Metabolic network analysis integrated with transcript verification for sequenced genomes

• Published in: Nature methods Vol. 6; no. 8; pp. 589 - 592
• Main Authors: Manichaikul, Ani, Ghamsari, Lila, Hom, Erik F Y, Lin, Chenwei, Murray, Ryan R, Chang, Roger L, Balaji, S, Hao, Tong, Shen, Yun, Chavali, Arvind K, Thiele, Ines, Yang, Xinping, Fan, Changyu, Mello, Elizabeth, Hill, David E, Vidal, Marc, Salehi-Ashtiani, Kourosh, Papin, Jason A
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.08.2009; Nature Publishing Group
• Subjects: Animals; Bioinformatics; Biological Microscopy; Biological Techniques; Biomedical Engineering/Biotechnology; brief-communication; Chlamydomonas reinhardtii; Chlamydomonas reinhardtii - enzymology; Chlamydomonas reinhardtii - genetics; Chlamydomonas reinhardtii - metabolism; Computational Biology - methods; Computer Simulation; DNA sequencing; Enzymes - genetics; Enzymes - metabolism; Genetic Engineering; Genetic transcription; Genome, Protozoan; Genomics; Life Sciences; Metabolic engineering; Metabolism; Methods; Models, Genetic; Molecular biology; Nucleotide sequencing; Open reading frames; Physiology; Proteomics; Protozoan Proteins - genetics; Protozoan Proteins - metabolism; Scientific method; Transcription, Genetic; United States
• ISSN: 1548-7091; 1548-7105; 1548-7105
• DOI: 10.1038/nmeth.1348

Iterative cycles of metabolic modeling and experimental open reading frame verification in Chlamydomonas reinhardtii lay the groundwork for more accurate gene annotation and provide resources for metabolic engineering. With sequencing of thousands of organisms completed or in progress, there is a growing need to integrate gene prediction with metabolic network analysis. Using Chlamydomonas reinhardtii as a model, we describe a systems-level methodology bridging metabolic network reconstruction with experimental verification of enzyme encoding open reading frames. Our quantitative and predictive metabolic model and its associated cloned open reading frames provide useful resources for metabolic engineering.