Protein Phosphorylation Dynamics Under Carbon/Nitrogen-Nutrient Stress and Identification of a Cell Death-Related Receptor-Like Kinase in Arabidopsis

Li, Xingwen; Sanagi, Miho; Lu, Yu; Nomura, Yuko; Stolze, Sara C.; Yasuda, Shigetaka; Saijo, Yusuke; Schulze, Waltraud X.; Feil, Regina; Stitt, Mark; Lunn, John E.; Nakagami, Hirofumi; Sato, Takeo; Yamaguchi, Junji

doi:10.3389/fpls.2020.00377

Cited by 29 publications

(24 citation statements)

References 89 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The genetic interaction between RIR1 and NILR2 is also supported by a recent in silico receptor interaction network analysis that indicated an association of RIR1, NILR2 and a so far uncharacterized LRR-RLK (At5g01950) (Xi et al, 2019). Interestingly, the phylogentically related MD-receptor-like kinase LMK1 (At1g07650) was reported to function as a cell death-related receptor as it induced cell death when ectopically expressed in N. benthamiana leaf epidermal cells (Li et al, 2020). While we did not observe such phenomenon for RIR1, we were indeed also unable to over-express NILR2 in these cell types (data not shown).…”

Section: Discussionmentioning

confidence: 99%

A hetero-oligomeric remorin-receptor complex regulates plant development

Abel

Buschle

Hernández‐Reyes

et al. 2021

Preprint

View full text Add to dashboard Cite

Plant growth and development are modulated by both biotic and abiotic stress. Increasing evidence suggests that cellular integration of the corresponding signals occurs within preformed hubs at the plasma membrane called nanodomains. These membrane sub-compartments are organized by multivalent molecular scaffold proteins, such as remorins. Here, we demonstrate that Group 1 remorins form a hetero-oligomeric complex at the plasma membrane. While these remorins are functionally redundant for some pathways their multivalency also allows the recruitment of specific interaction partners. One of them, the receptor-like kinase REMORIN-INTERACTING RECEPTOR 1 (RIR1), that acts redundantly with the closely related receptor NILR2, is specifically recruited by REM1.2 in a phosphorylation-dependent manner. Overlapping developmental phenotypes suggest that the REM/RIR complex regulates key developmental pathways.

show abstract

Section: Discussionmentioning

confidence: 99%

A hetero-oligomeric remorin-receptor complex regulates plant development

Abel

Buschle

Hernández‐Reyes

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…We evaluate our approach on previously published phosphoproteomic data. This includes data sets from more than one hundred public repositories [4] and additionally validate these results on recently published data [26, 27, 28, 29, 30] and in case of cross-linking data we use previously published data to evaluate our transfer learning approach [31, 32, 33].…”

Section: Introductionmentioning

confidence: 60%

“…For validation we use five data sets [28, 29, 30, 26, 27]. For each data set, we used the original search results from MaxQuant alongside the raw spectra.…”

Section: Methodsmentioning

confidence: 99%

AHLF: ad hoc learning of peptide fragmentation from mass spectra enables an interpretable detection of phosphorylated and cross-linked peptides

Altenburg

Wang

Muth

et al. 2020

Preprint

View full text Add to dashboard Cite

Motivation:Publicly available mass spectrometry-based proteomics data has grown exponentially in the recent past. Yet, large scale spectrum-centered analysis usually involves predefined fragmentation features that are limited and prone to be biased. Using deep learning, the decision making for a suitable fragmentation model can be carried out in a data-driven manner. Results: We introduce a framework that allows end-to-end training of generic deep learning models on a large collection of high resolution tandem mass spectra. In this case we used 19.2 million labeled spectra from more than a hundred individual PRIDE repositories. In our framework, we developed a representation that captures the complete information of a high-resolution spectrum facilitating a loss-less reduction of the number of features largely independent of the actual resolution. Additionally, it allows us to use common trainable layers, e.g. recurrent or convolutional operations. Specifically, we use a deep network of stacked dilated convolutions to model long range associations between any peaks within a tandem mass spectrum. We exemplify our approach by learning to detect post-translational modifications -in this case, protein phosphorylation -only based on a given mass spectrum in a fully data-driven manner. To the best of our knowledge, this is the first end-to-end trained deep learning model on tandem spectra that is able to ad hoc learn fragmentation patterns in high-resolution spectra. Our approach outperforms the current state-of-the-art in predicting if a mass spectrum originates from a phosphorylated peptide. Availability: Our deep learning framework is implemented in tensorflow. The open source code including trained weights is available at gitlab.com/dacs-hpi/ahlf Contact: bernhard.renard@hpi.de

