Insight into the biotechnology potential of Alicyclobacillus tolerans from whole genome sequence analysis and genome-scale metabolic network modeling.

Abstract

Extremophilic bacteria have numerous uncovered biotechnological potentials. Acidophilic bacteria are important iron oxidizers that are valuable in bioleaching and in studying extreme environments on earth and in space. Despite their obvious potential, little is known about the genetic traits that underpin their metabolic functions, which are equally poorly understood from a mechanistic perspective. Novel bioinformatics and computational biology pipelines can be used to analyze whole genomes to obtain insights into the phenotypic potential of organisms as well as develop a mathematical model representation of metabolism. Whole-genome sequence analysis and a genome-scale metabolic network model was curated for an iron-oxidizing bacterium initially isolated from an acid mine drainage in Turkey, previously identified as Alicyclobacillus tolerans. The genome contained a high proportion of genes for energy generation from carbohydrates, amino acids synthesis and conversion, nucleic acid metabolism and repair which contribute to robust adaption to their extreme environments. Several candidate genes for pyrite metabolism, iron uptake, regulation and storage, as well as genes for resistance to important heavy metals were annotated. A curated genome-scale metabolic network analysis accurately predicted facultative anaerobic growth, heterotrophic characteristics, and growth on a wide variety of carbon sources. This is the first in-depth in silico analysis of A. tolerans to the best of our knowledge which is expected to lay the groundwork for future research and drive innovations in environmental microbiology and biotechnological applications. The genomic data and mechanistic framework will have applications in biomining, synthetic geomicrobiology on earth, as well as for space exploration and settlement.