Abiotic stress induced miRNA-TF-gene regulatory network: A structural perspective

Sharma, R.C.; Upadhyay, Shashankaditya; Bhat, Basharat Ahmad; Singh, Garima; Bhattacharya, Sitangshu; Singh, Ashutosh

doi:10.1016/j.ygeno.2019.03.004

Cited by 17 publications

(15 citation statements)

References 58 publications

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“…Considering that the higher level of SmAP2-17 expression in the SmAP2-17 -overexpression was silenced after salt stress, we proposed that SmAP2-17 mRNA may be the target of a putative salt-induced miRNA molecule. Recently, a large number of abiotic stress-induced miRNAs, including the salt-induced miRNA gene ath-MIR167d, have been reported [ 31 ]. The secondary complementary structure of SmAP2-17 mRNA and a salt-induced miRNA ath-MIR167d suggest that SmAP2-17 mRNA may be digested through ath-MIR167d mediated RNAi process (Fig.…”

Section: Resultsmentioning

confidence: 99%

Overexpression of the Salix matsudana SmAP2-17 gene improves Arabidopsis salinity tolerance by enhancing the expression of SOS3 and ABI5

Chen

Dai

et al. 2022

BMC Plant Biol

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Background Salix matsudana (Koidz.) is a widely planted ornamental allotetraploid tree species. Genetic engineering can be used to enhance the tolerance of this species to soil salinization, endowing varieties with the ability to grow along coastlines, thereby mitigating afforestation and protecting the environment. The AP2/ERF family of transcription factors (TFs) plays multidimensional roles in plant biotic/abiotic stress tolerance and plant development. In this study, we cloned the SmAP2-17 gene and performed functional analysis of its role in salt tolerance. This study aims to identify key genes for future breeding of stress-resistant varieties of Salix matsudana. Results SmAP2-17 was predicted to be a homolog of AP2-like ethylene-responsive transcription factor ANT isoform X2 from Arabidopsis, with a predicted ORF of 2058 bp encoding an estimated protein of 685 amino acids containing two conserved AP2 domains (PF00847.20). SmAP2-17 had a constitutive expression pattern and was localized to the nucleus. The overexpression of the native SmAP2-17 CDS sequence in Arabidopsis did not increase salt tolerance because of the reduced expression level of ectopic SmAP2-17, potentially caused by salt-induced RNAi. Transgenic lines with high expression of optimized SmAP2-17 CDS under salt stress showed enhanced tolerance to salt. Moreover, the expression of general stress marker genes and important salt stress signaling genes, including RD29A, ABI5, SOS3, AtHKT1, and RBohF, were upregulated in SmAP2-17-overexpressed lines, with expression levels consistent with that of SmAP2-17 or optimized SmAP2-17. Promoter activity analysis using dual luciferase analysis showed that SmAP2-17 could bind the promoters of SOS3 and ABI5 to activate their expression, which plays a key role in regulating salt tolerance. Conclusions The SmAP2-17 gene isolated from Salix matsudana (Koidz.) is a positive regulator that improves the resistance of transgenic plants to salt stress by upregulating SOS3 and ABI5 genes. This study provides a potential functional gene resource for future generation of salt-resistant Salix lines by genetic engineering.

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Section: Resultsmentioning

confidence: 99%

Overexpression of the Salix matsudana SmAP2-17 gene improves Arabidopsis salinity tolerance by enhancing the expression of SOS3 and ABI5

Chen

Dai

et al. 2022

BMC Plant Biol

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Section: Discussionmentioning

confidence: 98%

“…Intriguingly, the differentially regulated miRNAs target a wide range of proteins involved in response to the stimulus, developmental processes, cellular component organization and biogenesis, biological regulation, cellular processes, metabolic processes and stress signaling ( Supplementary Table S1, Fig 7). Although many of the proteins targeted by specific miRNAs are still functionally not characterized, few of the target proteins have already been reported for their role in regulating various processes, including abiotic stresses such as cold (Megha et al 2017;Sharma et al 2019). Characterization of the other target proteins in this list will help to reveal the functional significance of these altered miRNAs in integrating auxin response and cold stress.…”

Section: Discussionmentioning

confidence: 99%

Deciphering miRNAs involved in crosstalk between auxin and cold stress in Arabidopsis roots

