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Yin Z, Zhao Q, Lv X, Zhang X, Wu Y. Circular RNA ath-circ032768, a competing endogenous RNA, response the drought stress by targeting miR472-RPS5 module. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:544-559. [PMID: 38588338 DOI: 10.1111/plb.13645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/21/2024] [Indexed: 04/10/2024]
Abstract
CircRNAs (circular RNAs) reduce the abundance of miRNAs through ceRNA (competing endogenous RNA), to regulate many physiological processes and stress responses in plants. However, the role of circRNA in drought stress is poorly understood. Through ring identification and sequencing verification of ath-circ032768, bioinformatics analysis predicted the interaction of ath-circ032768-miR472-RPS5, and further obtained transgenic plants overexpressing ath-circ032768 and silencing STTM-miR472. The change in drought stress was analysed using biochemical and molecular biological methods. Sequencing and biological analysis confirmed that ath-circ032768, miR472 and RPS5 were responsive to drought stress, and changes in gene expression were consistent with the prediction of ceRNA. The silencing vectors ath-circ032768 and STTM-miR472 were constructed using molecular biology techniques, and stable transgenic plants with drought tolerance obtained. Further physiological and biochemical studies showed that ath-circ032768 could bind to miR472, and that miR472 could bind to the RPS5 gene, resulting in decreased expression of RPS5. Hence, ath-circ032768 can competitively inhibit degradation of RPS5 by miR472 through ceRNA. This process is accompanied by increased expression of DREB2A, RD29A and RD29B genes. Through the ath-circ032768-miR472-RPS5 pathway, the RPS5 stress resistance protein interacts with DREB2A protein to enhance expression of downstream drought resistance genes, RD29A and RD29B, and participate in the regulation mechanism of plant drought resistance, thereby improving drought tolerance of plants.
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Affiliation(s)
- Z Yin
- College of Life Sciences, Northwest A&F University, Yangling, Shaan Xi, China
| | - Q Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Shaan Xi, China
| | - X Lv
- College of Life Sciences, Northwest A&F University, Yangling, Shaan Xi, China
| | - X Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaan Xi, China
| | - Y Wu
- College of Life Sciences, Northwest A&F University, Yangling, Shaan Xi, China
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3
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Li J, Zhang H, Yang R, Zeng Q, Han G, Du Y, Yang J, Yang G, Luo Q. Identification of miRNAs Contributing to the Broad-Spectrum and Durable Blast Resistance in the Yunnan Local Rice Germplasm. FRONTIERS IN PLANT SCIENCE 2021; 12:749919. [PMID: 34721478 PMCID: PMC8551726 DOI: 10.3389/fpls.2021.749919] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
MicroRNAs are 20-24 nucleotide non-coding RNAs and play important roles in plant-environment interactions. In recent years, many microRNAs (miRNAs) have been found to regulate rice immunity against rice blast fungus. However, there are limited studies about miRNAs that directly target resistance (R) genes to regulate rice immunity. In this study, by deep sequencing, small RNA libraries were constructed from four-leaf stage seedlings of the resistant variety Ziyu44 and susceptible variety Jiangnanxiangnuo (JNXN) upon Magnaporthe oryzae infection, we found that much more miRNAs were significantly differentially expressed in Ziyu44 than in JNXN. Among these miRNAs, we focused on miR9664, a newly identified rice miRNA in our sequencing, which was upregulated lightly in Ziyu44 and drastically in JNXN at 24-48 h post-inoculation (hpi). The transgenic plants overexpressing miR9664 (miR9664-oe) displayed reduced defense responses to M. oryzae, while those knocking down miR9664 (miR9664-m) displayed enhanced defense responses to M. oryzae. Most of the detected miR9664 predicted target genes were reduced in the miR9664-oe lines while increased in the miR9664-m lines. The cleavage site of LOC_Os08g07774 was confirmed by RLM-RACE. Meanwhile, after being inoculated with M. oryzae, the genes were expressed differently between Ziyu44 and JNXN. The results suggest that miR9664-mediated R gene turnover contributes to Ziyu44 broad-spectrum resistance to rice blast fungus. Taken together, our research identified a new rice miRNA that directly targets R genes to regulate rice immunity against rice blast fungus, adding significant information to the study of rice-M. oryzae interaction.
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Affiliation(s)
- Jinlu Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education Key Laboratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, China
| | - Hui Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Rui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education Key Laboratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, China
| | - Qianchun Zeng
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Guangyu Han
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education Key Laboratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, China
| | - Yunlong Du
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education Key Laboratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, China
| | - Jing Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education Key Laboratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, China
| | - Genhua Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education Key Laboratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, China
| | - Qiong Luo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education Key Laboratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, China
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4
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Lunardon A, Johnson NR, Hagerott E, Phifer T, Polydore S, Coruh C, Axtell MJ. Integrated annotations and analyses of small RNA-producing loci from 47 diverse plants. Genome Res 2020; 30:497-513. [PMID: 32179590 PMCID: PMC7111516 DOI: 10.1101/gr.256750.119] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/27/2020] [Indexed: 01/25/2023]
Abstract
Plant endogenous small RNAs (sRNAs) are important regulators of gene expression. There are two broad categories of plant sRNAs: microRNAs (miRNAs) and endogenous short interfering RNAs (siRNAs). MicroRNA loci are relatively well-annotated but compose only a small minority of the total sRNA pool; siRNA locus annotations have lagged far behind. Here, we used a large data set of published and newly generated sRNA sequencing data (1333 sRNA-seq libraries containing more than 20 billion reads) and a uniform bioinformatic pipeline to produce comprehensive sRNA locus annotations of 47 diverse plants, yielding more than 2.7 million sRNA loci. The two most numerous classes of siRNA loci produced mainly 24- and 21-nucleotide (nt) siRNAs, respectively. Most often, 24-nt-dominated siRNA loci occurred in intergenic regions, especially at the 5′-flanking regions of protein-coding genes. In contrast, 21-nt-dominated siRNA loci were most often derived from double-stranded RNA precursors copied from spliced mRNAs. Genic 21-nt-dominated loci were especially common from disease resistance genes, including from a large number of monocots. Individual siRNA sequences of all types showed very little conservation across species, whereas mature miRNAs were more likely to be conserved. We developed a web server where our data and several search and analysis tools are freely accessible.
