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Liu J, Ren Y, Sun Y, Yin Y, Han B, Zhang L, Song Y, Zhang Z, Xu Y, Fan D, Li J, Liu H, Ma C. Identification and Analysis of the MIR399 Gene Family in Grapevine Reveal Their Potential Functions in Abiotic Stress. Int J Mol Sci 2024; 25:2979. [PMID: 38474225 PMCID: PMC10931670 DOI: 10.3390/ijms25052979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
MiR399 plays an important role in plant growth and development. The objective of the present study was to elucidate the evolutionary characteristics of the MIR399 gene family in grapevine and investigate its role in stress response. To comprehensively investigate the functions of miR399 in grapevine, nine members of the Vvi-MIR399 family were identified based on the genome, using a miRBase database search, located on four chromosomes (Chr 2, Chr 10, Chr 15, and Chr 16). The lengths of the Vvi-miR399 precursor sequences ranged from 82 to 122 nt and they formed stable stem-loop structures, indicating that they could produce microRNAs (miRNAs). Furthermore, our results suggested that the 2 to 20 nt region of miR399 mature sequences were relatively conserved among family members. Phylogenetic analysis revealed that the Vvi-MIR399 members of dicots (Arabidopsis, tomato, and sweet orange) and monocots (rice and grapevine) could be divided into three clades, and most of the Vvi-MIR399s were closely related to sweet orange in dicots. Promoter analysis of Vvi-MIR399s showed that the majority of the predicted cis-elements were related to stress response. A total of 66.7% (6/9) of the Vvi-MIR399 promoters harbored drought, GA, and SA response elements, and 44.4% (4/9) of the Vvi-MIRR399 promoters also presented elements involved in ABA and MeJA response. The expression trend of Vvi-MIR399s was consistent in different tissues, with the lowest expression level in mature and young fruits and the highest expression level in stems and young leaves. However, nine Vvi-MIR399s and four target genes showed different expression patterns when exposed to low light, high light, heat, cold, drought, and salt stress. Interestingly, a putative target of Vvi-MIR399 targeted multiple genes; for example, seven Vvi-MIR399s simultaneously targeted VIT_213s0067g03280.1. Furthermore, overexpression of Vvi_MIR399e and Vvi_MIR399f in Arabidopsis enhanced tolerance to drought compared with wild-type (WT). In contrast, the survival rate of Vvi_MIR399d-overexpressed plants were zero after drought stress. In conclusion, Vvi-MIR399e and Vvi-MIR399f, which are related to drought tolerance in grapevine, provide candidate genes for future drought resistance breeding.
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Affiliation(s)
- Jingjing Liu
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Department of Horticulture, Agricultural College of Shihezi University, Shihezi 832003, China; (J.L.)
| | - Yi Ren
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China
| | - Yan Sun
- Changli Research Institute of Fruit Trees, Hebei Academy of Agricultural and Forestry Sciences, Changli 066600, China
| | - Yonggang Yin
- Changli Research Institute of Fruit Trees, Hebei Academy of Agricultural and Forestry Sciences, Changli 066600, China
| | - Bin Han
- Changli Research Institute of Fruit Trees, Hebei Academy of Agricultural and Forestry Sciences, Changli 066600, China
| | - Lipeng Zhang
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Department of Horticulture, Agricultural College of Shihezi University, Shihezi 832003, China; (J.L.)
| | - Yue Song
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhen Zhang
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuanyuan Xu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dongying Fan
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Junpeng Li
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huaifeng Liu
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Department of Horticulture, Agricultural College of Shihezi University, Shihezi 832003, China; (J.L.)
| | - Chao Ma
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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Pradhan M, Baldwin IT, Pandey SP. Argonaute7 (AGO7) optimizes arbuscular mycorrhizal fungal associations and enhances competitive growth in Nicotiana attenuata. THE NEW PHYTOLOGIST 2023; 240:382-398. [PMID: 37532924 DOI: 10.1111/nph.19155] [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: 03/23/2023] [Accepted: 07/02/2023] [Indexed: 08/04/2023]
Abstract
Plants interact with arbuscular mycorrhizal fungi (AMF) and in doing so, change transcript levels of many miRNAs and their targets. However, the identity of an Argonaute (AGO) that modulates this interaction remains unknown, including in Nicotiana attenuata. We examined how the silencing of NaAGO1/2/4/7/and 10 by RNAi influenced plant-competitive ability under low-P conditions when they interact with AMF. Furthermore, the roles of seven miRNAs, predicted to regulate signaling and phosphate homeostasis, were evaluated by transient overexpression. Only NaAGO7 silencing by RNAi (irAGO7) significantly reduced the competitive ability under P-limited conditions, without changes in leaf or root development, or juvenile-to-adult phase transitions. In plants growing competitively in the glasshouse, irAGO7 roots were over-colonized with AMF, but they accumulated significantly less phosphate and the expression of their AMF-specific transporters was deregulated. Furthermore, the AMF-induced miRNA levels were inversely regulated with the abundance of their target transcripts. miRNA overexpression consistently decreased plant fitness, with four of seven-tested miRNAs reducing mycorrhization rates, and two increasing mycorrhization rates. Overexpression of Na-miR473 and Na-miRNA-PN59 downregulated targets in GA, ethylene, and fatty acid metabolism pathways. We infer that AGO7 optimizes competitive ability and colonization by regulating miRNA levels and signaling pathways during a plant's interaction with AMF.
