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Correlation-Based Network Analysis of Metabolite and Enzyme Profiles Reveals a Role of Citrate Biosynthesis in Modulating N and C Metabolism in Zea mays.

Toubiana D, Xue W, Zhang N, Kremling K, Gur A, Pilosof S, Gibon Y, Stitt M, Buckler ES, Fernie AR, Fait A - Front Plant Sci (2016)

Bottom Line: The overall higher CV values for metabolites as compared to the tested enzymes are indicative for their greater phenotypic plasticity.H(2) tests revealed galactinol (1) and asparagine (0.91) as the highest scorers among metabolites and nitrate reductase (0.73), NAD-glutamate dehydrogenase (0.52), and phosphoglucomutase (0.51) among enzymes.The latter displayed the strongest node-betweenness value (185.25) of all nodes highlighting its fundamental structural role in the connectivity of the network by linking between different communities and to the also strongly connected enzyme aldolase.

View Article: PubMed Central - PubMed

Affiliation: Institute of Dryland Biotechnology and Agriculture, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev Midreshet Ben-Gurion, Israel.

ABSTRACT
To investigate the natural variability of leaf metabolism and enzymatic activity in a maize inbred population, statistical and network analyses were employed on metabolite and enzyme profiles. The test of coefficient of variation showed that sugars and amino acids displayed opposite trends in their variance within the population, consistently with their related enzymes. The overall higher CV values for metabolites as compared to the tested enzymes are indicative for their greater phenotypic plasticity. H(2) tests revealed galactinol (1) and asparagine (0.91) as the highest scorers among metabolites and nitrate reductase (0.73), NAD-glutamate dehydrogenase (0.52), and phosphoglucomutase (0.51) among enzymes. The overall low H(2) scores for metabolites and enzymes are suggestive for a great environmental impact or gene-environment interaction. Correlation-based network generation followed by community detection analysis, partitioned the network into three main communities and one dyad, (i) reflecting the different levels of phenotypic plasticity of the two molecular classes as observed for the CV values and (ii) highlighting the concerted changes between classes of chemically related metabolites. Community 1 is composed mainly of enzymes and specialized metabolites, community 2' is enriched in N-containing compounds and phosphorylated-intermediates. The third community contains mainly organic acids and sugars. Cross-community linkages are supported by aspartate, by the photorespiration amino acids glycine and serine, by the metabolically related GABA and putrescine, and by citrate. The latter displayed the strongest node-betweenness value (185.25) of all nodes highlighting its fundamental structural role in the connectivity of the network by linking between different communities and to the also strongly connected enzyme aldolase.

No MeSH data available.


Broad-sense heritability of maize metabolites. Broad-sense heritability (H2) values were calculated for all metabolites and enzymes of maize leaves in the background of the IBM population. Values of H2 were divided into bins of 0.1 intervals. Bars represent the relative number for each respective bin.
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Figure 3: Broad-sense heritability of maize metabolites. Broad-sense heritability (H2) values were calculated for all metabolites and enzymes of maize leaves in the background of the IBM population. Values of H2 were divided into bins of 0.1 intervals. Bars represent the relative number for each respective bin.

Mentions: To explore the level of heritability of metabolites and enzymes, broad-sense heritability values (H2) were computed. H2 estimates were divided into 10 bins of 0.1 intervals for which the relative frequencies are given (Figure 3). H2 values approaching one suggest for an increasingly unperturbed link between genotype and phenotype. The H2 bar-plot reveals a positive skewness for both metabolites and enzymes suggestive for a consistent environmental impact or genetic-environment interaction on their level. Indeed, 34 of the 43 (~79%) identified metabolites and 10 of the 13 enzymes (~77%) exhibit an H2 score below 0.5 (Supplementary Tables 1,2). Only nine metabolites displayed an H2 score greater than 0.5. Interestingly, galactinol and asparagine were the highest scorers among metabolites, with values of 1 and 0.91, respectively (Supplementary Table 1). For the enzymes, only nitrate reductase (0.73), NAD-glutamate dehydrogenase (0.52), and phosphoglucomutase (0.51) revealed H2 values above 0.5.