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Affiliation(s)
- Alice Lunardon
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Nathan R Johnson
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Emily Hagerott
- Department of Biology, Knox College, Galesburg, Illinois 61401, USA
| | - Tamia Phifer
- Department of Biology, Knox College, Galesburg, Illinois 61401, USA
| | - Seth Polydore
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Ceyda Coruh
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Michael J Axtell
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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5
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Zhang R, Huang S, Li S, Song G, Li Y, Li W, Li J, Gao J, Gu T, Li D, Zhang S, Li G. Evolution of PHAS loci in the young spike of Allohexaploid wheat. BMC Genomics 2020; 21:200. [PMID: 32131726 PMCID: PMC7057497 DOI: 10.1186/s12864-020-6582-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/17/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND PhasiRNAs (phased secondary siRNAs) play important regulatory roles in the development processes and biotic or abiotic stresses in plants. Some of phasiRNAs involve in the reproductive development in grasses, which include two categories, 21-nt (nucleotide) and 24-nt phasiRNAs. They are triggered by miR2118 and miR2275 respectively, in premeiotic and meiotic anthers of rice, maize and other grass species. Wheat (Triticum aestivum) with three closely related subgenomes (subA, subB and subD), is a model of allopolyploid in plants. Knowledge about the role of phasiRNAs in the inflorescence development of wheat is absent until now, and the evolution of PHAS loci in polyploid plants is also unavailable. RESULTS Using 261 small RNA expression datasets from various tissues, a batch of PHAS (phasiRNA precursors) loci were identified in the young spike of wheat, most of which were regulated by miR2118 and miR2275 in their target site regions. Dissection of PHAS and their trigger miRNAs among the diploid (AA and DD), tetraploid (AABB) and hexaploid (AABBDD) genomes of Triticum indicated that distribution of PHAS loci were dominant randomly in local chromosomes, while miR2118 was dominant only in the subB genome. The diversity of PHAS loci in the three subgenomes of wheat and their progenitor genomes (AA, DD and AABB) suggested that they originated or diverged at least before the occurrence of the tetraploid AABB genome. The positive correlation between the PHAS loci or the trigger miRNAs and the ploidy of genome indicated the expansion of genome was the major drive force for the increase of PHAS loci and their trigger miRNAs in Triticum. In addition, the expression profiles of the PHAS transcripts suggested they responded to abiotic stresses such as cold stress in wheat. CONCLUSIONS Altogether, non-coding phasiRNAs are conserved transcriptional regulators that display quick plasticity in Triticum genome. They may be involved in reproductive development and abiotic stress in wheat. It could be referred to molecular research on male reproductive development in Triticum.
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Affiliation(s)
- Rongzhi Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China. .,Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Ministry of Agriculture, Jinan, 250100, Shandong, China. .,National Engineering Laboratory for Wheat and Maize, Jinan, 250100, Shandong, China.
| | - Siyuan Huang
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Shiming Li
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Guoqi Song
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China.,Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Ministry of Agriculture, Jinan, 250100, Shandong, China.,National Engineering Laboratory for Wheat and Maize, Jinan, 250100, Shandong, China
| | - Yulian Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China.,Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Ministry of Agriculture, Jinan, 250100, Shandong, China.,National Engineering Laboratory for Wheat and Maize, Jinan, 250100, Shandong, China
| | - Wei Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China.,Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Ministry of Agriculture, Jinan, 250100, Shandong, China.,National Engineering Laboratory for Wheat and Maize, Jinan, 250100, Shandong, China
| | - Jihu Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China.,Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Ministry of Agriculture, Jinan, 250100, Shandong, China.,National Engineering Laboratory for Wheat and Maize, Jinan, 250100, Shandong, China
| | - Jie Gao
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China.,Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Ministry of Agriculture, Jinan, 250100, Shandong, China.,National Engineering Laboratory for Wheat and Maize, Jinan, 250100, Shandong, China
| | - Tiantian Gu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China.,Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Ministry of Agriculture, Jinan, 250100, Shandong, China.,National Engineering Laboratory for Wheat and Maize, Jinan, 250100, Shandong, China
| | - Dandan Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China.,Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Ministry of Agriculture, Jinan, 250100, Shandong, China.,National Engineering Laboratory for Wheat and Maize, Jinan, 250100, Shandong, China
| | - Shujuan Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China. .,Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Ministry of Agriculture, Jinan, 250100, Shandong, China. .,National Engineering Laboratory for Wheat and Maize, Jinan, 250100, Shandong, China.
| | - Genying Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China. .,Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Ministry of Agriculture, Jinan, 250100, Shandong, China. .,National Engineering Laboratory for Wheat and Maize, Jinan, 250100, Shandong, China.
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