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Affiliation(s)
- Maitree Pradhan
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Shree P Pandey
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
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Ma Z, Hu L. MicroRNA: A Dynamic Player from Signalling to Abiotic Tolerance in Plants. Int J Mol Sci 2023; 24:11364. [PMID: 37511124 PMCID: PMC10379455 DOI: 10.3390/ijms241411364] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 07/06/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of non-coding single-stranded RNA molecules composed of approximately 20-24 nucleotides in plants. They play an important regulatory role in plant growth and development and as a signal in abiotic tolerance. Some abiotic stresses include drought, salt, cold, high temperature, heavy metals and nutritional elements. miRNAs affect gene expression by manipulating the cleavage, translational expression or DNA methylation of target messenger RNAs (mRNAs). This review describes the current progress in the field considering two aspects: (i) the way miRNAs are produced and regulated and (ii) the way miRNA/target genes are used in plant responses to various abiotic stresses. Studying the molecular mechanism of action of miRNAs' downstream target genes could optimize the genetic manipulation of crop growth and development conditions to provide a more theoretically optimized basis for improving crop production. MicroRNA is a novel signalling mechanism in interplant communication relating to abiotic tolerance.
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Affiliation(s)
- Ziming Ma
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, 85354 Freising, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Lanjuan Hu
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China
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Wang J, Xu J, Wang L, Zhou M, Nian J, Chen M, Lu X, Liu X, Wang Z, Cen J, Liu Y, Zhang Z, Zeng D, Hu J, Zhu L, Dong G, Ren D, Gao Z, Shen L, Zhang Q, Li Q, Guo L, Yu S, Qian Q, Zhang G. SEMI-ROLLED LEAF 10 stabilizes catalase isozyme B to regulate leaf morphology and thermotolerance in rice (Oryza sativa L.). PLANT BIOTECHNOLOGY JOURNAL 2023; 21:819-838. [PMID: 36597711 PMCID: PMC10037157 DOI: 10.1111/pbi.13999] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 12/18/2022] [Accepted: 12/25/2022] [Indexed: 06/17/2023]
Abstract
Plant architecture and stress tolerance play important roles in rice breeding. Specific leaf morphologies and ideal plant architecture can effectively improve both abiotic stress resistance and rice grain yield. However, the mechanism by which plants simultaneously regulate leaf morphogenesis and stress resistance remains elusive. Here, we report that SRL10, which encodes a double-stranded RNA-binding protein, regulates leaf morphology and thermotolerance in rice through alteration of microRNA biogenesis. The srl10 mutant had a semi-rolled leaf phenotype and elevated sensitivity to high temperature. SRL10 directly interacted with catalase isozyme B (CATB), and the two proteins mutually increased one other's stability to enhance hydrogen peroxide (H2 O2 ) scavenging, thereby contributing to thermotolerance. The natural Hap3 (AGC) type of SRL10 allele was found to be present in the majority of aus rice accessions, and was identified as a thermotolerant allele under high temperature stress in both the field and the growth chamber. Moreover, the seed-setting rate was 3.19 times higher and grain yield per plant was 1.68 times higher in near-isogenic line (NIL) carrying Hap3 allele compared to plants carrying Hap1 allele under heat stress. Collectively, these results reveal a new locus of interest and define a novel SRL10-CATB based regulatory mechanism for developing cultivars with high temperature tolerance and stable yield. Furthermore, our findings provide a theoretical basis for simultaneous breeding for plant architecture and stress resistance.
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Affiliation(s)
- Jiajia Wang
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene ResearchCollege of Plant Science and Technology, Huazhong Agricultural UniversityWuhanChina
| | - Jing Xu
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang ProvinceResearch Institute of Subtropical Forestry, Chinese Academy of ForestryHangzhouChina
| | - Li Wang
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Mengyu Zhou
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Jinqiang Nian
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Minmin Chen
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Xueli Lu
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Xiong Liu
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Zian Wang
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Jiangsu Cen
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Yiting Liu
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Zhihai Zhang
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Dali Zeng
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Jiang Hu
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Li Zhu
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Guojun Dong
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Deyong Ren
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Zhenyu Gao
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Lan Shen
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Qiang Zhang
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Qing Li
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Longbiao Guo
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene ResearchCollege of Plant Science and Technology, Huazhong Agricultural UniversityWuhanChina
| | - Qian Qian
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
- Hainan Yazhou Bay Seed LaboratorySanyaChina
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural SciencesSanyaChina
| | - Guangheng Zhang
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
- Hainan Yazhou Bay Seed LaboratorySanyaChina
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural SciencesSanyaChina
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Li J, Zhou X, Xiong C, Zhou H, Li H, Ruan C. Yellowhorn Xso-miR5149-XsGTL1 enhances water-use efficiency and drought tolerance by regulating leaf morphology and stomatal density. Int J Biol Macromol 2023; 237:124060. [PMID: 36933587 DOI: 10.1016/j.ijbiomac.2023.124060] [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: 12/15/2022] [Revised: 03/06/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023]
Abstract
Yellowhorn (Xanthoceras sorbifolium) is a unique edible woody oil tree species in China. Drought stress is the major yield-limiting factor of yellowhorn. MicroRNAs play an important role in regulating the response of woody plants to drought stress. However, the regulatory function of miRNAs in yellowhorn remains unclear. Here, we first constructed coregulatory networks integrated with miRNAs and their target genes. According to GO function and expression pattern analysis, we selected the Xso-miR5149-XsGTL1 module for further study. Xso-miR5149 is a key regulator of leaf morphology and stomatal density by directly mediating the expression of the transcription factor XsGTL1. Downregulation of XsGTL1 in yellowhorn led to increased leaf area and reduced stomatal density. RNA-seq analysis indicated that downregulation of XsGTL1 increased the expression of genes involved in the negative control of stomatal density, leaf morphology, and drought tolerance. After drought stress treatments, the XsGTL1-RNAi yellowhorn plants were less damaged and had higher water-use efficiency than the WT plants, while destruction of Xso-miR5149 or overexpression of XsGTL1 had the opposite effect. Our findings indicated that the Xso-miR5149-XsGTL1 regulatory module plays a critical role in controlling leaf morphology and stomatal density; hence, it's a potential candidate module for engineering enhanced drought tolerance in yellowhorn.