Correlation-Based Network Analysis of Metabolite and Enzyme Profiles Reveals a Role of Citrate Biosynthesis in Modulating N and C Metabolism in Zea mays.

Toubiana D, Xue W, Zhang N, Kremling K, Gur A, Pilosof S, Gibon Y, Stitt M, Buckler ES, Fernie AR, Fait A - Front Plant Sci (2016)

Broad-sense heritability of maize metabolites. Broad-sense heritability (H2) values were calculated for all metabolites and enzymes of maize leaves in the background of the IBM population. Values of H2 were divided into bins of 0.1 intervals. Bars represent the relative number for each respective bin.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4940414&req=5

Figure 3: Broad-sense heritability of maize metabolites. Broad-sense heritability (H2) values were calculated for all metabolites and enzymes of maize leaves in the background of the IBM population. Values of H2 were divided into bins of 0.1 intervals. Bars represent the relative number for each respective bin.
Mentions: To explore the level of heritability of metabolites and enzymes, broad-sense heritability values (H2) were computed. H2 estimates were divided into 10 bins of 0.1 intervals for which the relative frequencies are given (Figure 3). H2 values approaching one suggest for an increasingly unperturbed link between genotype and phenotype. The H2 bar-plot reveals a positive skewness for both metabolites and enzymes suggestive for a consistent environmental impact or genetic-environment interaction on their level. Indeed, 34 of the 43 (~79%) identified metabolites and 10 of the 13 enzymes (~77%) exhibit an H2 score below 0.5 (Supplementary Tables 1,2). Only nine metabolites displayed an H2 score greater than 0.5. Interestingly, galactinol and asparagine were the highest scorers among metabolites, with values of 1 and 0.91, respectively (Supplementary Table 1). For the enzymes, only nitrate reductase (0.73), NAD-glutamate dehydrogenase (0.52), and phosphoglucomutase (0.51) revealed H2 values above 0.5.

Bottom Line: The overall higher CV values for metabolites as compared to the tested enzymes are indicative for their greater phenotypic plasticity.H(2) tests revealed galactinol (1) and asparagine (0.91) as the highest scorers among metabolites and nitrate reductase (0.73), NAD-glutamate dehydrogenase (0.52), and phosphoglucomutase (0.51) among enzymes.The latter displayed the strongest node-betweenness value (185.25) of all nodes highlighting its fundamental structural role in the connectivity of the network by linking between different communities and to the also strongly connected enzyme aldolase.

View Article: PubMed Central - PubMed

Affiliation: Institute of Dryland Biotechnology and Agriculture, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev Midreshet Ben-Gurion, Israel.

ABSTRACT
To investigate the natural variability of leaf metabolism and enzymatic activity in a maize inbred population, statistical and network analyses were employed on metabolite and enzyme profiles. The test of coefficient of variation showed that sugars and amino acids displayed opposite trends in their variance within the population, consistently with their related enzymes. The overall higher CV values for metabolites as compared to the tested enzymes are indicative for their greater phenotypic plasticity. H(2) tests revealed galactinol (1) and asparagine (0.91) as the highest scorers among metabolites and nitrate reductase (0.73), NAD-glutamate dehydrogenase (0.52), and phosphoglucomutase (0.51) among enzymes. The overall low H(2) scores for metabolites and enzymes are suggestive for a great environmental impact or gene-environment interaction. Correlation-based network generation followed by community detection analysis, partitioned the network into three main communities and one dyad, (i) reflecting the different levels of phenotypic plasticity of the two molecular classes as observed for the CV values and (ii) highlighting the concerted changes between classes of chemically related metabolites. Community 1 is composed mainly of enzymes and specialized metabolites, community 2' is enriched in N-containing compounds and phosphorylated-intermediates. The third community contains mainly organic acids and sugars. Cross-community linkages are supported by aspartate, by the photorespiration amino acids glycine and serine, by the metabolically related GABA and putrescine, and by citrate. The latter displayed the strongest node-betweenness value (185.25) of all nodes highlighting its fundamental structural role in the connectivity of the network by linking between different communities and to the also strongly connected enzyme aldolase.

No MeSH data available.