| | - Zhiyu Zhao
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, PR China
| | - Jinlian Li
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, PR China; Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi 154007, PR China.
| | - Hongkuan Shen
- Jiamusi Inspection and Testing Center, Jiamusi, Heilongjiang 154007, PR China.
| | - Dongmei Wu
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, PR China; Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi 154007, PR China.
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Zhang T, Wang X, Yuan Y, Zhu S, Liu C, Zhang Y, Gai S. PsmiR159b- PsMYB65 module functions in the resumption of bud growth after endodormancy by affecting the cell cycle in tree peony. HORTICULTURE RESEARCH 2024; 11:uhae052. [PMID: 38638681 PMCID: PMC11025381 DOI: 10.1093/hr/uhae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/16/2024] [Indexed: 04/20/2024]
Abstract
Bud endodormancy in perennial plants is a sophisticated system that adapts to seasonal climatic changes. Growth-promoting signals such as low temperature and gibberellins (GAs) are crucial for facilitating budbreak following endodormancy release (EDR). However, the regulatory mechanisms underlying GA-mediated budbreak in tree peony (Paeonia suffruticosa) remain unclear. In tree peony, the expression of PsmiR159b among three differentially expressed miR159 members was inhibited with the prolonged chilling, and overexpression of PsMIR159b delayed budbreak, whereas silencing PsmiR159b promoted budbreak after dormancy. PsMYB65, a downstream transcription factor in the GA pathway, was induced by prolonged chilling and exogenous GA3 treatments. PsMYB65 was identified as a target of PsmiR159b, and promoted budbreak in tree peony. RNA-seq of PsMYB65-slienced buds revealed significant enrichment in the GO terms regulation of 'cell cycle' and 'DNA replication' among differentially expressed genes. Yeast one-hybrid and electrophoretic mobility shift assays demonstrated that PsMYB65 directly bound to the promoter of the type-D cyclin gene PsCYCD3;1. Dual-luciferase reporter assay indicated that PsMYB65 positively regulate PsCYCD3;1 expression, suggesting that miR159b-PsMYB65 module contributes to budbreak by influencing the cell cycle. Our findings revealed that the PsmiR159b-PsMYB65 module functioned in budbreak after dormancy by regulating cell proliferation, providing valuable insights into the endodormancy release regulation mechanism.
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Affiliation(s)
- Tao Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
- University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, 266109, China
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xinyu Wang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
- University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, 266109, China
| | - Yanchao Yuan
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
- University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, 266109, China
| | - Shoujie Zhu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
- University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, 266109, China
| | - Chunying Liu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
- University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, 266109, China
| | - Yuxi Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
- University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, 266109, China
| | - Shupeng Gai
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
- University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, 266109, China
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Zhang Y, Zeng Z, Hu H, Zhao M, Chen C, Ma X, Li G, Li J, Liu Y, Hao Y, Xu J, Xia R. MicroRNA482/2118 is lineage-specifically involved in gibberellin signalling via the regulation of GID1 expression by targeting noncoding PHAS genes and subsequently instigated phasiRNAs. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:819-832. [PMID: 37966709 PMCID: PMC10955497 DOI: 10.1111/pbi.14226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 10/05/2023] [Accepted: 10/22/2023] [Indexed: 11/16/2023]
Abstract
MicroRNA482/2118 (miR482/2118) is a 22-nt miRNA superfamily, with conserved functions in disease resistance and plant development. It usually instigates the production of phased small interfering RNAs (phasiRNAs) from its targets to expand or reinforce its silencing effect. Using a new high-quality reference genome sequence and comprehensive small RNA profiling, we characterized a newly evolved regulatory pathway of miR482/2118 in litchi. In this pathway, miR482/2118 cleaved a novel noncoding trans-acting gene (LcTASL1) and triggered phasiRNAs to regulate the expression of gibberellin (GA) receptor gene GIBBERELLIN INSENSITIVE DWARF1 (GID1) in trans; another trans-acting gene LcTASL2, targeted by LcTASL1-derived phasiRNAs, produced phasiRNAs as well to target LcGID1 to reinforce the silencing effect of LcTASL1. We found this miR482/2118-TASL-GID1 pathway was likely involved in fruit development, especially the seed development in litchi. In vivo construction of the miR482a-TASL-GID1 pathway in Arabidopsis could lead to defects in flower and silique development, analogous to the phenotype of gid1 mutants. Finally, we found that a GA-responsive transcription factor, LcGAMYB33, could regulate LcMIR482/2118 as a feedback mechanism of the sRNA-silencing pathway. Our results deciphered a lineage-specifically evolved regulatory module of miR482/2118, demonstrating the high dynamics of miR482/2118 function in plants.
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Affiliation(s)
- Yanqing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Zaohai Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Huimin Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Minglei Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Chengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Xingshuai Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Guanliang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Jianguo Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Yuanlong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Yanwei Hao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
| | - Jing Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
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9
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Kaur A, Madhu, Sharma A, Singh K, Upadhyay SK. Investigation of two-pore K + (TPK) channels in Triticum aestivum L. suggests their role in stress response. Heliyon 2024; 10:e27814. [PMID: 38533012 PMCID: PMC10963239 DOI: 10.1016/j.heliyon.2024.e27814] [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: 10/17/2023] [Revised: 02/28/2024] [Accepted: 03/07/2024] [Indexed: 03/28/2024] Open
Abstract
Two-pore K+ (TPK) channels are voltage-independent and involved in stress response in plants. Herein, we identified 12 TaTPK genes located on nine chromosomes in the Triticum aestivum genome. The majority of TaTPK genes comprised two exons. Each TaTPK channel comprised four transmembrane (TM) helices, N- and C-terminal ion-channel domains, two EF-hand domains and one 14-3-3 binding site. Additionally, highly conserved 'GYGD' motif responsible for K+ ion specificity, was found in between the TMs in both the ion-channel domains. Nine TaTPK channels were predicted to be localised at the plasma membrane, while three were vacuolar. The protein-protein and protein-chemical interactions indicated the coordinated functioning of the TaTPK channels with the other K+ transporters and their possible interaction with the Ca2+-signaling pathway. Expression studies suggested their importance in both vegetative and reproductive tissues development. Significantly modulated expression of various TaTPK genes during heat, drought, combined heat and drought and salt stresses, and after fungal infestation, depicted their function in stress responses. The miRNAs and transcription factors interaction analyses suggested their role in the hormone, light, growth and development-related, and stress-responsive signaling cascades. The current study suggested vital functions of various TaTPK genes, especially in stress response, and would provide an opportunity for their detailed characterization in future studies.
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Affiliation(s)
- Amandeep Kaur
- Department of Botany, Panjab University, Chandigarh, India, 160014
| | - Madhu
- Department of Botany, Panjab University, Chandigarh, India, 160014
| | - Alok Sharma
- Department of Botany, Panjab University, Chandigarh, India, 160014
- Regional Ayurveda Research Institute, Gwalior, Madhya Pradesh, 474001, India
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, Chandigarh, India
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10
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Cao D, Liu C, Zhang W, Zheng C, Zhang S, Jia H, Yang Y. Characterization of the DUF868 gene family in Nicotiana and functional analysis of NtDUF868-E5 involved in pigment metabolism. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108493. [PMID: 38447423 DOI: 10.1016/j.plaphy.2024.108493] [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: 01/21/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/08/2024]
Abstract
Domains of unknown function (DUF) proteins represent a large group of uncharacterized protein families. The DUF868 gene family in Nicotiana has not yet been described. In the present study, we identified 12, 11, and 25 DUF868 family members in the genome of Nicotiana sylvestris, N. tomentosiformis, and N. tabacum, respectively. Based on phylogenetic analysis, these were categorized into five groups (A-E). Within each group, the gene structures, motifs, and tertiary structures showed high similarity. NtDUF868 family expansion during evolution was mainly driven by segmental duplication events. MicroRNA (miRNA) target site prediction identified 12 miRNA members that target 16 NtDUF868 family genes. The promoters of these genes contain cis-regulatory elements responsive to light, phytohormones, and abiotic stresses. Expression profiling revealed their tissue- and stage-specific expression patterns. RNA-sequencing and quantitative reverse transcription PCR revealed that the NtDUF868 family genes are potentially involved in the response to abiotic and biotic stresses, particularly drought and hormone stresses, and in the resistance to black shank and bacterial wilt. We generated transformed plants using NtDUF868-E5 overexpression and gene-editing vectors. NtDUF868-E5 overexpression resulted in enhanced tobacco plant growth and development, leading to increased leaf photosynthetic capacity and higher chlorophyll and carotenoid contents. This study provided a comprehensive genome-wide analysis of the DUF868 gene family, shedding light on their potential roles in plant growth and stress responses.
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Affiliation(s)
- Dejun Cao
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
| | - Che Liu
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
| | - Wenhan Zhang
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
| | - Cong Zheng
- China Tobacco Fujian Company, Pucheng Branch, Nanping, 353000, China.
| | - Songtao Zhang
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
| | - Hongfang Jia
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
| | - Yongxia Yang
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
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11
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Qian Z, Shi D, Zhang H, Li Z, Huang L, Yan X, Lin S. Transcription Factors and Their Regulatory Roles in the Male Gametophyte Development of Flowering Plants. Int J Mol Sci 2024; 25:566. [PMID: 38203741 PMCID: PMC10778882 DOI: 10.3390/ijms25010566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 12/30/2023] [Accepted: 12/30/2023] [Indexed: 01/12/2024] Open
Abstract
Male gametophyte development in plants relies on the functions of numerous genes, whose expression is regulated by transcription factors (TFs), non-coding RNAs, hormones, and diverse environmental stresses. Several excellent reviews are available that address the genes and enzymes associated with male gametophyte development, especially pollen wall formation. Growing evidence from genetic studies, transcriptome analysis, and gene-by-gene studies suggests that TFs coordinate with epigenetic machinery to regulate the expression of these genes and enzymes for the sequential male gametophyte development. However, very little summarization has been performed to comprehensively review their intricate regulatory roles and discuss their downstream targets and upstream regulators in this unique process. In the present review, we highlight the research progress on the regulatory roles of TF families in the male gametophyte development of flowering plants. The transcriptional regulation, epigenetic control, and other regulators of TFs involved in male gametophyte development are also addressed.
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Affiliation(s)
- Zhihao Qian
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Z.Q.); (D.S.); (H.Z.); (Z.L.)
| | - Dexi Shi
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Z.Q.); (D.S.); (H.Z.); (Z.L.)
| | - Hongxia Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Z.Q.); (D.S.); (H.Z.); (Z.L.)
| | - Zhenzhen Li
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Z.Q.); (D.S.); (H.Z.); (Z.L.)
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China;
| | - Xiufeng Yan
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Z.Q.); (D.S.); (H.Z.); (Z.L.)
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China
| | - Sue Lin
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Z.Q.); (D.S.); (H.Z.); (Z.L.)