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Affiliation(s)
- Jingbin Li
- Key Laboratory of Biotechnology and Bioresources Utilization-Ministry of Education, Institute of Plant Resources, Dalian Minzu University, 116600 Dalian, Liaoning Province, PR China
| | - Xudong Zhou
- College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, 311300 Lin'an, Zhejiang Province, PR China
| | - Chaowei Xiong
- College of Forestry, Northwest Agriculture and Forestry University, 712100 Yangling, Shaanxi Province, PR China
| | - Hui Zhou
- Key Laboratory of Biotechnology and Bioresources Utilization-Ministry of Education, Institute of Plant Resources, Dalian Minzu University, 116600 Dalian, Liaoning Province, PR China
| | - He Li
- Key Laboratory of Biotechnology and Bioresources Utilization-Ministry of Education, Institute of Plant Resources, Dalian Minzu University, 116600 Dalian, Liaoning Province, PR China
| | - Chengjiang Ruan
- Key Laboratory of Biotechnology and Bioresources Utilization-Ministry of Education, Institute of Plant Resources, Dalian Minzu University, 116600 Dalian, Liaoning Province, PR China.
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Pegler JL, Oultram JMJ, Mann CWG, Carroll BJ, Grof CPL, Eamens AL. Miniature Inverted-Repeat Transposable Elements: Small DNA Transposons That Have Contributed to Plant MICRORNA Gene Evolution. PLANTS (BASEL, SWITZERLAND) 2023; 12:1101. [PMID: 36903960 PMCID: PMC10004981 DOI: 10.3390/plants12051101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Angiosperms form the largest phylum within the Plantae kingdom and show remarkable genetic variation due to the considerable difference in the nuclear genome size of each species. Transposable elements (TEs), mobile DNA sequences that can amplify and change their chromosome position, account for much of the difference in nuclear genome size between individual angiosperm species. Considering the dramatic consequences of TE movement, including the complete loss of gene function, it is unsurprising that the angiosperms have developed elegant molecular strategies to control TE amplification and movement. Specifically, the RNA-directed DNA methylation (RdDM) pathway, directed by the repeat-associated small-interfering RNA (rasiRNA) class of small regulatory RNA, forms the primary line of defense to control TE activity in the angiosperms. However, the miniature inverted-repeat transposable element (MITE) species of TE has at times avoided the repressive effects imposed by the rasiRNA-directed RdDM pathway. MITE proliferation in angiosperm nuclear genomes is due to their preference to transpose within gene-rich regions, a pattern of transposition that has enabled MITEs to gain further transcriptional activity. The sequence-based properties of a MITE results in the synthesis of a noncoding RNA (ncRNA), which, after transcription, folds to form a structure that closely resembles those of the precursor transcripts of the microRNA (miRNA) class of small regulatory RNA. This shared folding structure results in a MITE-derived miRNA being processed from the MITE-transcribed ncRNA, and post-maturation, the MITE-derived miRNA can be used by the core protein machinery of the miRNA pathway to regulate the expression of protein-coding genes that harbor homologous MITE insertions. Here, we outline the considerable contribution that the MITE species of TE have made to expanding the miRNA repertoire of the angiosperms.