show abstract

“…Finally, some of the most highly and broadly induced xisRNAs are associated with subgroups of RLK/Pelle protein kinase of the DLSV subfamily (Figure 4C): the xisRNA010-associated protein kinase domain is closely related to the Arabidopsis CYSTEINE-RICH RECEPTOR-LIKE PROTEIN KINASE 2 (CRK2) which is required for PTI and defense against a bacterial pathogen (53). xisRNA004-associated protein kinase domain is closely related to Arabidopsis AT1G07650 / LMK1 which possesses cell death induction activity (54). Interestingly, in a sister clade, xiRNA001-3, 20, 27 and 118 cis -genes correspond to rice RLCKs phylogenetically closely related to the Arabidopsis RLCK AT1G16670.1 / COLD-RESPONSIVE PROTEIN KINASE 1 (55).…”

Section: Resultsmentioning

confidence: 99%

“…annotated with this latter term. In order to gain some insight on the family composition of kinase domain containing products of rice xisRNA loci cis-genes, they were annotated in Figure 3 and Supplementary Table S3 based on the kinase classification of Lehti-Shiu and Shiu (9) xisRNA004-associated protein kinase domain is closely related to Arabidopsis AT1G07650 / LMK1 which possesses cell death induction activity (54) xisRNA accumulation is DCL4-independent but requires expression of the cis-gene.…”

Section: A Broader Xisrnas Inventorymentioning

confidence: 99%

An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection

Reshetnyak

Jacobs

Auguy

et al. 2021

Preprint

View full text Add to dashboard Cite

Non-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth, development and stress responses. Early insights into plant sRNAs established a role in antiviral defense and they are now extensively studied across plant-microbe interactions. Here, sRNA sequencing discovered a class of sRNA in rice (Oryza sativa) specifically associated with foliar diseases caused by Xanthomonas oryzae bacteria. Xanthomonas-induced small RNAs (xisRNAs) loci were distinctively upregulated in response to diverse virulent strains at an early stage of infection producing a single duplex of 20-22nt sRNAs. xisRNAs production was dependent on the Type III secretion system, a major bacterial virulence factor for host colonization. xisRNA loci overlap with annotated transcripts sequences often encoding protein kinase domain proteins. A number of the corresponding rice cis-genes have documented functions in immune signaling and some xisRNA loci coincide with the coding sequence of a conserved kinase motif. xisRNAs exhibit features of small interfering RNAs and their biosynthesis depend on canonical components OsDCL1 and OsHEN1. xisRNA induction possibly mediates post-transcriptional gene silencing but they do not broadly suppress cis-genes expression on the basis of mRNA-seq data. Overall, our results identify a group of unusual sRNAs with a potential role in plant-microbe interactions.

show abstract

Protein Phosphorylation Dynamics Under Carbon/Nitrogen-Nutrient Stress and Identification of a Cell Death-Related Receptor-Like Kinase in Arabidopsis

Cited by 29 publications

References 89 publications

A hetero-oligomeric remorin-receptor complex regulates plant development

A hetero-oligomeric remorin-receptor complex regulates plant development

AHLF: ad hoc learning of peptide fragmentation from mass spectra enables an interpretable detection of phosphorylated and cross-linked peptides

An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection

Contact Info

Product

Resources

About