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China
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12
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Liu Y, Zhu QF, Li WY, Chen P, Xue J, Yu Y, Feng YZ. The Pivotal Role of Noncoding RNAs in Flowering Time Regulation. Genes (Basel) 2023; 14:2114. [PMID: 38136936 PMCID: PMC10742506 DOI: 10.3390/genes14122114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Noncoding RNAs constitute a substantial portion of the transcriptome and play pivotal roles in plant growth and development. Among these processes, flowering stands out as a crucial trait, ensuring reproductive success and seed set, and is meticulously controlled by genetic and environmental factors. With remarkable advancements in the identification and characterization of noncoding RNAs in plants, it has become evident that noncoding RNAs are intricately linked to the regulation of flowering time. In this article, we present an overview of the classification of plant noncoding RNAs and delve into their functions in the regulation of flowering time. Furthermore, we review their molecular mechanisms and their involvement in flowering pathways. Our comprehensive review enhances the understanding of how noncoding RNAs contribute to the regulation of flowering time and sheds light on their potential implications in crop breeding.
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Affiliation(s)
| | | | | | | | | | - Yang Yu
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (Y.L.); (Q.-F.Z.); (W.-Y.L.); (P.C.); (J.X.)
| | - Yan-Zhao Feng
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (Y.L.); (Q.-F.Z.); (W.-Y.L.); (P.C.); (J.X.)
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13
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Sun B, Zhao X, Gao J, Li J, Xin Y, Zhao Y, Liu Z, Feng H, Tan C. Genome-wide identification and expression analysis of the GASA gene family in Chinese cabbage (Brassica rapa L. ssp. pekinensis). BMC Genomics 2023; 24:668. [PMID: 37932701 PMCID: PMC10629197 DOI: 10.1186/s12864-023-09773-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 10/29/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND The Gibberellic Acid-Stimulated Arabidopsis (GASA) gene family is widely involved in the regulation of plant growth, development, and stress response. However, information on the GASA gene family has not been reported in Chinese cabbage (Brassica rapa L. ssp. pekinensis). RESULTS Here, we conducted genome-wide identification and analysis of the GASA genes in Chinese cabbage. In total, 15 GASA genes were identified in the Chinese cabbage genome, and the physicochemical property, subcellular location, and tertiary structure of the corresponding GASA proteins were elucidated. Phylogenetic analysis, conserved motif, and gene structure showed that the GASA proteins were divided into three well-conserved subfamilies. Synteny analysis proposed that the expansion of the GASA genes was influenced mainly by whole-genome duplication (WGD) and transposed duplication (TRD) and that duplication gene pairs were under negative selection. Cis-acting elements of the GASA promoters were involved in plant development, hormonal and stress responses. Expression profile analysis showed that the GASA genes were widely expressed in different tissues of Chinese cabbage, but their expression patterns appeared to diverse. The qRT-PCR analysis of nine GASA genes confirmed that they responded to salt stress, heat stress, and hormonal triggers. CONCLUSIONS Overall, this study provides a theoretical basis for further exploring the important role of the GASA gene family in the functional genome of Chinese cabbage.
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Affiliation(s)
- Bingxin Sun
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Xianlei Zhao
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Jiahui Gao
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Jie Li
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Yue Xin
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Yonghui Zhao
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Zhiyong Liu
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Hui Feng
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Chong Tan
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China.
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14
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Jing W, Gong F, Liu G, Deng Y, Liu J, Yang W, Sun X, Li Y, Gao J, Zhou X, Ma N. Petal size is controlled by the MYB73/TPL/HDA19-miR159-CKX6 module regulating cytokinin catabolism in Rosa hybrida. Nat Commun 2023; 14:7106. [PMID: 37925502 PMCID: PMC10625627 DOI: 10.1038/s41467-023-42914-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/25/2023] [Indexed: 11/06/2023] Open
Abstract
The size of plant lateral organs is determined by well-coordinated cell proliferation and cell expansion. Here, we report that miR159, an evolutionarily conserved microRNA, plays an essential role in regulating cell division in rose (Rosa hybrida) petals by modulating cytokinin catabolism. We uncover that Cytokinin Oxidase/Dehydrogenase6 (CKX6) is a target of miR159 in petals. Knocking down miR159 levels results in the accumulation of CKX6 transcripts and earlier cytokinin clearance, leading to a shortened cell division period and smaller petals. Conversely, knocking down CKX6 causes cytokinin accumulation and a prolonged developmental cell division period, mimicking the effects of exogenous cytokinin application. MYB73, a R2R3-type MYB transcription repressor, recruits a co-repressor (TOPLESS) and a histone deacetylase (HDA19) to form a suppression complex, which regulates MIR159 expression by modulating histone H3 lysine 9 acetylation levels at the MIR159 promoter. Our work sheds light on mechanisms for ensuring the correct timing of the exit from the cell division phase and thus organ size regulation by controlling cytokinin catabolism.
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Affiliation(s)
- Weikun Jing
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
- School of Food and Medicine, Shenzhen Polytechnic, Shenzhen, Guangdong, 518055, China
| | - Feifei Gong
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Guoqin Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yinglong Deng
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Jiaqi Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Wenjing Yang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xiaoming Sun
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yonghong Li
- School of Food and Medicine, Shenzhen Polytechnic, Shenzhen, Guangdong, 518055, China
| | - Junping Gao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xiaofeng Zhou
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China.
| | - Nan Ma
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China.
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15
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Xie L, Jian H, Dai H, Yang Y, Liu Y, Wei L, Tan M, Li J, Liu L. Screening of microRNAs and target genes involved in Sclerotinia sclerotiorum (Lib.) infection in Brassica napus L. BMC PLANT BIOLOGY 2023; 23:479. [PMID: 37807039 PMCID: PMC10561407 DOI: 10.1186/s12870-023-04501-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/30/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND Rapeseed (Brassica napus L.) is the third largest source of vegetable oil in the world, and Sclerotinia sclerotiorum (Lib.) is a major soil-borne fungal plant pathogen that infects more than 400 plant species, including B. napus. Sclerotinia stem rot caused an annual loss of 10 - 20% in rapeseed yield. Exploring the molecular mechanisms in response to S. sclerotiorum infection in B. napus is beneficial for breeding and cultivation of resistant varieties. To gain a better understanding of the mechanisms regarding B. napus tolerance to Sclerotinia stem rot, we employed a miRNAome sequencing approach and comprehensively investigated global miRNA expression profile among five relatively resistant lines and five susceptible lines of oilseed at 0, 24, and 48 h post-inoculation. RESULTS In this study, a total of 40 known and 1105 novel miRNAs were differentially expressed after S. sclerotiorum infection, including miR156, miR6028, miR394, miR390, miR395, miR166, miR171, miR167, miR164, and miR172. Furthermore, 8,523 genes were predicted as targets for these differentially expressed miRNAs. These target genes were mainly associated with disease resistance (R) genes, signal transduction, transcription factors, and hormones. Constitutively expressing miR156b (OX156b) plants strengthened Arabidopsis resistance against S. sclerotiorum accompanied by smaller necrotic lesions, whereas blocking miR156 expression in Arabidopsis (MIM156) led to greater susceptibility to S. sclerotiorum disease, associated with extensive cell death of necrotic lesions. CONCLUSIONS This study reveals the distinct difference in miRNA profiling between the relatively resistant lines and susceptible lines of B. napus in response to S. sclerotiorum. The identified differentially expressed miRNAs related to sclerotinia stem rot resistance are involved in regulating resistance to S. sclerotiorum in rapeseed by targeting genes related to R genes, signal transduction, transcription factors, and hormones. miR156 positively modulates the resistance to S. sclerotiorum infection by restricting colonization of S. sclerotiorum mycelia. This study provides a broad view of miRNA expression changes after S. sclerotiorum infection in oilseed and is the first to elucidate the function and mechanism underlying the miR156 response to S. sclerotiorum infection in oilseed rape.
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Affiliation(s)
- Ling Xie
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Hongju Jian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Haoxi Dai
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Youhong Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Yiling Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Lijuan Wei
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Min Tan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China.
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16
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Anand S, Lal M, Bhardwaj E, Shukla R, Pokhriyal E, Jain A, Sri T, Srivastava PS, Singh A, Das S. MIR159 regulates multiple aspects of stamen and carpel development and requires dissection and delimitation of differential downstream regulatory network for manipulating fertility traits. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1437-1456. [PMID: 38076769 PMCID: PMC10709278 DOI: 10.1007/s12298-023-01377-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/21/2023] [Accepted: 10/18/2023] [Indexed: 12/17/2023]
Abstract
Unravelling genetic networks regulating developmental programs are key to devising and implementing genomics assisted trait modification strategies. It is crucial to understand the role of small RNAs, and the basis of their ability to modify traits. MIR159 has been previously reported to cause defects in anther development in Arabidopsis; however, the complete spectrum and basis of the defects remained unclear. The present study was therefore undertaken to comprehensively investigate the role of miR159 from Brassica juncea in modulating vegetative and reproductive traits. Owing to the polyploid nature of Brassica, paralogous and homeologous copies of MIR159A, MIR159B, and, MIR159C were identified and analysis of the precursor uncovered extensive structural and sequence variation. The MIR159 locus with mature miR159 with perfect target complimentarily with MYB65, was cloned from Brassica juncea var. Varuna for functional characterization by generating constitutively over-expressing lines in Arabidopsis thaliana Col-0. Apart from statistically significant difference in multiple vegetative traits, drastic differences were observed in stamen and pistil. Over-expression of miR159a led to shortening of filament length and loss of tetradynamous condition. Anthers were apiculate, with improper lobe formation, and unsynchronized cellular growth between connective tissue and another lobe development. Analysis revealed arrested meiosis/cytokinesis in microspores, and altered lignin deposition pattern in endothecial walls thus affecting anther dehiscence. In the gynoecium, flaccid, dry stigmatic papillae, and large embryo sac in the female gametophyte was observed. Over-expression of miR159a thus severely affected pollination and seed-set. Analysis of the transcriptome data revealed components of regulatory networks of anther and carpel developmental pathway, and lignin metabolism that are affected. Expression analysis allowed us to position the miR159a-MYB65 module in the genetic network of stamen development, involved in pollen-grain maturation; in GA-mediated regulation of stamen development, and in lignin metabolism. The study, on one hand indicates role of miR159a-MYB65 in regulating multiple aspects of reproductive organ development that can be manipulated for trait modification, but also raises several unaddressed questions such as relationship between miR159a and male-meiosis, miR159a and filament elongation for future investigations. Accession numbers: KC204951-KC204960. Project number PRJNA1035268. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01377-7.