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Affiliation(s)
- Joseph L. Pegler
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Jackson M. J. Oultram
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Christopher W. G. Mann
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Bernard J. Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Christopher P. L. Grof
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Andrew L. Eamens
- School of Health, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
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Orellana D, Machuca D, Ibeas MA, Estevez JM, Poupin MJ. Plant-growth promotion by proteobacterial strains depends on the availability of phosphorus and iron in Arabidopsis thaliana plants. Front Microbiol 2022; 13:1083270. [PMID: 36583055 PMCID: PMC9792790 DOI: 10.3389/fmicb.2022.1083270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022] Open
Abstract
Phosphorus (as phosphate, Pi) and iron (Fe) are critical nutrients in plants that are often poorly available in the soil and can be microbially affected. This work aimed to evaluate how plant-rhizobacteria interaction changes due to different Pi or Fe nutritional scenarios and to study the underlying molecular mechanisms of the microbial modulation of these nutrients in plants. Thus, three proteobacteria (Paraburkholderia phytofirmans PsJN, Azospirillum brasilense Sp7, and Pseudomonas putida KT2440) were used to inoculate Arabidopsis seeds. Additionally, the seeds were exposed to a nutritional factor with the following levels for each nutrient: sufficient (control) or low concentrations of a highly soluble source or sufficient concentrations of a low solubility source. Then, the effects of the combinatorial factors were assessed in plant growth, nutrition, and genetic regulation. Interestingly, some bacterial effects in plants depended on the nutrient source (e.g., increased aerial zones induced by the strains), and others (e.g., decreased primary roots induced by Sp7 or KT2440) occurred regardless of the nutritional treatment. In the short-term, PsJN had detrimental effects on plant growth in the presence of the low-solubility Fe compound, but this was not observed in later stages of plant development. A thorough regulation of the phosphorus content was detected in plants independent of the nutritional treatment. Nevertheless, inoculation with KT2440 increased P content by 29% Pi-deficiency exposed plants. Conversely, the inoculation tended to decrease the Fe content in plants, suggesting a competition for this nutrient in the rhizosphere. The P-source also affected the effects of the PsJN strain in a double mutant of the phosphate starvation response (PSR). Furthermore, depending on the nutrient source, PsJN and Sp7 strains differentially regulated PSR and IAA- associated genes, indicating a role of these pathways in the observed differential phenotypical responses. In the case of iron, PsJN and SP7 regulated iron uptake-related genes regardless of the iron source, which may explain the lower Fe content in inoculated plants. Overall, the plant responses to these proteobacteria were not only influenced by the nutrient concentrations but also by their availabilities, the elapsed time of the interaction, and the specific identities of the beneficial bacteria. Graphical AbstractThe effects of the different nutritional and inoculation treatments are indicated for plant growth parameters (A), gene regulation (B) and phosphorus and iron content (C). Figures created with BioRender.com with an academic license.
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Affiliation(s)
- Daniela Orellana
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile,Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile,ANID - Millennium Science Initiative Program - Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - Daniel Machuca
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile,Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Miguel Angel Ibeas
- ANID - Millennium Science Initiative Program - Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile,Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - José Manuel Estevez
- ANID - Millennium Science Initiative Program - Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile,Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile,Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
| | - María Josefina Poupin
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile,Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile,ANID - Millennium Science Initiative Program - Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile,*Correspondence: María Josefina Poupin,
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Du J, Liu Y, Lu L, Shi J, Xu L, Li Q, Cheng X, Chen J, Zhang X. Accumulation of DNA damage alters microRNA gene transcription in Arabidopsis thaliana. BMC PLANT BIOLOGY 2022; 22:576. [PMID: 36503409 PMCID: PMC9743578 DOI: 10.1186/s12870-022-03951-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) and other epigenetic modifications play fundamental roles in all eukaryotic biological processes. DNA damage repair is a key process for maintaining the genomic integrity of different organisms exposed to diverse stresses. However, the reaction of miRNAs in the DNA damage repair process is unclear. RESULTS In this study, we found that the simultaneous mutation of zinc finger DNA 3'-phosphoesterase (ZDP) and AP endonuclease 2 (APE2), two genes that play overlapping roles in active DNA demethylation and base excision repair (BER), led to genome-wide alteration of miRNAs. The transcripts of newly transcribed miRNA-encoding genes (MIRs) decreased significantly in zdp/ape2, indicating that the mutation of ZDP and APE2 affected the accumulation of miRNAs at the transcriptional level. In addition, the introduction of base damage with the DNA-alkylating reagent methyl methanesulfonate (MMS) accelerated the reduction of miRNAs in zdp/ape2. Further mutation of FORMAMIDOPYRIMIDINE DNA GLYCOSYLASE (FPG), a bifunctional DNA glycosylase/lyase, rescued the accumulation of miRNAs in zdp/ape2, suggesting that the accumulation of DNA damage repair intermediates induced the transcriptional repression of miRNAs. CONCLUSIONS Our investigation indicates that the accumulation of DNA damage repair intermediates inhibit miRNAs accumulation by inhibiting MIR transcriptions.
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Affiliation(s)
- Juan Du
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lu Lu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jianfei Shi
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Longqian Xu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Department of Life Sciences, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Qi Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofei Cheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
| | - Jinfeng Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China.
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What Do We Know about Barley miRNAs? Int J Mol Sci 2022; 23:ijms232314755. [PMID: 36499082 PMCID: PMC9740008 DOI: 10.3390/ijms232314755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/09/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Plant miRNAs are powerful regulators of gene expression at the post-transcriptional level, which was repeatedly proved in several model plant species. miRNAs are considered to be key regulators of many developmental, homeostatic, and immune processes in plants. However, our understanding of plant miRNAs is still limited, despite the fact that an increasing number of studies have appeared. This systematic review aims to summarize our current knowledge about miRNAs in spring barley (Hordeum vulgare), which is an important agronomical crop worldwide and serves as a common monocot model for studying abiotic stress responses as well. This can help us to understand the connection between plant miRNAs and (not only) abiotic stresses in general. In the end, some future perspectives and open questions are summarized.
