Maize Metabolic Network Construction and Transcriptome Analysis

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 L. subsp. 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 identifi ed in the maize reference genome sequenced from the B73 variety. MaizeCyc version 2.0.2 is a collection of 391 maize pathways involving 8889 enzyme mapped to 2110 reactions and 1468 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 1062 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, genebased phylogeny trees, and comparison to known genes and pathways from rice (Oryza sativa L.) and Arabidopsis thaliana (L.) Heynh. 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. MAIZE (Zea mays subsp. mays) is one of the most agriculturally and economically important crops worldwide (FAOSTAT, 2011). Its widespread use is not limited to food and feedstock, but various commodities such as paint, plastics, soap, tiles, and packaging material are also made from maize. More recently it has been recognized as an excellent source of lignocellulosic biofuel. In addition, maize is one of the founding model organisms for genetics research and, along with rice and Arabidopsis thaliana, currently is one of the leading models for plant functional genomics (Gaut et al., 2000; Rabinowicz and Bennetzen, 2006; Strable and Scanlon, 2009). Th e discovery of molecular interactions that lead to desirable traits in this crop is ongoing. Th e availability of the draft reference genome sequence for the maize inbred cultivar B73 (Schnable et al., 2009) opened avenues to explore the interaction of genes, Published in The Plant Genome 6. doi: 10.3835/plantgenome2012.09.0025 © Crop Science Society of America 5585 Guilford Rd., Madison, WI 53711 USA An open-access publication All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. M.K. Monaco, L. Ren, J. Thomason, and D. Ware, Cold Spring Harbor Lab., 1 Bungtown Rd., Cold Spring Harbor, NY 11724; T.Z. Sen, M. Schaeffer, L. Harper, C.J. Lawrence, and D. Ware, USDAARS, Jamie L. Whitten Building, Room 302A, 1400 Independence Ave., S.W., Washington, DC 20250; T.Z. Sen, J. Gardiner, E.K.S. Cannon, and C.J. Lawrence, Dep. of Genetics, Development and Cell Biology, Iowa State Univ., Ames, IA 50011; P.D. Dharmawardhana, V. Amarasinghe, and P. Jaiswal, Dep. of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State Univ., Corvallis, OR 97331; M. Schaeffer, Division of Plant Sciences, Dep. of Agronomy, Univ. of Missouri, Columbia, MO 65211; S. Naithani, Dep. of Horticulture, 4017 ALS Bldg., Oregon State Univ., Corvallis, OR 97331; L. Harper, Dep. of Molecular and Cell Biology, Univ. of California, Berkeley, CA 94720; J. Gardiner, School of Plant Sciences, Univ. of Arizona, Tucson, AZ 85721. The gene expression data analysis was performed on the published and publicly available NCBI GEO record GSE27004. Received 20 Sept. 2012. *Corresponding author ([email protected]). Abbreviations: 16DAP, 16 d after pollination; CoA, coenzyme A; EC, Enzyme Commission; FGS, fi ltered gene set; GO, gene ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; Maize Core DB, MaizeSequence.org’s Ensembl Core Database; MaizeGDB, Maize Genetics and Genomics Database; ORF, open reading frame; PO, plant ontology. Published March 8, 2013