qPTMplants: an integrative database of quantitative post-translational modifications in plants

Han, Xue; Wang, Panqin; Cao, Bijin; Jia, Chongchong; Cheng, Ben; Shi, Yuhua; Guo, Weifeng; Wang, Zhenlong; Liu, Zexian; Cheng, Han

doi:10.1093/nar/gkab945

Cited by 19 publications

(23 citation statements)

References 55 publications

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“…Illustrated by the large number of phosphoproteomic studies and plant protein post translational modification (PTM) repositories reporting extensive phosphorylation of SR proteins and snRNPs [ 32 ], PTM viewer [ 33 ] https://www.psb.ugent.be/webtools/ptm-viewer/ ), qPTMplants [ 34 ] http://qptmplants.omicsbio.info/ , the plant spliceosome and its regulatory proteins (e.g. SR proteins) are a major targets of regulatory phosphorylation events.…”

Section: Introductionmentioning

confidence: 99%

Genome-scale analysis of Arabidopsis splicing-related protein kinase families reveals roles in abiotic stress adaptation

Gallo

Devang

et al. 2022

BMC Plant Biol

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Nearly 60 – 80 % of intron-containing plant genes undergo alternative splicing in response to either stress or plant developmental cues. RNA splicing is performed by a large ribonucleoprotein complex called the spliceosome in conjunction with associated subunits such as serine arginine (SR) proteins, all of which undergo extensive phosphorylation. In plants, there are three main protein kinase families suggested to phosphorylate core spliceosome subunits and related splicing factors based on orthology to human splicing-related kinases: the SERINE/ARGININE PROTEIN KINASES (SRPK), ARABIDOPSIS FUS3 COMPLEMENT (AFC), and Pre-mRNA PROCESSING FACTOR 4 (PRP4K) protein kinases. To better define the conservation and role(s) of these kinases in plants, we performed a genome-scale analysis of the three families across photosynthetic eukaryotes, followed by extensive transcriptomic and bioinformatic analysis of all Arabidopsis thaliana SRPK, AFC, and PRP4K protein kinases to elucidate their biological functions. Unexpectedly, this revealed the existence of SRPK and AFC phylogenetic groups with distinct promoter elements and patterns of transcriptional response to abiotic stress, while PRP4Ks possess no phylogenetic sub-divisions, suggestive of functional redundancy. We also reveal splicing-related kinase families are both diel and photoperiod regulated, implicating different orthologs as discrete time-of-day RNA splicing regulators. This foundational work establishes a number of new hypotheses regarding how reversible spliceosome phosphorylation contributes to both diel plant cell regulation and abiotic stress adaptation in plants.

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Section: Introductionmentioning

confidence: 99%

Genome-scale analysis of Arabidopsis splicing-related protein kinase families reveals roles in abiotic stress adaptation

Gallo

Devang

et al. 2022

BMC Plant Biol

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“…The latter offers an impressive array of new features for functional and evolutionary exploration including gene regulatory elements, target annotations, variants and phylogenetic trees. Finally, welcome new arrivals include PlantGSAD ( 104 ) which provides >200 000 gene sets across 44 families, sets based on a notably diverse set of properties; and qPTMplants ( 105 ) which curates data, including quantitative information, on post-translational modifications (PTM) across 43 species. The latter features an interesting discussion of PTM crosstalk identified in the database.…”

Section: New and Updated Databasesmentioning

confidence: 99%

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

Rigden

Fernández

2021

Nucleic Acids Research

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The 2022 Nucleic Acids Research Database Issue contains 185 papers, including 87 papers reporting on new databases and 85 updates from resources previously published in the Issue. Thirteen additional manuscripts provide updates on databases most recently published elsewhere. Seven new databases focus specifically on COVID-19 and SARS-CoV-2, including SCoV2-MD, the first of the Issue's Breakthrough Articles. Major nucleic acid databases reporting updates include MODOMICS, JASPAR and miRTarBase. The AlphaFold Protein Structure Database, described in the second Breakthrough Article, is the stand-out in the protein section, where the Human Proteoform Atlas and GproteinDb are other notable new arrivals. Updates from DisProt, FuzDB and ELM comprehensively cover disordered proteins. Under the metabolism and signalling section Reactome, ConsensusPathDB, HMDB and CAZy are major returning resources. In microbial and viral genomes taxonomy and systematics are well covered by LPSN, TYGS and GTDB. Genomics resources include Ensembl, Ensembl Genomes and UCSC Genome Browser. Major returning pharmacology resource names include the IUPHAR/BPS guide and the Therapeutic Target Database. New plant databases include PlantGSAD for gene lists and qPTMplants for post-translational modifications. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). Our latest update to the NAR online Molecular Biology Database Collection brings the total number of entries to 1645. Following last year's major cleanup, we have updated 317 entries, listing 89 new resources and trimming 80 discontinued URLs. The current release is available at http://www.oxfordjournals.org/nar/database/c/.

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“…We are particularly unsure of the precise mechanisms by which these candidates affect root traits because their PTM activity may be highly nonspecific and a majority of plant genes are likely to undergo PTMs. Evidence has been found for PTMs of over 12,000 substrates in Arabidopsis (Xue et al ., 2022), including arabinogalactans (Schultz et al 2004) and microtubule proteins involved in cell structure and division (Parrotta et al ., 2014) as well as hormone signal regulators (reviewed by Hill, 2015). Specific interactions between PTM catalysts and other gene candidates can be interrogated via statistical tests for epistasis.…”

Section: Discussionmentioning

confidence: 99%

GWAS identifies candidate genes controlling adventitious rooting in Populus trichocarpa

Nagle

Yuan

Kaur

et al. 2022

Preprint

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Adventitious rooting is critical to the propagation, breeding, and genetic engineering or editing of trees. The capacity for plants to undergo these processes is highly heritable; however, the basis of its genetic variation is largely uncharacterized. To identify genetic regulators of these processes, we performed a genome-wide association study (GWAS) using 1,148 genotypes of Populus trichocarpa. GWAS are often limited by the abilities of researchers to collect precise phenotype data on a high-throughput scale; to help overcome this limitation, we developed a computer vision system to measure an array of traits related to adventitious root development in poplar, including temporal measures of lateral and basal root length and area. GWAS was performed using multiple methods and significance thresholds to handle non-normal phenotype statistics, and to gain statistical power. These analyses yielded a total of 277 unique associations, suggesting that genes that control rooting include regulators of hormone signaling, cell division and structure, and reactive oxygen species signaling. Genes related to other processes with known roles in root development, and numerous genes with uncharacterized functions and/or cryptic roles, were also identified. These candidates provide targets for functional analysis, including physiological and epistatic analyses, to better characterize the complex polygenic regulation of adventitious rooting.

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qPTMplants: an integrative database of quantitative post-translational modifications in plants

Cited by 19 publications

References 55 publications

Genome-scale analysis of Arabidopsis splicing-related protein kinase families reveals roles in abiotic stress adaptation

Genome-scale analysis of Arabidopsis splicing-related protein kinase families reveals roles in abiotic stress adaptation

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

GWAS identifies candidate genes controlling adventitious rooting in Populus trichocarpa

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