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Divya D, Robin AHK, Cho LH, Kim D, Lee DJ, Kim CK, Chung MY. Genome-wide characterization and expression profiling of E2F/DP gene family members in response to abiotic stress in tomato (Solanum lycopersicum L.). BMC PLANT BIOLOGY 2024; 24:436. [PMID: 38773361 PMCID: PMC11110339 DOI: 10.1186/s12870-024-05107-3] [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: 06/19/2023] [Accepted: 05/05/2024] [Indexed: 05/23/2024]
Abstract
BACKGROUND E2F/DP (Eukaryotic 2 transcription factor/dimerization partner) family proteins play an essential function in the cell cycle development of higher organisms. E2F/DP family genes have been reported only in a few plant species. However, comprehensive genome-wide characterization analysis of the E2F/DP gene family of Solanum lycopersicum has not been reported so far. RESULTS This study identified eight nonredundant SlE2F/DP genes that were classified into seven groups in the phylogenetic analysis. All eight genes had a single E2F-TDP domain and few genes had additional domains. Two segmental duplication gene pairs were observed within tomato, in addition to cis-regulatory elements, miRNA target sites and phosphorylation sites which play an important role in plant development and stress response in tomato. To explore the three-dimensional (3D) models and gene ontology (GO) annotations of SlE2F/DP proteins, we pointed to their putative transporter activity and their interaction with several putative ligands. The localization of SlE2F/DP-GFP fused proteins in the nucleus and endoplasmic reticulum suggested that they may act in other biological functions. Expression studies revealed the differential expression pattern of most of the SlE2F/DP genes in various organs. Moreover, the expression of E2F/DP genes against abiotic stress, particularly SlE2F/DP2 and/or SlE2F/DP7, was upregulated in response to heat, salt, cold and ABA treatment. Furthermore, the co-expression analysis of SlE2F/DP genes with multiple metabolic pathways was co-expressed with defence genes, transcription factors and so on, suggested their crucial role in various biological processes. CONCLUSIONS Overall, our findings provide a way to understand the structure and function of SlE2F/DP genes; it might be helpful to improve fruit development and tolerance against abiotic stress through marker-assisted selection or transgenic approaches.
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Affiliation(s)
- Dhanasekar Divya
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea
| | - Arif Hasan Khan Robin
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Lae-Hyeon Cho
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang-si, Gyeongsangnam-do, 50463, Republic of Korea
| | - Dohyeon Kim
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang-si, Gyeongsangnam-do, 50463, Republic of Korea
| | - Do-Jin Lee
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea
| | - Chang-Kil Kim
- Department of Horticulture, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Mi-Young Chung
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea.
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Gao X, Du Z, Hao K, Zhang S, Li J, Guo J, Wang Z, Zhao S, Sang L, An M, Xia Z, Wu Y. ZmmiR398b negatively regulates maize resistance to sugarcane mosaic virus infection by targeting ZmCSD2/4/9. MOLECULAR PLANT PATHOLOGY 2024; 25:e13462. [PMID: 38695630 PMCID: PMC11064800 DOI: 10.1111/mpp.13462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/10/2024] [Accepted: 04/10/2024] [Indexed: 05/05/2024]
Abstract
MicroRNAs (miRNAs) are widely involved in various biological processes of plants and contribute to plant resistance against various pathogens. In this study, upon sugarcane mosaic virus (SCMV) infection, the accumulation of maize (Zea mays) miR398b (ZmmiR398b) was significantly reduced in resistant inbred line Chang7-2, while it was increased in susceptible inbred line Mo17. Degradome sequencing analysis coupled with transient co-expression assays revealed that ZmmiR398b can target Cu/Zn-superoxidase dismutase2 (ZmCSD2), ZmCSD4, and ZmCSD9 in vivo, of which the expression levels were all upregulated by SCMV infection in Chang7-2 and Mo17. Moreover, overexpressing ZmmiR398b (OE398b) exhibited increased susceptibility to SCMV infection, probably by increasing reactive oxygen species (ROS) accumulation, which were consistent with ZmCSD2/4/9-silenced maize plants. By contrast, silencing ZmmiR398b (STTM398b) through short tandem target mimic (STTM) technology enhanced maize resistance to SCMV infection and decreased ROS levels. Interestingly, copper (Cu)-gradient hydroponic experiments demonstrated that Cu deficiency promoted SCMV infection while Cu sufficiency inhibited SCMV infection by regulating accumulations of ZmmiR398b and ZmCSD2/4/9 in maize. These results revealed that manipulating the ZmmiR398b-ZmCSD2/4/9-ROS module provides a prospective strategy for developing SCMV-tolerant maize varieties.
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Affiliation(s)
- Xinran Gao
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Zhichao Du
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Kaiqiang Hao
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Sijia Zhang
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Jian Li
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Jinxiu Guo
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Zhiping Wang
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Shixue Zhao
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Lijun Sang
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Mengnan An
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Zihao Xia
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Yuanhua Wu
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
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Lian C, Zhang F, Yang H, Zhang X, Lan J, Zhang B, Liu X, Yang J, Chen S. Multi-omics analysis of small RNA, transcriptome, and degradome to identify putative miRNAs linked to MeJA regulated and oridonin biosynthesis in Isodon rubescens. Int J Biol Macromol 2024; 258:129123. [PMID: 38163496 DOI: 10.1016/j.ijbiomac.2023.129123] [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: 10/26/2023] [Revised: 12/13/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
Isodon rubescens has garnered much attention due to its anti-tumor or anti-cancer properties. However, little is known about the molecular mechanism of oridonin biosynthesis leveraging the regulatory network between small RNAs and mRNAs. In this study, the regulatory networks of miRNAs and targets were examined by combining mRNA, miRNA, and degradome. A total of 348 miRNAs, including 287 known miRNAs and 61 novel miRNAs, were identified. Among them, 51 miRNAs were significantly expressed, and 36 miRNAs responded to MeJA. A total of 3066 target genes were associated with 228 miRNAs via degradome sequencing. Multi-omics analysis demonstrated that 27 miRNA-mRNA pairs were speculated to be involved in MeJA regulation, and 36 miRNA-mRNA pairs were hypothesized to be involved in the genotype-dependence of I. rubescens. Furthermore, 151 and 7 miRNA-mRNA modules were likely engaged in oridonin biosynthesis as identified by psRNATarget and degradome sequencing, respectively. Some miRNA-mRNA modules were confirmed via RT-qPCR. Moreover, miRNAs targeting plant hormone signal transduction pathway genes were identified, such as miR156, miR167, miR393, and PC-3p-19822_242. Collectively, our results demonstrate for the first time that miRNAs are identified in I. rubescens, and laid a solid foundation for further research on the molecular mechanism of oridonin biosynthesis mediated by miRNA.
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Affiliation(s)
- Conglong Lian
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China; Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China
| | - Fei Zhang
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China; Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China
| | - Hao Yang
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China; Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China
| | - Xueyu Zhang
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China; Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China
| | - Jinxu Lan
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China; Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China
| | - Bao Zhang
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China; Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China
| | - Xiuyu Liu
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China; Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China
| | - Jingfan Yang
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China; Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China
| | - Suiqing Chen
- School of Pharmacy, Henan University of Chinese Medicine, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China; Henan Key Laboratory of Chinese Medicine Resources and Chemistry, 156 Esat Jin-shui Rd, Zhengzhou 450046, PR China.
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Guo S, Zhang M, Feng M, Liu G, Torregrosa L, Tao X, Ren R, Fang Y, Zhang Z, Meng J, Xu T. miR156b-targeted VvSBP8/13 functions downstream of the abscisic acid signal to regulate anthocyanins biosynthesis in grapevine fruit under drought. HORTICULTURE RESEARCH 2024; 11:uhad293. [PMID: 38371638 PMCID: PMC10873574 DOI: 10.1093/hr/uhad293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/20/2023] [Indexed: 02/20/2024]
Abstract
Anthocyanins are the primary color components of grapevine berries and wines. In cultivation practices, a moderate water deficit can promote anthocyanin accumulation in red grape skins. Our previous study showed that abscisic acid (ABA) plays a key role in this process. Herein, we identified a microRNA, vv-miR156b, that is generated in grapevine berries in response to drought stress, along with increasing anthocyanin content and biosynthetic structural gene transcripts. In contrast, vv-miR156b short tandem target mimic (STTM) function-loss callus exhibits the opposite phenotype. Results from in vivo and in vitro experiments revealed that the ABA-signaling-regulated transcription factor VvAREB2 binds directly to the ABA-responsive element (ABRE) of the MIR156b promoter and activates miR156b expression. Furthermore, two miR156b downstream targets, VvSBP8 and VvSBP13, exhibited reduced grape anthocyanin content in their overexpressors but there was a contrary result in their CRISPR-edited lines, the decrease in anthocyanin content was rescued in miR156b and SBP8/13 double overexpressors. We further demonstrated that both VvSBP8 and VvSBP13, encoding transcriptional repressors, displayed sufficient ability to interact with VvMYC1 and VvMYBA1, thereby interfering with MYB-bHLH-WD (MBW) repeat transcriptional complex formation, resulting in the repression of anthocyanin biosynthesis. Our findings demonstrate a direct functional relationship between ABA signaling and the miR156-SBP-MBW complex regulatory module in driving drought-induced anthocyanin accumulation in grape berries.
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Affiliation(s)
- Shuihuan Guo
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Meng Zhang
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingxin Feng
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Guipeng Liu
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Laurent Torregrosa
- UMR LEPSE, Université de Montpellier , CIRAD, INRAE, Institut Agro, 34060 Montpellier, France
| | - Xiaoqing Tao
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ruihua Ren
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yulin Fang
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhenwen Zhang
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiangfei Meng
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tengfei Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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Olmo R, Quijada NM, Morán-Diez ME, Hermosa R, Monte E. Identification of Tomato microRNAs in Late Response to Trichoderma atroviride. Int J Mol Sci 2024; 25:1617. [PMID: 38338899 PMCID: PMC10855890 DOI: 10.3390/ijms25031617] [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: 11/30/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
The tomato (Solanum lycopersicum) is an important crop worldwide and is considered a model plant to study stress responses. Small RNAs (sRNAs), 21-24 nucleotides in length, are recognized as a conserved mechanism for regulating gene expression in eukaryotes. Plant endogenous sRNAs, such as microRNA (miRNA), have been involved in disease resistance. High-throughput RNA sequencing was used to analyze the miRNA profile of the aerial part of 30-day-old tomato plants after the application of the fungus Trichoderma atroviride to the seeds at the transcriptional memory state. Compared to control plants, ten differentially expressed (DE) miRNAs were identified in those inoculated with Trichoderma, five upregulated and five downregulated, of which seven were known (miR166a, miR398-3p, miR408, miR5300, miR6024, miR6027-5p, and miR9471b-3p), and three were putatively novel (novel miR257, novel miR275, and novel miR1767). miRNA expression levels were assessed using real-time quantitative PCR analysis. A plant sRNA target analysis of the DE miRNAs predicted 945 potential target genes, most of them being downregulated (84%). The analysis of KEGG metabolic pathways showed that most of the targets harbored functions associated with plant-pathogen interaction, membrane trafficking, and protein kinases. Expression changes of tomato miRNAs caused by Trichoderma are linked to plant defense responses and appear to have long-lasting effects.
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Affiliation(s)
| | | | | | | | - Enrique Monte
- Institute for Agribiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, 37185 Villamayor, Salamanca, Spain; (R.O.); (N.M.Q.); (M.E.M.-D.); (R.H.)
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Lakshmi PTV, Kumar A, A. S. A, Raveendran AP, Chaudhary A, Shanmugam A, Arunachalam A. Comparative transcriptomic and weighted gene co-expression network analysis to identify the core genes in the cultivars of Musa acuminata under both infected and chemical perturbated conditions. PLANT SIGNALING & BEHAVIOR 2023; 18:2269675. [PMID: 37948570 PMCID: PMC10653623 DOI: 10.1080/15592324.2023.2269675] [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: 07/31/2023] [Accepted: 10/08/2023] [Indexed: 11/12/2023]
Abstract
Banana is a high nutrient crop, which ranks fourth in terms of gross value production. Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense tropical race 4 (FocTR4), is considered the most destructive disease leading to the complete loss of production of the Cavendish cultivars Berangan, Brazilian and Williams, which are vulnerable to the infection of FocTR4. However, the treatment with benzothiadiazole, a synthetic salicylic analog, is aimed to induce resistance in plants. Thus, the treatments pertaining to the banana plants subjected to the Foc infection within the chosen cultivars were compared with chemically treated samples obtained at different time intervals for a short duration (0-4 days). The integrated omics analyses considering the parameters of WGCNA, functional annotation, and protein-protein interactions revealed that many pathways have been negatively influenced in Cavendish bananas under FocTR4 infections and the number of genes influenced also increased over time in Williams cultivar. Furthermore, elevation in immune response and resistance genes were also observed in the roots of the Cavendish banana.
