Adaptive engineering of a hyperthermophilic archaeon on CO and discovering the underlying mechanism by multi-omics analysis

Abstract

Adaptive laboratory evolution is one of engineering approaches to produce new and fit phenotypes by long-term selection under a defined condition. To understand the molecular mechanisms driving adaptive phenotypic change, systems-level analysis such as comparative whole-genome sequencing and polyomic analysis has been performed. In this study, we evolved a hyperthermophilic archaeon Thermococcus onnurineus NA1 through serial transfers of a culture to fresh medium with carbonmonoxide (CO) over 100 times. The changes in the phenotype, genome sequence and transcriptome were analyzed. The growth rate, CO consumption rate and H2 production rate of the strain gradually increased with transfer time. The genome of evolved strains was sequenced and several mutations were identified in comparison with a parental strain. The gene expression pattern obtained by transcriptome analysis was consistent with the phenotypic changes, and some genes involved in COutilization such as carbon monoxide dehydrogenase, hydrogenase, Na+/H+-antiporter and ATP synthetase were significantly upregulated along with the adaption. This study demonstrates for the first time that CO-utilizing ability of microbes canbe improved by adaptive evolutionary approach.ysis such as comparative whole-genome sequencing and polyomic analysis has been performed. In this study, we evolved a hyperthermophilic archaeon Thermococcus onnurineus NA1 through serial transfers of a culture to fresh medium with carbonmonoxide (CO) over 100 times. The changes in the phenotype, genome sequence and transcriptome were analyzed. The growth rate, CO consumption rate and H2 production rate of the strain gradually increased with transfer time. The genome of evolved strains was sequenced and several mutations were identified in comparison with a parental strain. The gene expression pattern obtained by transcriptome analysis was consistent with the phenotypic changes, and some genes involved in COutilization such as carbon monoxide dehydrogenase, hydrogenase, Na+/H+-antiporter and ATP synthetase were significantly upregulated along with the adaption. This study demonstrates for the first time that CO-utilizing ability of microbes canbe improved by adaptive evolutionary approach.