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JXB Advance Access originally published online on May 23, 2005
Journal of Experimental Botany 2005 56(417):1887-1896; doi:10.1093/jxb/eri179
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© The Author [2005]. Published by Oxford University Press [on behalf of the Society for Experimental Biology]. All rights reserved.

RESEARCH PAPER

Integrative gene-metabolite network with implemented causality deciphers informational fluxes of sulphur stress response

Victoria J. Nikiforova1,2,*, Carsten O. Daub1 {dagger}, Holger Hesse1, Lothar Willmitzer1 and Rainer Hoefgen1

1Max Planck Institute of Molecular Plant Physiology, Department of Molecular Physiology, Am Mühlenberg 1, D-14476 Golm, Germany
2Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Str. 35, Moscow 127276, Russia

* To whom correspondence should be addressed in Germany. Fax: +49 331 567 8134. E-mail: nikiforova{at}mpimp-golm.mpg.de

The systematic accumulation of gene expression data, although revolutionary, is insufficient in itself for an understanding of system-level physiology. In the post-genomic era, the next cognitive step is linking genes to biological processes and assembling a mosaic of data into global models of biosystem function. A dynamic network of informational flows in Arabidopsis plants perturbed by sulphur depletion is presented here. With the use of an original protocol, the first biosystem response network was reconstructed from a time series of transcript and metabolite profiles, which, on the one hand, integrates complex metabolic and transcript data and, on the other hand, possesses a causal relationship. Using the informational fluxes within this reconstruction, it was possible to link system perturbation to response endpoints. Robustness and stress tolerance, as consequences of scale-free network topology, and hubs, as potential controllers of homeostasis maintenance, were revealed. Communication paths of propagating system excitement directed to physiological endpoints, such as anthocyanin accumulation and enforced root formation were dissected from the network. An auxin regulatory circuit involved in the control of a hypo-sulphur stress response was uncovered.

Key words: Auxin, causality, metabolome, network, network topology, plait concept, scale-free network, sulphur metabolism, systems biology, transcriptome


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