Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants

Abstract Plastids are morphologically and functionally diverse organelles that are dependent on nuclear-encoded, plastid-targeted proteins for all biochemical and regulatory functions. However, how plastid proteomes vary temporally, spatially, and taxonomically has been historically difficult to ana...

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Autores principales:	Ryan W. Christian, Seanna L. Hewitt, Eric H. Roalson, Amit Dhingra
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3e61fb8c81d94a60b169c41e5914d4bd
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spelling	oai:doaj.org-article:3e61fb8c81d94a60b169c41e5914d4bd2021-12-02T14:58:45ZGenome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants10.1038/s41598-020-64670-52045-2322https://doaj.org/article/3e61fb8c81d94a60b169c41e5914d4bd2020-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-64670-5https://doaj.org/toc/2045-2322Abstract Plastids are morphologically and functionally diverse organelles that are dependent on nuclear-encoded, plastid-targeted proteins for all biochemical and regulatory functions. However, how plastid proteomes vary temporally, spatially, and taxonomically has been historically difficult to analyze at a genome-wide scale using experimental methods. 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. Gene family grouping was then performed in parallel using modified approaches of reciprocal best BLAST hits (RBH) and UCLUST. A total of 628 protein families were found to have conserved plastid targeting across angiosperm species using RBH, and 828 using UCLUST. However, thousands of clusters were also detected where only one species had predicted plastid targeting, most notably in Panicum virgatum which had 1,458 proteins with species-unique targeting. An average of 45% overlap was found in plastid-targeted protein-coding gene families compared with Arabidopsis, but an additional 20% of proteins matched against the full Arabidopsis proteome, indicating a unique evolution of plastid targeting. Neofunctionalization through subcellular relocalization is known to impart novel biological functions but has not been described before on a genome-wide scale for the plastid proteome. Further work to correlate these predicted novel plastid-targeted proteins to transcript abundance and high-throughput proteomics will uncover unique aspects of plastid biology and shed light on how the plastid proteome has evolved to influence plastid morphology and biochemistry.Ryan W. ChristianSeanna L. HewittEric H. RoalsonAmit DhingraNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-22 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ryan W. Christian Seanna L. Hewitt Eric H. Roalson Amit Dhingra Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants
description	Abstract Plastids are morphologically and functionally diverse organelles that are dependent on nuclear-encoded, plastid-targeted proteins for all biochemical and regulatory functions. However, how plastid proteomes vary temporally, spatially, and taxonomically has been historically difficult to analyze at a genome-wide scale using experimental methods. 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. Gene family grouping was then performed in parallel using modified approaches of reciprocal best BLAST hits (RBH) and UCLUST. A total of 628 protein families were found to have conserved plastid targeting across angiosperm species using RBH, and 828 using UCLUST. However, thousands of clusters were also detected where only one species had predicted plastid targeting, most notably in Panicum virgatum which had 1,458 proteins with species-unique targeting. An average of 45% overlap was found in plastid-targeted protein-coding gene families compared with Arabidopsis, but an additional 20% of proteins matched against the full Arabidopsis proteome, indicating a unique evolution of plastid targeting. Neofunctionalization through subcellular relocalization is known to impart novel biological functions but has not been described before on a genome-wide scale for the plastid proteome. Further work to correlate these predicted novel plastid-targeted proteins to transcript abundance and high-throughput proteomics will uncover unique aspects of plastid biology and shed light on how the plastid proteome has evolved to influence plastid morphology and biochemistry.
format	article
author	Ryan W. Christian Seanna L. Hewitt Eric H. Roalson Amit Dhingra
author_facet	Ryan W. Christian Seanna L. Hewitt Eric H. Roalson Amit Dhingra
author_sort	Ryan W. Christian
title	Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants
title_short	Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants
title_full	Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants
title_fullStr	Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants
title_full_unstemmed	Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants
title_sort	genome-scale characterization of predicted plastid-targeted proteomes in higher plants
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/3e61fb8c81d94a60b169c41e5914d4bd
work_keys_str_mv	AT ryanwchristian genomescalecharacterizationofpredictedplastidtargetedproteomesinhigherplants AT seannalhewitt genomescalecharacterizationofpredictedplastidtargetedproteomesinhigherplants AT erichroalson genomescalecharacterizationofpredictedplastidtargetedproteomesinhigherplants AT amitdhingra genomescalecharacterizationofpredictedplastidtargetedproteomesinhigherplants
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Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants

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