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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Change history
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.).
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Authors and Affiliations
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.
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Supplementary information
Supplementary Text and Figures
Supplementary Figures 1–5, Supplementary Tables 2–3, 6–8 and Supplementary Note (PDF 1397 kb)
Supplementary Table 1
Our EC annotation of translated JGI v3.1 transcripts. (XLS 379 kb)
Supplementary Table 4
Transcripts annotation, sequences of experimentally tested transcripts; RT-PCR, 5′, and 3′ RACE summaries, and PA-SUB localization predictions. (XLS 670 kb)
Supplementary Table 5
Sequences of gene-specific primers used in transcript verification experiments. (XLS 90 kb)
Supplementary Table 9
Final metabolic network reconstruction sheet. (XLS 235 kb)
Supplementary Table 10
Results of in silico knockout experiments toward metabolic engineering. (XLS 74 kb)
Supplementary Data 1
Final metabolic network reconstruction in SBML format. (XML 276 kb)
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Manichaikul, A., Ghamsari, L., Hom, E. et al. Metabolic network analysis integrated with transcript verification for sequenced genomes. Nat Methods 6, 589–592 (2009). https://doi.org/10.1038/nmeth.1348
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DOI: https://doi.org/10.1038/nmeth.1348
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