Issue 12, 2009
From the journal:

Molecular BioSystems

A network-based method for predicting gene–nutrient interactions and its application to yeast amino-acidmetabolism†‡

Idit Diamant,a   Yonina C. Eldar,b   Oleg Rokhlenko,c   Eytan Ruppinad  and  Tomer Shlomi*c  

* Corresponding authors

a School of Computer Science, Tel-Aviv University, Tel-Aviv 69978, Israel

b Department of Electrical Engineering, Technion, Haifa 32000, Israel

c Department of Computer Science, Technion, Haifa 32000, Israel
E-mail: tomersh@cs.technion.ac.il

d School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel

Abstract

Cellular metabolism is highly dependent on environmental factors, such as nutrients, toxins and drugs, genetic factors, and interactions between the two. Previous experimental and computational studies of how environmental factors affect cellular metabolism were limited to the analysis of only a small set of growth media. In this study, we present a new computational method for predicting metabolic gene–nutrient interactions (GNI) that uncovers the dependence of gene essentiality on the presence or absence of nutrients in the growth medium. The method is based on constraint-based modeling, permitting the systematic exploration of a large putative growth media ‘space’. Applying this method to predict GNIs in the amino-acidmetabolism system of yeast reveals complex interdependencies between amino-acidbiosynthesis pathways. The predicted GNIs also enable the ‘reverse-prediction’ of growth media composition, based on gene essentiality data. These results suggest that our approach may be applied to learn about the host environment in which a microorganism is embedded given data pertaining to gene lethality, providing a means for the identification of a species’ natural habitat.

Graphical abstract: A network-based method for predicting gene–nutrient interactions and its application to yeast amino-acidmetabolism

About
Cited by
Related
Download options Please wait...

Supplementary files

Article information

DOI
https://doi.org/10.1039/B823287N
Article type
Paper
Submitted
24 Dec 2008
Accepted
07 May 2009
First published
18 Jun 2009

Mol. BioSyst., 2009,5, 1732-1739

Permissions

Request permissions

A network-based method for predicting gene–nutrient interactions and its application to yeast amino-acidmetabolism

I. Diamant, Y. C. Eldar, O. Rokhlenko, E. Ruppin and T. Shlomi, Mol. BioSyst., 2009, 5, 1732 DOI: 10.1039/B823287N

To request permission to reproduce material from this article, please go to the Copyright Clearance Center request page.

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page.

Read more about how to correctly acknowledge RSC content.

Spotlight

Advertisements