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10
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Sun J, Chen J, Si X, Liu W, Yuan M, Guo S, Wang Y. WRKY41/WRKY46-miR396b-5p-TPR module mediates abscisic acid-induced cold tolerance of grafted cucumber seedlings. FRONTIERS IN PLANT SCIENCE 2022; 13:1012439. [PMID: 36160963 PMCID: PMC9493262 DOI: 10.3389/fpls.2022.1012439] [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: 08/05/2022] [Accepted: 08/23/2022] [Indexed: 06/01/2023]
Abstract
Grafting is one of the key agronomic measures to enhance the tolerance to environmental stresses in horticultural plants, but the specific molecular regulation mechanism in this tolerance largely remains unclear. Here, we found that cucumber grafted onto figleaf gourd rootstock increased cold tolerance through abscisic acid (ABA) activating WRKY41/WRKY46-miR396b-5p-TPR (tetratricopeptide repeat-like superfamily protein) module. Cucumber seedlings grafted onto figleaf gourd increased cold tolerance and induced the expression of miR396b-5p. Furthermore, overexpression of cucumber miR396b-5p in Arabidopsis improved cold tolerance. 5' RNA ligase-mediated rapid amplification of cDNA ends (5' RLM-RACE) and transient transformation experiments demonstrated that TPR was the target gene of miR396b-5p, while TPR overexpression plants were hypersensitive to cold stress. The yeast one-hybrid and dual-luciferase assays showed that both WRKY41 and WRKY46 bound to MIR396b-5p promoter to induce its expression. Furthermore, cold stress enhanced the content of ABA in the roots and leaves of figleaf gourd grafted cucumber seedlings. Exogenous application of ABA induced the expression of WRKY41 and WRKY46, and cold tolerance of grafted cucumber seedlings. However, figleaf gourd rootstock-induced cold tolerance was compromised when plants were pretreated with ABA biosynthesis inhibitor. Thus, ABA mediated figleaf gourd grafting-induced cold tolerance of cucumber seedlings through activating the WRKY41/WRKY46-miR396b-5p-TPR module.
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11
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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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12
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A Combination of a Genome-Wide Association Study and a Transcriptome Analysis Reveals circRNAs as New Regulators Involved in the Response to Salt Stress in Maize. Int J Mol Sci 2022; 23:ijms23179755. [PMID: 36077153 PMCID: PMC9456493 DOI: 10.3390/ijms23179755] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/20/2022] [Accepted: 08/24/2022] [Indexed: 11/18/2022] Open
Abstract
Salinization seriously threatens the normal growth of maize, especially at the seedling stage. Recent studies have demonstrated that circular RNAs (circRNAs) play vital roles in the regulation of plant stress resistance. Here, we performed a genome-wide association study (GWAS) on the survival rate of 300 maize accessions under a salt stress treatment. A total of 5 trait-associated SNPs and 86 candidate genes were obtained by the GWAS. We performed RNA sequencing for 28 transcriptome libraries derived from 2 maize lines with contrasting salt tolerance under normal and salt treatment conditions. A total of 1217 highly expressed circRNAs were identified, of which 371 were responsive to a salt treatment. Using PCR and Sanger sequencing, we verified the reliability of these differentially expressed circRNAs. An integration of the GWAS and RNA-Seq analyses uncovered two differentially expressed hub genes (Zm00001eb013650 and Zm00001eb198930), which were regulated by four circRNAs. Based on these results, we constructed a regulation model of circRNA/miRNA/mRNA that mediated salt stress tolerance in maize. By conducting hub gene-based association analyses, we detected a favorable haplotype in Zm00001eb198930, which was responsible for high salt tolerance. These results help to clarify the regulatory relationship between circRNAs and their target genes as well as to develop salt-tolerant lines for maize breeding.
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13
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Miller SS, Dornbusch MR, Farmer AD, Huertas R, Gutierrez-Gonzalez JJ, Young ND, Samac DA, Curtin SJ. Alfalfa (Medicago sativa L.) pho2 mutant plants hyperaccumulate phosphate. G3 (BETHESDA, MD.) 2022; 12:jkac096. [PMID: 35471600 PMCID: PMC9157135 DOI: 10.1093/g3journal/jkac096] [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: 11/12/2021] [Accepted: 04/12/2022] [Indexed: 06/14/2023]
Abstract
In this article, we describe a set of novel alfalfa (Medicago sativa L.) plants that hyper-accumulate Phosphate ion (Pi) at levels 3- to 6-fold higher than wild-type. This alfalfa germplasm will have practical applications reclaiming Pi from contaminated or enriched soil or be used in conservation buffer strips to protect waterways from Pi run-off. Hyper-accumulating alfalfa plants were generated by targeted mutagenesis of PHOSPHATE2 (PHO2) using newly created CRISPR/Cas9 reagents and an improved mutant screening strategy. PHO2 encodes a ubiquitin conjugating E2 enzyme (UBC24) previously characterized in Arabidopsis thaliana, Medicago truncatula, and Oryza sativa. Mutations of PHO2 disrupt Pi homeostasis resulting in Pi hyper-accumulation. Successful CRISPR/Cas9 editing of PHO2 demonstrates that this is an efficient mutagenesis tool in alfalfa despite its complex autotetraploid genome structure. Arabidopsis and M. truncatula ortholog genes were used to identify PHO2 haplotypes in outcrossing tetraploid M. sativa with the aim of generating heritable mutations in both PHO2-like genes (PHO2-B and PHO2-C). After delivery of the reagent and regeneration from transformed leaf explants, plants with mutations in all haplotypes of PHO2-B and PHO2-C were identified. These plants were evaluated for morphology, Pi accumulation, heritable transmission of targeted mutations, segregation of mutant haplotypes and removal of T-DNA(s). The Agrobacterium-mediated transformation assay and gene editing reagents reported here were also evaluated for further optimization for future alfalfa functional genomic studies.
