Potential application of a knowledgebase of iron metabolism of Acidithiobacillus ferrooxidans as an alternative platform

Abstract Background Acidithiobacillus ferrooxidans is a facultative anaerobe that depends on ferrous ion oxidation as well as reduced sulfur oxidation to obtain energy and is widely applied in metallurgy, environmental protection and soil remediation. With the accumulation of experimental data, metabolic mechanisms, kinetic models and several databases have been established. However, scattered data are not conducive to understanding A. ferrooxidans, necessitating updated information informed by systems biology. Results Here, we constructed a knowledgebase of iron metabolism of A. ferrooxidans (KIMAf) system by integrating public databases and reviewing the literature, including the database of bioleaching substrates (DBS), the database of bioleaching metallic ion-related proteins (MIRP), the A. ferrooxidans bioinformation database (Af-info) and the database for dynamics model of bioleaching (DDMB). The DBS and MIRP incorporate common bioleaching substrates and metal ion-related proteins. Af-info and DDMB integrate nucleotide, gene, protein and kinetic model information. Statistical analysis was performed, elucidating the distribution of isolated A. ferrooxidans strains, evolutionary and metabolic advances and the development of bioleaching models. Conclusions This comprehensive system provides researchers with a platform of available iron metabolism-related resources of A. ferrooxidans and facilitates its application.