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Affiliation(s)
- PTV Lakshmi
- Phytomatics Lab, Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Amrendra Kumar
- Phytomatics Lab, Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Ajna A. S.
- Phytomatics Lab, Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Abitha P Raveendran
- Phytomatics Lab, Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Anjali Chaudhary
- Phytomatics Lab, Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Adhitthan Shanmugam
- Phytomatics Lab, Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Annamalai Arunachalam
- Department of Food Science and Technology, School of Life Sciences, Pondicherry University, Pondicherry, India
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Fang B, Huang Z, Sun Y, Zhang W, Yu J, Zhang J, Dong H, Wang S. Small RNA sequencing provides insights into molecular mechanism of flower development in Rhododendron pulchrum Sweet. Sci Rep 2023; 13:17912. [PMID: 37864069 PMCID: PMC10589353 DOI: 10.1038/s41598-023-44779-z] [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: 07/04/2023] [Accepted: 10/12/2023] [Indexed: 10/22/2023] Open
Abstract
Rhododendron pulchrum sweet, a member of the Ericaceae family possessing valuable horticultural properties, is widely distributed in the temperate regions. Though serving as bioindicator of metal pollution, the molecular mechanism regulating flowering in R. pulchrum is very limited. Illumina sequencing was performed to identify critical miRNAs in the synthesis of flavonoids at different developmental stages. Totally, 722 miRNAs belonging to 104 families were screened, and 84 novel mature miRNA sequences were predicted. The miR166, miR156, and miR167-1 families were dominant. In particular, 126 miRNAs were significantly differentially expressed among four different flowering stages. Totally, 593 genes were differentially regulated by miRNAs during the flower development process, which were mostly involved in "metabolic pathways", "plant hormone signal transduction", and "mitosis and regulation of biosynthetic processes". In pigment biosynthesis and signal transduction processes, gra-miR750 significantly regulated the expression of flavonoid 3',5'-hydroxylase; aof-miR171a, aof-miR171b, aof-miR171c, cas-miR171a-3p, and cas-miR171c-3p could regulate the expression of DELLA protein; aof-miR390, aof-miR396b, ath-miR3932b-5p, cas-miR171a-3p, aof-miR171a, and aof-miR171b regulated BAK1 expression. This research showed great potentials for genetic improvement of flower color traits for R. pulchrum and other Rhododendron species.
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Affiliation(s)
- Bo Fang
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei, People's Republic of China
| | - Zhiwei Huang
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei, People's Republic of China
| | - Yirong Sun
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei, People's Republic of China
| | - Wanjing Zhang
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei, People's Republic of China
| | - Jiaojun Yu
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei, People's Republic of China
| | - Jialiang Zhang
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei, People's Republic of China
| | - Hongjin Dong
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei, People's Republic of China
| | - Shuzhen Wang
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, Hubei, People's Republic of China.
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Juneja S, Saini R, Mukit A, Kumar S. Drought priming modulates ABF, GRFs, related microRNAs and induce metabolic adjustment during heat stress in chickpea. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108007. [PMID: 37714028 DOI: 10.1016/j.plaphy.2023.108007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/17/2023]
Abstract
Drought and high temperature stress may occur concomitantly or individually in succession causing cellular dysfunctions. Abscisic acid (ABA) is a key stress regulator, and its responsive genes are controlled by ABRE (Abscisic acid Responsive Element)-binding factors (ABFs)and G-Box Regulatory factors (GRFs). Here, we identify ABFs, GRFs and targeting miRNAs in desi and kabuli chickpea. To validate their role after drought priming and subsequent high temperature stress, two contrasting chickpea varieties (PBG1 and PBG5) were primed and exposed to 32 °C, 35 °C and 38 °C for 12, 6 and 2 h respectively and analyzed for Physio-biochemical, expression of ABFs, GRFs and MiRNAs, and GC-MS based metabolite analysis. To ascertain the ABF-GRF protein-protein interactions, docking studies were carried out between the ABF3 and GRF14. Genome-wide analysis identified total 9 & 11 ABFs, and 11 GRFsin desi and kabuli respectively. Their gene structure, and motif composition were conserved in all subfamilies and only 10 and 12 genes have undergone duplication in both desi and kabuli chickpea respectively. These genes were differentially expressed in-silico. MiR172 and miR396 were identified to target ABFs and GRFs respectively. Protein-protein interaction (ABF3 and GRF14) might be successful only when the ABF3 was phosphorylated. Drought priming downregulated miR172 and miR396 and eventually upregulated targeting ABFs, and GRFs. Metabolite profiling (GC-MS) revealed the accumulation of 87 metabolites in Primed (P) and Non-Primed (NP) Chickpea plants. Tolerant cultivar (PBG5) responded better in all respects however both severity of stress and exposure are important factors and can produce broadly similar cellular response.
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Affiliation(s)
- Sumandeep Juneja
- Centre for Biosciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Rashmi Saini
- Centre for Biosciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Abdul Mukit
- Department of Botany, School of Basic Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Sanjeev Kumar
- Centre for Biosciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151401, India; Department of Botany, School of Basic Sciences, Central University of Punjab, Bathinda, 151401, India.
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Riyazuddin R, Singh K, Iqbal N, Labhane N, Ramteke P, Singh VP, Gupta R. Unveiling the biosynthesis, mechanisms, and impacts of miRNAs in drought stress resilience in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107978. [PMID: 37660607 DOI: 10.1016/j.plaphy.2023.107978] [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: 04/04/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 09/05/2023]
Abstract
Drought stress is one of the most serious threats to sustainable agriculture and is predicted to be further intensified in the coming decades. Therefore, understanding the mechanism of drought stress tolerance and the development of drought-resilient crops are the major goals at present. In recent years, noncoding microRNAs (miRNAs) have emerged as key regulators of gene expressions under drought stress conditions and are turning out to be the potential candidates that can be targeted to develop drought-resilient crops in the future. miRNAs are known to target and decrease the expression of various genes to govern the drought stress response in plants. In addition, emerging evidence also suggests a regulatory role of long non-coding RNAs (lncRNAs) in the regulation of miRNAs and the expression of their target genes by a process referred as miRNA sponging. In this review, we present the regulatory roles of miRNAs in the modulation of drought-responsive genes along with discussing their biosynthesis and action mechanisms. Additionally, the interactive roles of miRNAs with phytohormone signaling components have also been highlighted to present the global view of miRNA functioning under drought-stress conditions.
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Affiliation(s)
- Riyazuddin Riyazuddin
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62, H-6726, Szeged, Hungary.
| | - Kalpita Singh
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, 2100, Gödöllő, Hungary; Department of Biological Resources, Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, H-2462, Martonvásár, Hungary.
| | - Nadeem Iqbal
- Department of Plant Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, 6726, Szeged, Hungary; Doctoral School of Environmental Sciences, University of Szeged, Szeged, Hungary.
| | - Nitin Labhane
- Department of Botany, Bhavan's College Andheri West, Mumbai, 400058, India.
| | - Pramod Ramteke
- Department of Biotechnology, Dr. Ambedkar College, Nagpur, India.
| | - Vijay Pratap Singh
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj, 211002, India
| | - Ravi Gupta
- College of General Education, Kookmin University, 02707, Seoul, Republic of Korea.
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Chen Y, Yu X. Endoplasmic reticulum stress-responsive microRNAs are involved in the regulation of abiotic stresses in wheat. PLANT CELL REPORTS 2023; 42:1433-1452. [PMID: 37341828 DOI: 10.1007/s00299-023-03040-7] [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: 01/15/2023] [Accepted: 06/08/2023] [Indexed: 06/22/2023]
Abstract
KEY MESSAGE ER stress-responsive miRNAs, tae-miR164, tae-miR2916, and tae-miR396e-5p, are essential in response to abiotic stress. Investigating ER stress-responsive miRNAs is necessary to improve plant tolerance to environmental stress. MicroRNAs (miRNAs) play vital regulatory roles in plant responses to environmental stress. Recently, the endoplasmic reticulum (ER) stress pathway, an essential signalling pathway in plants in response to adverse conditions, has been widely studied in model plants. However, miRNAs associated with ER stress response remain largely unknown. Using high-throughput sequencing, three ER stress-responsive miRNAs, tae-miR164, tae-miR2916, and tae-miR396e-5p were identified, and their target genes were confirmed. These three miRNAs and their target genes actively responded to dithiothreitol, polyethylene glycol, salt, heat, and cold stresses. Furthermore, in some instances, the expression patterns of the miRNAs and their corresponding target genes were contrasting. Knockdown of tae-miR164, tae-miR2916, or tae-miR396e-5p using a barley stripe mosaic virus-based miRNA silencing system substantially enhanced the tolerance of wheat plants to drought, salt, and heat stress. Under conditions involving these stresses, inhibiting the miR164 function by using the short tandem target mimic approach in Arabidopsis thaliana resulted in phenotypes consistent with those of miR164-silenced wheat plants. Correspondingly, overexpression of tae-miR164 in Arabidopsis resulted in a decreased tolerance to drought stress and, to some extent, a decrease in tolerance to salt and high temperature. These results revealed that tae-miR164 plays a negative regulatory role in wheat/Arabidopsis in response to drought, salt, and heat stress. Taken together, our study provides new insights into the regulatory role of ER stress-responsive miRNAs in abiotic stress responses.
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Affiliation(s)
- Yong Chen
- College of Mechanical and Electrical Engineering, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xing Yu
- Yellow River Institute of Hydraulic Research, Yellow River Conservancy Commission, Zhengzhou, 450003, China.
- Research Center on Rural Water Environment Improvement of Henan Province, Zhengzhou, 450003, China.
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11
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Mittal M, Dhingra A, Dawar P, Payton P, Rock CD. The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea). THE PLANT GENOME 2023; 16:e20350. [PMID: 37351954 DOI: 10.1002/tpg2.20350] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 06/24/2023]
Abstract
MicroRNAs (miRNAs) are 21-24 nt small RNAs (sRNAs) that negatively regulate protein-coding genes and/or trigger phased small-interfering RNA (phasiRNA) production. Two thousand nine hundred miRNA families, of which ∼40 are deeply conserved, have been identified in ∼80 different plant species genomes. miRNA functions in response to abiotic stresses is less understood than their roles in development. Only seven peanut MIRNA families are documented in miRBase, yet a reference genome assembly is now published and over 480 plant-like MIRNA loci were predicted in the diploid peanut progenitor Arachis duranensis genome. We explored by computational analysis of a leaf sRNA library and publicly available sRNA, degradome, and transcriptome datasets the miRNA and phasiRNA space associated with drought and heat stresses in peanut. We characterized 33 novel candidate and 33 ancient conserved families of MIRNAs and present degradome evidence for their cleavage activities on mRNA targets, including several noncanonical targets and novel phasiRNA-producing noncoding and mRNA loci with validated novel targets such as miR1509 targeting serine/threonine-protein phosphatase7 and miRc20 and ahy-miR3514 targeting penta-tricopeptide repeats (PPRs), in contradistinction to other claims of miR1509/173/7122 superfamily miRNAs indirectly targeting PPRs via TAS-like noncoding RNA loci. We characterized the inverse correlations of significantly differentially expressed drought- and heat-regulated miRNAs, assayed by sRNA blots or transcriptome datasets, with target mRNA expressions in the same datasets. Meta-analysis of an expression atlas and over representation of miRNA target genes in co-expression networks suggest that miRNAs have functions in unique aspects of peanut gynophore development. Genome-wide MIRNA annotation of the published allopolyploid peanut genome can facilitate molecular breeding of value-added traits.
