Unraveling Hidden Components of the Chloroplast Envelope Proteome: Opportunities and Limits of Better MS Sensitivity
The chloroplast is a major plant cell organelle that fulfills essential metabolic and biosynthetic functions. Located at the interface between the chloroplast and other cell compartments, the chloroplast envelope system is a strategic barrier controlling the exchange of ions, metabolites and protein...
Saved in:
Published in | Molecular & cellular proteomics Vol. 18; no. 7; p. 1285 |
---|---|
Main Authors | , , , , , , , |
Format | Journal Article |
Language | English |
Published |
United States
01.07.2019
|
Subjects | |
Online Access | Get full text |
Cover
Loading…
Abstract | The chloroplast is a major plant cell organelle that fulfills essential metabolic and biosynthetic functions. Located at the interface between the chloroplast and other cell compartments, the chloroplast envelope system is a strategic barrier controlling the exchange of ions, metabolites and proteins, thus regulating essential metabolic functions (synthesis of hormones precursors, amino acids, pigments, sugars, vitamins, lipids, nucleotides etc.) of the plant cell. However, unraveling the contents of the chloroplast envelope proteome remains a difficult challenge; many proteins constituting this functional double membrane system remain to be identified. Indeed, the envelope contains only 1% of the chloroplast proteins (i.e. 0.4% of the whole cell proteome). In other words, most envelope proteins are so rare at the cell, chloroplast, or even envelope level, that they remained undetectable using targeted MS studies. Cross-contamination of chloroplast subcompartments by each other and by other cell compartments during cell fractionation, impedes accurate localization of many envelope proteins. The aim of the present study was to take advantage of technologically improved MS sensitivity to better define the proteome of the chloroplast envelope (differentiate genuine envelope proteins from contaminants). This MS-based analysis relied on an enrichment factor that was calculated for each protein identified in purified envelope fractions as compared with the value obtained for the same protein in crude cell extracts. Using this approach, a total of 1269 proteins were detected in purified envelope fractions, of which, 462 could be assigned an envelope localization by combining MS-based spectral count analyses with manual annotation using data from the literature and prediction tools. Many of such proteins being previously unknown envelope components, these data constitute a new resource of significant value to the broader plant science community aiming to define principles and molecular mechanisms controlling fundamental aspects of plastid biogenesis and functions. |
---|---|
AbstractList | The chloroplast is a major plant cell organelle that fulfills essential metabolic and biosynthetic functions. Located at the interface between the chloroplast and other cell compartments, the chloroplast envelope system is a strategic barrier controlling the exchange of ions, metabolites and proteins, thus regulating essential metabolic functions (synthesis of hormones precursors, amino acids, pigments, sugars, vitamins, lipids, nucleotides etc.) of the plant cell. However, unraveling the contents of the chloroplast envelope proteome remains a difficult challenge; many proteins constituting this functional double membrane system remain to be identified. Indeed, the envelope contains