Rapid sequence and functional diversification of a miRNA superfamily targeting calcium signaling components in seed plants

Attri, Komal; Zhang, Zijie; Singh, Atinder; Sharrock, Robert A.; Xie, Zhixin

doi:10.1111/nph.18185

Cited by 5 publications

(4 citation statements)

References 80 publications

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“…Interestingly, the expression of miR391 was repressed to 6% by Sal‐deficiency, whereas it was decreased only to 20–40% in the case of other miRNAs. miR391 cleaves the mRNA of an autoinhibited Ca 2+ ‐ATPase controlling plant development, immunity, and responses to the environment in Arabidopsis (Attri et al 2022). Besides the member of the miR160 family, the lack of Sal also upregulated miR5664 targeting a sulphate transporter, which may indicate an association of Sal with sulphate reduction.…”

Section: Discussionmentioning

confidence: 99%

Identification of ascorbate‐ and salicylate‐responsive miRNAs and verification of the spectral control of miR395 in Arabidopsis

Székely,

Gulyás,

Balogh

et al. 2023

Physiologia Plantarum

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We assumed that miRNAs might regulate the physiological and biochemical processes in plants through their effects on the redox system and phytohormones. To check this hypothesis, the transcriptome profile of wild‐type Arabidopsis and lines with decreased ascorbate (Asc), glutathione (GSH), or salicylate (Sal) levels were compared. GSH deficiency did not influence the miRNA expression, whereas lower levels of Asc and Sal reduced the accumulation of 9 and 44 miRNAs, respectively, but only four miRNAs were upregulated. Bioinformatics analysis revealed that their over‐represented target genes are associated with the synthesis of nitrogen‐containing and aromatic compounds, nucleic acids, and sulphate assimilation. Among them, the sulphate reduction‐related miR395 – ATP‐sulfurylase couple was selected to check the assumed modulating role of the light spectrum. A greater induction of the Asc‐ and Sal‐responsive miR395 was observed under sulphur starvation in far‐red light compared to white and blue light in wild‐type and GSH‐deficient Arabidopsis lines. Sal deficiency inhibited the induction of miR395 by sulphur starvation in blue light, whereas Asc deficiency greatly reduced it independently of the spectrum. Interestingly, sulphur starvation decreased only the level of ATP sulfurylase 4 among the miR395 target genes in far‐red light. The expression level of ATP sulfurylase 3 was higher in far‐red light than in blue light in wild‐type and Asc‐deficient lines. The results indicate the coordinated control of miRNAs by the redox and hormonal system since 11 miRNAs were affected by both Asc and Sal deficiency. This process can be modulated by light spectrum, as shown for miR395.

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Section: Discussionmentioning

confidence: 99%

Identification of ascorbate‐ and salicylate‐responsive miRNAs and verification of the spectral control of miR395 in Arabidopsis

Székely,

Gulyás,

Balogh

et al. 2023

Physiologia Plantarum

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“…However, previous studies indicate that the ARF16 and ARF17 genes, which are involved in the regulation of root growth, are the targets of miR391 [49]. Recently, transgenic overexpression of miR391 in Arabidopsis demonstrated post-transcriptional silencing of the ACA-10 gene by this miRNA [50]. ACA-10 codes for a calcium-transporting pump (AtACA10) involved in plant development, immunity, and response to the environment.…”

Section: Identification and Characterization Of Micrornas And Target ...mentioning

confidence: 99%

Small RNA Differential Expression Analysis Reveals miRNAs Involved in Dormancy Progression in Sweet Cherry Floral Buds

