Nuclear dynamics: Formation of bodies and trafficking in plant nuclei

Muñoz-Díaz, Eduardo; Sáez‐Vasquez, Julio

doi:10.3389/fpls.2022.984163

Cited by 12 publications

(9 citation statements)

References 236 publications

(320 reference statements)

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“…2022 ; Meschichi and Rosa 2023 ) or the formation of foci with the assembly of repair factors ( Hirakawa et al . 2015 ; Hirakawa and Matsunaga 2019 ; Muñoz-Díaz and Sáez-Vásquez 2022 ). It remains to be investigated whether and how lncRNAs are involved in this compartmentalization, but the candidates identified in the course of the work presented and the improved techniques to visualize RNA molecules within cells ( Duncan and Rosa 2018 ; Huang et al .…”

Section: Discussionmentioning

confidence: 99%

Long noncoding RNAs contribute to DNA damage resistance in Arabidopsis thaliana

et al. 2023

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Efficient repair of DNA lesions is essential for faithful transmission of genetic information between somatic cells and for genome integrity across generations. Plants have multiple, partially redundant and overlapping DNA repair pathways, probably due to the less constricted germline and the inevitable exposure to light including higher energy wavelengths. Many proteins involved in DNA repair and their mode of actions are well described. In contrast, a role for DNA damage-associated RNA components, evident from many other organisms, is less well understood. Here, we have challenged young Arabidopsis thaliana plants with two different types of genotoxic stress and performed de novo assembly and transcriptome analysis. We identified three long non-coding RNAs (lncRNAs) that are lowly or not expressed under regular conditions but up-regulated or induced by DNA damage. We generated CRISPR/Cas deletion mutants and found that the absence of the lncRNAs impairs the recovery capacity of the plants from genotoxic stress. The genetic loci are highly conserved among world-wide distributed Arabidopsis accessions and within related species in the Brassicaceae group. Together, these results suggest that the lncRNAs have a conserved function in connection with DNA damage and provide a basis for a mechanistic analysis of their role.

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Section: Discussionmentioning

confidence: 99%

Long noncoding RNAs contribute to DNA damage resistance in Arabidopsis thaliana

et al. 2023

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“…Recently, a report on the lncRNA COOLAIR involved in the regulation of flowering time revealed that environmental conditions resulted in alternative processing and variability in secondary structures (Yang et al, 2022). In connection with DNA repair, there is growing evidence that this involves large scale reorganization of the chromatin, e.g., by changing chromatin mobility (Meschichi et al, 2022; Meschichi and Rosa, 2023) or the formation of foci with assembly of repair factors (Hirakawa et al, 2015; Hirakawa and Matsunaga, 2019; Muñoz-Díaz and Sáez-Vásquez, 2022). It remains to be investigated whether and how lncRNAs are involved in this compartmentalization, but the candidates identified in the course of the work presented and the improved techniques to visualize RNA molecules within cells (Duncan and Rosa, 2018; Huang et al, 2020) will make these approaches possible.…”

Section: Discussionmentioning

confidence: 99%

Long non-coding RNAs contribute to DNA damage resistance inArabidopsis thaliana

Durut

Kornienko

Schmidt

et al. 2023

Preprint

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Efficient repair of DNA lesions is essential for faithful transmission of genetic information between somatic cells and for genome integrity across generations. Plants have multiple, partially redundant and overlapping DNA repair pathways, probably due to the less constricted germline and the inevitable exposure to light including higher energy wavelengths. Many proteins involved in DNA repair and their mode of actions are well described. In contrast, a role for DNA damage-associated RNA components, evident from many other organisms, is less well understood. Here, we have challenged young Arabidopsis thaliana plants with two different types of genotoxic stress and performed de novo assembly and transcriptome analysis. We identified three long non-coding RNAs (lncRNAs) that are lowly or not expressed under regular conditions but up-regulated or induced by DNA damage. To understand their potential role in DNA repair, we generated CRISPR/Cas deletion mutants and found that the absence of the lncRNAs impairs the recovery capacity of the plants from genotoxic stress. The genetic loci are highly conserved among world-wide distributed Arabidopsis accessions and within related species in the Brassicaceae group. Together, these results suggest that the lncRNAs have a conserved function in connection with DNA damage and provide a basis for a mechanistic analysis of their role.

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“…When these arise in the cytosol, they can produce both phase-separated liquid droplets suspended in solution and phase-separated nanoclusters of signaling proteins at the cell membrane, as exemplified for the T-cell receptor, processing bodies, photobodies, Cajal bodies, and dicing nuclear bodies in the nucleus as well as stress granules and germ granules in the cytoplasm. Such membraneless bodies have also been described in mitochondria and chloroplasts of A. thaliana (Muñoz-D ıaz & S aez-V asquez, 2022;Su et al, 2016). By promoting nanoclustering and condensate formation, LLPS has emerged as an intracellular organizational mechanism that allows compartmentalization and leads to a local increase in enzyme and metabolite concentrations in and on the membrane and in the cytosol in both eukaryotic and prokaryotic cells (Banani et al, 2017;Emenecker et al, 2020;Feng et al, 2019;Shin & Brangwynne, 2017).…”

Section: Observations From Non-plant Systems Which Provide a Route To...mentioning

confidence: 95%

The formation and function of plant metabolons

et al. 2023

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SUMMARY Metabolons are temporary structural‐functional complexes of sequential enzymes of a metabolic pathway that are distinct from stable multi‐enzyme complexes. Here we provide a brief history of the study of enzyme–enzyme assemblies with a particular focus on those that mediate substrate channeling in plants. Large numbers of protein complexes have been proposed for both primary and secondary metabolic pathways in plants. However, to date only four substrate channels have been demonstrated. We provide an overview of current knowledge concerning these four metabolons and explain the methodologies that are currently being applied to unravel their functions. Although the assembly of metabolons has been documented to arise through diverse mechanisms, the physical interaction within the characterized plant metabolons all appear to be driven by interaction with structural elements of the cell. We therefore pose the question as to what methodologies could be brought to bear to enhance our knowledge of plant metabolons that assemble via different mechanisms? In addressing this question, we review recent findings in non‐plant systems concerning liquid droplet phase separation and enzyme chemotaxis and propose strategies via which such metabolons could be identified in plants. We additionally discuss the possibilities that could be opened up by novel approaches based on: (i) subcellular‐level mass spectral imaging, (ii) proteomics, and (iii) emergent methods in structural and computational biology.

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Nuclear dynamics: Formation of bodies and trafficking in plant nuclei

Cited by 12 publications

References 236 publications

Long noncoding RNAs contribute to DNA damage resistance in Arabidopsis thaliana

Long noncoding RNAs contribute to DNA damage resistance in Arabidopsis thaliana

Long non-coding RNAs contribute to DNA damage resistance inArabidopsis thaliana

The formation and function of plant metabolons

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