A Key Molecular Regulator, RNA G-Quadruplex and Its Function in Plants

Liu, Haifeng; Zhang, Chu; Yang, Xiaofei

doi:10.3389/fpls.2022.926953

Cited by 7 publications

(5 citation statements)

References 55 publications

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“…Transient reporter gene assay further revealed that this G4 inhibits translation, but not the transcription of the ATR gene in living plants [ 31 ]. G4s also have potential in applied/agronomic science, as it is believed that their formation and stability (and thereby the expression of genes containing PQS) could be affected by environmental conditions, e.g., macronutrient availability (mainly K + and Na + ions) and/or drought [ 30 ], temperature [ 32 ], irradiation [ 33 ], etc. From this point of view, it would be interesting to know which genes and pathways contain the highest amount/frequencies of PQS.…”

Section: Discussionmentioning

confidence: 99%

Analysis of G-Quadruplex-Forming Sequences in Drought Stress-Responsive Genes, and Synthesis Genes of Phenolic Compounds in Arabidopsis thaliana

Pečínka

Bohálová

Volná

et al. 2023

Life

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Sequences of nucleic acids with the potential to form four-stranded G-quadruplex structures are intensively studied mainly in the context of human diseases, pathogens, or extremophile organisms; nonetheless, the knowledge about their occurrence and putative role in plants is still limited. This work is focused on G-quadruplex-forming sites in two gene sets of interest: drought stress-responsive genes, and genes related to the production/biosynthesis of phenolic compounds in the model plant organism Arabidopsis thaliana. In addition, 20 housekeeping genes were analyzed as well, where the constitutive gene expression was expected (with no need for precise regulation depending on internal or external factors). The results have shown that none of the tested gene sets differed significantly in the content of G-quadruplex-forming sites, however, the highest frequency of G-quadruplex-forming sites was found in the 5′-UTR regions of phenolic compounds’ biosynthesis genes, which indicates the possibility of their regulation at the mRNA level. In addition, mainly within the introns and 1000 bp flanks downstream gene regions, G-quadruplex-forming sites were highly underrepresented. Finally, cluster analysis allowed us to observe similarities between particular genes in terms of their PQS characteristics. We believe that the original approach used in this study may become useful for further and more comprehensive bioinformatic studies in the field of G-quadruplex genomics.

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Section: Discussionmentioning

confidence: 99%

Analysis of G-Quadruplex-Forming Sequences in Drought Stress-Responsive Genes, and Synthesis Genes of Phenolic Compounds in Arabidopsis thaliana

Pečínka

Bohálová

Volná

et al. 2023

Life

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“…In plants, G4 and rG4 motifs appear widespread, but detecting them in vivo remains challenging, and their potential biological roles remain to be better understood (Griffin & Bass, 2018; Liu et al., 2022; Ma et al., 2022; Volnà et al., 2021). It was recently demonstrated that rG4 structures exist in vivo and can act as regulators (Yang et al., 2020).…”

Section: Discussionmentioning

confidence: 99%

“…For example, the crucial role of rhizobial tDRs in regulating nodulation is now ascertained (Ren et al, 2019). The existence of tDRs associated with Argonaute proteins was described (Alves et al, 2017;Cognat et al, 2017;Loss-Morais et al, 2013), and a report showed that AGO1associated tDRs can target and cleave transposable elements (Martinez et al, 2017). Hsieh and colleagues provided evidence that some tDRs are upregulated upon phosphate starvation (Hsieh et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

The Arabidopsis tDR Ala forms G‐quadruplex structures that can be unwound by the DExH1 DEA(D/H)‐box RNA helicase

Chery,

Berrissou,

Humbert

et al. 2023

The Plant Journal

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SUMMARYAs in many other organisms, tRNA‐derived RNAs (tDRs) exist in plants and likely have multiple functions. We previously showed that tDRs are present in Arabidopsis under normal growth conditions, and that the ones originating from alanine tRNAs are the most abundant in leaves. We also showed that tDRs Ala of 20 nt produced from mature tRNAAla (AGC) can block in vitro protein translation. Here, we report that first, these tDRs Ala (AGC) can be found within peculiar foci in the cell that are neither P‐bodies nor stress granules and, second, that they assemble into intermolecular RNA G‐quadruplex (rG4) structures. Such tDR Ala rG4 structures can specifically interact with an Arabidopsis DEA(D/H) RNA helicase, the DExH1 protein, and unwind them. The rG4‐DExH1 protein interaction relies on a glycine‐arginine domain with RGG/RG/GR/GRR motifs present at the N‐terminal extremity of the protein. Mutations on the four guanine residues located at the 5′ extremity of the tDR Ala abolish its rG4 structure assembly, association with the DExH1 protein, and foci formation, but they do not prevent protein translation inhibition in vitro. Our data suggest that the sequestration of tDRs Ala into rG4 complexes might represent a way to modulate accessible and functional tDRs for translation inhibition within the plant cell via the activity of a specific RNA helicase, DExH1.

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“…The pepino mosaic virus (PMV), which is threat to tomato production, contains pseudoknot structures in the 3′ UTR that overlap with the PolyA tail that is crucial for the replication of PMV RNA [ 153 ]. For more details, the roles of RNA conformers in plants are discussed in the articles by Liu et al [ 154 ], Griffin et al [ 155 ] and Yadav et al [ 156 ].…”

Section: Discussionmentioning

confidence: 99%

Alternative RNA Conformations: Companion or Combatant

Gupta

Khadake

Panja

et al. 2022

Genes

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RNA molecules, in one form or another, are involved in almost all aspects of cell physiology, as well as in disease development. The diversity of the functional roles of RNA comes from its intrinsic ability to adopt complex secondary and tertiary structures, rivaling the diversity of proteins. The RNA molecules form dynamic ensembles of many interconverting conformations at a timescale of seconds, which is a key for understanding how they execute their cellular functions. Given the crucial role of RNAs in various cellular processes, we need to understand the RNA molecules from a structural perspective. Central to this review are studies aimed at revealing the regulatory role of conformational equilibria in RNA in humans to understand genetic diseases such as cancer and neurodegenerative diseases, as well as in pathogens such as bacteria and viruses so as to understand the progression of infectious diseases. Furthermore, we also summarize the prior studies on the use of RNA structures as platforms for the rational design of small molecules for therapeutic applications.

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A Key Molecular Regulator, RNA G-Quadruplex and Its Function in Plants

Cited by 7 publications

References 55 publications

Analysis of G-Quadruplex-Forming Sequences in Drought Stress-Responsive Genes, and Synthesis Genes of Phenolic Compounds in Arabidopsis thaliana

Analysis of G-Quadruplex-Forming Sequences in Drought Stress-Responsive Genes, and Synthesis Genes of Phenolic Compounds in Arabidopsis thaliana

The Arabidopsis tDR Ala forms G‐quadruplex structures that can be unwound by the DExH1 DEA(D/H)‐box RNA helicase

Alternative RNA Conformations: Companion or Combatant

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