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Affiliation(s)
- Meenakshi Mittal
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Anuradha Dhingra
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Pranav Dawar
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Paxton Payton
- USDA-ARS Plant Stress and Germplasm Lab, Lubbock, Texas, USA
| | - Christopher D Rock
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
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12
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Hu Y, Ji J, Cheng H, Luo R, Zhang J, Li W, Wang X, Zhang J, Yao Y. The miR408a-BBP-LAC3/CSD1 module regulates anthocyanin biosynthesis mediated by crosstalk between copper homeostasis and ROS homeostasis during light induction in Malus plants. J Adv Res 2023; 51:27-44. [PMID: 36371057 PMCID: PMC10491975 DOI: 10.1016/j.jare.2022.11.005] [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: 08/10/2022] [Revised: 10/19/2022] [Accepted: 11/06/2022] [Indexed: 11/11/2022] Open
Abstract
INTRODUCTION The expression of miR408 is affected by copper (Cu) conditions and positively regulates anthocyanin biosynthesis in Arabidopsis. However, the underlying mechanisms by which miR408 regulates anthocyanin biosynthesis mediated by Cu homeostasis and reactive oxygen species (ROS) homeostasis remain unclear in Malus plants. OBJECTIVES Our study aims to elucidate how miR408a and its target, basic blue protein (BBP) regulate Cu homeostasis and ROS homeostasis, and anthocyanin biosynthesis in Malus plants. METHODS The roles of miR408a and its target BBP in regulating anthocyanin biosynthesis, Cu homeostasis, and ROS homeostasis were mainly identified in Malus plants. RESULTS We found that the BBP protein interacted with the copper-binding proteins LAC3 (laccase) and CSD1 (Cu/Zn SOD superoxide dismutase), indicating a potential crosstalk between Cu homeostasis and ROS homeostasis might be mediated by miR408 to regulate the anthocyanin accumulation. Further studies showed that overexpressing miR408a or suppressing BBP transiently significantly increased the expression of genes related to Cu binding and Cu transport, leading to anthocyanin accumulation under light induction in apple fruit and Malus plantlets. Consistently, opposite results were obtained when repressing miR408a or overexpressing BBP. Moreover, light induction significantly increased the expression of miR408a, CSD1, and LAC3, but significantly reduced the BBP expression, resulting in increased Cu content and anthocyanin accumulation. Furthermore, excessive Cu significantly increased the anthocyanin accumulation, accompanied by reduced expression of miR408a and Cu transport genes, and upregulated expression of Cu binding proteins including BBP, LAC3, and CSD1 to maintain the Cu homeostasis and ROS homeostasis in Malus plantlets. CONCLUSION Our findings provide new insights into the mechanism by which the miR408a-BBP-LAC3/CSD1 module perceives light and Cu signals regulating Cu and ROS homeostasis, ultimately affecting anthocyanin biosynthesis in Malus plants.
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Affiliation(s)
- Yujing Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Jiayi Ji
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China; Beijing Forestry University, China
| | - Hao Cheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Rongli Luo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Wenjing Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Xingsui Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China.
| | - Yuncong Yao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China.
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13
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Kaur S, Seem K, Kumar S, Kaundal R, Mohapatra T. Comparative Genome-Wide Analysis of MicroRNAs and Their Target Genes in Roots of Contrasting Indica Rice Cultivars under Reproductive-Stage Drought. Genes (Basel) 2023; 14:1390. [PMID: 37510295 PMCID: PMC10379292 DOI: 10.3390/genes14071390] [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: 05/21/2023] [Revised: 06/26/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Recurrent occurrence of drought stress in varying intensity has become a common phenomenon in the present era of global climate change, which not only causes severe yield losses but also challenges the cultivation of rice. This raises serious concerns for sustainable food production and global food security. The root of a plant is primarily responsible to perceive drought stress and acquire sufficient water for the survival/optimal growth of the plant under extreme climatic conditions. Earlier studies reported the involvement/important roles of microRNAs (miRNAs) in plants' responses to environmental/abiotic stresses. A number (738) of miRNAs is known to be expressed in different tissues under varying environmental conditions in rice, but our understanding of the role, mode of action, and target genes of the miRNAs are still elusive. Using contrasting rice [IR-64 (reproductive-stage drought sensitive) and N-22 (drought-tolerant)] cultivars, imposed with terminal (reproductive-stage) drought stress, we demonstrate differential expression of 270 known and 91 novel miRNAs in roots of the contrasting rice cultivars in response to the stress. Among the known miRNAs, osamiR812, osamiR166, osamiR156, osamiR167, and osamiR396 were the most differentially expressed miRNAs between the rice cultivars. In the root of N-22, 18 known and 12 novel miRNAs were observed to be exclusively expressed, while only two known (zero novels) miRNAs were exclusively expressed in the roots of IR-64. The majority of the target gene(s) of the miRNAs were drought-responsive transcription factors playing important roles in flower, grain development, auxin signaling, root development, and phytohormone-crosstalk. The novel miRNAs identified in this study may serve as good candidates for the genetic improvement of rice for terminal drought stress towards developing climate-smart rice for sustainable food production.
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Affiliation(s)
- Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
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14
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Liu G, Liu F, Zhang D, Zhao T, Yang H, Jiang J, Li J, Zhang H, Xu X. Integrating omics reveals that miRNA-guided genetic regulation on plant hormone level and defense response pathways shape resistance to Cladosporium fulvum in the tomato Cf-10-gene-carrying line. Front Genet 2023; 14:1158631. [PMID: 37303956 PMCID: PMC10248068 DOI: 10.3389/fgene.2023.1158631] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 05/18/2023] [Indexed: 06/13/2023] Open
Abstract
Invasion of C. fulvum causes the most serious diseases affecting the reproduction of tomatoes. Cf-10-gene-carrying line showed remarkable resistance to Cladosporium fulvum. To exploit its defense response mechanism, we performed a multiple-omics profiling of Cf-10-gene-carrying line and a susceptible line without carrying any resistance genes at non-inoculation and 3 days post-inoculation (dpi) of C. fulvum. We detected 54 differentially expressed miRNAs (DE-miRNAs) between the non-inoculation and 3 dpi in the Cf-10-gene-carrying line, which potentially regulated plant-pathogen interaction pathways and hormone signaling pathways. We also revealed 3,016 differentially expressed genes (DEGs) between the non-inoculated and 3 dpi in the Cf-10-gene-carrying line whose functions enriched in pathways that were potentially regulated by the DE-miRNAs. Integrating DE-miRNAs, gene expression and plant-hormone metabolites indicated a regulation network where the downregulation of miRNAs at 3 dpi activated crucial resistance genes to trigger host hypersensitive cell death, improved hormone levels and upregulated the receptors/critical responsive transcription factors (TFs) of plant hormones, to shape immunity to the pathogen. Notably, our transcriptome, miRNA and hormone metabolites profiling and qPCR analysis suggested that that the downregulation of miR9472 potentially upregulated the expression of SAR Deficient 1 (SARD1), a key regulator for ICS1 (Isochorismate Synthase 1) induction and salicylic acid (SA) synthesis, to improve the level of SA in the Cf-10-gene-carrying line. Our results exploited potential regulatory network and new pathways underlying the resistance to C. fulvum in Cf-10-gene-carrying line, providing a more comprehensive genetic circuit and valuable gene targets for modulating resistance to the virus.
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Affiliation(s)
- Guan Liu
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
| | - Fengjiao Liu
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Dongye Zhang
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Tingting Zhao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Huanhuan Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Jingbin Jiang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Jingfu Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - He Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Xiangyang Xu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
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15
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Asakura H, Tanaka M, Tamura T, Saito Y, Yamakawa T, Abe K, Asakura T. Genes related to cell wall metabolisms are targeted by miRNAs in immature tomato fruits under drought stress. Biosci Biotechnol Biochem 2023; 87:290-302. [PMID: 36572396 DOI: 10.1093/bbb/zbac209] [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: 10/17/2022] [Accepted: 12/18/2022] [Indexed: 12/28/2022]
Abstract
The metabolism of tomato fruits changes when plants experience drought stress. In this study, we investigated changes in microRNA (miRNA) abundance and detected 32 miRNAs whose expression changes in fruit. The candidate target genes for each miRNA were predicted from the differentially expressed genes identified by transcriptome analysis at the same fruit maturation stage. The predicted targeted genes were related to cell wall metabolisms, response to pathogens, and plant hormones. Among these, we focused on cell wall metabolism-related genes and performed a dual luciferase assay to assess the targeting of their mRNAs by their predicted miRNA. As a result, sly-miR10532 and sly-miR7981e suppress the expression of mRNAs of galacturonosyltransferase-10 like encoding the main enzyme of pectin biosynthesis, while sly-miR171b-5p targets β-1,3-glucosidase mRNAs involved in glucan degradation. These results will allow the systematic characterization of miRNA and their target genes in the tomato fruit under drought stress conditions.
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Affiliation(s)
- Hiroko Asakura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Mayui Tanaka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Tomoko Tamura
- Department of Nutritional Science and Food Safety, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo, Japan
| | - Yoshikazu Saito
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Takashi Yamakawa
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Keiko Abe
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, Japan.,Kanagawa Institute of Industrial Science and Technology (KISTEC), Life Science & Environmental Research Center (LiSE), 705-1, Imaizumi, Ebina, Kanagawa, Japan
| | - Tomiko Asakura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, Japan
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16
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Li Q, Shen H, Yuan S, Dai X, Yang C. miRNAs and lncRNAs in tomato: Roles in biotic and abiotic stress responses. FRONTIERS IN PLANT SCIENCE 2023; 13:1094459. [PMID: 36714724 PMCID: PMC9875070 DOI: 10.3389/fpls.2022.1094459] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Plants are continuously exposed to various biotic and abiotic stresses in the natural environment. To cope with these stresses, they have evolved a multitude of defenses mechanisms. With the rapid development of genome sequencing technologies, a large number of non-coding RNA (ncRNAs) have been identified in tomato, like microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Recently, more and more evidence indicates that many ncRNAs are involved in plant response to biotic and abiotic stresses in tomato. In this review, we summarize recent updates on the regulatory roles of ncRNAs in tomato abiotic/biotic responses, including abiotic (high temperature, drought, cold, salinization, etc.) and biotic (bacteria, fungi, viruses, insects, etc.) stresses. Understanding the molecular mechanisms mediated by ncRNAs in response to these stresses will help us to clarify the future directions for ncRNA research and resistance breeding in tomato.
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Affiliation(s)
- Qian Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Heng Shen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Shoujuan Yuan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Xigang Dai
- School of Life Sciences, Jianghan University/Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Wuhan, China
| | - Changxian Yang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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17
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Xu Y, Liu J, Ji X, Zhao G, Zhao T, Wang X, Wang L, Gao S, Hao Y, Gao Y, Gao Y, Weng X, Jia L, Chen Z. Integrative analysis of microRNAs and mRNAs reveals the regulatory networks of triterpenoid saponin metabolism in Soapberry ( Sapindus mukorossi Gaertn.). FRONTIERS IN PLANT SCIENCE 2023; 13:1037784. [PMID: 36699854 PMCID: PMC9869041 DOI: 10.3389/fpls.2022.1037784] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 12/19/2022] [Indexed: 06/13/2023]
Abstract
Triterpenoid saponin are important secondary metabolites and bioactive constituents of soapberry (Sapindus mukorossi Gaertn.) and are widely used in medicine and toiletry products. However, little is known about the roles of miRNAs in the regulation of triterpenoid saponin biosynthesis in soapberry. In this study, a total of 3036 miRNAs were identified, of which 1372 miRNAs were differentially expressed at different stages of pericarp development. Important KEGG pathways, such as terpenoid backbone biosynthesis, sesquiterpenoid and triterpenoid biosynthesis, and basal transcription factors were highlighted, as well the roles of some key miRNAs, such as ath-miR5021, han-miR3630-3p, and ppe-miR858, which may play important roles in regulating triterpenoid saponin biosynthesis. In addition, 58 miRNAs might participate in saponin biosynthesis pathways by predicting the targets of those miRNAs to 53 saponin biosynthesis structural genes. And 75 miRNAs were identified to potentially play vital role in saponin accumulation by targeting transcript factor genes, bHLH, bZIP, ERF, MYB, and WRKY, respectively, which are candidate regulatory genes in the pathway of saponin biosynthesis. The results of weighted gene coexpression network analysis (WGCNA) suggested that two saponin-specific miRNA modules and 10 hub miRNAs may participate in saponin biosynthesis. Furthermore, multiple miRNA-mRNA regulatory networks potentially involved in saponin biosynthesis were generated, e.g., ath-miR5021-SmIDI2/SmGPS5/SmbAS1/SmCYP71D-3/SmUGT74G-2, han-miR3630-3p-SmCYP71A-14/SmbHLH54/SmMYB135/SmWRKY32, and ppe-miR858-SmMYB5/SmMYB32. qRT-PCR analysis validated the expression patterns of nine miRNAs and 12 corresponding target genes. This study represents the first comprehensive analysis of miRNAs in soapberry and lays the foundation for further understanding of miRNA-based regulation in triterpenoid saponin biosynthesis.