Aslam

Sakai

Qin

et al. 2020

Preprint

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The phytohormone auxin and microRNA-mediated regulation of gene expressions are key regulators for plant growth and development at both optimal and under low-temperature stress conditions. However, the mechanistic link between microRNA and auxin in regulating plant cold stress response remains elusive. To better understand the role of microRNA in the crosstalk between auxin and cold stress responses, we took advantage of the mutants of Arabidopsis thaliana with altered response to auxin transport and signal. Screening of the mutants for root growth recovery after cold stress at 4°C revealed that the auxin signaling mutant, solitary root 1 ( slr1; mutation in Aux/IAA14), shows a hypersensitive response to cold stress. Genome-wide expression analysis of miRNA in wild-type and slr1 mutant roots using next-generation deep sequencing revealed 180 known and 86 novel cold-responsive microRNAs. Cold stress also increased the abundance of 26nt-31nt small RNA population in slr1 compared with wild-type. Comparative analysis of microRNA expression shows differential expression of 13 miRNAs in slr1 compared with wild-type. Target gene expression analysis of one of the potential candidate miRNAs, miR169 revelaed the possible involvement of miR169- NF-YA module in the auxin-mediated cold stress response. Taken together, these results indicate that SLR/IAA14, a transcriptional repressor of auxin signaling, plays a crucial role in integrating miRNA in auxin and cold responses.

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“…Previous studies suggest that during stress conditions, an increase in miRNA expression deregulates the negative regulators of stress. In contrast, a decrease in miRNAs expression leads to the accumulation of positive regulators of stress [107,108]. Signi cant reduction in the expression of several miRNAs in the slr1 mutant compared to Col-0 suggests that there could be an increased activity of negative regulators in mutant leading to a susceptible phenotype ( Table 3).…”

Section: Discussionmentioning

confidence: 99%

“…Intriguingly, the differentially regulated miRNAs target a wide range of proteins involved in response to the stimulus, developmental processes, cellular component organization and biogenesis, biological regulation, cellular processes, metabolic processes and stress signaling ( Supplementary Table S1, Fig 7). Although many of the proteins targeted by speci c miRNAs are still functionally not characterized, few of the target proteins have already been reported for their role in regulating various processes, including abiotic stresses such as cold [30,108]. Characterization of the other target proteins in this list will help to reveal the functional signi cance of these altered miRNAs in integrating auxin response and cold stress.…”

Section: Discussionmentioning

confidence: 99%

Deciphering miRNAs involved in crosstalk between auxin and cold stress in Arabidopsis roots

Aslam

Sakai

Yuan

et al. 2020

Preprint

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Background: The phytohormone auxin and microRNA-mediated regulation of gene expressions are key regulators for plant growth and development at both optimal and under low-temperature stress conditions. However, the mechanistic link between microRNA and auxin in regulating plant cold stress response remains elusive. Results: To better understand the role of microRNA in the crosstalk between auxin and cold stress responses, we took advantage of the mutants of Arabidopsis thaliana with altered response to auxin transport and signal. Screening of the mutants for root growth recovery after cold stress at 4°C revealed that the auxin signaling mutant, solitary root 1 ( slr1; mutation in Aux/IAA14), shows a hypersensitive response to cold stress. Genome-wide expression analysis of miRNA in wild-type and slr1 mutant roots using next-generation sequencing revealed 180 known and 71 novel cold-responsive microRNAs. Cold stress also increased the abundance of 26 nt-31 nt small RNA population in slr1 compared with wild-type. Comparative analysis of microRNA expression shows significant differential expression of 13 known and 7 novel miRNAs in slr1 at 4°C compared with wild-type. Target gene expression analysis of the members from one potential candidate miRNAs, miR169 revealed the possible involvement of miR169- NF-YA module in the auxin-mediated cold stress response. Conclusions: Taken together, these results indicate that SLR/IAA14, a transcriptional repressor of auxin signaling, plays a crucial role in integrating miRNA in auxin and cold responses.

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Abiotic stress induced miRNA-TF-gene regulatory network: A structural perspective

Cited by 17 publications

References 58 publications

Overexpression of the Salix matsudana SmAP2-17 gene improves Arabidopsis salinity tolerance by enhancing the expression of SOS3 and ABI5

Overexpression of the Salix matsudana SmAP2-17 gene improves Arabidopsis salinity tolerance by enhancing the expression of SOS3 and ABI5

Deciphering miRNAs involved in crosstalk between auxin and cold stress in Arabidopsis roots

Deciphering miRNAs involved in crosstalk between auxin and cold stress in Arabidopsis roots

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