Protein and metabolite composition of Arabidopsis stress granules

Kosmacz, Monika; Górka, Michał; Schmidt, Stephan; Luzarowski, Marcin; Moreno, Juan C.; Szlachetko, Jagoda; Leniak, Ewa; Sokołowska, Ewelina; Sofroni, Kostika; Schnittger, Arp

doi:10.1111/nph.15690

Cited by 115 publications

(159 citation statements)

References 56 publications

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“…Similar results were reported for other plant proteins such as the polyadenylated (poly(A)+) mRNA binding protein PAB-2 [7] and the VASCULAR PLANT ONE-ZINC FINGER (VOZ)1/and VOZ2 [36], which in normal conditions localize to the cytoplasm and the nucleus, and are translocated to stress granules upon stress. However, despite the fact that ArathEULS3 transcript levels are known to be upregulated in response to drought stress the ArathEULS3 protein was not identified in the proteome of heat/dark treated plants [10] nor was it identified when examining the changes in RNA-binding proteome under drought stress conditions [9,37]. This might be explained by the fact that the proteome of the stress granules might change depending on the nature and severity of the stress conditions as well as the developmental stage of the plant [1].…”

Section: Discussionmentioning

confidence: 93%

“…This might be explained by the fact that the proteome of the stress granules might change depending on the nature and severity of the stress conditions as well as the developmental stage of the plant [1]. Additionally the stress granules proteome analysis revealed elongation factors or chaperons, the presence of stress-related proteins such as receptors, kinases, and transcriptional regulators next to the predicted stress granule components like RNA-binding proteins [10]. Considering the stress-responsive nature of ArathEULS3, more proteomic analyses performed under different stress conditions will help to confirm the presence of ArathEULS3 protein in stress granules.…”

Section: Discussionmentioning

confidence: 99%

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The ArathEULS3 Lectin Ends up in Stress Granules and Can Follow an Unconventional Route for Secretion

Dubiel

Coninck

Osterne

et al. 2020

IJMS

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Stress granules are cytoplasmic compartments, which serve as mRNA storage units during stress, therefore regulating translation. The Arabidopsis thaliana lectin ArathEULS3 has been widely described as a stress inducible gene. This study aimed to examine in detail the localization of ArathEULS3 lectin in normal and stressed cells. Colocalization experiments revealed that the nucleo-cytoplasmic lectin ArathEULS3 relocates to stress granules after stress. The ArathEULS3 sequence encodes a protein with a EUL lectin domain and an N-terminal domain with unknown structure and function. Bioinformatics analyses showed that the N-terminal domain sequence contains intrinsically disordered regions and likely does not exhibit a stable protein fold. Plasmolysis experiments indicated that ArathEULS3 also localizes to the apoplast, suggesting that this protein might follow an unconventional route for secretion. As part of our efforts we also investigated the interactome of ArathEULS3 and identified several putative interaction partners important for the protein translation process.

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Section: Discussionmentioning

confidence: 93%

Section: Discussionmentioning

confidence: 99%

The ArathEULS3 Lectin Ends up in Stress Granules and Can Follow an Unconventional Route for Secretion

Dubiel

Coninck

Osterne

et al. 2020

IJMS

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“…While the protein components of SGs and siRNA bodies in plants are relatively well known 56 , the RNA composition of such cytoplasmic compartments are poorly understood. Studies in human and yeast have shown that transcriptome of cytoplasmic RNA granules are associated with strong translational repression 23,25,57,58 .…”

Section: Resultsmentioning

confidence: 99%

“…The enrichment of cytoplasmic bodies was carried out by employing the SG enrichment methods reported previously 25,56,59 . Briefly, 2 g of samples was ground with a precooled mortar and pestle in liquid nitrogen.…”

Section: Methodsmentioning

confidence: 99%

Translational inhibition and phase separation primes the epigenetic silencing of transposons

