Finding the Subcellular Location of Barley, Wheat, Rice and Maize Proteins: The Compendium of Crop Proteins with Annotated Locations (cropPAL).

@article{Hooper2016FindingTS,
  title={Finding the Subcellular Location of Barley, Wheat, Rice and Maize Proteins: The Compendium of Crop Proteins with Annotated Locations (cropPAL).},
  author={Cornelia M. Hooper and Ian R. Castleden and Nader Aryamanesh and Richard P. Jacoby and A. Harvey Millar},
  journal={Plant \& cell physiology},
  year={2016},
  volume={57 1},
  pages={
          e9
        }
}
Barley, wheat, rice and maize provide the bulk of human nutrition and have extensive industrial use as agricultural products. The genomes of these crops each contains >40,000 genes encoding proteins; however, the major genome databases for these species lack annotation information of protein subcellular location for >80% of these gene products. We address this gap, by constructing the compendium of crop protein subcellular locations called crop Proteins with Annotated Locations (cropPAL… 

Tables from this paper

CropPAL for discovering protein subcellular location divergence in crops to support strategies for molecular crop breeding.
TLDR
A comprehensive cross-species comparison showed that between 50-80% of the subcellulomes are conserved across species and that conservation only depends to some degree on the species phylogenetic relationship.
Subcellular Proteomics as a Unified Approach of Experimental Localizations and Computed Prediction Data for Arabidopsis and Crop Plants.
TLDR
Comprehensive cross-species comparison of these data shows that the sub-cellular proteomes (subcellulomes) depend only to some degree on phylogenetic relationship and are more conserved in major biosynthesis than in metabolic pathways.
Arabidopsis antibody resources for functional studies in plants
TLDR
It is shown that affinity purification of antibodies massively improved the detection rate of key proteins involved in hormone synthesis, transport and perception, membrane trafficking related proteins and several sub cellular marker proteins.
SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations
The SUBcellular location database for Arabidopsis proteins (SUBA4, http://suba.live) is a comprehensive collection of manually curated published data sets of large-scale subcellular proteomics,
LOCALIZER: subcellular localization prediction of both plant and effector proteins in the plant cell
TLDR
LOCALIZER is the first method for predicting effector localisation in plants and is a valuable tool for prioritizing effector candidates for functional investigations.
Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants
TLDR
A bioinformatics workflow was developed and evaluated using a combination of fast and user-friendly subcellular prediction programs to maximize performance and accuracy for chloroplast transit peptides and demonstrate this technique on the predicted proteomes of 15 sequenced plant genomes.
Conserved and Opposite Transcriptome Patterns during Germination in Hordeum vulgare and Arabidopsis thaliana
TLDR
Differences in expression of basic-leucine zippers and Apetala 2 (AP2)/ethylene-responsive element binding proteins (EREBPs) point to differences in regulatory processes at a high level, which provide opportunities to modify processes in order to enhance grain quality, germination, and storage as needed for different uses.
Sorghum’s Whole-Plant Transcriptome and Proteome Responses to Drought Stress: A Review
TLDR
An extensive review of current transcriptome and proteome works conducted with laboratory, greenhouse, or field-grown sorghum plants exposed to drought, osmotic stress, or treated with the drought stress-regulatory phytohormone, abscisic acid reveals that the overall functional classes of stress-responsive genes/proteins within sorghums are similar to those observed in equivalent studies of other drought-sensitive model species.
Plastid transit peptides—where do they come from and where do they all belong? Multi-genome and pan-genomic assessment of chloroplast transit peptide evolution
TLDR
A broad, multi-genome analysis of 15 phylogenetically diverse genera and in-depth analyses of pangenomes were performed to address the question of how proteins acquire or lose plastid targeting peptides, revealing that random insertions or deletions were the dominant mechanism by which novel transit peptides are gained by proteins.
Meta-Analysis of Yield-Related and N-Responsive Genes Reveals Chromosomal Hotspots, Key Processes and Candidate Genes for Nitrogen-Use Efficiency in Rice
TLDR
Functional annotations and PPIs for all the 1,064 NUE-related genes and also the shortlisted 62 candidates revealed transcription, redox, phosphorylation, transport, development, metabolism, photosynthesis, water deprivation, and hormonal and stomatal function among the prominent processes.
...
...

References

SHOWING 1-10 OF 49 REFERENCES
Combining Experimental and Predicted Datasets for Determination of the Subcellular Location of Proteins in Arabidopsis1[w]
TLDR
The subcellular location database for Arabidopsis proteins (SUBA) is merged, providing an integrated understanding of protein location, encompassing the plastid, mitochondrion, peroxisome, nucleus, plasma membrane, endoplasmic reticulum, vacuole, Golgi, cytoskeleton structures, and cytosol ( www.suba.uwa.edu.au).
Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis
TLDR
Rice DB, an Oryza information portal that is a functional genomics database, linking gene loci to comprehensive annotations, expression data and the subcellular location of encoded proteins is presented.
SUBA: the Arabidopsis Subcellular Database
TLDR
The localisation data in SUBA encompasses 10 distinct subcellular locations, >6743 non-redundant proteins and represents the proteins encoded in the transcripts responsible for 51% of Arabidopsis expressed sequence tags.
SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis
TLDR
SUBAcon is developed, a Bayesian approach that incorporates experimental localization and targeting prediction data to best estimate a protein’s location in the cell to determine as objectively as possible where a particular protein is located.
The map-based sequence of the rice genome
TLDR
A map-based, finished quality sequence that covers 95% of the 389 Mb rice genome, including virtually all of the euchromatin and two complete centromeres, and finds evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes.
Construction of plastid reference proteomes for maize and Arabidopsis and evaluation of their orthologous relationships; the concept of orthoproteomics.
Plastids are essential organelles because they contribute to primary and secondary metabolism and plant signaling networks. A high-quality inventory of the plastid proteome is therefore a critical
SUBAcon: a consensus algorithm for unifying the subcellular localization data of the Arabidopsis proteome
TLDR
The SUBcellular Arabidopsis consensus (SUBAcon) algorithm is developed, a naive Bayes classifier that integrates 22 computational prediction algorithms, experimental GFP and MS localizations, protein-protein interaction and co-expression data to derive a consensus call and probability.
Predicting subcellular localization of proteins based on their N-terminal amino acid sequence.
TLDR
A neural network-based tool, TargetP, for large-scale subcellular location prediction of newly identified proteins has been developed and it is estimated that 10% of all plant proteins are mitochondrial and 14% chloroplastic, and that the abundance of secretory proteins, in both Arabidopsis and Homo, is around 10%.
Identification of a Vacuolar Sucrose Transporter in Barley and Arabidopsis Mesophyll Cells by a Tonoplast Proteomic Approach1
TLDR
The Suc transporter (SUT) HvSUT2 was discovered among the 40 vacuolar proteins, which were previously not reported in Arabidopsis (Arabidopsis thaliana) vacUolar proteomic studies, and green fluorescence at the tonoplast indicated that these Suc transporters are indeed located at the vacuol membrane.
Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics
TLDR
The Rice Annotation Project Database (RAP-DB) is presented, based on the latest genome assembly, Os-Nipponbare-Reference-IRGSP-1.0), which was released in 2011 and detected 37,869 loci by mapping transcript and protein sequences of 150 monocot species.
...
...