Sorting signals, N-terminal modifications and abundance of the chloroplast proteome.

Characterization of the chloroplast proteome is needed to understand the essential contribution of the chloroplast to plant growth and development. Here we present a large scale analysis by nanoLC-Q-TOF and nanoLC-LTQ-Orbitrap mass spectrometry (MS) of ten independent chloroplast preparations from A...

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Autores principales:	Boris Zybailov, Heidi Rutschow, Giulia Friso, Andrea Rudella, Olof Emanuelsson, Qi Sun, Klaas J van Wijk
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2008
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/11a50ca9dcf8495e9e237d1dd8da8128
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spelling	oai:doaj.org-article:11a50ca9dcf8495e9e237d1dd8da81282021-11-25T06:12:45ZSorting signals, N-terminal modifications and abundance of the chloroplast proteome.1932-620310.1371/journal.pone.0001994https://doaj.org/article/11a50ca9dcf8495e9e237d1dd8da81282008-04-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18431481/?tool=EBIhttps://doaj.org/toc/1932-6203Characterization of the chloroplast proteome is needed to understand the essential contribution of the chloroplast to plant growth and development. Here we present a large scale analysis by nanoLC-Q-TOF and nanoLC-LTQ-Orbitrap mass spectrometry (MS) of ten independent chloroplast preparations from Arabidopsis thaliana which unambiguously identified 1325 proteins. Novel proteins include various kinases and putative nucleotide binding proteins. Based on repeated and independent MS based protein identifications requiring multiple matched peptide sequences, as well as literature, 916 nuclear-encoded proteins were assigned with high confidence to the plastid, of which 86% had a predicted chloroplast transit peptide (cTP). The protein abundance of soluble stromal proteins was calculated from normalized spectral counts from LTQ-Obitrap analysis and was found to cover four orders of magnitude. Comparison to gel-based quantification demonstrates that 'spectral counting' can provide large scale protein quantification for Arabidopsis. This quantitative information was used to determine possible biases for protein targeting prediction by TargetP and also to understand the significance of protein contaminants. The abundance data for 550 stromal proteins was used to understand abundance of metabolic pathways and chloroplast processes. We highlight the abundance of 48 stromal proteins involved in post-translational proteome homeostasis (including aminopeptidases, proteases, deformylases, chaperones, protein sorting components) and discuss the biological implications. N-terminal modifications were identified for a subset of nuclear- and chloroplast-encoded proteins and a novel N-terminal acetylation motif was discovered. Analysis of cTPs and their cleavage sites of Arabidopsis chloroplast proteins, as well as their predicted rice homologues, identified new species-dependent features, which will facilitate improved subcellular localization prediction. No evidence was found for suggested targeting via the secretory system. This study provides the most comprehensive chloroplast proteome analysis to date and an expanded Plant Proteome Database (PPDB) in which all MS data are projected on identified gene models.Boris ZybailovHeidi RutschowGiulia FrisoAndrea RudellaOlof EmanuelssonQi SunKlaas J van WijkPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 3, Iss 4, p e1994 (2008)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Boris Zybailov Heidi Rutschow Giulia Friso Andrea Rudella Olof Emanuelsson Qi Sun Klaas J van Wijk Sorting signals, N-terminal modifications and abundance of the chloroplast proteome.
description	Characterization of the chloroplast proteome is needed to understand the essential contribution of the chloroplast to plant growth and development. Here we present a large scale analysis by nanoLC-Q-TOF and nanoLC-LTQ-Orbitrap mass spectrometry (MS) of ten independent chloroplast preparations from Arabidopsis thaliana which unambiguously identified 1325 proteins. Novel proteins include various kinases and putative nucleotide binding proteins. Based on repeated and independent MS based protein identifications requiring multiple matched peptide sequences, as well as literature, 916 nuclear-encoded proteins were assigned with high confidence to the plastid, of which 86% had a predicted chloroplast transit peptide (cTP). The protein abundance of soluble stromal proteins was calculated from normalized spectral counts from LTQ-Obitrap analysis and was found to cover four orders of magnitude. Comparison to gel-based quantification demonstrates that 'spectral counting' can provide large scale protein quantification for Arabidopsis. This quantitative information was used to determine possible biases for protein targeting prediction by TargetP and also to understand the significance of protein contaminants. The abundance data for 550 stromal proteins was used to understand abundance of metabolic pathways and chloroplast processes. We highlight the abundance of 48 stromal proteins involved in post-translational proteome homeostasis (including aminopeptidases, proteases, deformylases, chaperones, protein sorting components) and discuss the biological implications. N-terminal modifications were identified for a subset of nuclear- and chloroplast-encoded proteins and a novel N-terminal acetylation motif was discovered. Analysis of cTPs and their cleavage sites of Arabidopsis chloroplast proteins, as well as their predicted rice homologues, identified new species-dependent features, which will facilitate improved subcellular localization prediction. No evidence was found for suggested targeting via the secretory system. This study provides the most comprehensive chloroplast proteome analysis to date and an expanded Plant Proteome Database (PPDB) in which all MS data are projected on identified gene models.
format	article
author	Boris Zybailov Heidi Rutschow Giulia Friso Andrea Rudella Olof Emanuelsson Qi Sun Klaas J van Wijk
author_facet	Boris Zybailov Heidi Rutschow Giulia Friso Andrea Rudella Olof Emanuelsson Qi Sun Klaas J van Wijk
author_sort	Boris Zybailov
title	Sorting signals, N-terminal modifications and abundance of the chloroplast proteome.
title_short	Sorting signals, N-terminal modifications and abundance of the chloroplast proteome.
title_full	Sorting signals, N-terminal modifications and abundance of the chloroplast proteome.
title_fullStr	Sorting signals, N-terminal modifications and abundance of the chloroplast proteome.
title_full_unstemmed	Sorting signals, N-terminal modifications and abundance of the chloroplast proteome.
title_sort	sorting signals, n-terminal modifications and abundance of the chloroplast proteome.
publisher	Public Library of Science (PLoS)
publishDate	2008
url	https://doaj.org/article/11a50ca9dcf8495e9e237d1dd8da8128
work_keys_str_mv	AT boriszybailov sortingsignalsnterminalmodificationsandabundanceofthechloroplastproteome AT heidirutschow sortingsignalsnterminalmodificationsandabundanceofthechloroplastproteome AT giuliafriso sortingsignalsnterminalmodificationsandabundanceofthechloroplastproteome AT andrearudella sortingsignalsnterminalmodificationsandabundanceofthechloroplastproteome AT olofemanuelsson sortingsignalsnterminalmodificationsandabundanceofthechloroplastproteome AT qisun sortingsignalsnterminalmodificationsandabundanceofthechloroplastproteome AT klaasjvanwijk sortingsignalsnterminalmodificationsandabundanceofthechloroplastproteome
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Sorting signals, N-terminal modifications and abundance of the chloroplast proteome.

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