Genetic Analysis of Central Carbon Metabolism Unveils an Amino Acid Substitution That Alters Maize NAD-Dependent Isocitrate Dehydrogenase Activity

Nengyi Zhang,Mark Stitt,Amit Gur,Sherry Flint-Garcia,Edward S Buckler,Yves Gibon,Ronan Sulpice,Michael D Mcmullen

doi:10.1371/journal.pone.0009991

Abstract

BackgroundCentral carbon metabolism (CCM) is a fundamental component of life. The participating genes and enzymes are thought to be structurally and functionally conserved across and within species. Association mapping utilizes a rich history of mutation and recombination to achieve high resolution mapping. Therefore, applying association mapping in maize (Zea mays ssp. mays), the most diverse model crop species, to study the genetics of CCM is a particularly attractive system.Methodology/Principal FindingsWe used a maize diversity panel to test the CCM functional conservation. We found heritable variation in enzyme activity for every enzyme tested. One of these enzymes was the NAD-dependent isocitrate dehydrogenase (IDH, E.C. 1.1.1.41), in which we identified a novel amino-acid substitution in a phylogenetically conserved site. Using candidate gene association mapping, we identified that this non-synonymous polymorphism was associated with IDH activity variation. The proposed mechanism for the IDH activity variation includes additional components regulating protein level. With the comparison of sequences from maize and teosinte (Zea mays ssp. Parviglumis), the maize wild ancestor, we found that some CCM genes had also been targeted for selection during maize domestication.Conclusions/SignificanceOur results demonstrate the efficacy of association mapping for dissecting natural variation in primary metabolic pathways. The considerable genetic diversity observed in maize CCM genes underlies heritable phenotypic variation in enzyme activities and can be useful to identify putative functional sites.

Highlights

Glycolysis and the tricarboxylic acid (TCA) cycle, known as Central carbon metabolism (CCM), are responsible for the production of accessible energy and the creation of primary building blocks of other metabolisms
We showed here the presence of substantial genetic variation among various CCM genes
The results showed that all nine enzymes tested from the glycolytic and TCA pathways had substantial differences in activity and significant genetic effects in leaf samples (Table 1)

Summary

Introduction

Glycolysis and the tricarboxylic acid (TCA) cycle, known as CCM, are responsible for the production of accessible energy and the creation of primary building blocks of other metabolisms. To study the genetics of CCM, the main focus to date has been on scoring gene expression [1,2] or metabolite levels [3,4,5]. Relatively little attention has been paid to adding protein levels or enzyme activities. There is evidence that protein levels and enzyme activities are more heritable because they integrate over time, in a manner analogous to whole plant phenotypes [6]. The participating genes and enzymes are thought to be structurally and functionally conserved across and within species. Mays), the most diverse model crop species, to study the genetics of CCM is a attractive system Applying association mapping in maize (Zea mays ssp. mays), the most diverse model crop species, to study the genetics of CCM is a attractive system

Methods

Results

Conclusion