Fibrillarin Genes Encode Both a Conserved Nucleolar Protein and a Novel Small Nucleolar RNA Involved in Ribosomal RNA Methylation inArabidopsis thaliana

Barneche, Frédy; Steinmetz, Florence; Echeverrı́a, Manuel

doi:10.1016/s0021-9258(19)61499-7

Cited by 106 publications

(12 citation statements)

References 54 publications

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“…Tiling array data also revealed that depletion of RRP4 and RRP41 resulted in dramatic increases in accumulation of poly(A) + snRNAs (Table S4) and snoRNAs (Table S5), including those encoded by free-standing polycistronic clusters (Figures S5A-S5C), solitary genes (Figure S8A), as well as those embedded in introns of genes functionally related to protein synthesis (Table S5). The latter gene arrangement may help to coordinate snoRNA biogenesis with cellular demands on translation and is prevalent in animals, but it has been observed in Arabidopsis only once (Barneche et al, 2000). Moreover, we identified 3 0 -extended upregulated poly(A) + snoRNAs (Figures S5A and S5B), which may represent either incompletely processed byproducts of snoRNA biogenesis targeted for degradation or normal processing intermediates.…”

Section: Rna Targets Of the Arabidopsis Exosomementioning

confidence: 86%

Genome-Wide High-Resolution Mapping of Exosome Substrates Reveals Hidden Features in the Arabidopsis Transcriptome

Chekanova

Gregory

Reverdatto

et al. 2007

Cell

303

398

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The exosome complex plays a central and essential role in RNA metabolism. However, comprehensive studies of exosome substrates and functional analyses of its subunits are lacking. Here, we demonstrate that as opposed to yeast and metazoans the plant exosome core possesses an unanticipated functional plasticity and present a genome-wide atlas of Arabidopsis exosome targets. Additionally, our study provides evidence for widespread polyadenylation- and exosome-mediated RNA quality control in plants, reveals unexpected aspects of stable structural RNA metabolism, and uncovers numerous novel exosome substrates. These include a select subset of mRNAs, miRNA processing intermediates, and hundreds of noncoding RNAs, the vast majority of which have not been previously described and belong to a layer of the transcriptome that can only be visualized upon inhibition of exosome activity. These first genome-wide maps of exosome substrates will aid in illuminating new fundamental components and regulatory mechanisms of eukaryotic transcriptomes.

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Section: Rna Targets Of the Arabidopsis Exosomementioning

confidence: 86%

Genome-Wide High-Resolution Mapping of Exosome Substrates Reveals Hidden Features in the Arabidopsis Transcriptome

Chekanova

Gregory

Reverdatto

et al. 2007

Cell

303

398

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“…However, NbNdhM‐ΔNES and NbNdhM‐NES 3L were not localized to the nucleolus in the presence of TuMV VPg (Figure 8). To further confirm this, we used Fib2‐mCherry as a nucleolus‐localized marker (Barneche, Steinmetz, & Echeverría, 2000). Similar localization patterns were observed when NbNdhM‐GFP, NbNdhM‐ΔNES‐GFP, NbNdhM‐NES 3L ‐GFP or NbNdhM‐NES 1,2,3,5,7 were co‐expressed with Fib‐mCherry and TuMV VPg‐cMyc (Figure S14a,b).…”

Section: Resultsmentioning

confidence: 99%

Turnip mosaic virus impairs perinuclear chloroplast clustering to facilitate viral infection