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Affiliation(s)
- Saurabh Anand
- Department of Botany, University of Delhi, Delhi, 110 007 India
| | - Mukund Lal
- Department of Botany, University of Delhi, Delhi, 110 007 India
| | - Ekta Bhardwaj
- Department of Botany, University of Delhi, Delhi, 110 007 India
| | - Richa Shukla
- Department of Botany, University of Delhi, Delhi, 110 007 India
| | - Ekta Pokhriyal
- Department of Botany, University of Delhi, Delhi, 110 007 India
| | - Aditi Jain
- Department of Botany, University of Delhi, Delhi, 110 007 India
| | - Tanu Sri
- TERI School of Advanced Studies, Plot No. 10, Institutional Area, Vasant Kunj, New Delhi, 110 070 India
| | - P. S. Srivastava
- Department of Biotechnology, Jamia Hamdard, Hamdard Nagar, New Delhi, Delhi 110 062 India
| | - Anandita Singh
- TERI School of Advanced Studies, Plot No. 10, Institutional Area, Vasant Kunj, New Delhi, 110 070 India
| | - Sandip Das
- Department of Botany, University of Delhi, Delhi, 110 007 India
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17
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Zhou Y, Zhao C, Du T, Li A, Qin Z, Zhang L, Dong S, Wang Q, Hou F. Overexpression of 9- cis-Epoxycarotenoid Dioxygenase Gene, IbNCED1, Negatively Regulates Plant Height in Transgenic Sweet Potato. Int J Mol Sci 2023; 24:10421. [PMID: 37445599 DOI: 10.3390/ijms241310421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/08/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023] Open
Abstract
Plant height is one of the key agronomic traits for improving the yield of sweet potato. Phytohormones, especially gibberellins (GAs), are crucial to regulate plant height. The enzyme 9-cis-epoxycarotenoid dioxygenase (NCED) is the key enzyme for abscisic acid (ABA) biosynthesis signalling in higher plants. However, its role in regulating plant height has not been reported to date. Here, we cloned a new NCED gene, IbNCED1, from the sweet potato cultivar Jishu26. This gene encoded the 587-amino acid polypeptide containing an NCED superfamily domain. The expression level of IbNCED1 was highest in the stem and the old tissues in the in vitro-grown and field-grown Jishu26, respectively. The expression of IbNCED1 was induced by ABA and GA3. Overexpression of IbNCED1 promoted the accumulation of ABA and inhibited the content of active GA3 and plant height and affected the expression levels of genes involved in the GA metabolic pathway. Exogenous application of GA3 could rescue the dwarf phenotype. In conclusion, we suggest that IbNCED1 regulates plant height and development by controlling the ABA and GA signalling pathways in transgenic sweet potato.
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Affiliation(s)
- Yuanyuan Zhou
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Chunling Zhao
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Taifeng Du
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Aixian Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Zhen Qin
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Liming Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Shunxu Dong
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Qingmei Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Fuyun Hou
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
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18
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Arora S, Singh AK, Chaudhary B. Coordination of floral and fiber development in cotton (Gossypium) by hormone- and flavonoid-signalling associated regulatory miRNAs. PLANT MOLECULAR BIOLOGY 2023; 112:1-18. [PMID: 37067671 DOI: 10.1007/s11103-023-01341-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 02/16/2023] [Indexed: 05/09/2023]
Abstract
Various plant development activities and stress responses are tightly regulated by various microRNAs (miRNA) and their target genes, or transcription factors in a spatiotemporal manner. Here, to exemplify how flowering-associated regulatory miRNAs synchronize their expression dynamics during floral and fiber development in cotton, constitutive expression diminution transgenic lines of auxin-signaling regulatory Gh-miR167 (35S-MIM167) were developed through target mimicry approach. 'Moderate' (58% to 80%)- and 'high' (> 80%)-Gh-miR167 diminution mimic lines showed dosage-dependent developmental deformities in anther development, pollen maturation, and fruit (= boll) formation. Cross pollination of 'moderate' 35S-MIM167 mimic lines with wild type (WT) plant partially restored boll formation and emergence of fiber initials on the ovule surface. Gh-miR167 diminution favored organ-specific transcription biases in miR159, miR166 as well as miR160, miR164, and miR172 along with their target genes during anther and petal development, respectively. Similarly, accumulative effect of percent Gh-miR167 diminution, cross regulation of its target ARF6/8 genes, and temporal mis-expression of hormone signaling- and flavonoid biosynthesis-associated regulatory miRNAs at early fiber initiation stage caused irregular fiber formation. Spatial and temporal transcription proportions of regulatory miRNAs were also found crucial for the execution of hormone- and flavonoid-dependent progression of floral and fiber development. These observations discover how assorted regulatory genetic circuits get organized in response to Gh-miR167 diminution and converge upon ensuing episodes of floral and fiber development in cotton.
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Affiliation(s)
- Sakshi Arora
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201312, India
| | - Amarjeet Kumar Singh
- Center for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Bhupendra Chaudhary
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201312, India.
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19
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Laanen P, Cuypers A, Saenen E, Horemans N. Flowering under enhanced ionising radiation conditions and its regulation through epigenetic mechanisms. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:246-259. [PMID: 36731286 DOI: 10.1016/j.plaphy.2023.01.049] [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: 06/27/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
As sessile organisms, plants have to deal with unfavourable conditions by acclimating or adapting in order to survive. Regulation of flower induction is one such mechanism to ensure reproduction and species survival. Flowering is a tightly regulated process under the control of a network of genes, which can be affected by environmental cues and stress. The effects of ionising radiation (IR) on flowering, however, have been poorly studied. Understanding the effects of ionising radiation on flowering, including the timing, gene pathways, and epigenetics involved, is crucial in the continuing effort of environmental radiation protection. The review shows that plants alter their flowering pattern in response to IR, with various flowering related genes (eg. FLOWERING LOCUS C (FLC), FLOWERING LOCUS T (FT), CONSTANS (CO), GIGANTEA (GI), APETALA1 (AP1), LEAFY (LFY)) and epigenetic processes (DNA methylation, and miRNA expression eg. miRNA169, miR156, miR172) being affected. Thereby, showing a hypothetical IR-induced flowering mechanism. Further research on the interaction between IR and flowering in plants is, however, needed to elucidate the mechanisms behind the stress-induced flowering response.
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Affiliation(s)
- Pol Laanen
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium; Centre for Environmental Research, University of Hasselt, Martelarenlaan 42, 3500, Hasselt, Belgium.
| | - Ann Cuypers
- Centre for Environmental Research, University of Hasselt, Martelarenlaan 42, 3500, Hasselt, Belgium.
| | - Eline Saenen
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium.
| | - Nele Horemans
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium; Centre for Environmental Research, University of Hasselt, Martelarenlaan 42, 3500, Hasselt, Belgium.
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20
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Pegler JL, Oultram JMJ, Mann CWG, Carroll BJ, Grof CPL, Eamens AL. Miniature Inverted-Repeat Transposable Elements: Small DNA Transposons That Have Contributed to Plant MICRORNA Gene Evolution. PLANTS (BASEL, SWITZERLAND) 2023; 12:1101. [PMID: 36903960 PMCID: PMC10004981 DOI: 10.3390/plants12051101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Angiosperms form the largest phylum within the Plantae kingdom and show remarkable genetic variation due to the considerable difference in the nuclear genome size of each species. Transposable elements (TEs), mobile DNA sequences that can amplify and change their chromosome position, account for much of the difference in nuclear genome size between individual angiosperm species. Considering the dramatic consequences of TE movement, including the complete loss of gene function, it is unsurprising that the angiosperms have developed elegant molecular strategies to control TE amplification and movement. Specifically, the RNA-directed DNA methylation (RdDM) pathway, directed by the repeat-associated small-interfering RNA (rasiRNA) class of small regulatory RNA, forms the primary line of defense to control TE activity in the angiosperms. However, the miniature inverted-repeat transposable element (MITE) species of TE has at times avoided the repressive effects imposed by the rasiRNA-directed RdDM pathway. MITE proliferation in angiosperm nuclear genomes is due to their preference to transpose within gene-rich regions, a pattern of transposition that has enabled MITEs to gain further transcriptional activity. The sequence-based properties of a MITE results in the synthesis of a noncoding RNA (ncRNA), which, after transcription, folds to form a structure that closely resembles those of the precursor transcripts of the microRNA (miRNA) class of small regulatory RNA. This shared folding structure results in a MITE-derived miRNA being processed from the MITE-transcribed ncRNA, and post-maturation, the MITE-derived miRNA can be used by the core protein machinery of the miRNA pathway to regulate the expression of protein-coding genes that harbor homologous MITE insertions. Here, we outline the considerable contribution that the MITE species of TE have made to expanding the miRNA repertoire of the angiosperms.
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Affiliation(s)
- Joseph L. Pegler
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Jackson M. J. Oultram
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Christopher W. G. Mann
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Bernard J. Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Christopher P. L. Grof
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Andrew L. Eamens
- School of Health, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
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21
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Lee S, Singh MB, Bhalla PL. Functional analysis of soybean miR156 and miR172 in tobacco highlights their role in plant morphology and floral transition. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:393-401. [PMID: 36753825 DOI: 10.1016/j.plaphy.2023.01.054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/23/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Soybean (Glycine max), a significant oilseed and protein source for humans and livestock feed, needs short day photoperiod for floral induction. Further, soybean has a paleopolyploid genome with multiple copies of flowering genes adding to the complexity of genetic regulation of flowering, and seed set, especially in investigating the role of the noncoding genome. microRNAs, a class of noncoding RNA, play a regulatory role in plant development. miR156 and miR172 are major components of the essential regulatory hub controlling juvenile and vegetative developments and initiation of reproductive phase change leading to flowering. These microRNAs have been originally isolated and studied from model plant, Arabidopsis. However, a study on soybean microRNAs is lacking. We investigated the temporal expression patterns of gma-miR156a and gma-miR172a and found inversely related - gma-miR156a expression was higher in the vegetative stage, and gma-miR172a expression was elevated under inductive flowering conditions. The functions of gma-miR156a and gma-miR172a were evaluated via heterologous expressions in transgenic tobacco plants (Nicotiana tabacum L.). The analysis of overexpression transgenic lines highlighted that gma-miR156a plays a role in juvenile development via repression of the SPL transcription factor family. In contrast, gma-miR172a plays a pivotal role in the reproductive development phase by down-regulating its target genes, AP2. In addition, ectopic expression of gma-miR156a and gma-miR172a affected plant morphology and physiology during plant growth. Collectively, our results suggest that gma-miR156a and gma-miR172a regulate multiple morpho-physiological traits that could be used to enhance crop yield under changing climate conditions.
