Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138.
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
Proc Natl Acad Sci U S A. 2021 Aug 10;118(32). doi: 10.1073/pnas.2101498118.
Trimethylamine (TMA) is an important gut microbial metabolite strongly associated with human disease. There are prominent gaps in our understanding of how TMA is produced from the essential dietary nutrient l-carnitine, particularly in the anoxic environment of the human gut where oxygen-dependent l-carnitine-metabolizing enzymes are likely inactive. Here, we elucidate the chemical and genetic basis for anaerobic TMA generation from the l-carnitine-derived metabolite γ-butyrobetaine (γbb) by the human gut bacterium We identify a set of genes up-regulated by γbb and demonstrate that the enzymes encoded by the induced γbb utilization () gene cluster convert γbb to TMA. The key TMA-generating step is catalyzed by a previously unknown type of TMA-lyase enzyme that utilizes a putative flavin cofactor to catalyze a redox-neutral transformation. We identify additional cultured and uncultured host-associated bacteria that possess the gene cluster, providing insights into the distribution of anaerobic γbb metabolism. Lastly, we present genetic, transcriptional, and metabolomic evidence that confirms the relevance of this metabolic pathway in the human gut microbiota. These analyses indicate that the anaerobic pathway is a more substantial contributor to TMA generation from l-carnitine in the human gut than the previously proposed aerobic pathway. The discovery and characterization of the pathway provides the critical missing link in anaerobic metabolism of l-carnitine to TMA, enabling investigation into the connection between this microbial function and human disease.
三甲胺 (TMA) 是一种重要的肠道微生物代谢物，与人类疾病密切相关。我们对 TMA 如何由必需的膳食营养物左旋肉碱产生的理解存在明显的空白，特别是在人类肠道的缺氧环境中，氧气依赖的左旋肉碱代谢酶可能不起作用。在这里，我们通过人类肠道细菌阐明了在无氧环境下由左旋肉碱衍生的代谢物γ-丁羟丁酸（γbb）生成 TMA 的化学和遗传基础。我们确定了一组由 γbb 上调的基因，并证明了由诱导的γbb 利用（gutB ）基因簇编码的酶将 γbb 转化为 TMA。关键的 TMA 生成步骤由一种以前未知的 TMA 裂解酶催化，该酶利用假定的黄素辅因子催化氧化还原中性转化。我们鉴定了其他具有 基因簇的培养和未培养的宿主相关细菌，为厌氧 γbb 代谢的分布提供了见解。最后，我们提出了遗传、转录和代谢组学证据，证实了该代谢途径在人类肠道微生物群中的相关性。这些分析表明，与先前提出的需氧途径相比，该厌氧途径是人类肠道中左旋肉碱生成 TMA 的更为重要的途径。gutB 途径的发现和特征提供了左旋肉碱厌氧代谢生成 TMA 的关键缺失环节，使我们能够研究这种微生物功能与人类疾病之间的联系。