Zhai

Yuan

Qiu

et al. 2021

Plant Cell & Environment

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Chloroplasts play crucial roles in plant defence against viral infection. We now report that chloroplast NADH dehydrogenase-like (NDH) complex M subunit gene (NdhM) was first up-regulated and then down-regulated in turnip mosaic virus (TuMV)infected N. benthamiana. NbNdhM-silenced plants were more susceptible to TuMV, whereas overexpression of NbNdhM inhibited TuMV accumulation. Overexpression of NbNdhM significantly induced the clustering of chloroplasts around the nuclei and disturbing this clustering facilitated TuMV infection, suggesting that the clustering mediated by NbNdhM is a defence against TuMV. It was then shown that NbNdhM interacted with TuMV VPg, and that the NdhMs of different plant species interacted with the proteins of different viruses, implying that NdhM may be a common target of viruses. In the presence of TuMV VPg, NbNdhM, which is normally localized in the nucleus, chloroplasts, cell periphery and chloroplast stromules, colocalized with VPg at the nucleus and nucleolus, with significantly increased nuclear accumulation, while NbNdhM-mediated chloroplast clustering was significantly impaired. This study therefore indicates that NbNdhM has a defensive role in TuMV infection probably by inducing the perinuclear clustering of chloroplasts, and that the localization of NbNdhM is altered by its interaction with TuMV VPg in a way that promotes virus infection.

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“…Remarkably, U3 in plants is transcribed by the RNA polymerase III and possess a different capping than found for U3 in yeast or human (Kiss et al, 1991). By dot-matrix analysis of Fib1 and Fib2, the plant-specific snoRNAs U60.1f and U60.2f were discovered (Barneche et al, 2000).…”

Section: The Snornas In Plantsmentioning

confidence: 99%

“…Initially, the analysis of the individual snoRNAs was accompanied by the analysis of the rRNA modification sites, e.g., by primer extension analysis (Barneche et al, 2000). Recently, genome-wide pseudouridine sequencing verified predicted pseudouridine modifications in cytosolic and plastidic ribosomes (Sun et al, 2019).…”

Section: The Rrna Modification In Plantsmentioning

confidence: 99%

The Arabidopsis 2′-O-Ribose-Methylation and Pseudouridylation Landscape of rRNA in Comparison to Human and Yeast

Streit

Schleiff

2021

Front. Plant Sci.

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Eukaryotic ribosome assembly starts in the nucleolus, where the ribosomal DNA (rDNA) is transcribed into the 35S pre-ribosomal RNA (pre-rRNA). More than two-hundred ribosome biogenesis factors (RBFs) and more than two-hundred small nucleolar RNAs (snoRNA) catalyze the processing, folding and modification of the rRNA in Arabidopsis thaliana. The initial pre-ribosomal 90S complex is formed already during transcription by association of ribosomal proteins (RPs) and RBFs. In addition, small nucleolar ribonucleoprotein particles (snoRNPs) composed of snoRNAs and RBFs catalyze the two major rRNA modification types, 2′-O-ribose-methylation and pseudouridylation. Besides these two modifications, rRNAs can also undergo base methylations and acetylation. However, the latter two modifications have not yet been systematically explored in plants. The snoRNAs of these snoRNPs serve as targeting factors to direct modifications to specific rRNA regions by antisense elements. Today, hundreds of different sites of modifications in the rRNA have been described for eukaryotic ribosomes in general. While our understanding of the general process of ribosome biogenesis has advanced rapidly, the diversities appearing during plant ribosome biogenesis is beginning to emerge. Today, more than two-hundred RBFs were identified by bioinformatics or biochemical approaches, including several plant specific factors. Similarly, more than two hundred snoRNA were predicted based on RNA sequencing experiments. Here, we discuss the predicted and verified rRNA modification sites and the corresponding identified snoRNAs on the example of the model plant Arabidopsis thaliana. Our summary uncovers the plant modification sites in comparison to the human and yeast modification sites.

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Fibrillarin Genes Encode Both a Conserved Nucleolar Protein and a Novel Small Nucleolar RNA Involved in Ribosomal RNA Methylation inArabidopsis thaliana

Cited by 106 publications

References 54 publications

Genome-Wide High-Resolution Mapping of Exosome Substrates Reveals Hidden Features in the Arabidopsis Transcriptome

Genome-Wide High-Resolution Mapping of Exosome Substrates Reveals Hidden Features in the Arabidopsis Transcriptome

Turnip mosaic virus impairs perinuclear chloroplast clustering to facilitate viral infection

The Arabidopsis 2′-O-Ribose-Methylation and Pseudouridylation Landscape of rRNA in Comparison to Human and Yeast

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