title: Genome-scale metabolic modeling and in silico analysis of lipid accumulating yeast Candida tropicalis for dicarboxylic acid production.
abstract: Recently, the bio-production of α,ω-dicarboxylic acids (DCAs) has gained significant attention, which potentially leads to the replacement of the conventional petroleum-based products. In this regard, the lipid accumulating yeast Candida tropicalis, has been recognized as a promising microbial host for DCA biosynthesis: it possess the unique ω-oxidation pathway where the terminal carbon of α-fatty acids is oxidized to form DCAs with varying chain lengths. However, despite such industrial importance, its cellular physiology and lipid accumulation capability remain largely uncharacterized. Thus, it is imperative to better understand the metabolic behavior of this lipogenic yeast, which could be achieved by a systems biological approach. To this end, herein, we reconstructed the genome-scale metabolic model of C. tropicalis, iCT646, accounting for 646 unique genes, 945 metabolic reactions, and 712 metabolites. Initially, the comparative network analysis of iCT646 with other yeasts revealed several distinctive metabolic reactions, mainly within the amino acid and lipid metabolism including the ω-oxidation pathway. Constraints-based flux analysis was, then, employed to predict the in silico growth rates of C. tropicalis which are highly consistent with the cellular phenotype observed in glucose and xylose minimal media chemostat cultures. Subsequently, the lipid accumulation capability of C. tropicalis was explored in comparison with Saccharomyces cerevisiae, indicating that the formation of "citrate pyruvate cycle" is essential to the lipid accumulation in oleaginous yeasts. The in silico flux analysis also highlighted the enhanced ability of pentose phosphate pathway as NADPH source rather than malic enzyme during lipogenesis. Finally, iCT646 was successfully utilized to highlight the key directions of C. tropicalis strain design for the whole cell biotransformation application to produce long-chain DCAs from alkanes. Biotechnol. Bioeng. 2016;113: 1993-2004. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585, Singapore.
authors.forename: Pranjul
authors.initials: P
authors.lastname: Mishra
authors.affiliation: Biotechnology Process Engineering Center, KRIBB, 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju, 363-883, Korea.|Bioprocess Department, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 305-350, Korea.
authors.forename: Gyu-Yeon
authors.initials: GY
authors.lastname: Park
authors.affiliation: Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, 138668, Singapore.
authors.forename: Meiyappan
authors.initials: M
authors.lastname: Lakshmanan
authors.affiliation: Biotechnology Process Engineering Center, KRIBB, 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju, 363-883, Korea.|Bioprocess Department, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 305-350, Korea.
authors.forename: Hee-Seok
authors.initials: HS
authors.lastname: Lee
authors.affiliation: Biotechnology Process Engineering Center, KRIBB, 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju, 363-883, Korea.|Bioprocess Department, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 305-350, Korea.
authors.forename: Hongweon
authors.initials: H
authors.lastname: Lee
authors.affiliation: Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.|NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore.
authors.forename: Matthew Wook
authors.initials: MW
authors.lastname: Chang
authors.affiliation: Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585, Singapore.
authors.forename: Chi Bun
authors.initials: CB
authors.lastname: Ching
authors.affiliation: Biotechnology Process Engineering Center, KRIBB, 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju, 363-883, Korea. ahnjo@kribb.re.kr.|Bioprocess Department, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 305-350, Korea. ahnjo@kribb.re.kr.
authors.forename: Jungoh
authors.initials: J
authors.lastname: Ahn
authors.affiliation: Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585, Singapore. cheld@nus.edu.sg.|Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, 138668, Singapore. cheld@nus.edu.sg.|NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore. cheld@nus.edu.sg.
authors.forename: Dong-Yup
authors.initials: DY
authors.lastname: Lee
mesh_terms: D041022:Candida tropicalis / Q000235:genetics* / Q000378:metabolism*; D003198:Computer Simulation; D003998:Dicarboxylic Acids / Q000032:analysis / Q000378:metabolism*; D016681:Genome, Fungal / Q000235:genetics*; D050356:Lipid Metabolism / Q000235:genetics*; D060847:Metabolic Engineering / Q000379:methods*; D053858:Metabolic Networks and Pathways; D008954:Models, Biological
chemical_list: D003998:Dicarboxylic Acids
keywords: Candida tropicalis; dicarboxylic acid; genome-scale metabolic model; lipid accumulating yeasts; systems biology