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Affiliation(s)
- Yuanyuan Xu
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Jiming Liu
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Xiangqin Ji
- Bioinformatics Analysis Department, Hangzhou KaiTai Biotechnology Co., Ltd, Hangzhou, Zhejiang, China
| | - Guochun Zhao
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Tianyun Zhao
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Xin Wang
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Lixian Wang
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Shilun Gao
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Yingying Hao
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Yuhan Gao
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Yuan Gao
- Planning and Design Institute of Forest Products Industry, National Forestry and Grassland Administration, Beijing, China
| | - Xuehuang Weng
- Research and Development Department, Yuanhua Forestry Biological Technology Co., Ltd., Sanming, Fujian, China
| | - Liming Jia
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Zhong Chen
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
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18
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Islam W, Idrees A, Waheed A, Zeng F. Plant responses to drought stress: microRNAs in action. ENVIRONMENTAL RESEARCH 2022; 215:114282. [PMID: 36122702 DOI: 10.1016/j.envres.2022.114282] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 06/15/2023]
Abstract
Drought is common in most regions of the world, and it has a significant impact on plant growth and development. Plants, on the other hand, have evolved their own defense systems to deal with the extreme weather. The reprogramming of gene expression by microRNAs (miRNAs) is one of these defense mechanisms. miRNAs are short noncoding RNAs that have emerged as key post-transcriptional gene regulators in a variety of species. Drought stress modulates the expression of certain miRNAs that are functionally conserved across plant species. These characteristics imply that miRNA-based genetic changes might improve drought resistance in plants. This study highlights current knowledge of plant miRNA biogenesis, regulatory mechanisms and their role in drought stress responses. miRNAs functions and their adaptations by plants during drought stress has also been explained that can be exploited to promote drought-resistance among economically important crops.
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Affiliation(s)
- Waqar Islam
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Atif Idrees
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China
| | - Abdul Waheed
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Fanjiang Zeng
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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19
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Guan R, Luan F, Li N, Qiu Z, Liu W, Cui Z, Zhao C, Li X. Identification of molecular initiating events and key events leading to endocrine disrupting effects of PFOA: Integrated molecular dynamic, transcriptomic, and proteomic analyses. CHEMOSPHERE 2022; 307:135881. [PMID: 35926748 DOI: 10.1016/j.chemosphere.2022.135881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/07/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Perfluorooctanoic acid (PFOA) can rapidly activate signaling pathways independent of nuclear hormone receptors through membrane receptor regulation, which leads to endocrine disrupting effects. In the present work, the molecular initiating event (MIE) and the key events (KEs) which cause the endocrine disrupting effects of PFOA have been explored and determined based on molecular dynamics simulation (MD), fluorescence analysis, transcriptomics, and proteomics. MD modeling and fluorescence analysis proved that, on binding to the G protein-coupled estrogen receptor-1 (GPER), PFOA could induce a conformational change in the receptor, turning it into an active state. The results also indicated that the binding to GPER was the MIE that led to the adverse outcome (AO) of PFOA. In addition, the downstream signal transduction pathways of GPER, as regulated by PFOA, were further investigated through genomics and proteomics to identify the KEs leading to thr endocrine disrupting effects. Two pathways (Endocrine resistance, ERP and Estrogen signaling pathway, ESP) containing GPER were regulated by different concentration of PFOA and identified as the KEs. The knowledge of MIE, KEs, and AO of PFOA is necessary to understand the links between PFOA and the possible pathways that lead to its negative effects.
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Affiliation(s)
- Ruining Guan
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Feng Luan
- College of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Ningqi Li
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Zhiqiang Qiu
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Wencheng Liu
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Zeyang Cui
- School of Information Science & Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Chunyan Zhao
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China.
| | - Xin Li
- Henan University of Science and Technology, Luoyang, 471023, China.
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20
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Tomato MicroRNAs and Their Functions. Int J Mol Sci 2022; 23:ijms231911979. [PMID: 36233279 PMCID: PMC9569937 DOI: 10.3390/ijms231911979] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 11/05/2022] Open
Abstract
MicroRNAs (miRNAs) define an essential class of non-coding small RNAs that function as posttranscriptional modulators of gene expression. They are coded by MIR genes, several hundreds of which exist in the genomes of Arabidopsis and rice model plants. The functional analysis of Arabidopsis and rice miRNAs indicate that their miRNAs regulate a wide range of processes including development, reproduction, metabolism, and stress. Tomato serves as a major model crop for the study of fleshy fruit development and ripening but until recently, information on the identity of its MIR genes and their coded miRNAs was limited and occasionally contradictory. As a result, the majority of tomato miRNAs remained uncharacterized. Recently, a comprehensive annotation of tomato MIR genes has been carried out by several labs and us. In this review, we curate and organize the resulting partially overlapping MIR annotations into an exhaustive and non-redundant atlas of tomato MIR genes. There are 538 candidate and validated MIR genes in the atlas, of which, 169, 18, and 351 code for highly conserved, Solanaceae-specific, and tomato-specific miRNAs, respectively. Furthermore, a critical review of functional studies on tomato miRNAs is presented, highlighting validated and possible functions, creating a useful resource for future tomato miRNA research.
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21
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Chen Y, Zhang Z, Zhang J, Chen X, Guo Y, Li C. RNA sequencing-based identification of microRNAs in the antler cartilage of Gansu red deer ( Cervus elaphus kansuensis). PeerJ 2022; 10:e13947. [PMID: 36164600 PMCID: PMC9508884 DOI: 10.7717/peerj.13947] [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: 05/30/2022] [Accepted: 08/03/2022] [Indexed: 01/19/2023] Open
Abstract
Background The velvet antler is a complex mammalian bone organ with unique biological characteristics, such as regeneration. The rapid growth stage (RGS) is a special period in the regeneration process of velvet antler. Methods To elucidate the functions of microRNAs (miRNAs) at the RGS of antler development in Gansu red deer (Cervus elaphus kansuensis), we used RNA sequencing (RNA-seq) to analyze miRNA expression profiles in cartilage tissues of deer antler tips at three different growth stages. Results The RNA-seq results revealed 1,073 known and 204 novel miRNAs, including 1,207, 1,242, and 1,204 from 30-, 60-, and 90-d antler cartilage tissues, respectively. To identify key miRNAs controlling rapid antler growth, we predicted target genes of screened 25 differentially expressed miRNAs (DEMs) and specifically expressed miRNAs (SEMs) in 60 d and annotated their functions. The KEGG results revealed that target genes of 25 DEMs and 30 SEMs were highly classified in the "Metabolic pathways", "Pathways in cancer", "Proteoglycans in cancer" and "PI3K-Akt signaling pathway". In addition, a novel miRNA (CM008039.1_315920), highly enriched in "NF-kappa B signaling pathway", may need further study. Conclusions The miRNAs identified in our study are potentially important in rapid antler growth. Our findings provide new insights to help elucidate the miRNA-mediated regulatory mechanisms involved during velvet antler development in C. elaphus kansuensis.
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Affiliation(s)
- Yanxia Chen
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Zhenxiang Zhang
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Jingjing Zhang
- School of Life Sciences and Engineering, Hexi University, Zhangye, Gansu, China
| | - Xiaxia Chen
- School of Life Sciences and Engineering, Hexi University, Zhangye, Gansu, China
| | - Yuqin Guo
- Research Monitoring and Evaluation Center of Qinghai National Park, Xining, Qinghai, China
| | - Changzhong Li
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
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22
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MicroRNAs Mediated Plant Responses to Salt Stress. Cells 2022; 11:cells11182806. [PMID: 36139379 PMCID: PMC9496875 DOI: 10.3390/cells11182806] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 12/17/2022] Open
Abstract
One of the most damaging issues to cultivatable land is soil salinity. While salt stress influences plant growth and yields at low to moderate levels, severe salt stress is harmful to plant growth. Mineral shortages and toxicities frequently exacerbate the problem of salinity. The growth of many plants is quantitatively reduced by various levels of salt stress depending on the stage of development and duration of stress. Plants have developed various mechanisms to withstand salt stress. One of the key strategies is the utilization of microRNAs (miRNAs) that can influence gene regulation at the post-transcriptional stage under different environmental conditions, including salinity. Here, we have reviewed the miRNA-mediated adaptations of various plant species to salt stress and other abiotic variables. Moreover, salt responsive (SR)-miRNAs, their targets, and corresponding pathways have also been discussed. The review article concludes by suggesting that the utilization of miRNAs may be a vital strategy to generate salt tolerant crops ensuring food security in the future.
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23
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Jiang J, Zhu H, Li N, Batley J, Wang Y. The miR393-Target Module Regulates Plant Development and Responses to Biotic and Abiotic Stresses. Int J Mol Sci 2022; 23:ijms23169477. [PMID: 36012740 PMCID: PMC9409142 DOI: 10.3390/ijms23169477] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
MicroRNAs (miRNAs), a class of endogenous small RNAs, are broadly involved in plant development, morphogenesis and responses to various environmental stresses, through manipulating the cleavage, translational expression, or DNA methylation of target mRNAs. miR393 is a conserved miRNA family present in many plants, which mainly targets genes encoding the transport inhibitor response1 (TIR1)/auxin signaling F-box (AFB) auxin receptors, and thus greatly affects the auxin signal perception, Aux/IAA degradation, and related gene expression. This review introduces the advances made on the miR393/target module regulating plant development and the plant’s responses to biotic and abiotic stresses. This module is valuable for genetic manipulation of optimized conditions for crop growth and development and would also be helpful in improving crop yield through molecular breeding.
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Affiliation(s)
- Jinjin Jiang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Haotian Zhu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Na Li
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
- Correspondence: (J.B.); (Y.W.)
| | - Youping Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: (J.B.); (Y.W.)
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24
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Fan B, Sun F, Yu Z, Zhang X, Yu X, Wu J, Yan X, Zhao Y, Nie L, Fang Y, Ma Y. Integrated analysis of small RNAs, transcriptome and degradome sequencing reveal the drought stress network in Agropyron mongolicum Keng. FRONTIERS IN PLANT SCIENCE 2022; 13:976684. [PMID: 36061788 PMCID: PMC9433978 DOI: 10.3389/fpls.2022.976684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Agropyron mongolicum (A. mongolicum) is an excellent gramineous forage with extreme drought tolerance, which lives in arid and semiarid desert areas. However, the mechanism that underlies the response of microRNAs (miRNAs) and their targets in A. mongolicum to drought stress is not well understood. In this study, we analyzed the transcriptome, small RNAome (specifically the miRNAome) and degradome to generate a comprehensive resource that focused on identifying key regulatory miRNA-target circuits under drought stress. The most extended transcript in each collection is known as the UniGene, and a total of 41,792 UniGenes and 1,104 miRNAs were identified, and 99 differentially expressed miRNAs negatively regulated 1,474 differentially expressed target genes. Among them, eight miRNAs were unique to A. mongolicum, and there were 36 target genes. A weighted gene co-expression network analysis identified five hub genes. The miRNAs of five hub genes were screened with an integration analysis of the degradome and sRNAs, such as osa-miR444a-3p.2-MADS47, bdi-miR408-5p_1ss19TA-CCX1, tae-miR9774_L-2R-1_1ss11GT-carC, ata-miR169a-3p-PAO2, and bdi-miR528-p3_2ss15TG20CA-HOX24. The functional annotations revealed that they were involved in mediating the brassinosteroid signal pathway, transporting and exchanging sodium and potassium ions and regulating the oxidation-reduction process, hydrolase activity, plant response to water deprivation, abscisic acid (ABA) and the ABA-activated signaling pathway to regulate drought stress. Five hub genes were discovered, which could play central roles in the regulation of drought-responsive genes. These results show that the combined analysis of miRNA, the transcriptome and degradation group provides a useful platform to investigate the molecular mechanism of drought resistance in A. mongolicum and could provide new insights into the genetic engineering of Poaceae crops in the future.
