Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii

Patrick May, Stefanie Wienkoop, Stefan Kempa, Bjorn Usadel, Nils Christian, Jens Rupprecht, Julia Weiss, Luis Recuenco-Munoz, Oliver Ebenhoeh, Wolfram Weckwerth, Dirk Walther

Research output: Contribution to journalArticle

115 Citations (Scopus)

Abstract

We present an integrated analysis of the molecular repertoire of Chlamydomonasreinhardtii under reference conditions. Bioinformatics annotationmethods combined with GCxGC/MS-based metabolomics and LC/MS-basedshotgun proteomics profiling technologies have been applied to characterizeabundant proteins and metabolites, resulting in the detection of1069 proteins and 159 metabolites. Of the measured proteins, 204currently do not have EST sequence support; thus a significant portionof the proteomics-detected proteins provide evidence for the validityof in silico gene models. Furthermore, the generated peptide datalend support to the validity of a number of proteins currently inthe proposed model stage. By integrating genomic annotation informationwith experimentally identified metabolites and proteins, we constructeda draft metabolic network for Chlamydomonas. Computational metabolicmodeling allowed an identification of missing enzymatic links. Someexperimentally detected metabolites are not producible by the currentlyknown and annotated enzyme set, thus suggesting entry points forfurther targeted gene discovery or biochemical pathway research.All data sets are made available as supplementary material as wellas web-accessible databases and within the functional context viathe Chlamydomonas-adapted MapMan annotation platform. Informationof identified peptides is also available directly via the JGI-Chlamydomonasgenomic resource database.
Original languageEnglish
Pages (from-to)157-166
Number of pages10
JournalGenetics
Volume179
Issue number1
DOIs
Publication statusPublished - May 2008

Fingerprint

Chlamydomonas reinhardtii
Metabolomics
Metabolic Networks and Pathways
Proteomics
Genome
Chlamydomonas
Proteins
Databases
Peptides
Expressed Sequence Tags
Genetic Association Studies
Computational Biology
Computer Simulation
Technology
Enzymes
Research
Genes

Keywords

  • Bioenergetic pathways
  • protein
  • identification
  • evolution
  • database
  • server
  • plants
  • sets
  • kegg

Cite this

May, P., Wienkoop, S., Kempa, S., Usadel, B., Christian, N., Rupprecht, J., ... Walther, D. (2008). Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii. Genetics, 179(1), 157-166. https://doi.org/10.1534/genetics.108.088336

Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii. / May, Patrick; Wienkoop, Stefanie; Kempa, Stefan; Usadel, Bjorn; Christian, Nils; Rupprecht, Jens; Weiss, Julia; Recuenco-Munoz, Luis; Ebenhoeh, Oliver; Weckwerth, Wolfram; Walther, Dirk.

In: Genetics, Vol. 179, No. 1, 05.2008, p. 157-166.

Research output: Contribution to journalArticle

May, P, Wienkoop, S, Kempa, S, Usadel, B, Christian, N, Rupprecht, J, Weiss, J, Recuenco-Munoz, L, Ebenhoeh, O, Weckwerth, W & Walther, D 2008, 'Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii', Genetics, vol. 179, no. 1, pp. 157-166. https://doi.org/10.1534/genetics.108.088336
May, Patrick ; Wienkoop, Stefanie ; Kempa, Stefan ; Usadel, Bjorn ; Christian, Nils ; Rupprecht, Jens ; Weiss, Julia ; Recuenco-Munoz, Luis ; Ebenhoeh, Oliver ; Weckwerth, Wolfram ; Walther, Dirk. / Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii. In: Genetics. 2008 ; Vol. 179, No. 1. pp. 157-166.
@article{c521cb615c0c4bb180651ff7a892827e,
title = "Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii",
abstract = "We present an integrated analysis of the molecular repertoire of Chlamydomonasreinhardtii under reference conditions. Bioinformatics annotationmethods combined with GCxGC/MS-based metabolomics and LC/MS-basedshotgun proteomics profiling technologies have been applied to characterizeabundant proteins and metabolites, resulting in the detection of1069 proteins and 159 metabolites. Of the measured proteins, 204currently do not have EST sequence support; thus a significant portionof the proteomics-detected proteins provide evidence for the validityof in silico gene models. Furthermore, the generated peptide datalend support to the validity of a number of proteins currently inthe proposed model stage. By integrating genomic annotation informationwith experimentally identified metabolites and proteins, we constructeda draft metabolic network for Chlamydomonas. Computational metabolicmodeling allowed an identification of missing enzymatic links. Someexperimentally detected metabolites are not producible by the currentlyknown and annotated enzyme set, thus suggesting entry points forfurther targeted gene discovery or biochemical pathway research.All data sets are made available as supplementary material as wellas web-accessible databases and within the functional context viathe Chlamydomonas-adapted MapMan annotation platform. Informationof identified peptides is also available directly via the JGI-Chlamydomonasgenomic resource database.",
keywords = "Bioenergetic pathways, protein, identification, evolution, database, server, plants, sets, kegg",
author = "Patrick May and Stefanie Wienkoop and Stefan Kempa and Bjorn Usadel and Nils Christian and Jens Rupprecht and Julia Weiss and Luis Recuenco-Munoz and Oliver Ebenhoeh and Wolfram Weckwerth and Dirk Walther",
year = "2008",
month = "5",
doi = "10.1534/genetics.108.088336",
language = "English",
volume = "179",
pages = "157--166",
journal = "Genetics",
issn = "0016-6731",
publisher = "Genetics Society of America",
number = "1",

