Finding the subcellular location of barley, wheat, rice and maize proteins: The compendium of crop proteins with annotated locations (cropPAL)

Cornelia M. Hooper, Ian R. Castleden, Nader Aryamanesh, Richard P. Jacoby, A. Harvey Millar

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

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). Subcellular location is most commonly determined by fluorescent protein tagging of live cells or mass spectrometry detection in subcellular purifications, but can also be predicted from amino acid sequence or protein expression patterns. The cropPAL database collates 556 published studies, from >300 research institutes in >30 countries that have been previously published, as well as compiling eight precomputed subcellular predictions for all Hordeum vulgare, Triticum aestivum, Oryza sativa and Zea mays protein sequences. The data collection including metadata for proteins and published studies can be accessed through a search portal http://crop-PAL.org. The subcellular localization information housed in cropPAL helps to depict plant cells as compartmentalized protein networks that can be investigated for improving crop yield and quality, and developing new biotechnological solutions to agricultural challenges.

LanguageEnglish
Pagese9
JournalPlant and Cell Physiology
Volume57
Issue number1
DOIs
Publication statusPublished - 1 Jan 2016

Keywords

  • Cell Biology
  • Compartments
  • Crop
  • Database
  • Proteomes
  • Subcellular localizations

ASJC Scopus subject areas

  • Physiology
  • Plant Science
  • Cell Biology

Cite this

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abstract = "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). Subcellular location is most commonly determined by fluorescent protein tagging of live cells or mass spectrometry detection in subcellular purifications, but can also be predicted from amino acid sequence or protein expression patterns. The cropPAL database collates 556 published studies, from >300 research institutes in >30 countries that have been previously published, as well as compiling eight precomputed subcellular predictions for all Hordeum vulgare, Triticum aestivum, Oryza sativa and Zea mays protein sequences. The data collection including metadata for proteins and published studies can be accessed through a search portal http://crop-PAL.org. The subcellular localization information housed in cropPAL helps to depict plant cells as compartmentalized protein networks that can be investigated for improving crop yield and quality, and developing new biotechnological solutions to agricultural challenges.",
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Finding the subcellular location of barley, wheat, rice and maize proteins : The compendium of crop proteins with annotated locations (cropPAL). / Hooper, Cornelia M.; Castleden, Ian R.; Aryamanesh, Nader; Jacoby, Richard P.; Millar, A. Harvey.

In: Plant and Cell Physiology, Vol. 57, No. 1, 01.01.2016, p. e9.

Research output: Contribution to journalArticle

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