Maximal sum of metabolic exchange fluxes outperforms biomass yield as a predictor of growth rate of microorganisms

PLoS One. 2014 May 27;9(5):e98372. doi: 10.1371/journal.pone.0098372. eCollection 2014.

Abstract

Growth rate has long been considered one of the most valuable phenotypes that can be measured in cells. Aside from being highly accessible and informative in laboratory cultures, maximal growth rate is often a prime determinant of cellular fitness, and predicting phenotypes that underlie fitness is key to both understanding and manipulating life. Despite this, current methods for predicting microbial fitness typically focus on yields [e.g., predictions of biomass yield using GEnome-scale metabolic Models (GEMs)] or notably require many empirical kinetic constants or substrate uptake rates, which render these methods ineffective in cases where fitness derives most directly from growth rate. Here we present a new method for predicting cellular growth rate, termed SUMEX, which does not require any empirical variables apart from a metabolic network (i.e., a GEM) and the growth medium. SUMEX is calculated by maximizing the SUM of molar EXchange fluxes (hence SUMEX) in a genome-scale metabolic model. SUMEX successfully predicts relative microbial growth rates across species, environments, and genetic conditions, outperforming traditional cellular objectives (most notably, the convention assuming biomass maximization). The success of SUMEX suggests that the ability of a cell to catabolize substrates and produce a strong proton gradient enables fast cell growth. Easily applicable heuristics for predicting growth rate, such as what we demonstrate with SUMEX, may contribute to numerous medical and biotechnological goals, ranging from the engineering of faster-growing industrial strains, modeling of mixed ecological communities, and the inhibition of cancer growth.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / growth & development*
  • Biochemical Phenomena
  • Biomass
  • Computer Simulation
  • Culture Media
  • Fungi
  • Metabolic Networks and Pathways
  • Models, Biological*
  • Software

Substances

  • Culture Media

Grants and funding

MO gratefully acknowledges funding from the Whitaker Foundation (Whitaker International Scholars Program) and the Dan David Fellowship; ER gratefully acknowledges support from the EU FP7 Microme project, the Israeli Science Foundation (ISF), the Israeli Centers of Research Excellence (I-CORE), and the McDonnell foundation. UG is supported by the McDonnell foundation, the Israeli Ministry of Health and the German-Israeli Project Cooperation (DIP). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.