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Affiliation(s)
- Susan S Miller
- United States Department of Agriculture, Plant Science Research Unit, St Paul, MN 55108, USA
| | - Melinda R Dornbusch
- United States Department of Agriculture, Plant Science Research Unit, St Paul, MN 55108, USA
| | - Andrew D Farmer
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | | | - Juan J Gutierrez-Gonzalez
- Facultad de Ciencias Biológicas y Ambientales, Departamento de Biología Molecular, Universidad de León, 24071 León, Spain
| | - Nevin D Young
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
- Department of Plant Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Deborah A Samac
- United States Department of Agriculture, Plant Science Research Unit, St Paul, MN 55108, USA
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
| | - Shaun J Curtin
- United States Department of Agriculture, Plant Science Research Unit, St Paul, MN 55108, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
- Center for Plant Precision Genomics, University of Minnesota, St. Paul, MN 55108, USA
- Center for Genome Engineering, University of Minnesota, St. Paul, MN 55108, USA
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14
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Val‐Torregrosa B, Bundó M, Martín‐Cardoso H, Bach‐Pages M, Chiou T, Flors V, Segundo BS. Phosphate-induced resistance to pathogen infection in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:452-469. [PMID: 35061924 PMCID: PMC9303409 DOI: 10.1111/tpj.15680] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 12/30/2021] [Accepted: 01/17/2022] [Indexed: 05/12/2023]
Abstract
In nature, plants are concurrently exposed to a number of abiotic and biotic stresses. Our understanding of convergence points between responses to combined biotic/abiotic stress pathways remains, however, rudimentary. Here we show that MIR399 overexpression, loss-of-function of PHOSPHATE2 (PHO2), or treatment with high phosphate (Pi) levels is accompanied by an increase in Pi content and accumulation of reactive oxygen species (ROS) in Arabidopsis thaliana. High Pi plants (e.g., miR399 overexpressors, pho2 mutants, and plants grown under high Pi supply) exhibited resistance to infection by necrotrophic and hemibiotrophic fungal pathogens. In the absence of pathogen infection, the expression levels of genes in the salicylic acid (SA)- and jasmonic acid (JA)-dependent signaling pathways were higher in high Pi plants compared to wild-type plants grown under control conditions, which is consistent with increased levels of SA and JA in non-infected high Pi plants. During infection, an opposite regulation in the two branches of the JA pathway (ERF1/PDF1.2 and MYC2/VSP2) occurs in high Pi plants. Thus, while pathogen infection induces PDF1.2 expression in miR399 OE and pho2 plants, VSP2 expression is downregulated by pathogen infection in these plants. This study supports the notion that Pi accumulation promotes resistance to infection by fungal pathogens in Arabidopsis, while providing a basis to better understand interactions between Pi signaling and hormonal signaling pathways for modulation of plant immune responses.
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Affiliation(s)
- Beatriz Val‐Torregrosa
- Centre for Research in Agricultural Genomics (CRAG) CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)BarcelonaSpain
| | - Mireia Bundó
- Centre for Research in Agricultural Genomics (CRAG) CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)BarcelonaSpain
| | - Héctor Martín‐Cardoso
- Centre for Research in Agricultural Genomics (CRAG) CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)BarcelonaSpain
| | - Marcel Bach‐Pages
- Centre for Research in Agricultural Genomics (CRAG) CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)BarcelonaSpain
| | - Tzyy‐Jen Chiou
- Agricultural Biotechnology Research Center, Academia SinicaTaipei 115Taiwan
| | - Victor Flors
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Superior de Tecnología y Ciencias ExperimentalesUniversitat Jaume ICastellóSpain
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG) CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)BarcelonaSpain
- Consejo Superior de Investigaciones Científicas (CSIC)BarcelonaSpain
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15
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Chen J, Han X, Ye S, Liu L, Yang B, Cao Y, Zhuo R, Yao X. Integration of small RNA, degradome, and transcriptome sequencing data illustrates the mechanism of low phosphorus adaptation in Camellia oleifera. FRONTIERS IN PLANT SCIENCE 2022; 13:932926. [PMID: 35979079 PMCID: PMC9377520 DOI: 10.3389/fpls.2022.932926] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/11/2022] [Indexed: 05/02/2023]
Abstract
Phosphorus (P) is an indispensable macronutrient for plant growth and development, and it is involved in various cellular biological activities in plants. Camellia oleifera is a unique high-quality woody oil plant that grows in the hills and mountains of southern China. However, the available P content is deficient in southern woodland soil. Until now, few studies focused on the regulatory functions of microRNAs (miRNAs) and their target genes under low inorganic phosphate (Pi) stress. In this study, we integrated small RNA, degradome, and transcriptome sequencing data to investigate the mechanism of low Pi adaptation in C. oleifera. We identified 40,689 unigenes and 386 miRNAs by the deep sequencing technology and divided the miRNAs into four different groups. We found 32 miRNAs which were differentially expressed under low Pi treatment. A total of 414 target genes of 108 miRNAs were verified by degradome sequencing. Gene ontology (GO) functional analysis of target genes found that they were related to the signal response to the stimulus and transporter activity, indicating that they may respond to low Pi stress. The integrated analysis revealed that 31 miRNA-target pairs had negatively correlated expression patterns. A co-expression regulatory network was established based on the profiles of differentially expressed genes. In total, three hub genes (ARF22, WRKY53, and SCL6), which were the targets of differentially expressed miRNAs, were discovered. Our results showed that integrated analyses of the small RNA, degradome, and transcriptome sequencing data provided a valuable basis for investigating low Pi in C. oleifera and offer new perspectives on the mechanism of low Pi tolerance in woody oil plants.
