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The YdiU Domain Modulates Bacterial Stress Signaling through Mn2+-dependent UMPylation

By Yinlong Yang, Yingying Yue, Nannan Song, Cuiling Li, Zenglin Yuan, Yan Wang, Yue Ma, Hui Li, Fengyu Zhang, Weiwei Wang, Haihong Jia, Peng Li, Xiaobing Li, Qi Wang, Zhe Ding, Hongjie Dong, Lichuan Gu, Bingqing Li

Posted 04 Jul 2019
bioRxiv DOI: 10.1101/692707 (published DOI: 10.1016/j.celrep.2020.108161)

Sensing stressful conditions and adjusting cellular metabolism to adapt to the environment is essential for bacteria to survive in variable situations. Here, we describe a new stress-related protein YdiU, and characterize YdiU as an enzyme that catalyzes the covalent attachment of uridine 5’-monophosphate to a protein tyrosine/histidine residue—a novel modification defined as UMPylation. Mn2+ serves as an essential co-factor for YdiU-mediated UMPylation. UTP and Mn2+-binding converts YdiU to an aggregate-prone state facilitating the recruitment of chaperones. The UMPylation of chaperones prevents them from binding co-factors or clients, thereby impairing their function. Consistent with the recent finding that YdiU acts as an AMPylator, we further demonstrate that the self-AMPylation of YdiU padlocks its chaperone-UMPylation activity. The detailed mechanism is proposed based on Apo-YdiU, YdiU-ATP, YdiU-AMP crystal structures and molecular dynamics simulation models of YdiU-UTP and YdiU-UTP-peptide. In vivo data demonstrate that YdiU effectively protects Salmonella from stress-induced ATP depletion through UMPylation. Highlights 1. YdiU involves in stress-resistance of Salmonella . 2. YdiU mediates protein UMPylation in a Mn2+-dependent manner. 3. Structural insights into YdiU-mediated UMPylation. 4. UMPylation of chaperones by YdiU modulates their function.

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