Soto

Sanchez

Núñez

et al. 2022

Plants

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In sweet cherry (Prunus avium), as in other temperate woody perennials, bud dormancy allows for survival in adverse environmental conditions during winter. During this process, environmental signals such as short days and/or low temperatures trigger internal signals that enable buds to become tolerant to the cold. The process involves tracking chilling units up to chilling the requirement fulfillment to resume growth, a transition involving transcriptional regulation, metabolic signaling, and epigenetic-related regulatory events. Massive sequencing of small RNAs was performed to identify miRNAs involved in sweet cherry dormancy by comparing their expression in field (regular seasonal) and controlled non-stop (continuous) chilling conditions. miRNAs highlighted by sequencing were validated using specific stem-loop PCR quantification, confirming expression patterns for known miRNAs such as miR156e, miR166c, miR172d, miR391, miR482c, and miR535b, as well as for newly proposed miRNAs. In silico prediction of the target genes was used to construct miRNA/target gene nodes. In particular, the involvement of the sweet cherry version for the miR156/SQUAMOSA PROMOTER-BINDING-LIKE PROTEIN genes whose expression was opposite in the two conditions suggests their involvement on dormancy regulation in sweet cherry. miRNA levels indicate that the regulation of stress-related genes and hormone synthesis modulates the expression of calcium metabolism and cell development-associated genes. Understanding the regulatory networks involved in sweet cherry dormancy, particularly in the context of miRNA involvement, represents the first step in the development of new agricultural strategies that may help overcome the increasing challenges presented by global climate change.

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“…The canonical targets of plant miRNAs are mostly transcription factor genes whose products are involved in various processes like abscisic acid (ABA) and auxin signaling pathways, cell growth, respiration, and photosynthesis (Koroban et al., 2016; Mukherjee et al., 2019). Although many miRNAs are highly conserved among various species of plants, the targets of these miRNAs might not be conserved and are subject to adaptive evolution (Attri et al., 2022). There is a need to validate noncanonical and novel targets of miRNAs involved in stress response in crops; such knowledge may be applied to engineer and breed stress‐tolerant crops and impact agronomic traits such as phenology (flowering time and bud break) and apomixis, an elusive target for rapid generation of elite crop hybrids (Liu et al., 2017; Long et al., 2016; Olmedo‐Monfil et al., 2010).…”

Section: Introductionmentioning

confidence: 99%

The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea)

et al. 2023

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MicroRNAs (miRNAs) are 21–24 nt small RNAs (sRNAs) that negatively regulate protein‐coding genes and/or trigger phased small‐interfering RNA (phasiRNA) production. Two thousand nine hundred miRNA families, of which ∼40 are deeply conserved, have been identified in ∼80 different plant species genomes. miRNA functions in response to abiotic stresses is less understood than their roles in development. Only seven peanut MIRNA families are documented in miRBase, yet a reference genome assembly is now published and over 480 plant‐like MIRNA loci were predicted in the diploid peanut progenitor Arachis duranensis genome. We explored by computational analysis of a leaf sRNA library and publicly available sRNA, degradome, and transcriptome datasets the miRNA and phasiRNA space associated with drought and heat stresses in peanut. We characterized 33 novel candidate and 33 ancient conserved families of MIRNAs and present degradome evidence for their cleavage activities on mRNA targets, including several noncanonical targets and novel phasiRNA‐producing noncoding and mRNA loci with validated novel targets such as miR1509 targeting serine/threonine‐protein phosphatase7 and miRc20 and ahy‐miR3514 targeting penta‐tricopeptide repeats (PPRs), in contradistinction to other claims of miR1509/173/7122 superfamily miRNAs indirectly targeting PPRs via TAS‐like noncoding RNA loci. We characterized the inverse correlations of significantly differentially expressed drought‐ and heat‐regulated miRNAs, assayed by sRNA blots or transcriptome datasets, with target mRNA expressions in the same datasets. Meta‐analysis of an expression atlas and over representation of miRNA target genes in co‐expression networks suggest that miRNAs have functions in unique aspects of peanut gynophore development. Genome‐wide MIRNA annotation of the published allopolyploid peanut genome can facilitate molecular breeding of value‐added traits.

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Rapid sequence and functional diversification of a miRNA superfamily targeting calcium signaling components in seed plants

Cited by 5 publications

References 80 publications

Identification of ascorbate‐ and salicylate‐responsive miRNAs and verification of the spectral control of miR395 in Arabidopsis

Identification of ascorbate‐ and salicylate‐responsive miRNAs and verification of the spectral control of miR395 in Arabidopsis

Small RNA Differential Expression Analysis Reveals miRNAs Involved in Dormancy Progression in Sweet Cherry Floral Buds

The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea)

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