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Affiliation(s)
- Sangil Lee
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
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22
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Zhang Y, Fan X, Wang Y, Kong P, Zhao L, Fan X, Zhang Y. OsNAR2.1 induced endogenous nitrogen concentration variation affects transcriptional expression of miRNAs in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1093676. [PMID: 36909394 PMCID: PMC9998545 DOI: 10.3389/fpls.2023.1093676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
The studies of rice nitrogen concentration on the expression of miRNA so far are mostly limited to the exogenous nitrogen, leaving the effect of endogenous nitrogen largely unexplored. OsNAR2.1 is a high-affinity nitrate transporter partner protein which plays a central role in nitrate absorption and translocation in rice. The expression of OsNAR2.1 could influence the concentration of the endogenous nitrogen in rice. We showed that the expression and production of miRNA in rice can be influenced by manipulating the endogenous nitrogen concentration via OsNAR2.1 transgenic lines. The small RNA content, particularly 24 nucleotides small RNA, expressed differently in two transgenic rice lines (nitrogen efficient line with overexpression of OsNAR2.1 (Ov199), nitrogen-inefficient line with knockdown OsNAR2.1 by RNAi (RNAi)) compared to the wild-type (NP). Comparative hierarchical clustering expression pattern analysis revealed that the expression profiles of mature miRNA in both transgenic lines were different from NP. Several previously unidentified miRNAs were identified to be differentially expressed under different nitrogen concentrations, namely miR1874, miR5150, chr3-36147, chr4-27017 and chr5-21745. In conclusion, our findings suggest that the level of endogenous nitrogen concentration variation by overexpression or knockdown OsNAR2.1 could mediate the expression pattern and intensity of miRNA in rice, which is of high potential to be used in molecular breeding to improve the rice responses towards nitrogen utilization.
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Affiliation(s)
- Yong Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Nanjing, China
| | - Xiaoru Fan
- School of Chemistry and Life Science, Anshan Normal University, Anshan, China
| | - Yulong Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Pulin Kong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Ling Zhao
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Nanjing, China
| | - Xiaorong Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Zhongshan Biological Breeding Laboratory, Nanjing, China
| | - Yadong Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Nanjing, China
- Zhongshan Biological Breeding Laboratory, Nanjing, China
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23
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Identification of Small RNAs Associated with Salt Stress in Chrysanthemums through High-Throughput Sequencing and Bioinformatics Analysis. Genes (Basel) 2023; 14:genes14030561. [PMID: 36980835 PMCID: PMC10048073 DOI: 10.3390/genes14030561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/12/2023] [Accepted: 02/20/2023] [Indexed: 02/27/2023] Open
Abstract
The Chrysanthemum variety “Niu 9717” exhibits excellent characteristics as an ornamental plant and has good salt resistance. In this study, this plant was treated with 200 mM NaCl for 12 h followed by high-throughput sequencing of miRNA and degradome. Subsequently, the regulatory patterns of potential miRNAs and their target genes were searched to elucidate how Chrysanthemum miRNAs respond to salt. From the root and leaf samples, we identified a total of 201 known miRNAs belonging to 40 families; furthermore, we identified 79 new miRNAs, of which 18 were significantly differentially expressed (p < 0.05). The expressed miRNAs, which targeted a total of 144 mRNAs in the leaf and 215 mRNAs in the root, formed 144 and 226 miRNA–target pairs in roots and leaves, respectively. Combined with the miRNA expression profile, degradome and transcriptome data were then analyzed to understand the possible effects of the miRNA target genes and their pathways on salt stress. The identified genes were mostly located in pathways related to hormone signaling during plant growth and development. Overall, these findings suggest that conserved and novel miRNAs may improve salt tolerance through the regulation of hormone signal synthesis or expression of genes involved in hormone synthesis.
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24
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Ahmad S, Lu C, Gao J, Wei Y, Xie Q, Jin J, Zhu G, Yang F. The Integrated mRNA and miRNA Approach Reveals Potential Regulators of Flowering Time in Arundina graminifolia. Int J Mol Sci 2023; 24:ijms24021699. [PMID: 36675213 PMCID: PMC9865619 DOI: 10.3390/ijms24021699] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Orchids are among the most precious flowers in the world. Regulation of flowering time is one of the most important targets to enhance their ornamental value. The beauty of Arundina graminifolia is its year-round flowering, although the molecular mechanism of this flowering ability remains masked. Therefore, we performed a comprehensive assessment to integrate transcriptome and miRNA sequencing to disentangle the genetic regulation of flowering in this valuable species. Clustering analyses provided a set of molecular regulators of floral transition and floral morphogenesis. We mined candidate floral homeotic genes, including FCA, FPA, GI, FT, FLC, AP2, SOC1, SVP, GI, TCP, and CO, which were targeted by a variety of miRNAs. MiR11091 targeted the highest number of genes, including candidate regulators of phase transition and hormonal control. The conserved miR156-miR172 pathway of floral time regulation was evident in our data, and we found important targets of these miRNAs in the transcriptome. Moreover, endogenous hormone levels were determined to decipher the hormonal control of floral buds in A. graminifolia. The qRT-PCR analysis of floral and hormonal integrators validated the transcriptome expression. Therefore, miRNA-mediated mining of candidate genes with hormonal regulation forms the basis for comprehending the complex regulatory network of perpetual flowering in precious orchids. The findings of this study can do a great deal to broaden the breeding programs for flowering time manipulation of orchids.
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Affiliation(s)
- Sagheer Ahmad
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Chuqiao Lu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jie Gao
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yonglu Wei
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Qi Xie
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jianpeng Jin
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Genfa Zhu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510640, China
| | - Fengxi Yang
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510640, China
- Correspondence: ; Tel.: +86-020-8516-1014
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25
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Shukla PS, Nivetha N, Nori SS, Bose D, Kumar S, Khandelwal S, Critchley A, Suryanarayan S. Understanding the mode of action of AgroGain ®, a biostimulant derived from the red seaweed Kappaphycus alvarezii in the stimulation of cotyledon expansion and growth of Cucumis sativa (cucumber). FRONTIERS IN PLANT SCIENCE 2023; 14:1136563. [PMID: 37089639 PMCID: PMC10118050 DOI: 10.3389/fpls.2023.1136563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/16/2023] [Indexed: 05/03/2023]
Abstract
Seaweed-based biostimulants are sustainable agriculture inputs that are known to have a multitude of beneficial effects on plant growth and productivity. This study demonstrates that Agrogain® (Product code: LBS6), a Kappaphycus alvarezii-derived biostimulant induced the expansion of cucumber cotyledons. Seven days treatment of LBS6-supplementation showed a 29.2% increase in area of expanded cotyledons, as compared to the control. LBS6-treated cotyledons also showed higher amylase activity, suggesting starch to sucrose conversion was used efficiently as an energy source during expansion. To understand the mechanisms of LBS6-induced expansion, real time gene expression analysis was carried out. This revealed that LBS6-treated cotyledons differentially modulated the expression of genes involved in cell division, cell number, cell expansion and cell size. LBS6 treatment also differentially regulated the expression of those genes involved in auxin and cytokinin metabolism. Further, foliar application of LBS6 on cucumber plants being grown under hydroponic conditions showed improved plant growth as compared to the control. The total leaf area of LBS6-sprayed plants increased by 19.1%, as compared to control. LBS6-sprayed plants efficiently regulated photosynthetic quenching by reducing loss via non-photochemical and non-regulatory quenching. LBS6 applications also modulated changes in the steady-state photosynthetic parameters of the cucumber leaves. It was demonstrated that LBS6 treatment modulated the electron and proton transport related pathways which help plants to efficiently utilize the photosynthetic radiation for optimal growth. These results provide clear evidence that bioactive compounds present in LBS6 improved the growth of cucumber plants by regulating the physiological as well as developmental pathways.
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Affiliation(s)
- Pushp Sheel Shukla
- Research and Development Division, Sea6 Energy Private Limited, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences-Tata Institute of Fundamental Research, Bengaluru, Karnataka, India
- *Correspondence: Pushp Sheel Shukla, ; Sri Sailaja Nori,
| | - Nagarajan Nivetha
- Research and Development Division, Sea6 Energy Private Limited, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences-Tata Institute of Fundamental Research, Bengaluru, Karnataka, India
| | - Sri Sailaja Nori
- Research and Development Division, Sea6 Energy Private Limited, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences-Tata Institute of Fundamental Research, Bengaluru, Karnataka, India
- *Correspondence: Pushp Sheel Shukla, ; Sri Sailaja Nori,
| | - Debayan Bose
- Research and Development Division, Sea6 Energy Private Limited, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences-Tata Institute of Fundamental Research, Bengaluru, Karnataka, India
| | - Sawan Kumar
- Research and Development Division, Sea6 Energy Private Limited, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences-Tata Institute of Fundamental Research, Bengaluru, Karnataka, India
| | - Sachin Khandelwal
- Research and Development Division, Sea6 Energy Private Limited, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences-Tata Institute of Fundamental Research, Bengaluru, Karnataka, India
| | - Alan Critchley
- Verschuren Centre for Sustainability in Energy and the Environment, Sydney, NS, Canada
| | - Shrikumar Suryanarayan
- Research and Development Division, Sea6 Energy Private Limited, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences-Tata Institute of Fundamental Research, Bengaluru, Karnataka, India
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26
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Yang X, Wang K, Ge L, Chen X, Zhang L, Song X. Transcription factor TaGAMYB from wheat (Triticum aestivum L.) regulates flowering time and fertility in transgenic Arabidopsis thaliana. PLANTA 2022; 257:16. [PMID: 36534157 DOI: 10.1007/s00425-022-04056-1] [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: 08/22/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
The loss of TaGAMYB function in Arabidopsis results in abnormal pollen development and leads to decreased fertility. This process may be regulated by microRNAs, which suppress the expression of fatty acid pathway genes. Development of the anthers and pollen is significantly influenced by the transcription factor GAMYB. However, our knowledge of GAMYB in wheat is limited. Here, under fertility and sterility conditions, we identified the distinct transcripts TaGAMYB-d and TaGAMYB-g in thermosensitive genic sterile wheat YanZhan 4110S and confirmed their functions. TaGAMYB-g overexpression decreased the pollen vigor and germination rates, thereby reducing fertility. TaGAMYB-d overexpression lines exhibited early flowering. Due to aberrant pollen germination, the mutant homologous TaGAMYB genes in Arabidopsis thaliana also resulted in lower fertility. Our findings indicate that TaGAMYB controls the fertility and flowering time in transgenic Arabidopsis thaliana.
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Affiliation(s)
- Xuetong Yang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Kai Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Limeng Ge
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xianning Chen
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Lingli Zhang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Xiyue Song
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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27
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Yang X, Wang K, Bu Y, Niu F, Ge L, Zhang L, Song X. The transcription factor TaGAMYB modulates tapetum and pollen development of TGMS wheat YanZhan 4110S via the gibberellin signaling. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111447. [PMID: 36041563 DOI: 10.1016/j.plantsci.2022.111447] [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: 06/22/2022] [Revised: 08/19/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Male reproductive development in higher plants experienced a series of complex biological processes, which can be regulated by Gibberellins (GA). The transcriptional factor GAMYB is a crucial component of GA signaling in anther development. However, the mechanism of GAMYB in wheat male reproduction is less understood. Here, we found that the thermo-sensitive genic male sterilitywheat line YanZhan 4110S displayed delayed tapetum programmed cell death and pollen abortive under the hot temperature stress. Combined with RNA-Sequencing data analysis, TaGAMYB associated with fertility conversion was isolated, which was located in the nucleus and highly expressed in fertility anthers. The silencing of TaGAMYB in wheat displayed fertility decline, defects in tapetum, pollen and exine formation, where the abortion characteristics were the same as YanZhan 4110S. In addition, either hot temperature or GA3 treatment in YanZhan 4110S caused the downregulation of TaGAMYB at binucleate stage and trinucleate stage, as well as fertility decrease. Further, the transcription factor TaWRKY2 significantly changed under GA3-treatment and directly interacted with the TaGAMYB promoter by W-box cis-element. Therefore, we suggested that TaGAMYB may be essential for anther development and male fertility, and GA3 activates TaGAMYB by TaWRKY2 to regulate fertility in wheat.
