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BioMed Research International - Volume 2016 2016, Article ID 8124636, 13 pages -

Research Article

Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand

Department of Physics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand

Computational Biomodelling Laboratory for Agricultural Science and Technology CBLAST, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand

Center of Advanced Science in Industrial Technology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand

Food Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology BIOTEC, National Science and Technology Development Agency NSTDA, Pathum Thani 12120, Thailand

Received 25 January 2016; Accepted 6 April 2016

Academic Editor: Luisa Di Paola

Copyright © 2016 Nachon Raethong et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Aspergillus oryzae is widely used for the industrial production of enzymes. In A. oryzae metabolism, transporters appear to play crucial roles in controlling the flux of molecules for energy generation, nutrients delivery, and waste elimination in the cell. While the A. oryzae genome sequence is available, transporter annotation remains limited and thus the connectivity of metabolic networks is incomplete. In this study, we developed a metabolic annotation strategy to understand the relationship between the sequence, structure, and function for annotation of A. oryzae metabolic transporters. Sequence-based analysis with manual curation showed that 58 genes of 12,096 total genes in the A. oryzae genome encoded metabolic transporters. Under consensus integrative databases, 55 unambiguous metabolic transporter genes were distributed into channels and pores 7 genes, electrochemical potential-driven transporters 33 genes, and primary active transporters 15 genes. To reveal the transporter functional role, a combination of homology modeling and molecular dynamics simulation was implemented to assess the relationship between sequence to structure and structure to function. As in the energy metabolism of A. oryzae, the H

-ATPase encoded by the AO090005000842 gene was selected as a representative case study of multilevel linkage annotation. Our developed strategy can be used for enhancing metabolic network reconstruction.





Autor: Nachon Raethong, Jirasak Wong-ekkabut, Kobkul Laoteng, and Wanwipa Vongsangnak

Fuente: https://www.hindawi.com/



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