CropPAL for discovering divergence in protein subcellular location in crops to support strategies for molecular crop breeding

Abstract

Agriculture faces increasing demand for yield, higher plant-derived protein content and diversity while facing pressure to achieve sustainability. Although the genomes of many of the important crops have been sequenced, the subcellular locations of most of the encoded proteins remain unknown or are only predicted. Protein subcellular location is crucial in determining protein function and accumulation patterns in plants, and is critical for targeted improvements in yield and resilience. Integrating location data from over 800 studies for 12 major crop species into the cropPAL2020 data collection showed that while >80% of proteins in most species are not localised by experimental data, combining species data or integrating predictions can help bridge gaps at similar accuracy. The collation and integration of over 61 505 experimental localisations and more than 6 million predictions showed that the relative sizes of the protein catalogues located in different subcellular compartments are comparable between crops and Arabidopsis. A comprehensive cross-species comparison showed that between 50% and 80% of the subcellulomes are conserved across species and that conservation only depends to some degree on the phylogenetic relationship of the species. Protein subcellular locations in major biosynthesis pathways are more often conserved than in metabolic pathways. Underlying this conservation is a clear potential for subcellular diversity in protein location between species by means of gene duplication and alternative splicing. Our cropPAL data set and search platform (https://crop-pal.org) provide a comprehensive subcellular proteomics resource to drive compartmentation-based approaches for improving yield, protein composition and resilience in future crop varieties.

Genome-Wide Characterization of Berberine Bridge Enzyme Gene Family in Wheat (Triticum aestivum L.) and the Positive Regulatory Role of TaBBE64 in Response to Wheat Stripe Rust

“…The subcellular localization prediction of TaBBEs was carried out by Crop-pal (https://crop-pal.org). 17 Analysis of Phylogenetic Relationships, Homologous Relationships, and Gene Repetitive Events. The protein sequences of soybean (Glycine max Wm82.a2.v1) and rice (Oryza sativa v7.0) were downloaded from the Phytozomev13 database (https://phytozomenext.jgi.doe.gov/blast-search).…”

Genome-wide survey and expression analysis of NIN-like Protein (NLP) genes reveals its potential roles in the response to nitrate signaling in tomato

“…The physicochemical properties of SlNLP proteins, including peptide length (aa), molecular weight (Mw), isoelectric point (pI) and grand average of hydrophilicity (GRAVY) were predicted using ExPASy ProtParam ( http://web.expasy.org/protparam/ ) [ 12 ]. Subcellular localizations of SlNLP proteins were predicted using CropPAL2020 ( https://www.crop-pal.org ) [ 17 ].…”

Title: Genome-Wide Survey and Expression Analysis of NIN-Like Protein (NLP) Genes Reveals Its Potential Roles in the Response to Nutrition Deficiency in Tomato

“…The physicochemical properties of SlNLP proteins, including peptide length (aa), molecular weight (Mw), isoelectric point (pI) and grand average of hydrophilicity (GRAVY) were predicted using ExPASy ProtParam (http://web.expasy.org/protparam/) (Gasteiger et al, 2005). Subcellular localizations of SlNLP proteins were predicted using CropPAL2020 (https://www.croppal.org) (Hooper et al, 2020).…”