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Affiliation(s)
- Xuetong Yang
- College of Agronomy, Northwest A&F University, Yangling 712100 Shaanxi, China.
| | - Kai Wang
- College of Agronomy, Northwest A&F University, Yangling 712100 Shaanxi, China.
| | - Yaning Bu
- College of Agronomy, Northwest A&F University, Yangling 712100 Shaanxi, China.
| | - Fuqiang Niu
- College of Agronomy, Northwest A&F University, Yangling 712100 Shaanxi, China.
| | - Limeng Ge
- College of Agronomy, Northwest A&F University, Yangling 712100 Shaanxi, China.
| | - Lingli Zhang
- College of Agronomy, Northwest A&F University, Yangling 712100 Shaanxi, China.
| | - Xiyue Song
- College of Agronomy, Northwest A&F University, Yangling 712100 Shaanxi, China.
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28
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Sekhar S, Das S, Panda D, Mohanty S, Mishra B, Kumar A, Navadagi DB, Sah RP, Pradhan SK, Samantaray S, Baig MJ, Behera L, Mohapatra T. Identification of microRNAs That Provide a Low Light Stress Tolerance-Mediated Signaling Pathway during Vegetative Growth in Rice. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11192558. [PMID: 36235424 PMCID: PMC9614602 DOI: 10.3390/plants11192558] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/16/2022] [Accepted: 09/22/2022] [Indexed: 05/27/2023]
Abstract
Low light intensity affects several physiological parameters during the different growth stages in rice. Plants have various regulatory mechanisms to cope with stresses. One of them is the differential and temporal expression of genes, which is governed by post-transcriptional gene expression regulation through endogenous miRNAs. To decipher low light stress-responsive miRNAs in rice, miRNA expression profiling was carried out using next-generation sequencing of low-light-tolerant (Swarnaprabha) and -sensitive (IR8) rice genotypes through Illumina sequencing. Swarnaprabha and IR8 were subjected to 25% low light treatment for one day, three days, and five days at the active tillering stage. More than 43 million raw reads and 9 million clean reads were identified in Swarnaprabha, while more than 41 million raw reads and 8.5 million clean reads were identified in IR8 after NGS. Importantly, 513 new miRNAs in rice were identified, whose targets were mostly regulated by the genes involved in photosynthesis and metabolic pathways. Additionally, 114 known miRNAs were also identified. Five novel (osa-novmiR1, osa-novmiR2, osa-novmiR3, osa-novmiR4, and osa-novmiR5) and three known (osa-miR166c-3p, osa-miR2102-3p, and osa-miR530-3p) miRNAs were selected for their expression validation through miRNA-specific qRT-PCR. The expression analyses of most of the predicted targets of corresponding miRNAs show negative regulation. Hence, miRNAs modulated the expression of genes providing tolerance/susceptibility to low light stress. This information might be useful in the improvement of crop productivity under low light stress.
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Affiliation(s)
- Sudhanshu Sekhar
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack 753006, India
| | - Swagatika Das
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack 753006, India
| | - Darshan Panda
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack 753006, India
| | - Soumya Mohanty
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack 753006, India
| | - Baneeta Mishra
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack 753006, India
| | - Awadhesh Kumar
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack 753006, India
| | | | - Rameswar Prasad Sah
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack 753006, India
| | - Sharat Kumar Pradhan
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack 753006, India
| | - Sanghamitra Samantaray
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack 753006, India
| | - Mirza Jaynul Baig
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack 753006, India
| | - Lambodar Behera
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack 753006, India
| | - Trilochan Mohapatra
- Former Secretary DARE, DG, ICAR, Government. of India, New Delhi 11001, India
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Zand Karimi H, Innes RW. Molecular mechanisms underlying host-induced gene silencing. THE PLANT CELL 2022; 34:3183-3199. [PMID: 35666177 PMCID: PMC9421479 DOI: 10.1093/plcell/koac165] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/08/2022] [Indexed: 05/05/2023]
Abstract
Host-induced gene silencing (HIGS) refers to the silencing of genes in pathogens and pests by expressing homologous double-stranded RNAs (dsRNA) or artificial microRNAs (amiRNAs) in the host plant. The discovery of such trans-kingdom RNA silencing has enabled the development of RNA interference-based approaches for controlling diverse crop pathogens and pests. Although HIGS is a promising strategy, the mechanisms by which these regulatory RNAs translocate from plants to pathogens, and how they induce gene silencing in pathogens, are poorly understood. This lack of understanding has led to large variability in the efficacy of various HIGS treatments. This variability is likely due to multiple factors, such as the ability of the target pathogen or pest to take up and/or process RNA from the host, the specific genes and target sequences selected in the pathogen or pest for silencing, and where, when, and how the dsRNAs or amiRNAs are produced and translocated. In this review, we summarize what is currently known about the molecular mechanisms underlying HIGS, identify key unanswered questions, and explore strategies for improving the efficacy and reproducibility of HIGS treatments in the control of crop diseases.
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Affiliation(s)
- Hana Zand Karimi
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
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30
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Molecular Aspects of MicroRNAs and Phytohormonal Signaling in Response to Drought Stress: A Review. Curr Issues Mol Biol 2022; 44:3695-3710. [PMID: 36005149 PMCID: PMC9406886 DOI: 10.3390/cimb44080253] [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: 06/26/2022] [Revised: 07/29/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
Phytohormones play an essential role in plant growth and development in response to environmental stresses. However, plant hormones require a complex signaling network combined with other signaling pathways to perform their proper functions. Thus, multiple phytohormonal signaling pathways are a prerequisite for understanding plant defense mechanism against stressful conditions. MicroRNAs (miRNAs) are master regulators of eukaryotic gene expression and are also influenced by a wide range of plant development events by suppressing their target genes. In recent decades, the mechanisms of phytohormone biosynthesis, signaling, pathways of miRNA biosynthesis and regulation were profoundly characterized. Recent findings have shown that miRNAs and plant hormones are integrated with the regulation of environmental stress. miRNAs target several components of phytohormone pathways, and plant hormones also regulate the expression of miRNAs or their target genes inversely. In this article, recent developments related to molecular linkages between miRNAs and phytohormones were reviewed, focusing on drought stress.
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31
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Cheng X, Pang F, Tian W, Tang X, Wu L, Hu X, Zhu H. Transcriptome analysis provides insights into the molecular mechanism of GhSAMDC 1 involving in rapid vegetative growth and early flowering in tobacco. Sci Rep 2022; 12:13612. [PMID: 35948667 PMCID: PMC9365820 DOI: 10.1038/s41598-022-18064-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
In previous study, ectopic expression of GhSAMDC1 improved vegetative growth and early flowering in tobacco, which had been explained through changes of polyamine content, polyamines and flowering relate genes expression. To further disclose the transcript changes of ectopic expression of GhSAMDC1 in tobacco, the leaves from wild type and two transgenic lines at seedling (30 days old), bolting (60 days old) and flowering (90 days old) stages were performed for transcriptome analysis. Compared to wild type, a total of 938 differentially expressed genes (DEGs) were found to be up- or down-regulated in the two transgenic plants. GO and KEGG analysis revealed that tobacco of wild-type and transgenic lines were controlled by a complex gene network, which regulated multiple metabolic pathways. Phytohormone detection indicate GhSAMDC1 affect endogenous phytohormone content, ABA and JA content are remarkably increased in transgenic plants. Furthermore, transcript factor analysis indicated 18 transcript factor families, including stress response, development and flowering related transcript factor families, especially AP2-EREBP, WRKY, HSF and Tify are the most over-represented in those transcript factor families. In conclusion, transcriptome analysis provides insights into the molecular mechanism of GhSAMDC1 involving rapid vegetative growth and early flowering in tobacco.
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Affiliation(s)
- Xinqi Cheng
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei, China.,Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang, 438000, Hubei, China
| | - Fangqin Pang
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei, China.,Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang, 438000, Hubei, China
| | - Wengang Tian
- College of Agronomy, Shihezi University, Shihezi, 832000, Xinjiang, China
| | - Xinxin Tang
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei, China.,Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang, 438000, Hubei, China
| | - Lan Wu
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei, China.,Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang, 438000, Hubei, China
| | - Xiaoming Hu
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei, China.,Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang, 438000, Hubei, China
| | - Huaguo Zhu
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei, China. .,Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang, 438000, Hubei, China.
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32
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Bai Y, Zhang X, Xuan X, Sadeghnezhad E, Liu F, Dong T, Pei D, Fang J, Wang C. miR3633a- GA3ox2 Module Conducts Grape Seed-Embryo Abortion in Response to Gibberellin. Int J Mol Sci 2022; 23:ijms23158767. [PMID: 35955901 PMCID: PMC9369392 DOI: 10.3390/ijms23158767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 07/28/2022] [Accepted: 07/28/2022] [Indexed: 12/04/2022] Open
Abstract
Seedlessness is one of the important quality and economic traits favored by grapevine consumers, which are mainly affected by phytohormones, especially gibberellin (GA). GA is widely utilized in seedless berry production and could effectively induce grape seed embryo abortion. However, the molecular mechanism underlying this process, like the role of RNA silencing in the biosynthesis pathway of GA remains elusive. Here, Gibberellin 3-β dioxygenase2 (GA3ox2) as the last key enzyme in GA biosynthesis was predicated as a potential target gene for miR3633a, and two of them were identified as a GA response in grape berries. We also analyzed the promoter regions of genes encoding GA biosynthesis and found the hormone-responsive elements to regulate grape growth and development. The cleavage interaction between VvmiR3633a and VvGA3ox2 was validated by RLM-RACE and the transient co-transformation technique in tobacco in vivo. Interestingly, during GA-induced grape seed embryo abortion, exogenous GA promoted the expression of VvmiR3633a, thereby mainly repressing the level of VvGA3ox2 in seed embryos. We also observed a negative correlation between down-regulated VvGA20ox2/VvGA3ox2 and up-regulated VvGA2ox3/VvGA2ox1, of which GA inactivation was greater than GA synthesis, inhibited active GA content, accompanied by the reduction of VvSOD and VvCAT expression levels and enzymatic activities. These series of changes might be the main causes of grape seed embryo abortion. In conclusion, we have preliminarily drawn a schematic mode of GA-mediated VvmiR3633a and related genes regulatory network during grape seed abortion induced by exogenous GA. Our findings provide novel insights into the GA-responsive roles of the VvmiR3633a-VvGA3ox2 module in the modulation of grape seed-embryo abortion, which has implications for the molecular breeding of high-quality seedless grape berries.
