Reference "Maize Metabolic Network Construction and Transcriptome Analysis"

Reference ID

54958

Title

Maize Metabolic Network Construction and Transcriptome Analysis

Source

The Plant Genome, 2013, vol. 1, pp. -

Authors (14)

Monaco-M-K	Sen-T-Z	Dharmawardhana-P-D	Ren-L
Schaeffer-M	Naithani-S	Amarasinghe-V	Thomason-J-T
Harper-L	Gardiner-J	Cannon-E-K-S	Lawrence-C-J
Ware-D	Jaiswal-P

Abstract

A framework for understanding the synthesis and catalysis of metabolites and
other biochemicals by proteins is crucial for unraveling the physiology of
cells. To create such a framework for Zea mays ssp. mays (maize), we developed
MaizeCyc, a metabolic network of enzyme catalysts, proteins, carbohydrates,
lipids, amino acids, secondary plant products, and other metabolites by
annotating the genes identified in the maize reference genome sequenced from the
B73 variety. MaizeCyc v2.0.2 is a collection of 391 maize pathways involving
8,889 enzyme mapped to 2,110 reactions and 1,468 metabolites. We used MaizeCyc
to describe the development and function of maize organs including leaf, root,
anther, embryo and endosperm by exploring the recently published microarray-
based maize gene expression atlas. We found that 1,062 differentially expressed
metabolic genes mapped to 524 unique enzymatic reactions associated with 310
pathways. The MaizeCyc pathway database was created by running a library of
evidences collected from the maize genome annotation, gene based phylogeny
trees, and comparison to known genes and pathways from rice and Arabidopsis
against the PathoLogic module of Pathway Tools. The network and the database
that were also developed as a community resource are freely accessible online at
http://maizecyc.maizegdb.org to facilitate analysis and promote studies on
metabolic genes in maize.