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Affiliation(s)
- Bobo Fan
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, China
| | - Fengcheng Sun
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, China
| | - Zhuo Yu
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, China
| | - Xuefeng Zhang
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaoxia Yu
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, China
| | - Jing Wu
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiuxiu Yan
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, China
| | - Yan Zhao
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Lizhen Nie
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, China
| | - Yongyu Fang
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, China
| | - Yanhong Ma
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, China
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25
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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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26
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Liu X, Cheng L, Li R, Cai Y, Wang X, Fu X, Dong X, Qi M, Jiang CZ, Xu T, Li T. The HD-Zip transcription factor SlHB15A regulates abscission by modulating jasmonoyl-isoleucine biosynthesis. PLANT PHYSIOLOGY 2022; 189:2396-2412. [PMID: 35522030 PMCID: PMC9342995 DOI: 10.1093/plphys/kiac212] [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: 12/09/2021] [Accepted: 04/04/2022] [Indexed: 05/08/2023]
Abstract
Plant organ abscission, a process that is important for development and reproductive success, is inhibited by the phytohormone auxin and promoted by another phytohormone, jasmonic acid (JA). However, the molecular mechanisms underlying the antagonistic effects of auxin and JA in organ abscission are unknown. We identified a tomato (Solanum lycopersicum) class III homeodomain-leucine zipper transcription factor, HOMEOBOX15A (SlHB15A), which was highly expressed in the flower pedicel abscission zone and induced by auxin. Knocking out SlHB15A using clustered regularly interspaced short palindromic repeats-associated protein 9 technology significantly accelerated abscission. In contrast, overexpression of microRNA166-resistant SlHB15A (mSlHB15A) delayed abscission. RNA sequencing and reverse transcription-quantitative PCR analyses showed that knocking out SlHB15A altered the expression of genes related to JA biosynthesis and signaling. Furthermore, functional analysis indicated that SlHB15A regulates abscission by depressing JA-isoleucine (JA-Ile) levels through inhabiting the expression of JASMONATE-RESISTANT1 (SlJAR1), a gene involved in JA-Ile biosynthesis, which could induce abscission-dependent and abscission-independent ethylene signaling. SlHB15A bound directly to the SlJAR1 promoter to silence SlJAR1, thus delaying abscission. We also found that flower removal enhanced JA-Ile content and that application of JA-Ile severely impaired the inhibitory effects of auxin on abscission. These results indicated that SlHB15A mediates the antagonistic effect of auxin and JA-Ile during tomato pedicel abscission, while auxin inhibits abscission through the SlHB15A-SlJAR1 module.
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Affiliation(s)
- Xianfeng Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang 110866, China
| | - Lina Cheng
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang 110866, China
| | - Ruizhen Li
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang 110866, China
| | - Yue Cai
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang 110866, China
| | - Xiaoyang Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang 110866, China
| | - Xin Fu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang 110866, China
| | - Xiufen Dong
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang 110866, China
| | - Mingfang Qi
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang 110866, China
| | - Cai-Zhong Jiang
- Department of Plant Sciences, University of California at Davis, Davis, California 95616, USA
- Crops Pathology and Genetic Research Unit, USDA-ARS, Davis, California 95616, USA
| | - Tao Xu
- Author for correspondence: (T.L.), (T.X.)
| | - Tianlai Li
- Author for correspondence: (T.L.), (T.X.)
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27
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Yang Z, Dong T, Dai X, Wei Y, Fang Y, Zhang L, Zhu M, Nawaz G, Cao Q, Xu T. Comparative Analysis of Salt Responsive MicroRNAs in Two Sweetpotato [ Ipomoea batatas (L.) Lam.] Cultivars With Different Salt Stress Resistance. FRONTIERS IN PLANT SCIENCE 2022; 13:879819. [PMID: 35874022 PMCID: PMC9302446 DOI: 10.3389/fpls.2022.879819] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Sweetpotato [Ipomoea batatas (L.) Lam.] is an important food, vegetable and economic crop, but its productivity is remarkably affected by soil salinity. MiRNAs are a class of endogenous non-coding small RNAs that play an important role in plant resistance to salt stress. However, the function of miRNAs still remains largely unknown in sweetpotato under salt stress. Previously, we identified salt-responsive miRNAs in one salt-sensitive sweetpotato cultivar "Xushu 32." In this study, we identified miRNAs in another salt-tolerant cultivar "Xushu 22" by high-throughput deep sequencing and compared the salt-responsive miRNAs between these two cultivars with different salt sensitivity. We identified 687 miRNAs in "Xushu 22," including 514 known miRNAs and 173 novel miRNAs. Among the 759 miRNAs from the two cultivars, 72 and 109 miRNAs were specifically expressed in "Xushu 32" and "Xushu 22," respectively, and 578 miRNAs were co-expressed. The comparison of "Xushu 32" and "Xushu 22" genotypes showed a total of 235 miRNAs with obvious differential expression and 177 salt-responsive miRNAs that were obviously differently expressed between "Xushu 32" and "Xushu 22" under salt stress. The target genes of the miRNAs were predicted and identified using the Target Finder tool and degradome sequencing. The results showed that most of the targets were transcription factors and proteins related to metabolism and stress response. Gene Ontology analysis revealed that these target genes are involved in key pathways related to salt stress response and secondary redox metabolism. The comparative analysis of salt-responsive miRNAs in sweetpotato cultivars with different salt sensitivity is helpful for understanding the regulatory pattern of miRNA in different sweetpotato genotypes and improving the agronomic traits of sweetpotato by miRNA manipulation in the future.
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Affiliation(s)
- Zhengmei Yang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Department of Applied Biology, Chonnam National University, Gwangju, South Korea
| | - Tingting Dong
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Xibin Dai
- Jiangsu Xuzhou Sweetpotato Research Center, Xuzhou, China
| | - Yiliang Wei
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yujie Fang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Lei Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Mingku Zhu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Ghazala Nawaz
- Department of Botanical and Environmental Sciences, Kohat University of Science and Technology, Kohat, Pakistan
| | - Qinghe Cao
- Jiangsu Xuzhou Sweetpotato Research Center, Xuzhou, China
| | - Tao Xu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics School of Life Sciences, Jiangsu Normal University, Xuzhou, China
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28
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Li L, Chen G, Yuan M, Guo S, Wang Y, Sun J. CsbZIP2-miR9748-CsNPF4.4 Module Mediates High Temperature Tolerance of Cucumber Through Jasmonic Acid Pathway. FRONTIERS IN PLANT SCIENCE 2022; 13:883876. [PMID: 35574100 PMCID: PMC9096661 DOI: 10.3389/fpls.2022.883876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/12/2022] [Indexed: 06/02/2023]
Abstract
High temperature stress seriously affects the growth of cucumber seedlings, and even leads to a decline in yield and quality. miRNAs have been shown to be involved in regulating the response to stress in plants, but little is known about its effects on cucumber high temperature stress tolerance. Here, we found that high temperature stress induced the expression of miR9748 in cucumber. Overexpression of cucumber miR9748 in Arabidopsis improved high temperature tolerance. Transcriptome analysis revealed that miR9748 might mediate high temperature tolerance through plant hormone signal pathway. 5' RNA ligase-mediated rapid amplification of cDNA ends (5' RLM-RACE) and transient transformation technology demonstrated that CsNPF4.4 was the target gene of miR9748. CsNPF4.4 overexpression plants decreased high temperature tolerance accompanied by reducing the content of jasmonic acid (JA), but alleviated by foliar application of methyl jasmonate, indicating that CsNPF4.4 negatively regulated high temperature stress tolerance through inhibition JA signal pathway. Furthermore, high temperature stress also increased the expression level of CsbZIP2. Yeast one-hybrid and dual-luciferase assays showed that CsbZIP2 directly bound to the promoter of MIR9748 to induce its expression. Taken together, our results indicated that CsbZIP2 directly regulated miR9748 expression to cleave CsNPF4.4 to mediate high temperature tolerance through JA pathway.
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29
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Li X, Zhang Y, Wu Y, Li B, Sun J, Gu S, Pang X. Lipid metabolism regulated by superoxide scavenger trypsin in
Hylocereus undatus
through multi‐omics analyses. J Food Biochem 2022; 46:e14144. [DOI: 10.1111/jfbc.14144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 02/24/2022] [Accepted: 03/03/2022] [Indexed: 12/09/2022]
Affiliation(s)
- Xin Li
- College of Food and Bioengineering Henan University of Science and Technology Luoyang China
- Key Laboratory of Microbial Resources Exploitation and Utilization Luoyang China
- National Demonstration Center for Experimental Food Processing and Safety Education Luoyang China
| | - Yinyin Zhang
- College of Food and Bioengineering Henan University of Science and Technology Luoyang China
| | - Ying Wu
- College of Food and Bioengineering Henan University of Science and Technology Luoyang China
| | - Bairu Li
- College of Food and Bioengineering Henan University of Science and Technology Luoyang China
| | - Jiaju Sun
- College of Food and Bioengineering Henan University of Science and Technology Luoyang China
| | - Shaobin Gu
- College of Food and Bioengineering Henan University of Science and Technology Luoyang China
| | - Xinyue Pang
- College of Medical Technology and Engineering Henan University of Science and Technology Luoyang China
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30
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Drought tolerance improvement in Solanum lycopersicum: an insight into "OMICS" approaches and genome editing. 3 Biotech 2022; 12:63. [PMID: 35186660 PMCID: PMC8825918 DOI: 10.1007/s13205-022-03132-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/24/2022] [Indexed: 12/16/2022] Open
Abstract
Solanum lycopersicum (tomato) is an internationally acclaimed vegetable crop that is grown worldwide. However, drought stress is one of the most critical challenges for tomato production, and it is a crucial task for agricultural biotechnology to produce drought-resistant cultivars. Although breeders have done a lot of work on the tomato to boost quality and quantity of production and enhance resistance to biotic and abiotic stresses, conventional tomato breeding approaches have been limited to improving drought tolerance because of the intricacy of drought traits. Many efforts have been made to better understand the mechanisms involved in adaptation and tolerance to drought stress in tomatoes throughout the years. "Omics" techniques, such as genomics, transcriptomics, proteomics, and metabolomics in combination with modern sequencing technologies, have tremendously aided the discovery of drought-responsive genes. In addition, the availability of biotechnological tools, such as plant transformation and the recently developed genome editing system for tomatoes, has opened up wider opportunities for validating the function of drought-responsive genes and the generation of drought-tolerant varieties. This review highlighted the recent progresses for tomatoes improvement against drought stress through "omics" and "multi-omics" technologies including genetic engineering. We have also discussed the roles of non-coding RNAs and genome editing techniques for drought stress tolerance improvement in tomatoes.
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Yao Y, Dong L, Fu X, Zhao L, Wei J, Cao J, Sun Y, Liu J. HrTCP20 dramatically enhance drought tolerance of sea buckthorn (Hippophae rhamnoides L). by mediating the JA signaling pathway. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 174:51-62. [PMID: 35144110 DOI: 10.1016/j.plaphy.2022.01.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/04/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Sea buckthorn, an important ecological and economical tree species, have remarkable drought and salt resistance. The plant-specific transcription factor TCPs play important roles in plant growth, development, and stress responses. However, in sea buckthorn, the molecular mechanism of TCP proteins and their involvement in drought stress are unknown. Here, we found that the expression of HrTCP20 was significantly up-regulated in sea buckthorn under drought stress. Overexpression of HrTCP20 in Arabidopsis thaliana showed that the superoxide dismutase (SOD), polyphenol oxidase (POD), and chlorophyll (SPAD) content was significantly increased by 1.37 and 1.35 times. However, the malondialdehyde (MDA) content decreased by 0.51 times. Our studies further confirmed that silencing HrTCP20 by virus-induced gene silencing (VIGS) led to a decrease in the content of defense enzymes, relative water content (RWC), and an increase of relative electrical conductivity (REC). Silencing HrTCP20 also caused the jasmonic acid (JA) content to decrease in the VIGS-treated tree. Interestingly, we found that JA accumulation content and the expression of HrLOX2, an essential enzyme for JA synthesis, was significantly inhibited in HrTCP20-silenced sea buckthorn under drought stress. Yeast two-hybrid analysis also showed that HrTCP20 is directly bound to HrLOX2. Taken together, the HrTCP20 transcription factor was a positive regulator in drought resistance of sea buckthorn. Further, our findings will provide comprehensive insights into the forest tree defence system of drought stress.
