The potato tuber mitochondrial proteome

Fernanda Salvato, Jesper Foged Havelund, Mingjie Chen, R. Shyama Prasad Rao, Adelina Rogowska-Wrzesinska, Ole Nørregaard Jensen, David R Gang, Jay J. Thelen, Ian Max Møller

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

Mitochondria are called the powerhouses of the cell. To better understand the role of mitochondria in maintaining and regulating metabolism in storage tissues, highly purified mitochondria were isolated from dormant potato tubers (Solanum tuberosum 'Folva') and their proteome investigated. Proteins were resolved by one-dimensional gel electrophoresis, and tryptic peptides were extracted from gel slices and analyzed by liquid chromatography-tandem mass spectrometry using an Orbitrap XL. Using four different search programs, a total of 1,060 nonredundant proteins were identified in a quantitative manner using normalized spectral counts including as many as 5-fold more "extreme" proteins (low mass, high isoelectric point, hydrophobic) than previous mitochondrial proteome studies. We estimate that this compendium of proteins represents a high coverage of the potato tuber mitochondrial proteome (possibly as high as 85%). The dynamic range of protein expression spanned 1,800-fold and included nearly all components of the electron transport chain, tricarboxylic acid cycle, and protein import apparatus. Additionally, we identified 71 pentatricopeptide repeat proteins, 29 membrane carriers/transporters, a number of new proteins involved in coenzyme biosynthesis and iron metabolism, the pyruvate dehydrogenase kinase, and a type 2C protein phosphatase that may catalyze the dephosphorylation of the pyruvate dehydrogenase complex. Systematic analysis of prominent posttranslational modifications revealed that more than 50% of the identified proteins harbor at least one modification. The most prominently observed class of posttranslational modifications was oxidative modifications. This study reveals approximately 500 new or previously unconfirmed plant mitochondrial proteins and outlines a facile strategy for unbiased, near-comprehensive identification of mitochondrial proteins and their modified forms.
OriginalsprogEngelsk
TidsskriftPlant Physiology
Vol/bind164
Udgave nummer2
Sider (fra-til)637-653
ISSN0032-0889
DOI
StatusUdgivet - 2014

Fingeraftryk

Proteome
proteome
tubers
potatoes
Proteins
proteins
Mitochondrial Proteins
mitochondria
post-translational modification
pyruvate dehydrogenase (lipoamide)
pyruvate dehydrogenase (acetyl-transferring) kinase
Plant Proteins
Citric Acid Cycle
Coenzymes
Isoelectric Point
Electron Transport
Tandem Mass Spectrometry
metabolism
Liquid Chromatography
coenzymes

Citer dette

Salvato, Fernanda ; Havelund, Jesper Foged ; Chen, Mingjie ; Rao, R. Shyama Prasad ; Rogowska-Wrzesinska, Adelina ; Jensen, Ole Nørregaard ; Gang, David R ; Thelen, Jay J. ; Møller, Ian Max. / The potato tuber mitochondrial proteome. I: Plant Physiology. 2014 ; Bind 164, Nr. 2. s. 637-653.
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title = "The potato tuber mitochondrial proteome",
abstract = "Mitochondria are called the powerhouses of the cell. To better understand the role of mitochondria in maintaining and regulating metabolism in storage tissues, highly purified mitochondria were isolated from dormant potato tubers (Solanum tuberosum 'Folva') and their proteome investigated. Proteins were resolved by one-dimensional gel electrophoresis, and tryptic peptides were extracted from gel slices and analyzed by liquid chromatography-tandem mass spectrometry using an Orbitrap XL. Using four different search programs, a total of 1,060 nonredundant proteins were identified in a quantitative manner using normalized spectral counts including as many as 5-fold more {"}extreme{"} proteins (low mass, high isoelectric point, hydrophobic) than previous mitochondrial proteome studies. We estimate that this compendium of proteins represents a high coverage of the potato tuber mitochondrial proteome (possibly as high as 85{\%}). The dynamic range of protein expression spanned 1,800-fold and included nearly all components of the electron transport chain, tricarboxylic acid cycle, and protein import apparatus. Additionally, we identified 71 pentatricopeptide repeat proteins, 29 membrane carriers/transporters, a number of new proteins involved in coenzyme biosynthesis and iron metabolism, the pyruvate dehydrogenase kinase, and a type 2C protein phosphatase that may catalyze the dephosphorylation of the pyruvate dehydrogenase complex. Systematic analysis of prominent posttranslational modifications revealed that more than 50{\%} of the identified proteins harbor at least one modification. The most prominently observed class of posttranslational modifications was oxidative modifications. This study reveals approximately 500 new or previously unconfirmed plant mitochondrial proteins and outlines a facile strategy for unbiased, near-comprehensive identification of mitochondrial proteins and their modified forms.",
author = "Fernanda Salvato and Havelund, {Jesper Foged} and Mingjie Chen and Rao, {R. Shyama Prasad} and Adelina Rogowska-Wrzesinska and Jensen, {Ole N{\o}rregaard} and Gang, {David R} and Thelen, {Jay J.} and M{\o}ller, {Ian Max}",
year = "2014",
doi = "10.1104/pp.113.229054",
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volume = "164",
pages = "637--653",
journal = "Plant Physiology",
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Salvato, F, Havelund, JF, Chen, M, Rao, RSP, Rogowska-Wrzesinska, A, Jensen, ON, Gang, DR, Thelen, JJ & Møller, IM 2014, 'The potato tuber mitochondrial proteome', Plant Physiology, bind 164, nr. 2, s. 637-653. https://doi.org/10.1104/pp.113.229054

