The role of microRNA in abiotic stress response in plants

Koroban, N. V.; Kudryavtseva, Anna V.; Krasnov, George S.; Садритдинова, А. Ф.; Fedorova, Maria S.; Snezhkina, Anastasiya V.; Bolsheva, Nadezhda L.; Muravenko, Olga V.; Dmitriev, Alexey A.; Melnikova, N. V.

doi:10.1134/s0026893316020102

Cited by 33 publications

(22 citation statements)

References 74 publications

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“…MiRNAs, one of small noncoding RNA, are comprising 21–24 nucleotides 20 . They have essential functions in plant such as development, growth, maturation, cell differentiation, and response to various abiotic and biotic stresses 21 – 24 .…”

Section: Introductionmentioning

confidence: 99%

Degradome, small RNAs and transcriptome sequencing of a high-nicotine cultivated tobacco uncovers miRNA’s function in nicotine biosynthesis

Jin

et al. 2020

Sci Rep

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tobacco (Nicotiana tabacum) is considered as the model plant for alkaloid research, of which nicotine accounts for 90%. Many nicotine biosynthetic genes have been identified and were known to be regulated by jasmonate-responsive transcription factors. As an important regulator in plant physiological processes, whether small RNAs are involved in nicotine biosynthesis is largely unknown. Here, we combine transcriptome, small RnAs and degradome analysis of two native tobacco germplasms YJ1 and ZY100 to investigate small RNA's function. YJ1 leaves accumulate twofold higher nicotine than ZY100. Transcriptome analysis revealed 3,865 genes which were differently expressed in leaf and root of two germplasms, including some known nicotine and jasmonate pathway genes. By small RNA sequencing, 193 miRNAs were identified to be differentially expressed between YJ1 and ZY100. Using in silico and degradome sequencing approaches, six nicotine biosynthetic genes and seven jasmonate pathway genes were predicted to be targeted by 77 miRNA loci. Three pairs among them were validated by transient expression in vivo. Combined analysis of degradome and transcriptome datasets revealed 51 novel miRNA-mRNA interactions that may regulate nicotine biosynthesis. The comprehensive analysis of our study may provide new insights into the regulatory network of nicotine biosynthesis. Around 20% of plants are known to produce alkaloids, a diverse class of more than 12,000 different N-containing natural product compounds which are important for plant defense and medical use 1,2. Cultivated tobacco (Nicotiana tabacum), as a natural allotetraploid, is possibly evolved from hybridization of two diploids N. tomentosiformis and N. sylvestris 3,4. Nicotine accounts for around 90% of total alkaloids in tobacco, which made tobacco as a model plant to study the biosynthesis, transportation, accumulation, and degradation of alkaloids. Extensive studies have established that nicotine is produced in roots before being transported to and accumulating in leaves 5-7. Nicotine functions as a defense toxin to many insect herbivores 8. Mechanical wounding and woundingelicited jasmonate signaling are known to increase the accumulation of nicotine 9-11. For instance, substantially increased nicotine synthesis and accumulation is known to result from the agricultural practice known as topping, wherein the early developing inflorescence organs are removed by producers to prevent seed production 12,13. Nicotine is synthesized from putrescine, which is derived from arginine or ornithine 14. Most of the enzymes involved in this pathway have been identified and characterized in the course of many decades of research, including ornithine decarboxylase (ODC), putrescine N-methyltransferase (PMT), aspartate oxidase (AO), quinolinate synthase (QS), quinolinate phosphoribosyl transferase (QPT), N-methylputrescine oxidase (MPO), and berberine bridge enzyme-like (BBL), among others 4,6,14. There has also been extensive research about the genetic control

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Section: Introductionmentioning

confidence: 99%

Degradome, small RNAs and transcriptome sequencing of a high-nicotine cultivated tobacco uncovers miRNA’s function in nicotine biosynthesis

Jin

et al. 2020

Sci Rep

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“…By functioning in RNA silencing and posttranscriptional regulation of gene expression, plant miRNAs coordinate a wide range of biological processes in different cells, tissues, and organs. Since their initial discovery, several functional analyses elucidated the importance of these bio-regulators in almost all aspects of plant growth and development 3,4 , in the crosstalk between phytohormone signaling pathways 5 , and in response to environmental stimuli 6 , abiotic stresses 7 , and pathogen invasions 8 . Besides their relevance in fundamental research, miRNAs are also very important from an applicative point of view to manipulate specific agricultural traits by modulation of plant gene expression [9][10][11] .…”

Section: Introductionmentioning

confidence: 99%

Transcriptional regulation of MdmiR285N microRNA in apple (Malus x domestica) and the heterologous plant system Arabidopsis thaliana