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Affiliation(s)
- Ying Yao
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Lijun Dong
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Xiaohong Fu
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Lin Zhao
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Jianrong Wei
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Jinfeng Cao
- Hebei Key Laboratory of Crop Salt-Alkali Stress Tolerance Evaluation and Genetic Improvement, Cangzhou, China
| | - Yongyuan Sun
- Hebei Key Laboratory of Crop Salt-Alkali Stress Tolerance Evaluation and Genetic Improvement, Cangzhou, China.
| | - Jianfeng Liu
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China.
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Insight into gene regulatory networks involved in sesame (Sesamum indicum L.) drought response. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01009-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Li X, Chen L, Zhou H, Wang J, Zhao C, Pang X. PFOA regulate adenosine receptors and downstream concentration-response cAMP-PKA pathway revealed by integrated omics and molecular dynamics analyses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 803:149910. [PMID: 34500266 DOI: 10.1016/j.scitotenv.2021.149910] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 08/20/2021] [Accepted: 08/22/2021] [Indexed: 06/13/2023]
Abstract
As an important pollutant, perfluorooctane acid (PFOA) has been widely concerned and reported by thousands of times, while less is known about the concentration-response pathway of PFOA. The aim of the present work was to reveal the concentration-response mechanism of PFOA in human cells. Omics results showed that calcium-related pathways play key roles in PFOA injury mechanisms. The results of GO and KEGG analyses showed that the cAMP signaling pathway was presented as the top one in all of the regulatory patterns and concentrations groups of PFOA. In the cAMP signaling pathway, the adenosine A1 receptor (ADORA1) recognized the low concentration of PFOA and induced pathway "Gi-cAMP-PKA" to decrease the concentration of cAMP. This indicated that the low concentration of PFOA may promote breast hyperplasia and inhibit lactation. While adenosine A2A receptor (ADORA2A) recognized the high concentration of PFOA and induced pathway "GS-AC-cAMP-RKA" to increase the concentration of cAMP, induce cell damage and may lead to the deterioration of breast cancer. The results of molecular dynamics simulation showed that PFOA could bind to ADORA1 and ADORA2A, thus cause subsequent signal transduction. Furthermore, considering the strong binding ability of PFOA with ADORA1, PFOA tends to bind to ADORA1 at a low concentration. On the other side, PFOA at high concentration will continue to bind to another receptor protein, ADORA2A, and activate subsequent signaling pathways. Combined analyses of transcriptomic and proteomic revealed that different concentrations of PFOA regulate cellular calcium-related pathways. The cAMP pathway showed a concentration-response effect of PFOA. After treatment with different concentrations of PFOA, ADORA1 and ADORA2A were activated respectively, showing opposite cellular effects, leading to kinds of breast lesions. In the nervous system, PFOA might induce a variety of nervous system diseases. The present work was an exploration on the toxicological mechanism of PFOA, providing important information on the health impacts of PFOA in humans.
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Affiliation(s)
- Xin Li
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China; National Demonstration Center for Experimental Food Processing and Safety Education, Luoyang 471000, China
| | - Lei Chen
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China
| | - Haitao Zhou
- Neurology Department, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, China
| | - Jie Wang
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China
| | - Chunyan Zhao
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China.
| | - Xinyue Pang
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang 471023, China.
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The Evolution and Functional Roles of miR408 and Its Targets in Plants. Int J Mol Sci 2022; 23:ijms23010530. [PMID: 35008962 PMCID: PMC8745667 DOI: 10.3390/ijms23010530] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/21/2021] [Accepted: 12/29/2021] [Indexed: 12/20/2022] Open
Abstract
MicroRNA408 (miR408) is an ancient and highly conserved miRNA, which is involved in the regulation of plant growth, development and stress response. However, previous research results on the evolution and functional roles of miR408 and its targets are relatively scattered, and there is a lack of a systematic comparison and comprehensive summary of the detailed evolutionary pathways and regulatory mechanisms of miR408 and its targets in plants. Here, we analyzed the evolutionary pathway of miR408 in plants, and summarized the functions of miR408 and its targets in regulating plant growth and development and plant responses to various abiotic and biotic stresses. The evolutionary analysis shows that miR408 is an ancient and highly conserved microRNA, which is widely distributed in different plants. miR408 regulates the growth and development of different plants by down-regulating its targets, encoding blue copper (Cu) proteins, and by transporting Cu to plastocyanin (PC), which affects photosynthesis and ultimately promotes grain yield. In addition, miR408 improves tolerance to stress by down-regulating target genes and enhancing cellular antioxidants, thereby increasing the antioxidant capacity of plants. This review expands and promotes an in-depth understanding of the evolutionary and regulatory roles of miR408 and its targets in plants.
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Palakolanu SR, Gupta S, Yeshvekar RK, Chakravartty N, Kaliamoorthy S, Shankhapal AR, Vempati AS, Kuriakose B, Lekkala SP, Philip M, Perumal RC, Lachagari VBR, Bhatnagar-Mathur P. Genome-wide miRNAs profiles of pearl millet under contrasting high vapor pressure deficit reveal their functional roles in drought stress adaptations. PHYSIOLOGIA PLANTARUM 2022; 174:e13521. [PMID: 34392545 DOI: 10.1111/ppl.13521] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/22/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
Pearl millet (Pennisetum glaucum [L.] R. Br.) is an important crop capable of growing in harsh and marginal environments, with the highest degree of tolerance to drought and heat stresses among cereals. Diverse germplasm of pearl millet shows a significant phenotypic variation in response to abiotic stresses, making it a unique model to study the mechanisms responsible for stress mitigation. The present study focuses on identifying the physiological response of two pearl millet high-resolution cross (HRC) genotypes, ICMR 1122 and ICMR 1152, in response to low and high vapor pressure deficit (VPD). Under high VPD conditions, ICMR 1152 exhibited a lower transpiration rate (Tr), higher transpiration efficiency, and lower root sap exudation than ICMR 1122. Further, Pg-miRNAs expressed in the contrasting genotypes under low and high VPD conditions were identified by deep sequencing analysis. A total of 116 known and 61 novel Pg-miRNAs were identified from ICMR 1152, while 26 known and six novel Pg-miRNAs were identified from ICMR 1122 genotypes, respectively. While Pg-miR165, 168, 170, and 319 families exhibited significant differential expression under low and high VPD conditions in both genotypes, ICMR 1152 showed abundant expression of Pg-miR167, Pg-miR172, Pg-miR396 Pg-miR399, Pg-miR862, Pg-miR868, Pg-miR950, Pg-miR5054, and Pg-miR7527 indicating their direct and indirect role in root physiology and abiotic stress responses. Drought responsive Pg-miRNA targets showed upregulation in response to high VPD stress, further narrowing down the miRNAs involved in regulation of drought tolerance in pearl millet.
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Affiliation(s)
- Sudhakar Reddy Palakolanu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
| | - Saurabh Gupta
- AgriGenome Labs Pvt. Ltd, Hyderabad, Telangana, India
| | - Richa K Yeshvekar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds, UK
| | | | - Sivasakthi Kaliamoorthy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
| | | | - Ashwini Soumya Vempati
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
| | | | | | | | | | | | - Pooja Bhatnagar-Mathur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
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Zhang M, Cheng W, Yuan X, Wang J, Cheng T, Zhang Q. Integrated transcriptome and small RNA sequencing in revealing miRNA-mediated regulatory network of floral bud break in Prunus mume. FRONTIERS IN PLANT SCIENCE 2022; 13:931454. [PMID: 35937373 PMCID: PMC9355595 DOI: 10.3389/fpls.2022.931454] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/30/2022] [Indexed: 05/08/2023]
Abstract
MicroRNAs is one class of small non-coding RNAs that play important roles in plant growth and development. Though miRNAs and their target genes have been widely studied in many plant species, their functional roles in floral bud break and dormancy release in woody perennials is still unclear. In this study, we applied transcriptome and small RNA sequencing together to systematically explore the transcriptional and post-transcriptional regulation of floral bud break in P. mume. Through expression profiling, we identified a few candidate genes and miRNAs during different developmental stage transitions. In total, we characterized 1,553 DEGs associated with endodormancy release and 2,084 DEGs associated with bud flush. Additionally, we identified 48 known miRNAs and 53 novel miRNAs targeting genes enriched in biological processes such as floral organ morphogenesis and hormone signaling transudation. We further validated the regulatory relationship between differentially expressed miRNAs and their target genes combining computational prediction, degradome sequencing, and expression pattern analysis. Finally, we integrated weighted gene co-expression analysis and constructed miRNA-mRNA regulatory networks mediating floral bud flushing competency. In general, our study revealed the miRNA-mediated networks in modulating floral bud break in P. mume. The findings will contribute to the comprehensive understanding of miRNA-mediated regulatory mechanism governing floral bud break and dormancy cycling in wood perennials.
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Baloch AA, Raza AM, Rana SSA, Ullah S, Khan S, Zaib-un-Nisa, Zahid H, Malghani GK, Kakar KU. BrCNGC gene family in field mustard: genome-wide identification, characterization, comparative synteny, evolution and expression profiling. Sci Rep 2021; 11:24203. [PMID: 34921218 PMCID: PMC8683401 DOI: 10.1038/s41598-021-03712-y] [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: 08/27/2021] [Accepted: 12/03/2021] [Indexed: 12/30/2022] Open
Abstract
CNGCs are ligand-gated calcium signaling channels, which participate in important biological processes in eukaryotes. However, the CNGC gene family is not well-investigated in Brassica rapa L. (i.e., field mustard) that is economically important and evolutionary model crop. In this study, we systematically identified 29 member genes in BrCNGC gene family, and studied their physico-chemical properties. The BrCNGC family was classified into four major and two sub phylogenetic groups. These genes were randomly localized on nine chromosomes, and dispersed into three sub-genomes of B. rapa L. Both whole-genome triplication and gene duplication (i.e., segmental/tandem) events participated in the expansion of the BrCNGC family. Using in-silico bioinformatics approaches, we determined the gene structures, conserved motif compositions, protein interaction networks, and revealed that most BrCNGCs can be regulated by phosphorylation and microRNAs of diverse functionality. The differential expression patterns of BrCNGC genes in different plant tissues, and in response to different biotic, abiotic and hormonal stress types, suggest their strong role in plant growth, development and stress tolerance. Notably, BrCNGC-9, 27, 18 and 11 exhibited highest responses in terms of fold-changes against club-root pathogen Plasmodiophora brassicae, Pseudomonas syringae pv. maculicola, methyl-jasmonate, and trace elements. These results provide foundation for the selection of candidate BrCNGC genes for future breeding of field mustard.
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Affiliation(s)
- Akram Ali Baloch
- grid.440526.10000 0004 0609 3164Department of Biotechnology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering, and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Agha Muhammad Raza
- grid.440526.10000 0004 0609 3164Department of Microbiology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Shahjahan Shabbir Ahmed Rana
- grid.440526.10000 0004 0609 3164Department of Biotechnology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering, and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Saad Ullah
- grid.440526.10000 0004 0609 3164Department of Microbiology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Samiullah Khan
- grid.440526.10000 0004 0609 3164Department of Biotechnology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering, and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Zaib-un-Nisa
- grid.411555.10000 0001 2233 7083Department of Botany, GC University Lahore, Lahore, Pakistan
| | - Humera Zahid
- grid.413062.2Department of Zoology, University of Balochistan, Quetta, Pakistan
| | - Gohram Khan Malghani
- grid.440526.10000 0004 0609 3164Department of Environmental Sciences, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Kaleem U. Kakar
- grid.440526.10000 0004 0609 3164Department of Microbiology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
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Liang Y, Wei K, Wei F, Qin S, Deng C, Lin Y, Li M, Gu L, Wei G, Miao J, Zhang Z. Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis. BMC PLANT BIOLOGY 2021; 21:566. [PMID: 34856930 PMCID: PMC8641164 DOI: 10.1186/s12870-021-03334-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Sophora tonkinensis Gagnep is a traditional Chinese medical plant that is mainly cultivated in southern China. Drought stress is one of the major abiotic stresses that negatively impacts S. tonkinensis growth. However, the molecular mechanisms governing the responses to drought stress in S. tonkinensis at the transcriptional and posttranscriptional levels are not well understood. RESULTS To identify genes and miRNAs involved in drought stress responses in S. tonkinensis, both mRNA and small RNA sequencing was performed in root samples under control, mild drought, and severe drought conditions. mRNA sequencing revealed 66,476 unigenes, and the differentially expressed unigenes (DEGs) were associated with several key pathways, including phenylpropanoid biosynthesis, sugar metabolism, and quinolizidine alkaloid biosynthesis pathways. A total of 10 and 30 transcription factors (TFs) were identified among the DEGs under mild and severe drought stress, respectively. Moreover, small RNA sequencing revealed a total of 368 miRNAs, including 255 known miRNAs and 113 novel miRNAs. The differentially expressed miRNAs and their target genes were involved in the regulation of plant hormone signal transduction, the spliceosome, and ribosomes. Analysis of the regulatory network involved in the response to drought stress revealed 37 differentially expressed miRNA-mRNA pairs. CONCLUSION This is the first study to simultaneously profile the expression patterns of mRNAs and miRNAs on a genome-wide scale to elucidate the molecular mechanisms of the drought stress responses of S. tonkinensis. Our results suggest that S. tonkinensis implements diverse mechanisms to modulate its responses to drought stress.