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Affiliation(s)
- Yunhe Bai
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaowen Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuxian Xuan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ehsan Sadeghnezhad
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Department of Plant Biology, Faculty of Biological Science, Tarbiat Modares University, Tehran P.O. Box 14115-111, Iran
| | - Fei Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianyu Dong
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Dan Pei
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinggui Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Chen Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence:
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Imran M, Liu T, Wang Z, Wang M, Liu S, Gao X, Wang A, Liu S, Tian Z, Zhang M. Evolutionary conservation of nested MIR159 structural microRNA genes and their promoter characterization in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:948751. [PMID: 35958213 PMCID: PMC9361848 DOI: 10.3389/fpls.2022.948751] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
MicroRNAs (miRNAs) are endogenous small RNAs, that are vital for gene expression regulation in eukaryotes. Whenever a pri-miRNA precursor includes another miRNA precursor, and both of these precursors may generate independent, non-overlapping mature miRNAs, we named them nested miRNAs. However, the extent of nested miR159 structural evolutionary conservation and its promoter characterization remains unknown. In this study, the sequence alignment and phylogenetic analysis reveal that the MIR159 family is ancient, and its nested miR159 structures are evolutionary conserved in different plant species. The overexpression of ath-MIR159a, including the 1.2 kb downstream region, has no effect on rescuing the mir159ab phenotype. The promoter truncation results revealed that the 1.0 kb promoter of ath-MIR159a is sufficient for rescuing the mir159ab phenotype. The cis-regulatory elements in the ath-miR159a promoters indicated functions related to different phytohormones, abiotic stresses, and transcriptional activation. While the MybSt1 motif-containing region is not responsible for activating the regulation of the miR159a promoter. The qRT-PCR results showed that overexpression of ath-MIR159a led to high expression levels of miR159a.1-5 and miR159a.1-3 and complemented the growth defect of mir159ab via downregulation of MYB33 and MYB65. Furthermore, continuously higher expression of the miR159a.2 duplex in transgenic lines with the curly leaf phenotype indicates that miR159a.2 is functional in Arabidopsis and suggests that it is possible for a miRNA precursor to encode several regulatory small RNAs in plants. Taken together, our study demonstrates that the nested miR159 structure is evolutionary conserved and miRNA-mediated gene regulation is more complex than previously thought.
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Affiliation(s)
- Muhammad Imran
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Tengfei Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zheng Wang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
| | - Min Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Xinyan Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Anning Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Songfeng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
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Zhao P, Wang F, Deng Y, Zhong F, Tian P, Lin D, Deng J, Zhang Y, Huang T. Sly-miR159 regulates fruit morphology by modulating GA biosynthesis in tomato. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:833-845. [PMID: 34882929 PMCID: PMC9055814 DOI: 10.1111/pbi.13762] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 11/28/2021] [Indexed: 05/29/2023]
Abstract
Fruit morphology is an important agronomical trait of many crops. Here, we identify Sly-miR159 as an important regulator of fruit morphology in tomato, a model species of fleshy-fruit development. We show that Sly-miR159 functions through its target SlGAMYB2 to control fruit growth. Suppression of Sly-miR159 and overexpression of SlGAMYB2 result in larger fruits with a reduced length/width ratio, while loss of function of SlGAMYB2 leads to the formation of smaller and more elongated fruits. Gibberellin (GA) is a major phytohormone that regulates fruit development in tomato. We show the Sly-miR159-SlGAMYB2 pathway controls fruit morphology by modulating GA biosynthesis. In particular, we demonstrate that Sly-miR159 promotes GA biosynthesis largely through the direct repression of the GA biosynthetic gene SlGA3ox2 by SlGAMYB2. Together, our findings reveal the action of Sly-miR159 on GA biosynthesis as a previously unidentified mechanism that controls fruit morphology in tomato. Modulating this pathway may have potential applications in tomato breeding for manipulating fruit growth and facilitating the process of fruit improvement.
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Affiliation(s)
- Panpan Zhao
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and GuangdongCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenGuangdongChina
| | - Fengpan Wang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and GuangdongCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenGuangdongChina
| | - Yinjiao Deng
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| | - Fanjia Zhong
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| | - Peng Tian
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and GuangdongCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenGuangdongChina
| | - Dongbo Lin
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and GuangdongCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenGuangdongChina
| | - Juhui Deng
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| | - Yongxia Zhang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| | - Tengbo Huang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
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35
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Wang J, Jiang X, Bai H, Liu C. Genome-wide identification, classification and expression analysis of the JmjC domain-containing histone demethylase gene family in Jatropha curcas L. Sci Rep 2022; 12:6543. [PMID: 35449230 PMCID: PMC9023485 DOI: 10.1038/s41598-022-10584-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 04/05/2022] [Indexed: 12/20/2022] Open
Abstract
JmjC domain-containing proteins, an important family of histone lysine demethylase, play significant roles in maintaining the homeostasis of histone methylation. In this study, we comprehensively analyzed the JmjC domain-containing gene family in Jatropha curcas and found 20 JmjC domain-containing genes (JcJMJ genes). Phylogenetic analysis revealed that these JcJMJ genes can be classified into five major subgroups, and genes in each subgroup had similar motif and domain composition. Cis-regulatory element analysis showed that the number and types of cis-regulatory elements owned by the promoter of JcJMJ genes in different subgroup were significantly different. Moreover, miRNA target prediction result revealed a complicated miRNA-mediated post-transcriptional regulatory network, in which JcJMJ genes were regulated by different numbers and types of miRNAs. Further analysis of the tissue and stress expression profiles showed that many JcJMJ genes had tissue and stress expression specificity. All these results provided valuable information for understanding the evolution of JcJMJ genes and the complex transcriptional and post transcriptional regulation involved, and laid the foundation for further functional analysis of JcJMJ genes.
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Affiliation(s)
- Jie Wang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoke Jiang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hanrui Bai
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
- College of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China.
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, MenglaYunnan, 666303, China.
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Ma X, Zhao F, Zhou B. The Characters of Non-Coding RNAs and Their Biological Roles in Plant Development and Abiotic Stress Response. Int J Mol Sci 2022; 23:ijms23084124. [PMID: 35456943 PMCID: PMC9032736 DOI: 10.3390/ijms23084124] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/30/2022] [Accepted: 04/06/2022] [Indexed: 02/07/2023] Open
Abstract
Plant growth and development are greatly affected by the environment. Many genes have been identified to be involved in regulating plant development and adaption of abiotic stress. Apart from protein-coding genes, more and more evidence indicates that non-coding RNAs (ncRNAs), including small RNAs and long ncRNAs (lncRNAs), can target plant developmental and stress-responsive mRNAs, regulatory genes, DNA regulatory regions, and proteins to regulate the transcription of various genes at the transcriptional, posttranscriptional, and epigenetic level. Currently, the molecular regulatory mechanisms of sRNAs and lncRNAs controlling plant development and abiotic response are being deeply explored. In this review, we summarize the recent research progress of small RNAs and lncRNAs in plants, focusing on the signal factors, expression characters, targets functions, and interplay network of ncRNAs and their targets in plant development and abiotic stress responses. The complex molecular regulatory pathways among small RNAs, lncRNAs, and targets in plants are also discussed. Understanding molecular mechanisms and functional implications of ncRNAs in various abiotic stress responses and development will benefit us in regard to the use of ncRNAs as potential character-determining factors in molecular plant breeding.
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Affiliation(s)
- Xu Ma
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Ministry of Education, Harbin 150040, China;
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Fei Zhao
- Horticulture Science and Engineering, Shandong Agricultural University, Taian 271018, China
- Correspondence: (F.Z.); (B.Z.); Tel.: +86-0538-8243-965 (F.Z.); +86-0451-8219-1738 (B.Z.)
| | - Bo Zhou
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Ministry of Education, Harbin 150040, China;
- College of Life Science, Northeast Forestry University, Harbin 150040, China
- Correspondence: (F.Z.); (B.Z.); Tel.: +86-0538-8243-965 (F.Z.); +86-0451-8219-1738 (B.Z.)
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37
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Ivanova Z, Minkov G, Gisel A, Yahubyan G, Minkov I, Toneva V, Baev V. The Multiverse of Plant Small RNAs: How Can We Explore It?
. Int J Mol Sci 2022; 23:ijms23073979. [PMID: 35409340 PMCID: PMC8999349 DOI: 10.3390/ijms23073979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 12/22/2022] Open
Abstract
Plant small RNAs (sRNAs) are a heterogeneous group of noncoding RNAs with a length of 20–24 nucleotides that are widely studied due to their importance as major regulators in various biological processes. sRNAs are divided into two main classes—microRNAs (miRNAs) and small interfering RNAs (siRNAs)—which differ in their biogenesis and functional pathways. Their identification and enrichment with new structural variants would not be possible without the use of various high-throughput sequencing (NGS) techniques, allowing for the detection of the total population of sRNAs in plants. Classifying sRNAs and predicting their functional role based on such high-performance datasets is a nontrivial bioinformatics task, as plants can generate millions of sRNAs from a variety of biosynthetic pathways. Over the years, many computing tools have been developed to meet this challenge. Here, we review more than 35 tools developed specifically for plant sRNAs over the past few years and explore some of their basic algorithms for performing tasks related to predicting, identifying, categorizing, and quantifying individual sRNAs in plant samples, as well as visualizing the results of these analyzes. We believe that this review will be practical for biologists who want to analyze their plant sRNA datasets but are overwhelmed by the number of tools available, thus answering the basic question of how to choose the right one for a particular study.
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Affiliation(s)
- Zdravka Ivanova
- Institute of Molecular Biology and Biotechnologies, 4108 Markovo, Bulgaria; (Z.I.); (G.M.); (I.M.); (V.T.)
| | - Georgi Minkov
- Institute of Molecular Biology and Biotechnologies, 4108 Markovo, Bulgaria; (Z.I.); (G.M.); (I.M.); (V.T.)
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 4000 Plovdiv, Bulgaria;
| | - Andreas Gisel
- Institute of Biomedical Technologies (ITB), CNR, 70126 Bari, Italy;
| | - Galina Yahubyan
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 4000 Plovdiv, Bulgaria;
| | - Ivan Minkov
- Institute of Molecular Biology and Biotechnologies, 4108 Markovo, Bulgaria; (Z.I.); (G.M.); (I.M.); (V.T.)
- Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Valentina Toneva
- Institute of Molecular Biology and Biotechnologies, 4108 Markovo, Bulgaria; (Z.I.); (G.M.); (I.M.); (V.T.)
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 4000 Plovdiv, Bulgaria;
| | - Vesselin Baev
- Institute of Molecular Biology and Biotechnologies, 4108 Markovo, Bulgaria; (Z.I.); (G.M.); (I.M.); (V.T.)
