A transcriptomics-based kinetic model for ethylene biosynthesis in tomato (Solanum lycopersicum) fruit: development, validation and exploration of novel regulatory mechanisms
Article first published online: 21 JAN 2014
© 2014 The Authors. New Phytologist © 2014 New Phytologist Trust
Volume 202, Issue 3, pages 952–963, May 2014
How to Cite
Van de Poel, B., Bulens, I., Hertog, M. L. A. T. M., Nicolai, B. M. and Geeraerd, A. H. (2014), A transcriptomics-based kinetic model for ethylene biosynthesis in tomato (Solanum lycopersicum) fruit: development, validation and exploration of novel regulatory mechanisms. New Phytologist, 202: 952–963. doi: 10.1111/nph.12685
- Issue published online: 10 APR 2014
- Article first published online: 21 JAN 2014
- Manuscript Accepted: 17 DEC 2013
- Manuscript Received: 29 SEP 2013
- Research Council of KU Leuven. Grant Number: OT/12/055
- Institute for the Promotion of Innovation through Science and Technology in Flanders
- B.V.d.P. and I.B. Grant Number: FA1106
- ethylene biosynthesis;
- gene expression;
- kinetic modeling;
- network model;
- systems biology;
- The gaseous plant hormone ethylene is involved in many physiological processes including climacteric fruit ripening, in which it is a key determinant of fruit quality. A detailed model that describes ethylene biochemistry dynamics is missing. Often, kinetic modeling is used to describe metabolic networks or signaling cascades, mostly ignoring the link with transcriptomic data.
- We have constructed an elegant kinetic model that describes the transfer of genetic information into abundance and metabolic activity of proteins for the entire ethylene biosynthesis pathway during fruit development and ripening of tomato (Solanum lycopersicum).
- Our model was calibrated against a vast amount of transcriptomic, proteomic and metabolic data and showed good descriptive qualities. Subsequently it was validated successfully against several ripening mutants previously described in the literature. The model was used as a predictive tool to evaluate novel and existing hypotheses regarding the regulation of ethylene biosynthesis.
- This bottom-up kinetic network model was used to indicate that a side-branch of the ethylene pathway, the formation of the dead-end product 1-(malonylamino)-1-aminocyclopropane-1-carboxylic acid (MACC), might have a strong effect on eventual ethylene production. Furthermore, our in silico analyses indicated potential (post-) translational regulation of the ethylene-forming enzyme ACC oxidase.