Progress Toward Deep Sequencing-Based Discovery of Stress-Related MicroRNA in Plants and Available Bioinformatics Tools

Hannoufa, Abdelali; Matthews, Craig J.; Feyissa, Biruk A.; Gruber, Margaret Y.; Arshad, Muhammad

doi:10.1007/124_2018_25

Cited by 7 publications

(7 citation statements)

References 211 publications

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“…MicroRNAs have emerged as a vital component of post-transcriptional regulation of genes involved in numerous growth, development and stress responses in plants. The inhibitory effect of abiotic stress on photosynthesis is mainly linked to stomatal conductivity and metabolic limitations that have widely been described in several other studies, including studies on heat shock response [19,41,42]. In our current study, a number of proteins with altered abundance became prominent when heat stress was imposed on controls and miR156OE plants.…”

Section: Functional Processes Affected By Mir156 Under Heat Stresssupporting

confidence: 59%

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Label-free quantitative proteomic analysis of alfalfa in response to microRNA156 under high temperature

Arshad

Puri

Simkovich

et al. 2020

Preprint

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Background Abiotic stress, including heat, is one of the major factors that affect alfalfa growth and forage yield. The small RNA, microRNA156 (miR156), regulates multiple traits in alfalfa during abiotic stress. The aim of this study was to explore the role of miR156 in regulating heat response in alfalfa at the protein level. Results In this study, we compared an empty vector control and miR156 overexpressing (miR156OE) alfalfa plants after exposing them to heat stress (40 ° C) for 24 hours. We measured physiological parameters of control and miR156OE plants under heat stress, and collected leaf samples for protein analysis. A higher proline and antioxidant contents were detected in miR156OE plants than in controls under heat stress. Protein samples were analyzed by label-free quantification proteomics. Across all samples, a total of 1878 protein groups were detected. Under heat stress, 45 protein groups in the empty vector plants were significantly altered (P < 0.05; |log 2 FC| > 2). Conversely, 105 protein groups were significantly altered when miR156OE alfalfa was subjected to heat stress, of which 91 were unique to miR156OE plants. The identified protein groups unique to miR156OE plants were related to diverse functions including metabolism, photosynthesis, stress-response and plant defenses. Furthermore, we identified transcription factors in miR156OE plants, which belonged to squamosa promoter binding-like protein, MYB, ethylene responsive factors, AP2 domain, ABA response element binding factor and bZIP families of transcription factors. Conclusions These results suggest a positive role for miR156 in heat stress response in alfalfa. They reveal a miR156-regulated network of mechanisms at the protein level to modulate heat responses in alfalfa.

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Section: Functional Processes Affected By Mir156 Under Heat Stresssupporting

confidence: 59%

“…The microRNAs (miRNAs) are key regulators of gene expression at both the transcriptional and posttranscriptional levels [18,19]. These miRNAs are approximately 18-24 nt long and are grouped based on the differences in their biogenesis and functional characteristics [20].…”

Section: Introductionmentioning

confidence: 99%

Label-free quantitative proteomic analysis of alfalfa in response to microRNA156 under high temperature

Arshad

Puri

Simkovich

et al. 2020

Preprint

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“…To cope with these weather events, plants respond by developing different resilience strategies at the phenotypic, physiological, and molecular levels (Theocharis et al, 2012;Hasanuzzaman et al, 2013). Among the molecular strategies, the role of microRNAs in regulating various plant processes to enhance stress tolerance has been reported in a variety of crops (Hannoufa et al, 2018). Of the hundreds of plant microRNAs, microRNA156 (miR156) is highly conserved across species and regulates plant development as well as tolerance to biotic and abiotic stresses (Hasanuzzaman et al, 2013;Aung et al, 2015aAung et al, , 2015bArshad et al, 2017;Gao et al, 2018;Hannoufa et al, 2018;Feyissa et al, 2019;Matthews et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Transcriptome-IPMS analysis reveals a tissue-dependent miR156/SPL13 regulatory mechanism in alfalfa drought tolerance