Kim

Lei

et al. 2020

Preprint

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19Transposons are mobile DNAs that can cause fatal mutations. To counteract these 20 genome invaders, the host genomes deploy small interfering (si) RNAs to initiate and 21 establish the epigenetic silencing. However, the regulatory mechanisms for the selective 22 recognition of transposons by the host genomes remain still elusive. Here we show that plant 23 transposon RNAs undergo frequent ribosome stalling caused by their inherently unfavourable 24 codon sequence usage. The ribosome stalling then causes the RNA truncation and the 25 localization to siRNA bodies, which are both critical prerequisites for the siRNA processing. 26 In addition, SGS3, the key protein in the siRNA biogenesis pathway, forms liquid droplets in 27 vitro through its prion-like domains implicating the role of liquid-liquid phase separation in 28 the formation of the siRNA bodies. Our study provides a novel insight into the regulatory 29 mechanisms for the recognition of invasive genetic elements which is essential for the 30 maintenance of genome integrity. 31 32 33 Keywords 34 transposon, codon optimality, ribosome stalling, easiRNA, RDR6-RdDM, liquid-liquid phase 35 separation, siRNA body, stress granule 36 37 38 45 of transposons 5 . While the canonical RdDM is mainly for reinforcing the silent state of 46 transposons, the recently proposed alternative RdDM pathway suppresses the active 47 transposons that are induced upon the epigenetic mutations and in several development 48 stages 3,6-10 . RNA-DEPENDENT RNA POLYMERASE 6 (RDR6)-SUPPRESSOR OF GENE 49 SILENCING 3 (SGS3) complex serves as a detector of transposon RNAs that selectively 50 processes them into 21 or 22-nt siRNAs (also referred to as epigenetically activated siRNAs, 51 easiRNAs) 11,12 . Transposon-derived siRNAs trigger both post-transcriptional repression by 52 cleaving the transposon RNAs (and then subsequently initiating the secondary siRNA 53 biogenesis) and establishment of the epigenetic silencing by recruiting DNA 54 methyltransferases to the target TE chromatin 5,7,8 . The biogenesis of 21 or 22-nt siRNAs in 55 plants is initiated by RDR6 which is an RNA-dependent RNA polymerase that forms double-56stranded RNAs by templating directly the target RNAs 13 . SGS3 is an RNA-binding protein 57 that interacts with RDR6 and is essential for its function 13 . The duplex RNAs are then sliced 58 to 21 or 22-nt siRNAs by DICER-LIKE 3 or 4 (DCL3/4) 8,14,15 . Since RDR6 templates are 59 directly derived from the RNAs of those mobile elements, RDR6 and the resulting easiRNAs 60 are deemed the first line of the host immune system against the invasive genetic elements. 61The RDR6-mediated easiRNA production pathway (RDR6-RdDM) is usually 62 prevented in the transcripts derived from genes by the RNA decay pathways [16][17][18] . This raises 63 4 an important question of how RDR6 specifically recognizes its TE targets and establish their 64 epigenetic silencing. Previous reports showed that the initial cleavage of target transcripts is a 65 critical prerequisite for RDR6 recog...

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“…MCs of plants and other eukaryotes contain overlapping sets of proteins, indicating a common function in eukaryotic metabolism. For example, stress granules, small cytoplasmic MCs that form upon a variety of stresses contain RNA, translation initiation factors, RNA-binding, and other proteins [75,76]. Curiously, also components of the cell cycle regulation machinery (see paragraph below), such as cyclin-dependent kinases localize to stress granules in both plant and human cells [76,77].…”

Section: Protein Disorder As a Driving Force For Liquid-liquid Phase mentioning

confidence: 99%

Common Functions of Disordered Proteins across Evolutionary Distant Organisms

Wallmann

Kesten

2020

IJMS

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Intrinsically disordered proteins and regions typically lack a well-defined structure and thus fall outside the scope of the classic sequence-structure-function relationship. Hence, classic sequence-or structure-based bioinformatic approaches are often not well suited to identify homology or predict the function of unknown intrinsically disordered proteins. Here, we give selected examples of intrinsic disorder in plant proteins and present how protein function is shared, altered or distinct in evolutionary distant organisms. Furthermore, we explore how examining the specific role of disorder across different phyla can provide a better understanding of the common features that protein disorder contributes to the respective biological mechanism. being defined by a separate set of parameters compared to their structured and globular counterparts [7]. Hence, identification of distantly related IDPs cannot rely on structure, which can help to detect relationships of folded proteins that would remain undetected by conventional sequence-based methods [8]. Methods that use antibodies to metazoan proteins to identify putative plant homologues may result in a higher incidence of artefacts when compared to folded protein targets, due to the smaller size of disordered epitopes and their comparably higher sensitivity to epitope variation [9].In contrast to folded proteins, IDPs and IDRs show an overall increased rate of evolution, while these rates can strongly vary between different parts of the IDP [10,11]. Moreover, disordered regions appear to be more permissive to mutation, further complicating sequence-function analysis. Overall, genome duplication events seem to influence the distribution of IDRs within genomes, as the amount of identical paralogous IDRs positively correlates with the number of chromosomes [12]. Interestingly, proteins can display different modes of how sequence conservation can relate to disorder as a functional feature [13]. While in some cases only the disorder itself is conserved, but not the sequence facilitating it (flexible disorder), other IDPs retain disorder together with a highly conserved sequence (constrained disorder). Short-linear motifs (SLiMs) represent conserved functional modules that can mediate low-affinity interactions and are often interspersed by regions of flexible disorder [14]. As many alignment algorithms require long stretches of sequence similarity to satisfy statistical significance, the high modality and low complexity of SLiMs can obscure the search for homologous sequences considerably. Due to their limited size (7-12 residues), these motifs can easily develop in unrelated proteins in convergent evolution. Furthermore, post-translational modifications (PTMs) that often regulate IDP function complicate the analysis, as they can drastically alter the biophysical features of a protein and phosphorylation sites display short and weakly conserved motifs that are often difficult to detect via computational sequence analysis [15].Within protein interaction networks, IDPs ofte...

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Protein and metabolite composition of Arabidopsis stress granules

Cited by 115 publications

References 56 publications

The ArathEULS3 Lectin Ends up in Stress Granules and Can Follow an Unconventional Route for Secretion

The ArathEULS3 Lectin Ends up in Stress Granules and Can Follow an Unconventional Route for Secretion

Translational inhibition and phase separation primes the epigenetic silencing of transposons

Common Functions of Disordered Proteins across Evolutionary Distant Organisms

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