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 4000 Plovdiv, Bulgaria;
- Correspondence:
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Yan W, Cao S, Wu Y, Ye Z, Zhang C, Yao G, Yu J, Yang D, Zhang J. Integrated Analysis of Physiological, mRNA Sequencing, and miRNA Sequencing Data Reveals a Specific Mechanism for the Response to Continuous Cropping Obstacles in Pogostemon cablin Roots. FRONTIERS IN PLANT SCIENCE 2022; 13:853110. [PMID: 35432413 PMCID: PMC9010791 DOI: 10.3389/fpls.2022.853110] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/07/2022] [Indexed: 06/02/2023]
Abstract
Pogostemon cablin (patchouli) is a commercially important medicinal and industrial crop grown worldwide for its medicinal and aromatic properties. Patchoulol and pogostone, derived from the essential oil of patchouli, are considered valuable components in the cosmetic and pharmaceutical industries. Due to its high application value in the clinic and industry, the demand for patchouli is constantly growing. Unfortunately, patchouli cultivation has suffered due to severe continuous cropping obstacles, resulting in a significant decline in yield and quality. Moreover, the physiological and transcriptional changes in patchouli in response to continuous cropping obstacles remain unclear. This has greatly restricted the development of the patchouli industry. To explore the mechanism underlying the rapid response of patchouli roots to continuous cropping stress, integrated analysis of the transcriptome and miRNA profiles of patchouli roots under continuous and noncontinuous cropping conditions in different growth periods was conducted using RNA sequencing (RNA-seq) and miRNA-seq and complemented with physiological data. The physiological and biochemical results showed that continuous cropping significantly inhibited root growth, decreased root activity, and increased the activity of antioxidant enzymes (superoxide dismutase, peroxidase, and catalase) and the levels of osmoregulators (malondialdehyde, soluble protein, soluble sugar, and proline). Subsequently, we found 4,238, 3,494, and 7,290 upregulated and 4,176, 3,202, and 8,599 downregulated differentially expressed genes (DEGs) in the three growth periods of continuously cropped patchouli, many of which were associated with primary carbon and nitrogen metabolism, defense responses, secondary metabolite biosynthesis, and transcription factors. Based on miRNA-seq, 927 known miRNAs and 130 novel miRNAs were identified, among which 67 differentially expressed miRNAs (DEMIs) belonging to 24 miRNA families were induced or repressed by continuous cropping. By combining transcriptome and miRNA profiling, we obtained 47 miRNA-target gene pairs, consisting of 18 DEMIs and 43 DEGs, that likely play important roles in the continuous cropping response of patchouli. The information provided in this study will contribute to clarifying the intricate mechanism underlying the patchouli response to continuous cropping obstacles. In addition, the candidate miRNAs and genes can provide a new strategy for breeding continuous cropping-tolerant patchouli.
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An Integrated Analysis of Transcriptome and miRNA Sequencing Provides Insights into the Dynamic Regulations during Flower Morphogenesis in Petunia. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8040284] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Published genome sequences can facilitate multiple genome sequencing studies of flower development, which can serve as the basis for later analysis of variation in flower phenotypes. To identify potential regulators related to flower morphology, we captured dynamic expression patterns under five different developmental stages of petunia flowers, a popular bedding plant, using transcriptome and miRNA sequencing. The significant transcription factor (TF) families, including MYB, MADS, and bHLH, were elucidated. MADS-box genes exhibited co-expression patterns with BBR-BPC, GATA, and Dof genes in different modules according to a weighted gene co-expression network analysis. Through miRNA sequencing, a total of 45 conserved and 26 novel miRNAs were identified. According to GO and KEGG enrichment analysis, the carbohydrate metabolic process, photosynthesis, and phenylalanine metabolism were significant at the transcriptomic level, while the response to hormone pathways was significantly enriched by DEmiR-targeted genes. Finally, an miRNA–RNA network was constructed, which suggested the possibility of novel miRNA-mediated regulation pathways being activated during flower development. Overall, the expression data in the present study provide novel insights into the developmental gene regulatory network facilitated by TFs, miRNA, and their target genes.
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Su Z, Xuan X, Sheng Z, Wang F, Zhang X, Ye D, Wang X, Dong T, Pei D, Zhang P, Fang J, Wang C. Characterization and regulatory mechanism analysis of VvmiR156a-VvAGL80 pair during grapevine flowering and parthenocarpy process induced by gibberellin. THE PLANT GENOME 2022; 15:e20181. [PMID: 34882981 DOI: 10.1002/tpg2.20181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
MicroRNA156 (miR156) is an important conserved miRNA family in plants. Recently, we revealed VvmiR156a could involve in the modulation of gibberellin (GA)-mediated flower and berry development process of grapevine (Vitis vinifera L.). However, how to manipulate this process is unclear. For this, we used the GA-induced grapevine parthenocarpy system to investigate the regulatory roles of VvmiR156a during this process. Here, we cloned the mature and precursor sequences of VvmiR156a in Wink grape and identified its potential target gene VvAGL80, which belongs to the MADS-box gene family. Moreover, using RNA ligase-mediated 5' rapid amplification of cDNA ends (RLM-RACE) and poly(A)polymerase-mediated 3' rapid amplification of cDNA (PPM-RACE) technologies, it confirmed that VvAGL80 was the true target gene of VvmiR159a. Analysis of promoter cis-elements and β-glucuronidase (GUS) staining showed that both VvmiR156a and VvAGL80 contained GA-responsive elements and could respond to GA treatments. Quantitative real-time-polymerase chain reaction (qRT-PCR) analysis exhibited the VvmiR156a and VvAGL80 showed opposite expression trends during grapevine flower and berry development, indicating that VvmiR156a negatively regulated the expression of VvAGL80 during this process. After GA treatment, the expression of miR156 in flowers was downregulated significantly, while that of VvAGL80 was upregulated, thereby accelerating grapevine flowering. Furthermore, GA treatment enhanced the negative regulation of VvmiR156a on VvAGL80 in seed, especially at the seed-coat hardening stage, which was the key period of seed growth and development. Our findings enriched the knowledge of the regulatory mechanism of the miRNA-mediated grapevine parthenocarpy process.
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Affiliation(s)
- Ziwen Su
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, China
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Xuxian Xuan
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, China
| | - Zilu Sheng
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, China
| | - Fei Wang
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, China
| | - Xiaowen Zhang
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, China
| | - Dongdong Ye
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, China
| | - Xicheng Wang
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Tianyu Dong
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, China
| | - Dan Pei
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, China
| | - Peian Zhang
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, China
| | - Jinggui Fang
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, China
| | - Chen Wang
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, China
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Dong Q, Hu B, Zhang C. microRNAs and Their Roles in Plant Development. FRONTIERS IN PLANT SCIENCE 2022; 13:824240. [PMID: 35251094 PMCID: PMC8895298 DOI: 10.3389/fpls.2022.824240] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/27/2022] [Indexed: 05/26/2023]
Abstract
Small RNAs are short non-coding RNAs with a length ranging between 20 and 24 nucleotides. Of these, microRNAs (miRNAs) play a distinct role in plant development. miRNAs control target gene expression at the post-transcriptional level, either through direct cleavage or inhibition of translation. miRNAs participate in nearly all the developmental processes in plants, such as juvenile-to-adult transition, shoot apical meristem development, leaf morphogenesis, floral organ formation, and flowering time determination. This review summarizes the research progress in miRNA-mediated gene regulation and its role in plant development, to provide the basis for further in-depth exploration regarding the function of miRNAs and the elucidation of the molecular mechanism underlying the interaction of miRNAs and other pathways.
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Affiliation(s)
- Qingkun Dong
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Binbin Hu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Cui Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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42
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The Genetic and Hormonal Inducers of Continuous Flowering in Orchids: An Emerging View. Cells 2022; 11:cells11040657. [PMID: 35203310 PMCID: PMC8870070 DOI: 10.3390/cells11040657] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 02/07/2023] Open
Abstract
Orchids are the flowers of magnetic beauty. Vivid and attractive flowers with magnificent shapes make them the king of the floriculture industry. However, the long-awaited flowering is a drawback to their market success, and therefore, flowering time regulation is the key to studies about orchid flower development. Although there are some rare orchids with a continuous flowering pattern, the molecular regulatory mechanisms are yet to be elucidated to find applicable solutions to other orchid species. Multiple regulatory pathways, such as photoperiod, vernalization, circadian clock, temperature and hormonal pathways are thought to signalize flower timing using a group of floral integrators. This mini review, thus, organizes the current knowledge of floral time regulators to suggest future perspectives on the continuous flowering mechanism that may help to plan functional studies to induce flowering revolution in precious orchid species.
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RNA-Binding Protein MAC5A Is Required for Gibberellin-Regulated Stamen Development. Int J Mol Sci 2022; 23:ijms23042009. [PMID: 35216125 PMCID: PMC8874600 DOI: 10.3390/ijms23042009] [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: 01/25/2022] [Revised: 02/09/2022] [Accepted: 02/09/2022] [Indexed: 11/23/2022] Open
Abstract
The development of floral organs is coordinated by an elaborate network of homeotic genes, and gibberellin (GA) signaling is involved in floral organ development; however, the underlying molecular mechanisms remain elusive. In the present study, we found that MOS4-ASSOCIATED COMPLEX 5A (MAC5A), which is a protein containing an RNA-binding motif, was involved in the development of sepals, petals, and stamens; either the loss or gain of MAC5A function resulted in stamen malformation and a reduced seed set. The exogenous application of GA considerably exacerbated the defects in mac5a null mutants, including fewer stamens and male sterility. MAC5A was predominantly expressed in pollen grains and stamens, and overexpression of MAC5A affected the expression of homeotic genes such as APETALA1 (AP1), AP2, and AGAMOUS (AG). MAC5A may interact with RABBIT EARS (RBE), a repressor of AG expression in Arabidopsis flowers. The petal defect in rbe null mutants was at least partly rescued in mac5a rbe double mutants. These findings suggest that MAC5A is a novel factor that is required for the normal development of stamens and depends on the GA signaling pathway.
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Luo P, Di D, Wu L, Yang J, Lu Y, Shi W. MicroRNAs Are Involved in Regulating Plant Development and Stress Response through Fine-Tuning of TIR1/AFB-Dependent Auxin Signaling. Int J Mol Sci 2022; 23:ijms23010510. [PMID: 35008937 PMCID: PMC8745101 DOI: 10.3390/ijms23010510] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/27/2021] [Accepted: 01/01/2022] [Indexed: 11/30/2022] Open
Abstract
Auxin, primarily indole-3-acetic acid (IAA), is a versatile signal molecule that regulates many aspects of plant growth, development, and stress response. Recently, microRNAs (miRNAs), a type of short non-coding RNA, have emerged as master regulators of the auxin response pathways by affecting auxin homeostasis and perception in plants. The combination of these miRNAs and the autoregulation of the auxin signaling pathways, as well as the interaction with other hormones, creates a regulatory network that controls the level of auxin perception and signal transduction to maintain signaling homeostasis. In this review, we will detail the miRNAs involved in auxin signaling to illustrate its in planta complex regulation.
