Plant RNA Interactome Capture: Revealing the Plant RBPome

Bach‐Pages, Marcel; Castelló, Alfredo; Preston, Gail M.

doi:10.1016/j.tplants.2017.04.006

Cited by 12 publications

(6 citation statements)

References 13 publications

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“…Firstly, the intensity of most of these photosynthetic proteins in ptRIC was relatively high, suggesting that these were bona fide RBPs ( Figure S4B). Secondly, 33 leaf RBPs involved in photosynthesis have also been independently shown to associate with RNA in other Arabidopsis tissues by RIC analyses [32,33], with the exception of seedlings grown in the dark [34]. Thirdly, five leaf RBPs with GO annotations related to photosynthesis were also annotated as 'RNA binding' (OEE1, OEE2, HPR1, WTF1 homolog and the uncharacterised PPR-containing protein AT3G46610).…”

Section: Proteins Of the Photosynthetic Apparatus Moonlight As Rna Bimentioning

confidence: 99%

“…This has greatly expanded the repertoire of RBPs, and with it our knowledge of RNA biology [32]. RIC has also been applied to different tissues of the model plant Arabidopsis thaliana [33]: etiolated seedlings [34], cell cultures [35,36] and protoplasts derived from the mesophyll [37,38]. Although a recent work applied RIC to plant leaves [35], this study only identified 27 leaf RBPs, which is a very small fraction of the expected plant RBPome.…”

Section: Introductionmentioning

confidence: 99%

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Discovering the RNA-Binding Proteome of Plant Leaves with an Improved RNA Interactome Capture Method

et al. 2020

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RNA-binding proteins (RBPs) play a crucial role in regulating RNA function and fate. However, the full complement of RBPs has only recently begun to be uncovered through proteome-wide approaches such as RNA interactome capture (RIC). RIC has been applied to various cell lines and organisms, including plants, greatly expanding the repertoire of RBPs. However, several technical challenges have limited the efficacy of RIC when applied to plant tissues. Here, we report an improved version of RIC that overcomes the difficulties imposed by leaf tissue. Using this improved RIC method in Arabidopsis leaves, we identified 717 RBPs, generating a deep RNA-binding proteome for leaf tissues. While 75% of these RBPs can be linked to RNA biology, the remaining 25% were previously not known to interact with RNA. Interestingly, we observed that a large number of proteins related to photosynthesis associate with RNA in vivo, including proteins from the four major photosynthetic supercomplexes. As has previously been reported for mammals, a large proportion of leaf RBPs lack known RNA-binding domains, suggesting unconventional modes of RNA binding. We anticipate that this improved RIC method will provide critical insights into RNA metabolism in plants, including how cellular RBPs respond to environmental, physiological and pathological cues.

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Section: Proteins Of the Photosynthetic Apparatus Moonlight As Rna Bimentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Discovering the RNA-Binding Proteome of Plant Leaves with an Improved RNA Interactome Capture Method

et al. 2020

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“…The Arabidopsis leaf RBPome and its responses to flg22 Multiple RBPs have been described to have crucial roles during plant immune responses. Hence, we hypothesised that the Arabidopsis RBPome is modulated during immune responses, and that these changes in RNA binding activity could be profiled using RIC 17 .…”

Section: Resultsmentioning

confidence: 99%

Proteome-wide Profiling of RNA-Binding Protein Responses to flg22 Reveals Novel Components of Plant Immunity

Bach‐Pages

Chen

Sanguankiattichai

et al. 2020

Preprint

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RNA-binding proteins (RBPs) play critical roles in post-transcriptional gene regulation and are known to contribute to plant immunity. To understand the responses of cellular RBPs to an immune elicitor, we applied RNA interactome capture to Arabidopsis leaves treated with flg22. Strikingly, flg22 induced a pervasive remodelling of the cellular RBPome affecting 186 proteins. Flg22-responsive RBPs included classical RBPs involved in RNA metabolism as well as non-canonical RBPs. RBP responders detected after 2h of treatment are enriched in putative sites for post-translational modifications, which may play a regulatory role. By contrast, changes in RBP abundance becomes increasingly important for the RBPome responses to flg22 after 12h. Plant resistance to Pseudomonas syringae is strongly altered in mutant lines lacking individual flg22-responsive RBPs, supporting the importance of RBP dynamics in plant immunity. This study provides a comprehensive and systematic census of flg22 responsive plant RBPs, discovering novel components of plant immunity.

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“…The cell lysate is then passed over oligo(dT)-magnetic beads under denaturing conditions to pull down polyA RNAs and the denatured proteins covalently bonded to them. After stringent washes to elute any non-covalently interacting proteins, the RNA is enzymatically digested and the protein sample is subjected for proteomics via mass spectrometry [70] (Figure 3). This technique is powerful but limited by its restriction to polyA RNA.…”

Section: Global Rna-protein Interactomementioning

confidence: 99%

The Landscape of RNA-Protein Interactions in Plants: Approaches and Current Status

Burjoski

Reddy

2021

IJMS

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RNAs transmit information from DNA to encode proteins that perform all cellular processes and regulate gene expression in multiple ways. From the time of synthesis to degradation, RNA molecules are associated with proteins called RNA-binding proteins (RBPs). The RBPs play diverse roles in many aspects of gene expression including pre-mRNA processing and post-transcriptional and translational regulation. In the last decade, the application of modern techniques to identify RNA–protein interactions with individual proteins, RNAs, and the whole transcriptome has led to the discovery of a hidden landscape of these interactions in plants. Global approaches such as RNA interactome capture (RIC) to identify proteins that bind protein-coding transcripts have led to the identification of close to 2000 putative RBPs in plants. Interestingly, many of these were found to be metabolic enzymes with no known canonical RNA-binding domains. Here, we review the methods used to analyze RNA–protein interactions in plants thus far and highlight the understanding of plant RNA–protein interactions these techniques have provided us. We also review some recent protein-centric, RNA-centric, and global approaches developed with non-plant systems and discuss their potential application to plants. We also provide an overview of results from classical studies of RNA–protein interaction in plants and discuss the significance of the increasingly evident ubiquity of RNA–protein interactions for the study of gene regulation and RNA biology in plants.

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Plant RNA Interactome Capture: Revealing the Plant RBPome

Cited by 12 publications

References 13 publications

Discovering the RNA-Binding Proteome of Plant Leaves with an Improved RNA Interactome Capture Method

Discovering the RNA-Binding Proteome of Plant Leaves with an Improved RNA Interactome Capture Method

Proteome-wide Profiling of RNA-Binding Protein Responses to flg22 Reveals Novel Components of Plant Immunity

The Landscape of RNA-Protein Interactions in Plants: Approaches and Current Status

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