Proteomics and transcriptomics analyses of Methylophaga thiooxydans reveal adaptations for growth on dimethylsulfide in a marine model organism

Dimethylsulfide is a volatile organic sulfur compound that provides the largest input of biogenic sulfur from the oceans to the atmosphere, and thence back to land, constituting an important link in the global sulfur cycle. Microorganisms degrading DMS affect fluxes of DMS in the environment, but the underlying metabolic pathways are still poorly understood. Methylophaga thiooxydans is a marine methylotrophic bacterium capable of growth on DMS as sole source of carbon and energy. Using proteomics and transcriptomics we identified genes expressed during growth on dimethylsulfide and methanol to refine our knowledge of the metabolic pathways that are involved in DMS and methanol degradation in this strain. Amongst the most highly expressed genes on DMS were the two methanethiol oxidases driving the oxidation of this reactive and toxic intermediate of DMS metabolism. Growth on DMS also increased expression of the enzymes of the tetrahydrofolate linked pathway of formaldehyde oxidation, in addition to the tetrahydromethanopterin linked pathway. Key enzymes of the inorganic sulfur oxidation pathway included flavocytochrome c sulfide dehydrogenase, sulfide quinone oxidoreductase, and persulfide dioxygenases. A sulP permease was also expressed during growth on DMS. Other enzymes of organic and inorganic sulfur metabolism previously detected in cell extracts of Methylophaga have not been characterised at the genetic level yet; their expression level and regulation could not be analysed. A pan-genome analysis of six available Methylophaga genomes suggests that only two of the six investigated bacteria have the metabolic potential to utilize methanethiol, the degradation product of DMS. These results mirror phenotypic analyses and demonstrate that DMS-utilization and subsequent C1 and sulfur oxidation are not conserved across the entire genus.

二甲基硫（Dimethylsulfide，DMS）是一种挥发性有机硫化合物，是海洋向大气输入生物源硫的最主要途径，随后经大气沉降返还至陆地，构成全球硫循环中的重要一环。降解二甲基硫的微生物会影响环境中二甲基硫的通量，但其中的核心代谢途径仍未得到充分解析。氧化甲基单胞菌（Methylophaga thiooxydans）是一种海洋甲基营养型细菌，能够以二甲基硫作为唯一碳源与能源进行生长。本研究通过蛋白质组学（proteomics）与转录组学（transcriptomics）技术，鉴定了该菌株在以二甲基硫或甲醇为唯一碳源与能源生长时的表达基因，以完善我们对该菌株中二甲基硫与甲醇降解相关代谢途径的认知。在二甲基硫培养条件下的高表达基因中，包含两种负责催化该二甲基硫代谢过程中活性毒性中间产物——甲硫醇氧化的甲硫醇氧化酶。以二甲基硫为碳源生长时，除四氢甲烷蝶呤结合的甲醛氧化途径外，依赖四氢叶酸的甲醛氧化途径相关酶的表达量也显著上调。无机硫氧化途径的关键酶包括黄素细胞色素c硫化物脱氢酶、硫化物醌氧化还原酶与过硫化物双加氧酶。在以二甲基硫生长的过程中，还检测到了SulP通透酶（sulP permease）的表达。此前在该菌株细胞提取物中检测到的其他有机与无机硫代谢相关酶，尚未在基因层面完成功能鉴定，因此无法对其表达水平与调控机制进行分析。对已公开的6株甲基单胞菌属（Methylophaga）基因组进行泛基因组分析后发现，6株受试菌株中仅2株具备利用二甲基硫降解产物甲硫醇的代谢潜能。上述研究结果与表型分析结果相吻合，证实了二甲基硫利用能力及后续的一碳与硫氧化代谢途径在该属内并非保守存在的。