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Affiliation(s)
- Pan Luo
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
- Correspondence: (P.L.); (D.D.)
| | - Dongwei Di
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (Y.L.); (W.S.)
- Correspondence: (P.L.); (D.D.)
| | - Lei Wu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China;
| | - Jiangwei Yang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
| | - Yufang Lu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (Y.L.); (W.S.)
| | - Weiming Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (Y.L.); (W.S.)
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Kumar S, Abass Ahanger M, Alshaya H, Latief Jan B, Yerramilli V. Salicylic acid mitigates salt induced toxicity through the modifications of biochemical attributes and some key antioxidants in capsicum annuum. Saudi J Biol Sci 2022. [DOI: 10.1016/j.sjbs.2022.01.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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46
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Lei P, Qi N, Zhou Y, Wang Y, Zhu X, Xuan Y, Liu X, Fan H, Chen L, Duan Y. Soybean miR159 -GmMYB33 Regulatory Network Involved in Gibberellin-Modulated Resistance to Heterodera glycines. Int J Mol Sci 2021; 22:13172. [PMID: 34884977 PMCID: PMC8658632 DOI: 10.3390/ijms222313172] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 11/16/2022] Open
Abstract
Soybean cyst nematode (SCN, Heterodera glycines) is an obligate sedentary biotroph that poses major threats to soybean production globally. Recently, multiple miRNAome studies revealed that miRNAs participate in complicated soybean-SCN interactions by regulating their target genes. However, the functional roles of miRNA and target genes regulatory network are still poorly understood. In present study, we firstly investigated the expression patterns of miR159 and targeted GmMYB33 genes. The results showed miR159-3p downregulation during SCN infection; conversely, GmMYB33 genes upregulated. Furthermore, miR159 overexpressing and silencing soybean hairy roots exhibited strong resistance and susceptibility to H. glycines, respectively. In particular, miR159-GAMYB genes are reported to be involve in GA signaling and metabolism. Therefore, we then investigated the effects of GA application on the expression of miR159-GAMYB module and the development of H. glycines. We found that GA directly controls the miR159-GAMYB module, and exogenous GA application enhanced endogenous biologically active GA1 and GA3, the abundance of miR159, lowered the expression of GmMYB33 genes and delayed the development of H. glycines. Moreover, SCN infection also results in endogenous GA content decreased in soybean roots. In summary, the soybean miR159-GmMYB33 module was directly involved in the GA-modulated soybean resistance to H. glycines.
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Affiliation(s)
- Piao Lei
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (N.Q.); (Y.Z.); (Y.W.); (X.Z.); (Y.X.); (X.L.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Nawei Qi
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (N.Q.); (Y.Z.); (Y.W.); (X.Z.); (Y.X.); (X.L.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuan Zhou
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (N.Q.); (Y.Z.); (Y.W.); (X.Z.); (Y.X.); (X.L.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuanyuan Wang
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (N.Q.); (Y.Z.); (Y.W.); (X.Z.); (Y.X.); (X.L.); (H.F.); (L.C.)
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaofeng Zhu
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (N.Q.); (Y.Z.); (Y.W.); (X.Z.); (Y.X.); (X.L.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuanhu Xuan
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (N.Q.); (Y.Z.); (Y.W.); (X.Z.); (Y.X.); (X.L.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaoyu Liu
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (N.Q.); (Y.Z.); (Y.W.); (X.Z.); (Y.X.); (X.L.); (H.F.); (L.C.)
- College of Sciences, Shenyang Agricultural University, Shenyang 110866, China
| | - Haiyan Fan
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (N.Q.); (Y.Z.); (Y.W.); (X.Z.); (Y.X.); (X.L.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Lijie Chen
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (N.Q.); (Y.Z.); (Y.W.); (X.Z.); (Y.X.); (X.L.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuxi Duan
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (N.Q.); (Y.Z.); (Y.W.); (X.Z.); (Y.X.); (X.L.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
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miRNAomic Approach to Plant Nitrogen Starvation. Int J Genomics 2021; 2021:8560323. [PMID: 34796230 PMCID: PMC8595019 DOI: 10.1155/2021/8560323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/02/2022] Open
Abstract
Nitrogen (N) is one of the indispensable nutrients required by plants for their growth, development, and survival. Being a limited nutrient, it is mostly supplied exogenously to the plants, to maintain quality and productivity. The increased use of N fertilizers is associated with high-cost inputs and negative environmental consequences, which necessitates the development of nitrogen-use-efficient plants for sustainable agriculture. Understanding the regulatory mechanisms underlying N metabolism in plants under low N is one of the prerequisites for the development of nitrogen-use-efficient plants. One of the important and recently discovered groups of regulatory molecules acting at the posttranscriptional and translational levels are microRNAs (miRNAs). miRNAs are known to play critical roles in the regulation of gene expression in plants under different stress conditions including N stress. Several classes of miRNAs associated with N metabolism have been identified so far. These nitrogen-responsive miRNAs may provide a platform for a better understanding of the regulation of N metabolism and pave a way for the development of genotypes for better N utilization. The current review presents a brief outline of miRNAs and their regulatory role in N metabolism.
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Gelaw TA, Sanan-Mishra N. Non-Coding RNAs in Response to Drought Stress. Int J Mol Sci 2021; 22:12519. [PMID: 34830399 PMCID: PMC8621352 DOI: 10.3390/ijms222212519] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 02/06/2023] Open
Abstract
Drought stress causes changes in the morphological, physiological, biochemical and molecular characteristics of plants. The response to drought in different plants may vary from avoidance, tolerance and escape to recovery from stress. This response is genetically programmed and regulated in a very complex yet synchronized manner. The crucial genetic regulations mediated by non-coding RNAs (ncRNAs) have emerged as game-changers in modulating the plant responses to drought and other abiotic stresses. The ncRNAs interact with their targets to form potentially subtle regulatory networks that control multiple genes to determine the overall response of plants. Many long and small drought-responsive ncRNAs have been identified and characterized in different plant varieties. The miRNA-based research is better documented, while lncRNA and transposon-derived RNAs are relatively new, and their cellular role is beginning to be understood. In this review, we have compiled the information on the categorization of non-coding RNAs based on their biogenesis and function. We also discuss the available literature on the role of long and small non-coding RNAs in mitigating drought stress in plants.
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Affiliation(s)
- Temesgen Assefa Gelaw
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
- Department of Biotechnology, College of Natural and Computational Science, Debre Birhan University, Debre Birhan P.O. Box 445, Ethiopia
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
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Identification and profiling of conserved microRNAs in different developmental stages of crown imperial (Fritillaria imperialis L.) using high-throughput sequencing. Mol Biol Rep 2021; 49:1121-1132. [PMID: 34779986 DOI: 10.1007/s11033-021-06938-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/05/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Novel strategies for improvement of ornamental plants and their properties relay on miRNA control of differential plant gene expression modulation. Still, in response to the same abiotic stresses, some conserved miRNA families show different expression patterns in different plant species. In parallel, the use of deep sequencing technologies reveals new levels of complexity of regulatory networks in plants through identification of new miRNAs. METHODS AND RESULTS Fritillaria imperialis plants were collected from their natural habitats in Koohrang, Chaharmahal va Bakhtiari, Iran. Several tissues including stamen, pistil, petal, sepal, leaf, stem, bulb and fruit were collected during three developmental stages (stem elongation, flower development and seed head stages). Using RNAseq and qRT-PCR approach, this research revealed 21 conserved miRNAs, matching 15 miRNA families, in Fritilaria imperialis. CONCLUSIONS The expression of seven conserved miRNAs (Fim-miR156b, Fim-miR159, Fim-miR166a-5p, Fim-miR169d-5p, Fim-miR171c, Fim-miR393 and Fim-miR396e-3p) was further investigated in different tissues and three developmental stages, suggesting different roles for these miRNAs during growth and development of crown imperial. Gained knowledge from this research can open the door to find efficient ways to secure crown imperial survival, preservation and utilization and if proven useful may be applied in other plant species as well.
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50
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Wang M, Yang C, Wei K, Zhao M, Shen L, Ji J, Wang L, Zhang D, Guo J, Zheng Y, Yu J, Zhu M, Liu H, Li YF. Temporal expression study of miRNAs in the crown tissues of winter wheat grown under natural growth conditions. BMC Genomics 2021; 22:793. [PMID: 34736408 PMCID: PMC8567549 DOI: 10.1186/s12864-021-08048-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 09/30/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Winter wheat requires prolonged exposure to low temperature to initiate flowering (vernalization). Shoot apical meristem of the crown is the site of cold perception, which produces leaf primordia during vegetative growth before developing into floral primordia at the initiation of the reproductive phase. Although many essential genes for winter wheat cold acclimation and floral initiation have been revealed, the importance of microRNA (miRNA) meditated post-transcriptional regulation in crowns is not well understood. To understand the potential roles of miRNAs in crown tissues, we performed a temporal expression study of miRNAs in crown tissues at the three-leaf stage, winter dormancy stage, spring green-up stage, and jointing stage of winter wheat grown under natural growth conditions. RESULTS In total, 348 miRNAs belonging to 298 miRNA families, were identified in wheat crown tissues. Among them, 92 differentially expressed miRNAs (DEMs) were found to be significantly regulated from the three-leaf stage to the jointing stage. Most of these DEMs were highly expressed at the three-leaf stage and winter dormancy stage, and then declined in later stages. Six DEMs, including miR156a-5p were markedly induced during the winter dormancy stage. Eleven DEMs, including miR159a.1, miR390a-5p, miR393-5p, miR160a-5p, and miR1436, were highly expressed at the green-up stage. Twelve DEMs, such as miR172a-5p, miR394a, miR319b-3p, and miR9676-5p were highly induced at the jointing stage. Moreover, 14 novel target genes of nine wheat or Pooideae-specific miRNAs were verified using RLM-5' RACE assay. Notably, six mTERFs and two Rf1 genes, which are associated with mitochondrial gene expression, were confirmed as targets of three wheat-specific miRNAs. CONCLUSIONS The present study not only confirmed the known miRNAs associated with phase transition and floral development, but also identified a number of wheat or Pooideae-specific miRNAs critical for winter wheat cold acclimation and floral development. Most importantly, this study provided experimental evidence that miRNA could regulate mitochondrial gene expression by targeting mTERF and Rf1 genes. Our study provides valuable information for further exploration of the mechanism of miRNA mediated post-transcriptional regulation during winter wheat vernalization and inflorescent initiation.
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Affiliation(s)
- Menglei Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China.,Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, 453007, China.,Present address: National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Chenhui Yang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Kangning Wei
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Miao Zhao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Liqiang Shen
- Jindal School of Management, University of Texas at Dallas, 800 W Campbell RD, Richardson, TX, 75080, USA
| | - Jie Ji
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Li Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China.,Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, 453007, China
| | - Daijing Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Junqiang Guo
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Yun Zheng
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Juanjuan Yu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China.,Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, 453007, China
| | - Mo Zhu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China.,Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, 453007, China
| | - Haiying Liu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Yong-Fang Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China. .,Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, 453007, China.
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