Feyissa

Renaud

Nasrollahi

et al. 2020

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Background : We previously reported on the interplay between miR156/SPL13 and WD40-1/DFR to improve response to drought stress in alfalfa ( Medicago sativa L.). Here we aimed to investigate whether the role of miR156/SPL13 module in drought response is tissue-specific, and to identify SPL13-interacting proteins. We analyzed the global transcript profiles of leaf, stem, and root tissues of one-month old RNAi-silenced SPL13 ( SPL13 RNAi) alfalfa plants exposed to drought stress and conducted protein-protein interaction analysis to identify SPL13 interacting partners. Result : Transcript analysis combined with weighted gene co-expression network analysis showed tissue and genotype-specific gene expression patterns. Moreover, pathway analysis of stem-derived differentially expressed genes (DEG) revealed upregulation of genes associated with stress mitigating primary and specialized metabolites, whereas genes associated with photosynthesis light reactions were silenced in SPL13 RNAi plants. Leaf-derived DEG were attributed to enhanced light reactions, largely photosystem I, II, and electron transport chains, while roots of SPL13 RNAi plants upregulated transcripts associated with metal ion transport, carbohydrate, and primary metabolism. Using immunoprecipitation combined with mass spectrometry (IPMS) we showed that SPL13 interacts with proteins involved in photosynthesis, specialized metabolite biosynthesis, and stress tolerance. Conclusions : We conclude that the miR156/SPL13 module mitigates drought stress in alfalfa by regulating molecular and physiological processes in a tissue-dependent manner.

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“…The microRNAs (miRNAs) are key regulators of gene expression at both the transcriptional and post-transcriptional levels [ 18 , 19 ]. These miRNAs are approximately 18–24 nt long and are grouped based on the differences in their biogenesis and functional characteristics [ 20 ].…”

Section: Introductionmentioning

confidence: 99%

Label-free quantitative proteomic analysis of alfalfa in response to microRNA156 under high temperature

et al. 2020

Self Cite

View full text Add to dashboard Cite

Background Abiotic stress, including heat, is one of the major factors that affect alfalfa growth and forage yield. The small RNA, microRNA156 (miR156), regulates multiple traits in alfalfa during abiotic stress. The aim of this study was to explore the role of miR156 in regulating heat response in alfalfa at the protein level. Results In this study, we compared an empty vector control and miR156 overexpressing (miR156OE) alfalfa plants after exposing them to heat stress (40 °C) for 24 h. We measured physiological parameters of control and miR156OE plants under heat stress, and collected leaf samples for protein analysis. A higher proline and antioxidant contents were detected in miR156OE plants than in controls under heat stress. Protein samples were analyzed by label-free quantification proteomics. Across all samples, a total of 1878 protein groups were detected. Under heat stress, 45 protein groups in the empty vector plants were significantly altered (P < 0.05; |log2FC| > 2). Conversely, 105 protein groups were significantly altered when miR156OE alfalfa was subjected to heat stress, of which 91 were unique to miR156OE plants. The identified protein groups unique to miR156OE plants were related to diverse functions including metabolism, photosynthesis, stress-response and plant defenses. Furthermore, we identified transcription factors in miR156OE plants, which belonged to squamosa promoter binding-like protein, MYB, ethylene responsive factors, AP2 domain, ABA response element binding factor and bZIP families of transcription factors. Conclusions These results suggest a positive role for miR156 in heat stress response in alfalfa. They reveal a miR156-regulated network of mechanisms at the protein level to modulate heat responses in alfalfa.

show abstract

Progress Toward Deep Sequencing-Based Discovery of Stress-Related MicroRNA in Plants and Available Bioinformatics Tools

Cited by 7 publications

References 211 publications

Label-free quantitative proteomic analysis of alfalfa in response to microRNA156 under high temperature

Label-free quantitative proteomic analysis of alfalfa in response to microRNA156 under high temperature

Transcriptome-IPMS analysis reveals a tissue-dependent miR156/SPL13 regulatory mechanism in alfalfa drought tolerance

Label-free quantitative proteomic analysis of alfalfa in response to microRNA156 under high temperature

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