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Affiliation(s)
- Juanjuan Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- Forestry Faculty, Nanjing Forestry University, Nanjing, China
| | - Xiaojiao Han
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Sicheng Ye
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Linxiu Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Bingbing Yang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Yongqing Cao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- *Correspondence: Renying Zhuo,
| | - Xiaohua Yao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- Xiaohua Yao,
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16
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Negi P, Mishra S, Ganapathi TR, Srivastava AK. Regulatory short RNAs: A decade's tale for manipulating salt tolerance in plants. PHYSIOLOGIA PLANTARUM 2021; 173:1535-1555. [PMID: 34227692 DOI: 10.1111/ppl.13492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/25/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
Salt stress is a globally increasing environmental detriment to crop growth and productivity. Exposure to salt stress evokes a complex medley of cellular signals, which rapidly reprogram transcriptional and metabolic networks to shape plant phenotype. To date, genetic engineering approaches were used with success to enhance salt tolerance; however, their performance is yet to be evaluated under realistic field conditions. Regulatory short non-coding RNAs (rsRNAs) are emerging as next-generation candidates for engineering salt tolerance in crops. In view of this, the present review provides a comprehensive analysis of a decade's worth of functional studies on non-coding RNAs involved in salt tolerance. Further, we have integrated this knowledge of rsRNA-mediated regulation with the current paradigm of salt tolerance to highlight two regulatory complexes (RCs) for regulating salt tolerance in plants. Finally, a knowledge-driven roadmap is proposed to judiciously utilize RC component(s) for enhancing salt tolerance in crops.
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Affiliation(s)
- Pooja Negi
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Shefali Mishra
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Thumballi Ramabhatta Ganapathi
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Ashish Kumar Srivastava
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
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17
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Pegler JL, Nguyen DQ, Oultram JMJ, Grof CPL, Eamens AL. Molecular Manipulation of the miR396 and miR399 Expression Modules Alters the Response of Arabidopsis thaliana to Phosphate Stress. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122570. [PMID: 34961041 PMCID: PMC8706208 DOI: 10.3390/plants10122570] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 05/03/2023]
Abstract
In plant cells, the molecular and metabolic processes of nucleic acid synthesis, phospholipid production, coenzyme activation and the generation of the vast amount of chemical energy required to drive these processes relies on an adequate supply of the essential macronutrient, phosphorous (P). The requirement of an appropriate level of P in plant cells is evidenced by the intricately linked molecular mechanisms of P sensing, signaling and transport. One such mechanism is the posttranscriptional regulation of the P response pathway by the highly conserved plant microRNA (miRNA), miR399. In addition to miR399, numerous other plant miRNAs are also required to respond to environmental stress, including miR396. Here, we exposed Arabidopsis thaliana (Arabidopsis) transformant lines which harbor molecular modifications to the miR396 and miR399 expression modules to phosphate (PO4) starvation. We show that molecular alteration of either miR396 or miR399 abundance afforded the Arabidopsis transformant lines different degrees of tolerance to PO4 starvation. Furthermore, RT-qPCR assessment of PO4-starved miR396 and miR399 transformants revealed that the tolerance displayed by these plant lines to this form of abiotic stress most likely stemmed from the altered expression of the target genes of these two miRNAs. Therefore, this study forms an early step towards the future development of molecularly modified plant lines which possess a degree of tolerance to growth in a PO4 deficient environment.
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Affiliation(s)
- Joseph L. Pegler
- Centre for Plant Science, School of Environmental and Life Sciences, Faculty of Science, University of Newcastle, Callaghan, NSW 2308, Australia; (J.L.P.); (D.Q.N.); (J.M.J.O.); (C.P.L.G.)
| | - Duc Quan Nguyen
- Centre for Plant Science, School of Environmental and Life Sciences, Faculty of Science, University of Newcastle, Callaghan, NSW 2308, Australia; (J.L.P.); (D.Q.N.); (J.M.J.O.); (C.P.L.G.)
