{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Yu S"],"funding":["R&D Program of Guangzhou National Laboratory","福 建 省 科 技 厅 | Natural Science Foundation of Fujian Province","MOST | National Natural Science Foundation of China (NSFC)","| Natural Science Foundation of Fujian Province (Fujian Natural Science Foundation)","R&D Program of Guangzhou National Laboratory","The Fourteenth Five-Year National Key Reaech and Development Program of China","MOST | National Natural Science Foundation of China"],"pagination":["1367-1384"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11894153"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["26(5)"],"pubmed_abstract":["Cyclic diguanosine monophosphate (c-di-GMP) is a ubiquitous bacterial secondary messenger with diverse functions. A previous Escherichia coli proteome microarray identified that c-di-GMP binds to the 23S rRNA methyltransferases RlmI and RlmE. Here we show that c-di-GMP inhibits RlmI activity in rRNA methylation assays, and that it modulates ribosome assembly in the presence of kanamycin. Molecular dynamics simulation and mutagenesis studies reveal that c-di-GMP binds to RlmI at residues R64, R103, G114, and K201. Structural simulations indicate that c-di-GMP quenches RlmI activity by inducing the closure of the catalytic pocket. We also show that c-di-GMP promotes antibiotic tolerance through RlmI. Binding and methylation assays indicate that the inhibitory effect of c-di-GMP on RlmI is co"],"journal":["EMBO reports"],"pubmed_title":["c-di-GMP inhibits rRNA methylation and impairs ribosome assembly in the presence of kanamycin."],"pmcid":["PMC11894153"],"funding_grant_id":["32000027","2022J01197","GZNL2023A01005","92374110","2023YFC2307200"],"pubmed_authors":["Shen J","Yu S","Hu Z","Liang X","Liu M","Chen H","Xu X","Lin M","Tao SC","Xu Z","Marti J"],"additional_accession":[]},"is_claimable":false,"name":"c-di-GMP inhibits rRNA methylation and impairs ribosome assembly in the presence of kanamycin.","description":"Cyclic diguanosine monophosphate (c-di-GMP) is a ubiquitous bacterial secondary messenger with diverse functions. A previous Escherichia coli proteome microarray identified that c-di-GMP binds to the 23S rRNA methyltransferases RlmI and RlmE. Here we show that c-di-GMP inhibits RlmI activity in rRNA methylation assays, and that it modulates ribosome assembly in the presence of kanamycin. Molecular dynamics simulation and mutagenesis studies reveal that c-di-GMP binds to RlmI at residues R64, R103, G114, and K201. Structural simulations indicate that c-di-GMP quenches RlmI activity by inducing the closure of the catalytic pocket. We also show that c-di-GMP promotes antibiotic tolerance through RlmI. Binding and methylation assays indicate that the inhibitory effect of c-di-GMP on RlmI is co","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Mar","modification":"2026-06-02T19:18:17.199Z","creation":"2025-04-04T02:50:58.473Z"},"accession":"S-EPMC11894153","cross_references":{"pubmed":["39870966"],"doi":["10.1038/s44319-025-00377-w"]}}