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Affiliation(s)
- Ying Liang
- College of Agriculture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou, 350002, People's Republic of China
- Guangxi key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, No. 189 Changgang Road, Xingning District, Nanning, 530023, People's Republic of China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Kunhua Wei
- Guangxi key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, No. 189 Changgang Road, Xingning District, Nanning, 530023, People's Republic of China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Fan Wei
- Guangxi key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, No. 189 Changgang Road, Xingning District, Nanning, 530023, People's Republic of China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Shuangshuang Qin
- Guangxi key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, No. 189 Changgang Road, Xingning District, Nanning, 530023, People's Republic of China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Chuanhua Deng
- Guangxi Forest Inventory and Planning Institute, Nanning, 530011, China
| | - Yang Lin
- Guangxi key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, No. 189 Changgang Road, Xingning District, Nanning, 530023, People's Republic of China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Mingjie Li
- College of Agriculture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou, 350002, People's Republic of China
| | - Li Gu
- College of Agriculture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou, 350002, People's Republic of China
| | - Guili Wei
- Guangxi key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, No. 189 Changgang Road, Xingning District, Nanning, 530023, People's Republic of China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Jianhua Miao
- Guangxi key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, No. 189 Changgang Road, Xingning District, Nanning, 530023, People's Republic of China.
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China.
| | - Zhongyi Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou, 350002, People's Republic of China.
- Key Laboratory of Genetics, Breeding and Comprehensive Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Wang Z, Li N, Yu Q, Wang H. Genome-Wide Characterization of Salt-Responsive miRNAs, circRNAs and Associated ceRNA Networks in Tomatoes. Int J Mol Sci 2021; 22:12238. [PMID: 34830118 PMCID: PMC8625345 DOI: 10.3390/ijms222212238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 11/28/2022] Open
Abstract
Soil salinization is a major environmental stress that causes crop yield reductions worldwide. Therefore, the cultivation of salt-tolerant crops is an effective way to sustain crop yield. Tomatoes are one of the vegetable crops that are moderately sensitive to salt stress. Global market demand for tomatoes is huge and growing. In recent years, the mechanisms of salt tolerance in tomatoes have been extensively investigated; however, the molecular mechanism through which non-coding RNAs (ncRNAs) respond to salt stress is not well understood. In this study, we utilized small RNA sequencing and whole transcriptome sequencing technology to identify salt-responsive microRNAs (miRNAs), messenger RNAs (mRNAs), and circular RNAs (circRNAs) in roots of M82 cultivated tomato and Solanum pennellii (S. pennellii) wild tomato under salt stress. Based on the theory of competitive endogenous RNA (ceRNA), we also established several salt-responsive ceRNA networks. The results showed that circRNAs could act as miRNA sponges in the regulation of target mRNAs of miRNAs, thus participating in the response to salt stress. This study provides insights into the mechanisms of salt tolerance in tomatoes and serves as an effective reference for improving the salt tolerance of salt-sensitive cultivars.
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Affiliation(s)
- Zhongyu Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Ning Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
- Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Qinghui Yu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
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Guo M, Li H, Zhu L, Wu Z, Li J, Li Z. Genome-wide identification of microRNAs associated with osmotic stress and elucidation of the role of miR319 in Medicago ruthenica seedlings. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 168:53-61. [PMID: 34619598 DOI: 10.1016/j.plaphy.2021.09.033] [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: 07/09/2021] [Revised: 09/06/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Drought is a major environmental stress that affects plant growth, development, and productivity. Medicago ruthenica, a leguminous forage, has garnered attention owing to its resistance to abiotic stress. The purpose of the current study was to explore genes conferring drought resistance to M. ruthenica. MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression in plants and are associated with developmental plasticity and abiotic/biotic stress responses. Here, high-throughput small RNA, mRNA, and degradome sequencing analyses were performed to analyze miRNAs and their potential target genes in the leaves of M. ruthenica seedlings under osmotic stress conditions. In total, 591 miRNAs were identified. A comparison of the expression levels showed that 15 miRNAs (14 upregulated and 1 downregulated) were significantly differentially expressed following PEG6000 treatment compared with those in the control (0 h). Most miRNAs are highly conserved between M. ruthenica and Medicago truncatula. Using TargetFinder, 11 target genes were predicted; the expression of these target genes negatively correlated with that of five miRNAs related to osmotic stress response. miR319 downregulated the expression of teosinte branched/cycloidea/proliferating cell factor 4 (TCP4), which encodes plant-specific transcription factors, more significantly in the leaves than in the roots. These results were confirmed using quantitative real-time polymerase chain reaction, northern blotting, RLM 5'RACE, and a Nicotiana benthamiana transient expression system. The miR319-TCP4 module may act as a homeostasis factor in M. ruthenica roots following drought injury, and it is conserved among plant species.
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Affiliation(s)
- Maowei Guo
- Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Hongyan Li
- Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Lin Zhu
- Grassland and Resources Environment Institute, Inner Mongolia Agriculture University, Hohhot, China
| | - Zinian Wu
- Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Jun Li
- Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China; Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.
| | - Zhiyong Li
- Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China.
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Liu X, Xia B, Purente N, Chen B, Zhou Y, He M. Transgenic Chrysanthemum indicum overexpressing cin-miR396a exhibits altered plant development and reduced salt and drought tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 168:17-26. [PMID: 34619595 DOI: 10.1016/j.plaphy.2021.09.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 05/02/2023]
Abstract
The conserved microRNA396 (miR396) is involved in growth, development, and abiotic stress responses in a variety of plants by regulating target genes. Here, we obtained transgenic Chrysanthemum indicum (C. indicum) overexpressing the cin-miR396a gene. The transgenic plants (TGs) had longer internodes and fewer epidermal hairs in contrast with the wild-type (WT) control. cin-miR396a overexpression in C. indicum reduced salt tolerance and drought tolerance. After salt and drought stress compared with WT plants, the transgenic C. indicum exhibited a relative decrease in leaf water content, and the leaf free proline content, also exhibited a relative increase, in the leaf conductivity and leaf Malondialdehyde content, while the total chlorophyll content did not differ significantly from WT, and the Na+/K+ ratio in the roots of transgenic C. indicum increased after salt stress. We also identified two target genes of cin-miR396a, CiGRF1 and CiGRF5, whose expression was induced by salt and drought treatments and suppressed in transgenic C. indicum. Taken together, our results reveal a unique role for the regulatory module of miR396a-GRFs in C. indicum development and response to abiotic stresses. cin-miR396a plays a negative regulatory role in C. indicum in response to salt and drought stresses.
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Affiliation(s)
- Xiaowei Liu
- College of Landscape Architecture, Northeast Forestry University, Harbin, 150040, China
| | - Bin Xia
- College of Landscape Architecture, Northeast Forestry University, Harbin, 150040, China
| | - Nuananong Purente
- College of Traditional Chinese Medicine, Jilin Agriculture Science and Technology University, Jilin, 132000, China
| | - Bin Chen
- College of Landscape Architecture, Northeast Forestry University, Harbin, 150040, China
| | - Yunwei Zhou
- College of Horticulture, Jilin Agricultural University, Changchun, 130118, China
| | - Miao He
- College of Landscape Architecture, Northeast Forestry University, Harbin, 150040, China.
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Li X, Chen L, Zhou H, Gu S, Wu Y, Wang B, Zhang M, Ding N, Sun J, Pang X, Lu D. LsrB, the hub of ABC transporters involved in the membrane damage mechanisms of heavy ion irradiation in Escherichia coli. Int J Radiat Biol 2021; 97:1731-1740. [PMID: 34597255 DOI: 10.1080/09553002.2021.1987565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Ionizing radiation, especially heavy ion (HI) beams, has been widely used in biology and medicine. However, the mechanism of membrane damage by such radiation remains primarily uncharacterized. PURPOSE Transcriptomic profiles of Escherichia coli (E. coli) treated with HI illustrated the response mechanisms of the membrane, mainly ABC transporters, related genes regulated by antibiotics treatment through enrichment analyses of GO and KEGG. The networks of protein-protein interactions indicated that LsrB was the crucial one among the ABC transporters specially regulated by HI through the calculation of plugins MCODE and cytoHubba of Cytoscape. Finally, the expression pattern, GO/KEGG enrichment terms, and the interaction between nine LuxS/AI-2 quorum sensing system members were investigated. CONCLUSIONS Above all, results suggested that HI might perform membrane damage through regulated material transport, inhibited LuxS/AI-2 system, finally impeded biofilm formation. This work provides further evidence for the role of ABC transporters, especially LsrB, in membrane damage of E. coli to HI. It will provide new strategies for improving the precise application of HI.
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Affiliation(s)
- Xin Li
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China.,Key Laboratory of Microbial Resources Exploitation and Utilization, Luoyang, China.,National Demonstration Center for Experimental Food Processing and Safety Education, Luoyang, China
| | - Lei Chen
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Haitao Zhou
- Neurology Department, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, China
| | - Shaobin Gu
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Ying Wu
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Bing Wang
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Miaomiao Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Nan Ding
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jiaju Sun
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Xinyue Pang
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - Dong Lu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
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43
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Li X, Zhang Y, Zhao S, Li B, Cai L, Pang X. Omics analyses indicate the routes of lignin related metabolites regulated by trypsin during storage of pitaya (Hylocereus undatus). Genomics 2021; 113:3681-3695. [PMID: 34509619 DOI: 10.1016/j.ygeno.2021.08.005] [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: 12/24/2020] [Revised: 07/30/2021] [Accepted: 08/10/2021] [Indexed: 10/20/2022]
Abstract
The storage quality of Hylocereus undatus was significantly improved by trypsin, a novel preservative. The transcriptomic results revealed that antioxidant signal pathways were induced, while lignin catabolic process was impeded by trypsin. In addition, the results of protein-protein interaction (PPI) network networks suggested that flavone 3'-O-methyltransferase 1 (OMT1), ferulic acid 5-hydroxylase 1 (CYP84A1), cellulose synthase isomer (CEV1), and 4-coumarate-CoA ligase 3 (4CL3) act as hubs of peroxidases, lignin related proteins, and proteins involved in the phenylpropanoid metabolism (PLPs) induced by trypsin. Trypsin also regulated the biosynthesis of lignin, chlorogenic acid, and flavonoids. Caffeic acid might be the hub in the metabolic network of the early pathways of phenylpropanoid biosynthesis. It has been hypothesized that trypsin might quickly induce lignin biosynthesis and then up-regulated bioactive metabolites to enhance storage quality of H. undatus.
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Affiliation(s)
- Xin Li
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China; Key Laboratory of Microbial Resources Exploitation and Utilization, Luoyang 471023, China; National Demonstration Center for Experimental Food Processing and Safety Education, Luoyang 471000, China
| | - Yinyin Zhang
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China
| | - Shoujing Zhao
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China
| | - Bairu Li
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China
| | - Luning Cai
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China
| | - Xinyue Pang
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang 471023, China.
