Mechanistic Insight into Trimethylamine N-Oxide Recognition by the Marine Bacterium Ruegeria pomeroyi DSS-3
Mechanistic Insight into Trimethylamine N-Oxide Recognition by the Marine Bacterium Ruegeria pomeroyi DSS-3
复制标题
海洋细菌 Ruegeria pomeroyi DSS-3 识别三甲胺 N-氧化物的机制
DOI：
10.1128/jb.00542-15
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发表时间：
2015-11-01
影响因子：
3.2
通讯作者：
Zhang, Yu-Zhong
中科院分区：
文献类型：
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作者：
Li, Chun-Yang;Chen, Xiu-Lan;Zhang, Yu-Zhong
三甲胺氮氧化物(TMAO)是海洋细菌的重要氮源。海洋细菌还可以将TMAO代谢成挥发性甲基化胺，后者是温室气体一氧化二氮的前体。然而，目前尚不清楚细菌是如何识别和输入TMAO的。Pomeroyi Regeria pomeroyi DSS-3是一株海洋玫瑰杆菌，具有TMAO特异的三磷酸腺苷结合盒转运体TmoXWV。TmoX是TmoXWV转运蛋白的底物结合蛋白。本研究对Pomeroyi DSS-3菌株TmoX的底物特异性进行了研究。我们进一步确定了TmoX/TMAO复合体的结构，并通过生化、结构和突变分析研究了TmoX与TMAO的结合机制。在TmoX中，钙离子被一个扩展的环络合，这对维持TmoX的稳定性是重要的。分子动力学模拟表明，TmoX可以在“开放”和“关闭”状态之间交替结合TMAO。在底物结合口袋中，四个色氨酸残基通过阳离子-pi相互作用与TMAO的季胺相互作用，Glu131与TMAO的极性氧原子形成氢键。Phe和Trp侧链之间的pi-pi堆积作用也是TMAO结合所必需的。序列分析表明，TmoX的TMAO结合机制可能在海洋细菌中具有普遍意义，特别是在海洋玫瑰杆菌分支中。本研究揭示了海洋微生物如何利用TMAO。三甲胺N-氧化物(TMAO)是海洋细菌的重要氮源。细菌代谢TMAO的产物是温室气体一氧化二氮前体的一部分。目前还不清楚细菌是如何识别和输入TMAO的。TmoX是TMAO特异性转运蛋白的底物结合蛋白。在此，我们对Pomeroyi Regeria pomeroyi DSS-3的TmoX底物特异性进行了研究。通过生化、结构和突变分析，研究了TmoX与TMAO的结合机制。此外，我们的结果表明，TMAO结合机制可能在海洋细菌中具有普遍意义。这项研究揭示了海洋微生物如何利用TMAO，并应有助于更好地理解海洋氮循环。
Trimethylamine N-oxide (TMAO) is an important nitrogen source for marine bacteria. TMAO can also be metabolized by marine bacteria into volatile methylated amines, the precursors of the greenhouse gas nitrous oxide. However, it was not known how TMAO is recognized and imported by bacteria. Ruegeria pomeroyi DSS-3, a marine Roseobacter, has an ATP-binding cassette transporter, TmoXWV, specific for TMAO. TmoX is the substrate-binding protein of the TmoXWV transporter. In this study, the substrate specificity of TmoX of R. pomeroyi DSS-3 was characterized. We further determined the structure of the TmoX/TMAO complex and studied the TMAO-binding mechanism of TmoX by biochemical, structural, and mutational analyses. A Ca2+ ion chelated by an extended loop in TmoX was shown to be important for maintaining the stability of TmoX. Molecular dynamics simulations indicate that TmoX can alternate between "open" and "closed" states for binding TMAO. In the substrate-binding pocket, four tryptophan residues interact with the quaternary amine of TMAO by cation-pi interactions, and Glu131 forms a hydrogen bond with the polar oxygen atom of TMAO. The pi-pi stacking interactions between the side chains of Phe and Trp are also essential for TMAO binding. Sequence analysis suggests that the TMAO-binding mechanism of TmoX may have universal significance in marine bacteria, especially in the marine Roseobacter clade. This study sheds light on how marine microorganisms utilize TMAO.IMPORTANCETrimethylamine N-oxide (TMAO) is an important nitrogen source for marine bacteria. The products of TMAO metabolized by bacteria are part of the precursors of the greenhouse gas nitrous oxide. It is unclear how TMAO is recognized and imported by bacteria. TmoX is the substrate-binding protein of a TMAO-specific transporter. Here, the substrate specificity of TmoX of Ruegeria pomeroyi DSS-3 was characterized. The TMAO-binding mechanism of TmoX was studied by biochemical, structural, and mutational analyses. Moreover, our results suggest that the TMAO-binding mechanism may have universal significance in marine bacteria. This study sheds light on how marine microorganisms utilize TMAO and should lead to a better understanding of marine nitrogen cycling.