Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species

Esa Pitkänen (Corresponding Author), Paula Jouhten, Jian Hou, Muhammad Fahad Syed, Peter Blomberg, Jana Kludas, Merja Oja, Liisa Holm, Merja Penttilä, Juho Rousu, Mikko Arvas

Research output: Contribution to journalArticleScientificpeer-review

34 Citations (Scopus)

Abstract

We introduce a novel computational approach, CoReCo, for comparative metabolic reconstruction and provide genome-scale metabolic network models for 49 important fungal species. Leveraging on the exponential growth in sequenced genome availability, our method reconstructs genome-scale gapless metabolic networks simultaneously for a large number of species by integrating sequence data in a probabilistic framework. High reconstruction accuracy is demonstrated by comparisons to the well-curated Saccharomyces cerevisiae consensus model and large-scale knock-out experiments. Our comparative approach is particularly useful in scenarios where the quality of available sequence data is lacking, and when reconstructing evolutionary distant species. Moreover, the reconstructed networks are fully carbon mapped, allowing their use in 13C flux analysis. We demonstrate the functionality and usability of the reconstructed fungal models with computational steady-state biomass production experiment, as these fungi include some of the most important production organisms in industrial biotechnology. In contrast to many existing reconstruction techniques, only minimal manual effort is required before the reconstructed models are usable in flux balance experiments. CoReCo is available at http://esaskar.github.io/CoReCo/.

Original languageEnglish
Article numbere1003465
JournalPLoS Computational Biology
Volume10
Issue number2
DOIs
Publication statusPublished - 1 Jan 2014
MoE publication typeA1 Journal article-refereed

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Metabolic Network
Metabolic Networks and Pathways
Genome
genome
Genes
Experiment
Biotechnology
Saccharomyces Cerevisiae
Exponential Growth
Biomass
Fluxes
Usability
Network Model
Saccharomyces cerevisiae
experiment
Experiments
Carbon
Fungi
biotechnology
Availability

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Pitkänen, Esa ; Jouhten, Paula ; Hou, Jian ; Syed, Muhammad Fahad ; Blomberg, Peter ; Kludas, Jana ; Oja, Merja ; Holm, Liisa ; Penttilä, Merja ; Rousu, Juho ; Arvas, Mikko. / Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species. In: PLoS Computational Biology. 2014 ; Vol. 10, No. 2.
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Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species. / Pitkänen, Esa (Corresponding Author); Jouhten, Paula; Hou, Jian; Syed, Muhammad Fahad; Blomberg, Peter; Kludas, Jana; Oja, Merja; Holm, Liisa; Penttilä, Merja; Rousu, Juho; Arvas, Mikko.

In: PLoS Computational Biology, Vol. 10, No. 2, e1003465, 01.01.2014.

Research output: Contribution to journalArticleScientificpeer-review

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