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Metabolic network analysis integrated with transcript verification for sequenced genomes

Nature Methods volume 6, pages 589592 (2009) | Download Citation

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Abstract

With sequencing of thousands of organisms completed or in progress, there is a growing need to integrate gene prediction with metabolic network analysis. Using Chlamydomonas reinhardtii as a model, we describe a systems-level methodology bridging metabolic network reconstruction with experimental verification of enzyme encoding open reading frames. Our quantitative and predictive metabolic model and its associated cloned open reading frames provide useful resources for metabolic engineering.

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  • 20 July 2009

    In the version of this article initially published online, the email address of one of the Corresponding authors was spelled incorrectly. The correct email address is papin@virginia.edu. The error has been corrected for the print, PDF and HTML versions of this article.

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Acknowledgements

This research was supported by the Office of Science (Biological and Environmental Research), US Department of Energy, grant DE-FG02-07ER64496 (to J.A.P. and K.S.-A.), the Jane Coffin Childs Memorial Fund for Medical Research (to E.F.Y.H.) and by National Science Foundation IGERT training grant DGE0504645 (to R.L.C.).

Author information

Author notes

    • Ines Thiele

    Present address: Center for Systems Biology, University of Iceland, Reykjavik, Iceland.

    • Ani Manichaikul
    • , Lila Ghamsari
    • , Erik F Y Hom
    • , Chenwei Lin
    • , Ryan R Murray
    •  & Roger L Chang

    These authors contributed equally to this work.

Affiliations

  1. Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA.

    • Ani Manichaikul
    • , Arvind K Chavali
    •  & Jason A Papin
  2. Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.

    • Lila Ghamsari
    • , Chenwei Lin
    • , Ryan R Murray
    • , S Balaji
    • , Tong Hao
    • , Yun Shen
    • , Xinping Yang
    • , Changyu Fan
    • , Elizabeth Mello
    • , David E Hill
    • , Marc Vidal
    •  & Kourosh Salehi-Ashtiani
  3. Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA.

    • Erik F Y Hom
  4. Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.

    • Roger L Chang
    •  & Ines Thiele

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Contributions

A.M., A.K.C., R.L.C. and I.T. reconstructed metabolic networks; L.G., R.R.M., X.Y. and E.M. performed transcript verification experiments, E.F.Y.H. performed localization prediction; L.G., C.L., Y.S., C.F. and T.H., annotated transcripts and analyzed sequences; S.B. annotated transcripts; D.E.H. and M.V. initially developed the transcript verification pipeline; A.M., L.G., E.F.Y.H., K.S.A., J.P., development of pipeline to integrate model with experiments; A.M., L.G., E.F.Y.H., C.L., R.L.C., R.R.M., K.S.-A. and J.A.P. wrote and edited the manuscript; D.E.H. and M.V. edited the manuscript; K.S.-A. guided transcript verification experiments and transcript annotation; J.A.P. guided the metabolic network reconstruction; J.A.P. and K.S.-A. conceived the study.

Corresponding authors

Correspondence to Kourosh Salehi-Ashtiani or Jason A Papin.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–5, Supplementary Tables 2–3, 6–8 and Supplementary Note

Excel files

  1. 1.

    Supplementary Table 1

    Our EC annotation of translated JGI v3.1 transcripts.

  2. 2.

    Supplementary Table 4

    Transcripts annotation, sequences of experimentally tested transcripts; RT-PCR, 5′, and 3′ RACE summaries, and PA-SUB localization predictions.

  3. 3.

    Supplementary Table 5

    Sequences of gene-specific primers used in transcript verification experiments.

  4. 4.

    Supplementary Table 9

    Final metabolic network reconstruction sheet.

  5. 5.

    Supplementary Table 10

    Results of in silico knockout experiments toward metabolic engineering.

XML files

  1. 1.

    Supplementary Data 1

    Final metabolic network reconstruction in SBML format.

About this article

Publication history

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DOI

https://doi.org/10.1038/nmeth.1348

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