Role of miRNAs in regulation of SA-mediated upregulation of genes involved in folate and methionine metabolism in foxtail millet

The effect of exogenous salicylic acid (SA) on folate metabolism and the related gene regulatory mechanisms is still unclear. In this study, the panicle of foxtail millet treated with different SA concentrations showed that 6 mM SA doubled the 5-methyltetrahydrofolate content compared to that of the control. An untargeted metabolomic analysis revealed that 275 metabolites were enriched in amino acid metabolic pathways. Significantly, the relative content of methionine (Met) after 6 mM SA treatment was 3.14 times higher than the control. Transcriptome analysis revealed that differentially expressed genes were mainly enriched in the folate and amino acid biosynthesis pathways (including Met, Cys, Pro, Ser et al.). The miRNA−mRNA interactions related to the folate and Met metabolic pathways were analyzed and several likely structural gene targets for miRNAs were identified, miRNA-seq analysis revealed that 33 and 51 miRNAs targeted 11 and 15 genes related to the folate and Met pathways, respectively. Eight key genes in the folate metabolism pathway were likely to be up-regulated by 14 new miRNAs and 20 new miRNAs up-regulated the 9 key genes in the Met metabolism pathway. The 6 miRNA−mRNA interactions related to the folate and Met metabolism pathways were verified by qRT−PCR, and consistent with the prediction. The results showed that DHFR1 gene expression level related to folate synthesis was directly up-regulated by Nov-m0139-3p with 3.8 times, but DHFR2 was down-regulated by Nov-m0731-5p with 0.62 times. The expression level of CYSC1 and APIP related to Met synthesis were up-regulated by Nov-m0461-5p and Nov-m0664-3p with 4.27 and 1.32 times, respectively. Our results suggested that exogenous SA could induce the folate and Met accumulated in the panicle of foxtail millet. The higher expression level of DHFR1, FTHFD, CYSC1 and APIP in the folate and Met metabolism pathway and their regulators, including Nov-m0139-3p, Nov-m0717-5p, Nov-m0461-5p and Nov-m0664-3p, could be responsible for these metabolites accumulation. This study lays the theoretical foundation for elucidating the post-transcription regulatory mechanisms of folate and Met metabolism.

[1]  Zhaoxia Sun,et al.  Heterologous Expression of SiFBP, a Folate-Binding Protein from Foxtail Millet, Confers Increased Folate Content and Altered Amino Acid Profiles with Nutritional Potential to Arabidopsis. , 2022, Journal of agricultural and food chemistry.

[2]  Zheng Kuang,et al.  The Construction and Exploration of a Comprehensive MicroRNA Centered Regulatory Network in Foxtail Millet (Setaria italica L.) , 2022, Frontiers in Plant Science.

[3]  Xiaochen Bo,et al.  clusterProfiler 4.0: A universal enrichment tool for interpreting omics data , 2021, Innovation.

[4]  Zhaoxia Sun,et al.  Folate metabolic profiling and expression of folate metabolism-related genes during panicle development in foxtail millet (Setaria italica (L.) P. Beauv). , 2021, Journal of the science of food and agriculture.

[5]  Jun Ma,et al.  MicroRNAs Roles in Plants Secondary Metabolism , 2021, Plant signaling & behavior.

[6]  F. Rahmani,et al.  Pre- sowing seed treatment with salicylic acid and sodium hydrosulfide confers Pb toxicity tolerance in maize (Zea mays L.). , 2020, Ecotoxicology and environmental safety.

[7]  Bin Zhang,et al.  A mini foxtail millet with an Arabidopsis-like life cycle as a C4 model system , 2020, Nature Plants.

[8]  Margaret H. Frank,et al.  TBtools - an integrative toolkit developed for interactive analyses of big biological data. , 2020, Molecular plant.

[9]  Jiwen Yu,et al.  Analysis of the MIR160 gene family and the role of MIR160a_A05 in regulating fiber length in cotton , 2019, Planta.

[10]  B. González,et al.  Folate Metabolism Interferes with Plant Immunity through 1C Methionine Synthase-Directed Genome-wide DNA Methylation Enhancement. , 2019, Molecular plant.

[11]  Jun Meng,et al.  Overexpression of MiR482c in Tomato Induces Enhanced Susceptibility to Late Blight , 2019, Cells.

[12]  Chunyi Zhang,et al.  Simultaneous extraction and determination of mono-/polyglutamyl folates using high-performance liquid chromatography-tandem mass spectrometry and its applications in starchy crops , 2019, Analytical and Bioanalytical Chemistry.

[13]  X. Estivill,et al.  miRTrace reveals the organismal origins of microRNA sequencing data , 2018, Genome Biology.

[14]  N. Sui,et al.  Regulation mechanism of microRNA in plant response to abiotic stress and breeding , 2018, Molecular Biology Reports.

