Sequence- and Structure-Based Functional Annotation and Assessment of Metabolic Transporters inAspergillus oryzae: A Representative Case Study

Abstract

Aspergillus oryzaeis widely used for the industrial production of enzymes. InA. oryzaemetabolism, transporters appear to play crucial roles in controlling the flux of molecules for energy generation, nutrients delivery, and waste elimination in the cell. While theA. oryzaegenome 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 ofA. oryzaemetabolic transporters. Sequence-based analysis with manual curation showed that 58 genes of 12,096 total genes in theA. oryzaegenome 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 ofA. 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.