- Institute of Genome Research, Vietnam Academy of Research and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam
| | - Jackson M. J. Oultram
- Centre for Plant Science, School of Environmental and Life Sciences, Faculty of Science, University of Newcastle, Callaghan, NSW 2308, Australia; (J.L.P.); (D.Q.N.); (J.M.J.O.); (C.P.L.G.)
| | - Christopher P. L. Grof
- Centre for Plant Science, School of Environmental and Life Sciences, Faculty of Science, University of Newcastle, Callaghan, NSW 2308, Australia; (J.L.P.); (D.Q.N.); (J.M.J.O.); (C.P.L.G.)
| | - Andrew L. Eamens
- Centre for Plant Science, School of Environmental and Life Sciences, Faculty of Science, University of Newcastle, Callaghan, NSW 2308, Australia; (J.L.P.); (D.Q.N.); (J.M.J.O.); (C.P.L.G.)
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Correspondence:
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18
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Targeted designing functional markers revealed the role of retrotransposon derived miRNAs as mobile epigenetic regulators in adaptation responses of pistachio. Sci Rep 2021; 11:19751. [PMID: 34611187 PMCID: PMC8492636 DOI: 10.1038/s41598-021-98402-0] [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: 05/13/2021] [Accepted: 09/06/2021] [Indexed: 02/08/2023] Open
Abstract
We developed novel miRNA-based markers based on salt responsive miRNA sequences to detect polymorphisms in miRNA sequences and locations. The validation of 76 combined miRNA + miRNA and miRNA + ISSR markers in the three extreme pistachio populations led to the identification of three selected markers that could link salt tolerance phenotype to genotype and divided pistachio genotypes and Pistacia species into three clusters. This novel functional marker system, in addition to more efficient performance, has higher polymorphisms than previous miRNA-based marker systems. The functional importance of the target gene of five miRNAs in the structure of the three selected markers in regulation of different genes such as ECA2, ALA10, PFK, PHT1;4, PTR3, KUP2, GRAS, TCP, bHLH, PHD finger, PLATZ and genes involved in developmental, signaling and biosynthetic processes shows that the polymorphism associated with these selected miRNAs can make a significant phenotypic difference between salt sensitive and tolerant pistachio genotypes. The sequencing results of selected bands showed the presence of conserved miRNAs in the structure of the mitochondrial genome. Further notable findings of this study are that the sequences of PCR products of two selected markers were annotated as Gypsy and Copia retrotransposable elements. The transposition of retrotransposons with related miRNAs by increasing the number of miRNA copies and changing their location between nuclear and organellar genomes can affect the regulatory activity of these molecules. These findings show the crucial role of retrotransposon-derived miRNAs as mobile epigenetic regulators between intracellular genomes in regulating salt stress responses as well as creating new and tolerant phenotypes for adaptation to environmental conditions.
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19
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Yang X, Kang Y, Liu Y, Shi M, Zhang W, Fan Y, Yao Y, Li H, Qin S. Integrated analysis of miRNA-mRNA regulatory networks of potato (Solanum tuberosum L.) in response to cadmium stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 224:112682. [PMID: 34419646 DOI: 10.1016/j.ecoenv.2021.112682] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/14/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Cadmium (Cd) stress is a ubiquitous abiotic stress affecting plant growth worldwide and negatively impacting crop yield and food safety. Potato is the most important non-grain crop globally, but there is limited research available on the response of this crop to Cd stress. This study explored the coping mechanism for Cd stress in potato through analyses of miRNA and mRNA. Tissue culture seedlings (20-day-old) of potato variety 'Atlantic' were cultured for up to 48 h in liquid medium containing 5 mmol/L CdCl2, and phenotypic, physiological, and transcriptomic changes were observed at specific times. With the extension of Cd stress time, the potato leaves gradually wilted and curled, and root salicylic acid (SA), glutathione (GSH), and lignin contents and peroxidase (POD) activity increased, while indole-3-acetic acid (IAA) and zeatin (ZT) contents decreased. Using miRNA-seq, 161 existing miRNAs, 383 known miRNAs, and 7361 novel miRNAs were identified, and, 18 miRNAs were differentially expressed in response to Cd stress. Based on mRNA-seq, 7340 differentially expressed mRNAs (DEGs) were found. Through mRNA-miRNA integrated analysis, miRNA-target gene pairs consisting of 23 DEGs and 33 miRNAs were identified. Furthermore, "glutathione metabolism" "plant hormone signal transduction" and "phenylpropanoid biosynthesis" were established as crucial pathways in the Cd stress response of potato. Novel miRNAs novel-m3483-5p and novel-m2893-5p participate in these pathways through targeted regulation of cinnamic alcohol dehydrogenase (CAD; PG0005359) and alanine aminotransferase (POP; PG0024281), respectively. This study provides information that will help elucidate the complex mechanism of the Cd stress response in potato. Moreover, candidate miRNAs and mRNAs could yield new strategies for the development of Cd-tolerant potato breeding.
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Affiliation(s)
- Xinyu Yang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Yichen Kang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China
| | - Yuhui Liu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China
| | - Mingfu Shi
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Weina Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Yanling Fan
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Yanhong Yao
- Dingxi Academy of Agricultural Sciences, Dingxi 743000, China
| | - Hong Li
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; College of Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Shuhao Qin
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China.
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