[15]  S. Gupta,et al.  Tuning of SlARF10A dosage by sly-miR160a is critical for auxin-mediated compound leaf and flower development. , 2018, The Plant journal : for cell and molecular biology.

[16]  F. Rahmani,et al.  Impacts of seed priming with salicylic acid and sodium hydrosulfide on possible metabolic pathway of two amino acids in maize plant under lead stress , 2018, Molecular biology research communications.

[17]  Bijesh Puthusseri,et al.  Evaluation of folate-binding proteins and stability of folates in plant foliages. , 2018, Food chemistry.

[18]  B. Meyers,et al.  Despacito: the slow evolutionary changes in plant microRNAs. , 2018, Current opinion in plant biology.

[19]  R. Visser,et al.  Folate Biofortification of Potato by Tuber-Specific Expression of Four Folate Biosynthesis Genes. , 2018, Molecular plant.

[20]  M. Veysey,et al.  Folate and microRNA: Bidirectional interactions. , 2017, Clinica chimica acta; international journal of clinical chemistry.

[21]  D. Van Der Straeten,et al.  Folate biofortification in food crops. , 2017, Current opinion in biotechnology.

[22]  F. Rébeillé,et al.  Folates in Plants: Research Advances and Progress in Crop Biofortification , 2017, Front. Chem..

[23]  Juan Ni,et al.  Response of MiRNA-22-3p and MiRNA-149-5p to Folate Deficiency and the Differential Regulation of MTHFR Expression in Normal and Cancerous Human Hepatocytes , 2017, PloS one.

[24]  K. Ghassemi-Golezani,et al.  Improving amino acid composition of soybean under salt stress by salicylic acid and jasmonic acid , 2016 .

[25]  P. A. Ramos-Parra,et al.  Ethylene treatment induces changes in folate profiles in climacteric fruit during postharvest ripening , 2016 .

[26]  Md. Abu Reza,et al.  Remediation of Chromium Toxicity Through Exogenous Salicylic Acid in Rice (Oryza sativa L.) , 2016, Water, Air, & Soil Pollution.

[27]  Chunyi Zhang,et al.  Genome-wide identification and transcriptional analysis of folate metabolism-related genes in maize kernels , 2015, BMC Plant Biology.

[28]  W. Schwab,et al.  Folic acid induces salicylic acid-dependent immunity in Arabidopsis and enhances susceptibility to Alternaria brassicicola. , 2015, Molecular plant pathology.

[29]  N. Anjum,et al.  Salicylic acid-induced abiotic stress tolerance and underlying mechanisms in plants , 2015, Front. Plant Sci..

[30]  Shaojun Xie,et al.  Genome-wide characterization of microRNA in foxtail millet (Setaria italica) , 2013, BMC Plant Biology.

[31]  F. Vázquez-Flota,et al.  Salicylic acid induces vanillin synthesis through the phospholipid signaling pathway in Capsicum chinense cell cultures , 2013, Plant signaling & behavior.

[32]  Ming Chen,et al.  MicroRNAs and their cross-talks in plant development. , 2013, Journal of genetics and genomics = Yi chuan xue bao.

[33]  R. Hell,et al.  Methionine salvage and S-adenosylmethionine: essential links between sulfur, ethylene and polyamine biosynthesis. , 2013, The Biochemical journal.

[34]  Bijesh Puthusseri,et al.  Salicylic acid-induced elicitation of folates in coriander (Coriandrum sativum L.) improves bioaccessibility and reduces pro-oxidant status. , 2013, Food chemistry.

[35]  Q. Ge,et al.  Early millet use in northern China , 2012, Proceedings of the National Academy of Sciences.

[36]  J. Gregory,et al.  Folate biosynthesis, turnover, and transport in plants. , 2011, Annual review of plant biology.

[37]  Kam‐biu Liu,et al.  Earliest domestication of common millet (Panicum miliaceum) in East Asia extended to 10,000 years ago , 2009, Proceedings of the National Academy of Sciences.

[38]  C. Job,et al.  Proteomic Investigation of the Effect of Salicylic Acid on Arabidopsis Seed Germination and Establishment of Early Defense Mechanisms1[W][OA] , 2006, Plant Physiology.

[39]  D. Bartel,et al.  MicroRNAS and their regulatory roles in plants. , 2006, Annual review of plant biology.

[40]  F. Parvez,et al.  Folate and cobalamin deficiencies and hyperhomocysteinemia in Bangladesh. , 2005, The American journal of clinical nutrition.

[41]  Thomas D. Schmittgen,et al.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.

[42]  A. Hanson,et al.  ONE-CARBON METABOLISM IN HIGHER PLANTS. , 2001, Annual review of plant physiology and plant molecular biology.