A miRNA-Encoded Small Peptide, vvi-miPEP171d1, Regulates Adventitious Root Formation

Chen, Qiuju; Deng, Bohan; Gao, Jie; Zhao, Zhongyang; Chen, Zili; Song, Shiren; Wang, Lei; Zhao, Liping; Xu, Wenping; Zhang, Caixi; Ma, Chao; Wang, Shiping

doi:10.1104/pp.20.00197

Cited by 99 publications

(75 citation statements)

References 77 publications

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“…To date, in addition to the miPEP156a found in the Brassicaceae family, there are data on several other miPEPs in plants. These peptides are miPEP165a and miPEP858 from Arabidopsis thaliana (Lauressergues et al, 2015; Sharma et al, 2020), miPEP171b from Medicago truncatula and miPEP172c from Glycine max (Couzigou et al, 2015, 2016), and vvi-miPEP171d1 from Vitis vinifera (Chen et al, 2020). In our work, we have identified some common features of miPEP156a functioning with the peptides listed above.…”

Section: Resultsmentioning

confidence: 99%

Possible functions of the conserved peptide encoded by the RNA-precursor of miR-156a in plants of the familyBrassicaceae

Erokhina

Ryazantsev

et al. 2020

Preprint

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Recent studies have shown that the primary transcripts of some microRNA genes (pri-miRNAs) are able to express short proteins (peptides) ranging usually from 12-15 amino acid residues to around 30 residues in length. These peptides, called miPEPs, may participate in the regulation of transcription of their own pri-miRNAs. Using bioinformatic comparative analysis of pri-miRNA sequences in plant genomes, we previously discovered a new group of miPEPs (miPEP-156a), which is encoded by pri-miR156a in several dozen species from the Brassicaceae family. Exogenous peptides miPEP-156a can effectively penetrate plant seedlings through the root system and spread systemically to the leaves of young seedlings. At the same time, a moderate morphological effect is observed, which consists in accelerated growth of the main root of the seedling. In parallel, a positive effect is observed at the level of pri-miR156a expression. It is important that the effects at the morphological and molecular levels are seemingly related to the ability of the peptide to quickly transfer into the cell nuclei and bind to nuclear chromatin. In this work, the secondary structure of the peptide was also experimentally established, and changes in this structure in the complex with DNA were shown.

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Section: Resultsmentioning

confidence: 99%

Possible functions of the conserved peptide encoded by the RNA-precursor of miR-156a in plants of the familyBrassicaceae

Erokhina

Ryazantsev

et al. 2020

Preprint

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“…Regarding the previously cited example of the effects of miR828 and miR858 on anthocyanin and flavonol synthesis in grapevine ( Tirumalai et al, 2019 ), Sharma et al (2020) demonstrated that pri-miR858a of Arabidopsis thaliana encodes a small peptide, miPEP858a, which regulates the expression of miR858a and associated target genes ( Figure 2 ). Chen et al (2020) also shown that a miRNA-encoded small peptide, miPEP171d1, regulates the formation of adventitious roots. These results increase the complexity of mechanisms of the regulation of gene expression but provide us with tools to better control the phenotypes of grapevine under changing environmental conditions.…”

Section: Molecular Tools For Understanding the Response Of Grapevinementioning

confidence: 94%

Molecular Tools for Adapting Viticulture to Climate Change

2021

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Adaptation of viticulture to climate change includes exploration of new geographical areas, new training systems, new management practices, or new varieties, both for rootstocks and scions. Molecular tools can be defined as molecular approaches used to study DNAs, RNAs, and proteins in all living organisms. We present here the current knowledge about molecular tools and their potential usefulness in three aspects of grapevine adaptation to the ongoing climate change. (i) Molecular tools for understanding grapevine response to environmental stresses. A fine description of the regulation of gene expression is a powerful tool to understand the physiological mechanisms set up by the grapevine to respond to abiotic stress such as high temperatures or drought. The current knowledge on gene expression is continuously evolving with increasing evidence of the role of alternative splicing, small RNAs, long non-coding RNAs, DNA methylation, or chromatin activity. (ii) Genetics and genomics of grapevine stress tolerance. The description of the grapevine genome is more and more precise. The genetic variations among genotypes are now revealed with new technologies with the sequencing of very long DNA molecules. High throughput technologies for DNA sequencing also allow now the genetic characterization at the same time of hundreds of genotypes for thousands of points in the genome, which provides unprecedented datasets for genotype-phenotype associations studies. We review the current knowledge on the genetic determinism of traits for the adaptation to climate change. We focus on quantitative trait loci and molecular markers available for developmental stages, tolerance to water stress/water use efficiency, sugar content, acidity, and secondary metabolism of the berries. (iii) Controlling the genome and its expression to allow breeding of better-adapted genotypes. High-density DNA genotyping can be used to select genotypes with specific interesting alleles but genomic selection is also a powerful method able to take into account the genetic information along the whole genome to predict a phenotype. Modern technologies are also able to generate mutations that are possibly interesting for generating new phenotypes but the most promising one is the direct editing of the genome at a precise location.

