MassIVE MSV000094475

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Pulsed SILAC proteomics analysis of Escherichia coli RPL11 methyltransferase PrmA mutant

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Description

For the pulse-chase experiment, E. coli BW25113 and its isogenic delta prmA strains were grown in M9 minimal medium and L-Lysine-2HCl (13C6, 15N2) was added to cultures in exponential and stationary phase. The cells were cultured for an additional 2 hr and harvested. Proteins from the wild-type and delta prmA strains were extracted, digested with trypsin, and analyzed by LC-MS/MS on a Q-Exactive HF-X. LC-MS/MS data was processed with MaxQuant v2.2.0.0, identifying peptides by searching tandem mass spectra against the E. coli K12 sequences from Uniprot Knowledgebase downloaded on December 19, 2022. The search parameters included fully LysC digestion with 2 missed cleavage sites, oxidation of methionine as variable modifications, and precursor mass tolerances of 20 ppm and 4.5 ppm for the first and main searches, respectively. Multiplicity was set as 2 of a light channel, and a heavy channel with Lys8. The "requantify" function was enabled. [doi:10.25345/C51J97K3Q] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: bacteria ; methylation ; ribosome ; PrmA

Contact

Principal Investigators:
(in alphabetical order) 		Ernesto Nakayasu, Pacific Northwest National Laboratory, United States
Submitting User: alchemistmatt

Publications

Walukiewicz HE, Farris Y, Burnet MC, Feid SC, You Y, Kim H, Bank T, Christensen D, Payne SH, Wolfe AJ, Rao CV, Nakayasu ES.
Regulation of bacterial stringent response by an evolutionarily conserved ribosomal protein L11 methylation.
mBio. 2024 Oct 16;15(10):e0177324. Epub 2024 Aug 27.

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