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44
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Jacques C, Salon C, Barnard RL, Vernoud V, Prudent M. Drought Stress Memory at the Plant Cycle Level: A Review. PLANTS (BASEL, SWITZERLAND) 2021; 10:1873. [PMID: 34579406 PMCID: PMC8466371 DOI: 10.3390/plants10091873] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/07/2021] [Accepted: 09/07/2021] [Indexed: 05/25/2023]
Abstract
Plants are sessile organisms whose survival depends on their strategy to cope with dynamic, stressful conditions. It is urgent to improve the ability of crops to adapt to recurrent stresses in order to alleviate the negative impacts on their productivity. Although our knowledge of plant adaptation to drought has been extensively enhanced during the last decades, recent studies have tackled plant responses to recurrent stresses. The present review synthesizes the major findings from studies addressing plant responses to multiple drought events, and demonstrates the ability of plants to memorize drought stress. Stress memory is described as a priming effect allowing a different response to a reiterated stress when compared to a single stress event. Here, by specifically focusing on water stress memory at the plant cycle level, we describe the different underlying processes at the molecular, physiological and morphological levels in crops as well as in the model species Arabidopsis thaliana. Moreover, a conceptual analysis framework is proposed to study drought stress memory. Finally, the essential role of interactions between plants and soil microorganisms is emphasized during reiterated stresses because their plasticity can play a key role in supporting overall plant resilience.
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Affiliation(s)
| | | | | | | | - Marion Prudent
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université Bourgogne Franche-Comté, F-21000 Dijon, France; (C.J.); (C.S.); (R.L.B.); (V.V.)
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Bread Wheat ( Triticum aestivum) Responses to Arbuscular Mycorrhizae Inoculation under Drought Stress Conditions. PLANTS 2021; 10:plants10091756. [PMID: 34579289 PMCID: PMC8466081 DOI: 10.3390/plants10091756] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 11/17/2022]
Abstract
Abiotic constraints such as water deficit reduce cereal production. Plants have different strategies against these stresses to improve plant growth, physiological metabolism and crop production. For example, arbuscular mycorrhiza (AM)—bread wheat association has been shown to improve tolerance to drought stress conditions. The objective of this study was to determine the effect of AM inoculation on plant characteristics, lipid peroxidation, solute accumulation, water deficit saturation, photosynthetic activity, total phenol secretion and enzymatic activities including peroxidise (PO) and polyphenol oxidase (PPO) in two bread wheat cultivars (PAN3497 and SST806) under well-watered and drought-stressed conditions in plants grown under greenhouse conditions, to determine whether AM can enhance drought tolerance in wheat. AM inoculation improved morphological and physiological parameters in plants under stress. The leaf number increased by 35% and 5%, tiller number by 25% and 23%, chlorophyll content by 7% and 10%, accumulation of soluble sugars by 33% and 14%, electrolyte leakage by 26% and 32%, PPO by 44% and 47% and PO by 30% and 37% respectively, in PAN3497 and SST806, respectively. However, drought stress decreased proline content by 20% and 24%, oxidative damage to lipids measured as malondialdehyde by 34% and 60%, and total phenol content by 55% and 40% respectively, in AM treated plants of PAN3497 and SST806. PAN3497 was generally more drought-sensitive than SST806. This study showed that AM can contribute to protect plants against drought stress by alleviating water deficit induced oxidative stress.
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46
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Singroha G, Sharma P, Sunkur R. Current status of microRNA-mediated regulation of drought stress responses in cereals. PHYSIOLOGIA PLANTARUM 2021; 172:1808-1821. [PMID: 33956991 DOI: 10.1111/ppl.13451] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 04/20/2021] [Accepted: 05/04/2021] [Indexed: 05/03/2023]
Abstract
Drought is one of the most important abiotic stress factors impeding crop productivity. With the uncovering of their role as potential regulators of gene expression, microRNAs (miRNAs) have been recognized as new targets for developing stress resistance. MicroRNAs are small noncoding RNAs whose abundance is significantly altered under stress conditions. Interestingly, plant miRNAs predominantly targets transcription factors (TFs), and some of which are also the most critical drought-responsive genes that in turn could regulate the expression of numerous loci with drought-adaptive potential. The phytohormone ABA plays important roles in regulating stomatal conductance and in initiating an adaptive response to drought stress. miRNAs are implicated in regulating ABA-(abscisic acid) and non-ABA-mediated drought resistance pathways. For instance, miR159-MYB module and miR169-NFYA module participates in an ABA-dependent pathway, whereas several other ABA-independent miRNA-target modules (miR156-SPL; miR393-TIR1; miR160-ARF10, ARF16, ARF17; miR167-ARF6 and ARF8; miR390/TAS3siRNA-ARF2, ARF3, ARF4) collectively regulate drought responses in plants. Overall, miRNA-mediated drought response manifests diverse molecular, biochemical and physiological processes. Because of their immense role in controlling gene expression, miRNA manipulation has significant potential to augment plant tolerance to drought stress. This review compiles the current understanding of drought-responsive miRNAs in major cereals. Also, potential miRNA manipulation strategies currently in use along with the challenges and future perspectives are discussed.
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Affiliation(s)
- Garima Singroha
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Pradeep Sharma
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Ramanjulu Sunkur
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, USA
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47
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Hang N, Shi T, Liu Y, Ye W, Taier G, Sun Y, Wang K, Zhang W. Overexpression of Os-microRNA408 enhances drought tolerance in perennial ryegrass. PHYSIOLOGIA PLANTARUM 2021; 172:733-747. [PMID: 33215699 DOI: 10.1111/ppl.13276] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/26/2020] [Accepted: 11/10/2020] [Indexed: 05/29/2023]
Abstract
As a conserved microRNA (miRNA) family in plants, miR408 is known to be involved in different abiotic stress responses, including drought. Interestingly, some studies indicated a species- and/or cultivar-specific drought-responsive characteristic of miR408 in plant drought stress. Moreover, the functions of miR408 in perennial grass species are unknown. In this study, we investigated the role of miR408 in perennial ryegrass (Lolium perenne L.) by withholding water for 10 days for both wild type and transgenic plants with heterologous expression of rice (Oryza sativa L.) miR408 gene, Os-miR408. The results showed that transgenic perennial ryegrass plants displayed morphological changes under normal growth conditions, such as curl leaves and sunken stomata, which could be related to decreased leaf water loss. Moreover, transgenic perennial ryegrass exhibited improved drought tolerance, as demonstrated by maintaining higher leaf relative water content (RWC), lower electrolyte leakage (EL), and less lipid peroxidation compared to WT plants under drought stress. Furthermore, the transgenic plants showed higher antioxidative capacity under drought. These results showed that the improved drought tolerance in Os-miR408 transgenic plants could be due to leaf morphological changes favoring the maintenance of water status and to increased antioxidative capacity protecting against the reactive oxygen species damages under stress. These findings implied that miR408 could serve as a potential target for genetic manipulations to engineer perennial grass plants for improved water stress tolerance.
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Affiliation(s)
- Nan Hang
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Tianran Shi
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Yanrong Liu
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wenxin Ye
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Huhehaote, China
| | - Geli Taier
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Yan Sun
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Kehua Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Wanjun Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
- National Energy R&D Center for Biomass, China Agricultural University, Beijing, China
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48
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Knockout of Auxin Response Factor SlARF4 Improves Tomato Resistance to Water Deficit. Int J Mol Sci 2021; 22:ijms22073347. [PMID: 33805879 PMCID: PMC8037468 DOI: 10.3390/ijms22073347] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/20/2021] [Accepted: 03/22/2021] [Indexed: 12/25/2022] Open
Abstract
Auxin response factors (ARFs) play important roles in various plant physiological processes; however, knowledge of the exact role of ARFs in plant responses to water deficit is limited. In this study, SlARF4, a member of the ARF family, was functionally characterized under water deficit. Real-time fluorescence quantitative polymerase chain reaction (PCR) and β-glucuronidase (GUS) staining showed that water deficit and abscisic acid (ABA) treatment reduced the expression of SlARF4. SlARF4 was expressed in the vascular bundles and guard cells of tomato stomata. Loss of function of SlARF4 (arf4) by using Clustered Regularly Interspaced Short Palindromic Repeats/Cas 9 (CRISPR/Cas 9) technology enhanced plant resistance to water stress and rehydration ability. The arf4 mutant plants exhibited curly leaves and a thick stem. Malondialdehyde content was significantly lower in arf4 mutants than in wildtype plants under water stress; furthermore, arf4 mutants showed higher content of antioxidant substances, superoxide dismutase, actual photochemical efficiency of photosystem II (PSII), and catalase activities. Stomatal and vascular bundle morphology was changed in arf4 mutants. We identified 628 differentially expressed genes specifically expressed under water deficit in arf4 mutants; six of these genes, including ABA signaling pathway-related genes, were differentially expressed between the wildtype and arf4 mutants under water deficit and unlimited water supply. Auxin responsive element (AuxRE) elements were found in these genes' promoters indicating that SlARF4 participates in ABA signaling pathways by regulating the expression of SlABI5/ABF and SCL3, thereby influencing stomatal morphology and vascular bundle development and ultimately improving plant resistance to water deficit.
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49
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Sun Y, Xiong X, Wang Q, Zhu L, Wang L, He Y, Zeng H. Integrated Analysis of Small RNA, Transcriptome, and Degradome Sequencing Reveals the MiR156, MiR5488 and MiR399 are Involved in the Regulation of Male Sterility in PTGMS Rice. Int J Mol Sci 2021; 22:ijms22052260. [PMID: 33668376 PMCID: PMC7956645 DOI: 10.3390/ijms22052260] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 02/07/2023] Open
Abstract
A photoperiod- and thermo-sensitive genic male sterile (PTGMS) line is the basic material for two-hybrid rice and is an important genetic breeding resource. Peiai64S (PA64S) is an important germplasm resource of PTGMS rice, and it has been applied to two-line hybrid rice systems in China. Pollen fertility in PA64S is regulated by the temperature and photoperiod, but the mechanism of the fertility transition is unclear. In this study, we obtained the male fertile plant PA64S(F) and the male sterile plant PA64S(S) by controlling different temperatures under long light conditions and used the male fertile and sterile plants to investigate the role of microRNAs (miRNAs) in regulating male fertility in rice. We performed the small RNA library sequencing of anthers from PA64S(S) and PA64S(F). A total of 196 miRNAs were identified-166 known miRNAs among 27 miRNA families and 30 novel miRNAs. In the transcriptome analysis, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of differentially expressed genes revealed significant enrichment in the synthesis and metabolism of fatty acids and some secondary metabolism pathways such as fatty acid metabolism and phenylalanine metabolism. With a comprehensive analysis of miRNA, transcriptome, and degradome sequencing, we identified that 13 pairs of miRNA/target genes regulated male fertility in rice by responding to temperature change, among which the miR156, miR5488, and miR399 affect the male fertility of PA64S by influencing SPLs, the lignin synthesis of anther walls, and the flavonoid metabolism pathway. The results provide a new understanding of PTGMS rice, which will help us better understand the potential regulatory mechanisms of male sterility in the future.
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Affiliation(s)
| | | | | | | | | | - Ying He
- Correspondence: (Y.H.); (H.Z.)
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50
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Fracasso A, Vallino M, Staropoli A, Vinale F, Amaducci S, Carra A. Increased water use efficiency in miR396-downregulated tomato plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 303:110729. [PMID: 33487336 DOI: 10.1016/j.plantsci.2020.110729] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 06/12/2023]
Abstract
MicroRNAs regulate plant development and responses to biotic and abiotic stresses but their impact on water use efficiency (WUE) is poorly known. Increasing WUE is a major task in crop improvement programs aimed to meet the challenges posed by the reduction in water availability associated with the ongoing climatic change. We have examined the physiological and molecular response to water stress of tomato (Solanum lycopersicum L.) plants downregulated for miR396 by target mimicry. In water stress conditions, miR396-downregulated plants displayed reduced transpiration and a less then proportional decrease in the photosynthetic rate that resulted in higher WUE. The increase in WUE was associated with faster foliar accumulation of abscisic acid (ABA), with the induction of several drought-protective genes and with the activation of the jasmonic acid (JA) and γ-aminobutyric acid (GABA) pathways. We propose a model in which the downregulation of miR396 leads to the activation of a complex molecular response to water stress. This response acts synergistically with a set of leaf morphological modifications to increase stomatal closure and preserve the efficiency of the photosynthetic activity, ultimately resulting in higher WUE.
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Affiliation(s)
- Alessandra Fracasso
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), 10135 Torino, Italy
| | - Alessia Staropoli
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), 80055 Portici, Italy
| | - Francesco Vinale
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), 80055 Portici, Italy; Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, 80137, Italy
| | - Stefano Amaducci
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Andrea Carra
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), 10135 Torino, Italy.
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