Pompili

Piazza

et al. 2020

Hortic Res

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Malus x domestica microRNA MdmiR285N is a potential key regulator of plant immunity, as it has been predicted to target 35 RNA transcripts coding for different disease resistance proteins involved in plant defense to pathogens. In this study, the promoter region of MdmiR285N was isolated from the apple genome and analyzed in silico to detect potential regulatory regions controlling its transcription. A complex network of putative regulatory elements involved in plant growth and development, and in response to different hormones and stress conditions, was identified. Activity of the β-Glucoronidase (GUS) reporter gene driven by the promoter of MdmiR285N was examined in transgenic apple, demonstrating that MdmiR285N was expressed during the vegetative growth phase. Similarly, in transgenic Arabidopsis thaliana, spatial and temporal patterns of GUS expression revealed that MdmiR285N was differentially regulated during seed germination, vegetative phase change, and reproductive development. To elucidate the role of MdmiR285N in plant immunity, MdmiR285N expression in wild-type apple plants and GUS activity in transgenic apple and Arabidopsis thaliana plants were monitored in response to Erwinia amylovora and Pseudomonas syringae pv. Tomato DC3000. A significant decrease of MdmiR285N levels and GUS expression was observed during host-pathogen infections. Overall, these data suggest that MdmiR285N is involved in the biotic stress response, plant growth, and reproductive development.

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“…miRNA is a cluster of 21-22-nt-long regulatory RNAs formed as a result of the activity of MIR genes in certain tissues and at certain developmental stages [14][15][16], and also in response to environmental stimuli [17][18][19]. MIR genes encode two consecutively formed precursor RNAs, first pri-miRNAs and then pre-miRNAs, which are subsequently processed by DCL1 (Dicer-like enzyme) into mature miRNAs [20,21].…”

Section: Introductionmentioning

confidence: 99%

“…miRNA sequences of 19-21 nucleotides are long enough to enable binding particular mRNAs by complementary base pairing, and allow either for cutting within a recognized sequence or for translational repression (reviewed in [23]). Plant miRNAs are involved in, for instance, regulating leaf morphogenesis, establishment of flower identity, and stress response [17][18][19][24][25][26].…”

Section: Introductionmentioning

confidence: 99%

Integrated analysis of small RNA, transcriptome and degradome sequencing provides new insights into floral development and abscission in yellow lupine (Lupines luteus L.)

Glazińska

Kulasek

Glinkowski

et al. 2019

Preprint

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Background Yellow lupine (Lupinus luteus L., Taper c.) is an important legume crop. However, its flower development and pod formation are often affected by excessive abscission. Organ detachment occurs within the abscission zone (AZ) and in L. luteus primarily affects flowers formed at the top of the inflorescence. The top flowers’ fate appears determined before anthesis. The organ development and abscission mechanisms utilize a complex molecular network, not yet not fully understood, especially as to the role of miRNAs and siRNAs. We aimed at identifying differentially expressed (DE) small ncRNAs in lupine by comparing small RNA-seq libraries generated from developing upper and lower raceme flowers, and flower pedicels with active and inactive AZs. Their target genes were also identified using transcriptome and degradome sequencing. Results Within all the libraries, 394 known and 28 novel miRNAs and 316 phased siRNAs were identified. In flowers at different stages of development, 30 miRNAs displayed DE in the upper and 29 in the lower parts of the raceme. In comparisons between upper and lower raceme flowers, a total of 46 DE miRNAs were identified. miR393 and miR160 were related to the upper and miR396 to the lower flowers and pedicels of non-abscising flowers. In flower pedicels we identified 34 DE miRNAs, with miR167 being the most abundant of all. Most siRNAs seem to play a marginal role in the processes studied herein, with the exception of tasiR-ARFs, which were DE in the developing flowers. The target genes of these miRNAs were predominantly categorized into the following Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways: ‘Metabolism’ (15,856), ‘Genetic information processing’ (5,267), and ‘Environmental information processing’ (1,517). Over 700 putative targets were categorized as belonging to the ‘Plant Hormone Signal Transduction pathway’. 26,230 target genes exhibited Gene Ontology (GO) terms: 23,092 genes were categorized into the ‘Cellular component’, 23,501 into the ‘Molecular function’, and 22,939 into the ’Biological process’. Conclusion Our results indicate that miRNAs and siRNAs in yellow lupine may influence the development of flowers and, consequently, their fate by repressing their target genes, particularly those associated with the homeostasis of phytohormones, mainly auxins.

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The role of microRNA in abiotic stress response in plants

Cited by 33 publications

References 74 publications

Degradome, small RNAs and transcriptome sequencing of a high-nicotine cultivated tobacco uncovers miRNA’s function in nicotine biosynthesis

Degradome, small RNAs and transcriptome sequencing of a high-nicotine cultivated tobacco uncovers miRNA’s function in nicotine biosynthesis

Transcriptional regulation of MdmiR285N microRNA in apple (Malus x domestica) and the heterologous plant system Arabidopsis thaliana

Integrated analysis of small RNA, transcriptome and degradome sequencing provides new insights into floral development and abscission in yellow lupine (Lupines luteus L.)

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