only 1% of the chloroplast proteins (i.e. 0.4% of the whole cell proteome). In other words, most envelope proteins are so rare at the cell, chloroplast, or even envelope level, that they remained undetectable using targeted MS studies. Cross-contamination of chloroplast subcompartments by each other and by other cell compartments during cell fractionation, impedes accurate localization of many envelope proteins. The aim of the present study was to take advantage of technologically improved MS sensitivity to better define the proteome of the chloroplast envelope (differentiate genuine envelope proteins from contaminants). This MS-based analysis relied on an enrichment factor that was calculated for each protein identified in purified envelope fractions as compared with the value obtained for the same protein in crude cell extracts. Using this approach, a total of 1269 proteins were detected in purified envelope fractions, of which, 462 could be assigned an envelope localization by combining MS-based spectral count analyses with manual annotation using data from the literature and prediction tools. Many of such proteins being previously unknown envelope components, these data constitute a new resource of significant value to the broader plant science community aiming to define principles and molecular mechanisms controlling fundamental aspects of plastid biogenesis and functions. |
Author | Kuntz, Marcel Salvi, Daniel Bouchnak, Imen Moyet, Lucas Rolland, Norbert Brugière, Sabine Le Gall, Sophie Tardif, Marianne |
Author_xml | – sequence: 1 givenname: Imen surname: Bouchnak fullname: Bouchnak, Imen organization: From the ‡University Grenoble Alpes, INRA, CNRS, CEA, IRIG-LPCV, 38000 Grenoble, France – sequence: 2 givenname: Sabine surname: Brugière fullname: Brugière, Sabine organization: §University Grenoble Alpes, CEA, Inserm, IRIG-BGE, 38000 Grenoble, France – sequence: 3 givenname: Lucas surname: Moyet fullname: Moyet, Lucas organization: From the ‡University Grenoble Alpes, INRA, CNRS, CEA, IRIG-LPCV, 38000 Grenoble, France – sequence: 4 givenname: Sophie surname: Le Gall fullname: Le Gall, Sophie organization: From the ‡University Grenoble Alpes, INRA, CNRS, CEA, IRIG-LPCV, 38000 Grenoble, France – sequence: 5 givenname: Daniel surname: Salvi fullname: Salvi, Daniel organization: From the ‡University Grenoble Alpes, INRA, CNRS, CEA, IRIG-LPCV, 38000 Grenoble, France – sequence: 6 givenname: Marcel surname: Kuntz fullname: Kuntz, Marcel organization: From the ‡University Grenoble Alpes, INRA, CNRS, CEA, IRIG-LPCV, 38000 Grenoble, France – sequence: 7 givenname: Marianne surname: Tardif fullname: Tardif, Marianne organization: §University Grenoble Alpes, CEA, Inserm, IRIG-BGE, 38000 Grenoble, France – sequence: 8 givenname: Norbert surname: Rolland fullname: Rolland, Norbert email: norbert.rolland@cea.fr organization: From the ‡University Grenoble Alpes, INRA, CNRS, CEA, IRIG-LPCV, 38000 Grenoble, France;. Electronic address: norbert.rolland@cea.fr |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/33451516$$D View this record in MEDLINE/PubMed |
BookMark | eNqFzs1qwkAUhuGhKNXY3oKcGwgkTaZ_S4PFhWIhug5TcqxTMucMM0chd9-Aunb1bZ4XvkSNiAkf1DTXhU4_yvdyopIY_7LsJcvf9KOaFEWpc52_TpXsKZgzdpZ-YWXbFgkqdn7oSSLwAeSIUB07Duw7EwWWNGj2CN-BBdnhJ2y95yAnsmIxgqEW1tbZS75AEQywqaFGioM4W-mf1PhguojP152p-ddyV61Sf_px2DY-WGdC39xuFnfBP_iqS70 |
ContentType | Journal Article |
Copyright | Copyright © 2019 © 2019 Bouchnak et al. Published by Elsevier Inc. All rights reserved. |
