Sequence- and Structure-Based Functional Annotation and Assessment of Metabolic Transporters in Aspergillus oryzae: A Representative Case Study.
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.
Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
Nachon
N
Raethong
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.
Jirasak
J
Wong-Ekkabut
Food Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand.
Kobkul
K
Laoteng
Department of Zoology, 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.
Wanwipa
W
Vongsangnak
D001236:Aspergillus oryzae / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D066289:Data Curation; D005800:Genes, Fungal; D026901:Membrane Transport Proteins / Q000378:metabolism*; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D016415:Sequence Alignment
D026901:Membrane Transport Proteins