}

TY - JOUR

T1 - Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii

AU - May, Patrick

AU - Wienkoop, Stefanie

AU - Kempa, Stefan

AU - Usadel, Bjorn

AU - Christian, Nils

AU - Rupprecht, Jens

AU - Weiss, Julia

AU - Recuenco-Munoz, Luis

AU - Ebenhoeh, Oliver

AU - Weckwerth, Wolfram

AU - Walther, Dirk

PY - 2008/5

Y1 - 2008/5

N2 - We present an integrated analysis of the molecular repertoire of Chlamydomonasreinhardtii under reference conditions. Bioinformatics annotationmethods combined with GCxGC/MS-based metabolomics and LC/MS-basedshotgun proteomics profiling technologies have been applied to characterizeabundant proteins and metabolites, resulting in the detection of1069 proteins and 159 metabolites. Of the measured proteins, 204currently do not have EST sequence support; thus a significant portionof the proteomics-detected proteins provide evidence for the validityof in silico gene models. Furthermore, the generated peptide datalend support to the validity of a number of proteins currently inthe proposed model stage. By integrating genomic annotation informationwith experimentally identified metabolites and proteins, we constructeda draft metabolic network for Chlamydomonas. Computational metabolicmodeling allowed an identification of missing enzymatic links. Someexperimentally detected metabolites are not producible by the currentlyknown and annotated enzyme set, thus suggesting entry points forfurther targeted gene discovery or biochemical pathway research.All data sets are made available as supplementary material as wellas web-accessible databases and within the functional context viathe Chlamydomonas-adapted MapMan annotation platform. Informationof identified peptides is also available directly via the JGI-Chlamydomonasgenomic resource database.

AB - We present an integrated analysis of the molecular repertoire of Chlamydomonasreinhardtii under reference conditions. Bioinformatics annotationmethods combined with GCxGC/MS-based metabolomics and LC/MS-basedshotgun proteomics profiling technologies have been applied to characterizeabundant proteins and metabolites, resulting in the detection of1069 proteins and 159 metabolites. Of the measured proteins, 204currently do not have EST sequence support; thus a significant portionof the proteomics-detected proteins provide evidence for the validityof in silico gene models. Furthermore, the generated peptide datalend support to the validity of a number of proteins currently inthe proposed model stage. By integrating genomic annotation informationwith experimentally identified metabolites and proteins, we constructeda draft metabolic network for Chlamydomonas. Computational metabolicmodeling allowed an identification of missing enzymatic links. Someexperimentally detected metabolites are not producible by the currentlyknown and annotated enzyme set, thus suggesting entry points forfurther targeted gene discovery or biochemical pathway research.All data sets are made available as supplementary material as wellas web-accessible databases and within the functional context viathe Chlamydomonas-adapted MapMan annotation platform. Informationof identified peptides is also available directly via the JGI-Chlamydomonasgenomic resource database.

KW - Bioenergetic pathways

KW - protein

KW - identification

KW - evolution

KW - database

KW - server

KW - plants

KW - sets

KW - kegg

U2 - 10.1534/genetics.108.088336

DO - 10.1534/genetics.108.088336

M3 - Article

VL - 179

SP - 157

EP - 166

JO - Genetics

JF - Genetics

SN - 0016-6731

IS - 1

ER -