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

Abstract

The hyperthermophilic archaeon Thermococcus onnurineus NA1 can grow and produce H2 on carbon monoxide (CO) and its H2 production rates have been improved through metabolic engineering. In this study, we applied adaptive evolution to enhance H2 productivity. After over 150 serial transfers onto CO medium, cell density, CO consumption rate and H2 production rate increased. The underlying mechanism for those physiological changes could be explained by using multi-omics approaches including genomic, transcriptomic and epigenomic analyses. A putative transcriptional regulator was newly identified to regulate the expression levels of genes related to CO oxidation. Transcriptome analysis revealed significant changes in the transcript levels of genes belonging to the categories of transcription, translation and energy metabolism. Our study presents the first genome-scale methylation pattern of hyperthermophilic archaea. Adaptive evolution led to highly enhanced H2 productivity at high CO flow rates using synthesis gas produced from coal gasification.

The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology

“…A main source of difficulty lies in the conflict between fast, robust strain growth and the fitness-counterproductive repurposing of cellular resources to produce large amounts of a desirable compound. Nevertheless, ALE studies with proper experimental design can be used to overcome this conflict and optimize metabolite production and increase titer (Basso et al, 2011;Charusanti et al, 2012;Fong et al, 2005a;Fu et al, 2013;Grabar et al, 2006;Jiang et al, 2013;Lee et al, 2016Lee et al, , 2014Lu et al, 2012;Luo et al, 2019;Mahr et al, 2015;Otero et al, 2013;Pontrelli et al, 2018;Reyes et al, 2014;Royce et al, 2015;Shen et al, 2012;Smith and Liao, 2011;Vilela et al, 2015;Wang et al, 2012;Wisselink et al, 2007;Zhang et al, 2007;Zhao et al, 2013;Zhou et al, 2005Zhou et al, , 2003.…”

Adaptive evolution of a hyperthermophilic archaeon pinpoints a formate transporter as a critical factor for the growth enhancement on formate

“…Previously, the strain has been adapted on CO by serial transfer on CO-containing medium, accompanying a genomic change with beneficial mutations 23 . In this study, we investigated molecular changes associated with cell growth on formate as an energy source.…”

“…During adaptation, genetic variations occur all over the chromosome, and beneficial mutations can improve the ability to handle the stress 22 . Previously, it has been demonstrated that the serial transfer of T. onnurineus NA1 under the CO condition greatly improved growth and CO tolerance 23 , due to mutations including a mutation at a putative DNA-binding protein (TON_1525 T55I).…”

Biohydrogen production of obligate anaerobic archaeon Thermococcus onnurineus NA1 under oxic conditions via overexpression of frhAGB-encoding hydrogenase genes

“…In particular, H 2 production by T. onnurineus NA1 using steel-mill waste gas was successfully demonstrated, indicating that environmentally friendly H 2 production is feasible [18, 19]. Over the years, H 2 production by this strain has been improved by employing various strategies of genetic engineering [18, 20, 21], adaptive laboratory evolution [22, 23], and fermentation process engineering [24]. Even though the strain has great potential for practical applications as an H 2 producer, it must be carefully handled and cultivated to prevent exposure to O 2 in all the steps.…”