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“…In addition to producing miRNAs, it was found that the pri-miRNAs can contain short ORFs in the 5’ upstream of pre-miRNA, which encode for regulatory peptides, called miPEPs. This coding ability of pri-miRNAs has first been discovered in Arabidopsis and Medicago truncatula and has since been studied in soybeans, grapes, and even mammalian cells ( Lauressergues et al, 2015 ; Couzigou et al, 2016 ; Fang et al, 2017 ; Chen Q. J. et al, 2020 ; Sharma et al, 2020 ). The endogenous miPEPs have been detected by Western blotting, demonstrating significant levels of peptide accumulation ( Lauressergues et al, 2015 ; Sharma et al, 2020 ; Table 1 ).…”

Section: Regulatory Functions Of Primary Microrna-derived Peptidesmentioning

confidence: 99%

“…It is also reasonably speculated that the upstream of pre-miRNAs, which possibly contain sORF, is exported to the cytoplasm for guiding peptide translation ( Figure 2 ). For example, the pri-miR171d is mainly accumulated in the nucleus and also slightly detected in the cytoplasm of grape, implying that the coding region of pri-miRNA is possibly transported into the cytoplasm after they are cleaved ( Lauressergues et al, 2015 ; Chen Q. J. et al, 2020 ). The possibility that the cleaved upstream fragments of the pre-miRNAs are protected by re-polyadenylation is still unknown and requires investigation ( Figure 2 ).…”

Section: Regulatory Functions Of Primary Microrna-derived Peptidesmentioning

confidence: 99%

Coding of Non-coding RNA: Insights Into the Regulatory Functions of Pri-MicroRNA-Encoded Peptides in Plants

et al. 2021

Self Cite

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Peptides composed of a short chain of amino acids can play significant roles in plant growth, development, and stress responses. Most of these functional peptides are derived by either processing precursor proteins or direct translation of small open reading frames present in the genome and sometimes located in the untranslated region sequence of a messenger RNA. Generally, canonical peptides serve as local signal molecules mediating short- or long-distance intercellular communication. Also, they are commonly used as ligands perceived by an associated receptor, triggering cellular signaling transduction. In recent years, increasing pieces of evidence from studies in both plants and animals have revealed that peptides are also encoded by RNAs currently defined as non-coding RNAs (ncRNAs), including long ncRNAs, circular RNAs, and primary microRNAs. Primary microRNAs (miRNAs) have been reported to encode regulatory peptides in Arabidopsis, grapevine, soybean, and Medicago, called miRNA-encoded peptides (miPEPs). Remarkably, overexpression or exogenous applications of miPEPs specifically increase the expression level of their corresponding miRNAs by enhancing the transcription of the MIRNA (MIR) genes. Here, we first outline the current knowledge regarding the coding of putative ncRNAs. Notably, we review in detail the limited studies available regarding the translation of miPEPs and their relevant regulatory mechanisms. Furthermore, we discuss the potential cellular and molecular mechanisms in which miPEPs might be involved in plants and raise problems that needed to be solved.

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A miRNA-Encoded Small Peptide, vvi-miPEP171d1, Regulates Adventitious Root Formation

Cited by 99 publications

References 77 publications

Possible functions of the conserved peptide encoded by the RNA-precursor of miR-156a in plants of the familyBrassicaceae

Possible functions of the conserved peptide encoded by the RNA-precursor of miR-156a in plants of the familyBrassicaceae

Molecular Tools for Adapting Viticulture to Climate Change

Coding of Non-coding RNA: Insights Into the Regulatory Functions of Pri-MicroRNA-Encoded Peptides in Plants

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