The potato tuber mitochondrial proteome. / Salvato, Fernanda; Havelund, Jesper Foged; Chen, Mingjie; Rao, R. Shyama Prasad; Rogowska-Wrzesinska, Adelina; Jensen, Ole Nørregaard; Gang, David R; Thelen, Jay J.; Møller, Ian Max.

I: Plant Physiology, Bind 164, Nr. 2, 2014, s. 637-653.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - The potato tuber mitochondrial proteome

AU - Salvato, Fernanda

AU - Havelund, Jesper Foged

AU - Chen, Mingjie

AU - Rao, R. Shyama Prasad

AU - Rogowska-Wrzesinska, Adelina

AU - Jensen, Ole Nørregaard

AU - Gang, David R

AU - Thelen, Jay J.

AU - Møller, Ian Max

PY - 2014

Y1 - 2014

N2 - Mitochondria are called the powerhouses of the cell. To better understand the role of mitochondria in maintaining and regulating metabolism in storage tissues, highly purified mitochondria were isolated from dormant potato tubers (Solanum tuberosum 'Folva') and their proteome investigated. Proteins were resolved by one-dimensional gel electrophoresis, and tryptic peptides were extracted from gel slices and analyzed by liquid chromatography-tandem mass spectrometry using an Orbitrap XL. Using four different search programs, a total of 1,060 nonredundant proteins were identified in a quantitative manner using normalized spectral counts including as many as 5-fold more "extreme" proteins (low mass, high isoelectric point, hydrophobic) than previous mitochondrial proteome studies. We estimate that this compendium of proteins represents a high coverage of the potato tuber mitochondrial proteome (possibly as high as 85%). The dynamic range of protein expression spanned 1,800-fold and included nearly all components of the electron transport chain, tricarboxylic acid cycle, and protein import apparatus. Additionally, we identified 71 pentatricopeptide repeat proteins, 29 membrane carriers/transporters, a number of new proteins involved in coenzyme biosynthesis and iron metabolism, the pyruvate dehydrogenase kinase, and a type 2C protein phosphatase that may catalyze the dephosphorylation of the pyruvate dehydrogenase complex. Systematic analysis of prominent posttranslational modifications revealed that more than 50% of the identified proteins harbor at least one modification. The most prominently observed class of posttranslational modifications was oxidative modifications. This study reveals approximately 500 new or previously unconfirmed plant mitochondrial proteins and outlines a facile strategy for unbiased, near-comprehensive identification of mitochondrial proteins and their modified forms.

AB - Mitochondria are called the powerhouses of the cell. To better understand the role of mitochondria in maintaining and regulating metabolism in storage tissues, highly purified mitochondria were isolated from dormant potato tubers (Solanum tuberosum 'Folva') and their proteome investigated. Proteins were resolved by one-dimensional gel electrophoresis, and tryptic peptides were extracted from gel slices and analyzed by liquid chromatography-tandem mass spectrometry using an Orbitrap XL. Using four different search programs, a total of 1,060 nonredundant proteins were identified in a quantitative manner using normalized spectral counts including as many as 5-fold more "extreme" proteins (low mass, high isoelectric point, hydrophobic) than previous mitochondrial proteome studies. We estimate that this compendium of proteins represents a high coverage of the potato tuber mitochondrial proteome (possibly as high as 85%). The dynamic range of protein expression spanned 1,800-fold and included nearly all components of the electron transport chain, tricarboxylic acid cycle, and protein import apparatus. Additionally, we identified 71 pentatricopeptide repeat proteins, 29 membrane carriers/transporters, a number of new proteins involved in coenzyme biosynthesis and iron metabolism, the pyruvate dehydrogenase kinase, and a type 2C protein phosphatase that may catalyze the dephosphorylation of the pyruvate dehydrogenase complex. Systematic analysis of prominent posttranslational modifications revealed that more than 50% of the identified proteins harbor at least one modification. The most prominently observed class of posttranslational modifications was oxidative modifications. This study reveals approximately 500 new or previously unconfirmed plant mitochondrial proteins and outlines a facile strategy for unbiased, near-comprehensive identification of mitochondrial proteins and their modified forms.

U2 - 10.1104/pp.113.229054

DO - 10.1104/pp.113.229054

M3 - Journal article

VL - 164

SP - 637

EP - 653

JO - Plant Physiology

JF - Plant Physiology

SN - 0032-0889

IS - 2

ER -