The hidden metabolic versatility of ubiquitous Marine bacteria

Abstract

The bacterial clade SAR11 is known for its abundance and ecological significance in marine environments. A representative member of the SAR11 clade is Pelagibacter ubique HTCC1062, which is a highly abundant marine bacterium. By utilizing a variety of single-carbon (C1) and short-chain methylated compounds for their development, P. ubique plays crucial role in the carbon cycles of the ocean. While the genome of P. ubique encodes various enzymes involve in metabolism of these carbon sources, many of which are waiting to be characterized. Among these enzymes, SAR11_1287 and SAR11_0272 are proposed to be involves in the methanol utilization, yet they have not been experimentally characterized. This study aimed to experimentally validate whether these enzymes functions as methanol dehydrogenase through a combination of bioinformatic analysis and protein expression and purification in E. coli, followed by in vitro enzyme assays. While SAR11_1287 could be successfully expressed and purified for enzymatic assays, SAR11_0272 proved difficult to express under the tested conditions. Enzymatic assays demonstrated that SAR11_1287 displayed broad substrate specificity by utilizing several short-chain alcohols, meanwhile it did not oxidize methanol under the experimental conditions. In contrast to the previous bioinformatic analysis, which suggest that SAR11_1287 can oxidize methanol, the results obtained in this study revealed that SAR11_1287 is likely not the methanol dehydrogenase for SAR11 clade. This study provided important insights into the substrate specificity of SAR11_1287 and provided preliminary data for further experimental validation.