Copyright_xml | – notice: Copyright © 2019 © 2019 Bouchnak et al. Published by Elsevier Inc. All rights reserved. |
DBID | NPM |
DatabaseName | PubMed |
DatabaseTitle | PubMed |
DatabaseTitleList | PubMed |
Database_xml | – sequence: 1 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database |
DeliveryMethod | fulltext_linktorsrc |
Discipline | Anatomy & Physiology Biology |
EISSN | 1535-9484 |
ExternalDocumentID | 33451516 |
Genre | Journal Article |
GroupedDBID | --- 0R~ 0SF 123 18M 29M 2WC 34G 39C 4.4 53G 5VS AAEDW AAFWJ AALRI AAXUO ABDNZ ACGFO ACIWK ACPRK ACYGS ADBBV ADVLN AENEX AEXQZ AFPKN AFRAH AITUG AKRWK ALMA_UNASSIGNED_HOLDINGS AMRAJ AOIJS BAWUL BTFSW C1A CS3 DIK DU5 E3Z EBS EJD F5P FDB FRP GROUPED_DOAJ GX1 H13 HH5 HYE KQ8 NPM OK1 P2P RHF RHI RNS ROL RPM TBC TR2 W8F WOQ |
ID | FETCH-pubmed_primary_334515163 |
IngestDate | Sat Sep 28 08:25:22 EDT 2024 |
IsPeerReviewed | true |
IsScholarly | true |
Issue | 7 |
Keywords | Chloroplast envelope Plant Biology Cell fractionation Chloroplast Subcellular Separation Subcellular analysis Cellular organelles |
Language | English |
License | Copyright © 2019 © 2019 Bouchnak et al. Published by Elsevier Inc. All rights reserved. |
LinkModel | OpenURL |
MergedId | FETCHMERGED-pubmed_primary_334515163 |
PMID | 33451516 |
ParticipantIDs | pubmed_primary_33451516 |
PublicationCentury | 2000 |
PublicationDate | 2019-Jul |
PublicationDateYYYYMMDD | 2019-07-01 |
PublicationDate_xml | – month: 07 year: 2019 text: 2019-Jul |
PublicationDecade | 2010 |
PublicationPlace | United States |
PublicationPlace_xml | – name: United States |
PublicationTitle | Molecular & cellular proteomics |
PublicationTitleAlternate | Mol Cell Proteomics |
PublicationYear | 2019 |
SSID | ssj0020175 |
Score | 4.256057 |
Snippet | The chloroplast is a major plant cell organelle that fulfills essential metabolic and biosynthetic functions. Located at the interface between the chloroplast... |
SourceID | pubmed |
SourceType | Index Database |
StartPage | 1285 |
Title | Unraveling Hidden Components of the Chloroplast Envelope Proteome: Opportunities and Limits of Better MS Sensitivity |
URI | https://www.ncbi.nlm.nih.gov/pubmed/33451516 |
Volume | 18 |
hasFullText | 1 |
inHoldings | 1 |
isFullTextHit | |
isPrint | |
link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3NT4MwFG_cEhMvRje_denBeFkwI8AC3rZlBs3Qw7Zkt4VCcTusEAOH-df7-roKLi5RLwQKNMDvx-tr3xcht4nLXa-TcMNL7I5hxwkzmB26RmxaScQiOcrI9Y7gpetP7eeZMysdMjG6JGf30cePcSX_QRXaAFcZJfsHZL86hQbYB3xhCwjD9lcYT4UsHoQB5b5MBSLw904F3_i2SKVysIAZeZqBkpy3hwI9hLgMD8i5LJBu9dqvmVTBC4GpVdGWgEFP2EEfg33aMNkfS0d3VWmiqs8GurouUkhaAfAgU_1XPOn7aREtRIiy92lVxp8Bt96WaK13N6vhIauY-oN0rawlI1mcTbeOgNqhspeM02yx5NW1CwyX0msXXMtbx_BUOtMfBHKh3YiVdIWx1KmKffhI2QqxtSwbFDNzK6m2GqY3p2qkZpmYB9gvszGCPJK1i_Q1W3ML1DEmR-RwMzmgPYX0MdnjokGaPRHm6WpN7yi666IdpEH2VRXRdZPkJQ2oogEtaUDThAINaIUGVNOAaho80G8koEACqkggb1ckoMGYVkhwQlqPw8nAN9SbzDOVtWSu39E6JXUBj3BOqOfGLvNsHlmgpIWJw7qOzBMbha5ns9j0LsjZjk4ud565Igcl0teknr8X_Ab0tpy18NN_AkV8ULI |
link.rule.ids | 315,786,790 |
linkProvider | ABC ChemistRy |
openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Unraveling+Hidden+Components+of+the+Chloroplast+Envelope+Proteome%3A+Opportunities+and+Limits+of+Better+MS+Sensitivity&rft.jtitle=Molecular+%26+cellular+proteomics&rft.au=Bouchnak%2C+Imen&rft.au=Brugi%C3%A8re%2C+Sabine&rft.au=Moyet%2C+Lucas&rft.au=Le+Gall%2C+Sophie&rft.date=2019-07-01&rft.eissn=1535-9484&rft.volume=18&rft.issue=7&rft.spage=1285&rft_id=info%3Apmid%2F33451516&rft.externalDocID=33451516 |