Dataset Information

Pulsed SILAC proteomics analysis of Escherichia coli RPL11 methyltransferase PrmA mutant

ABSTRACT: 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.

INSTRUMENT(S): Q Exactive HF-X

ORGANISM(S): Escherichia Coli Bw25113 (ncbitaxon:679895)

SUBMITTER: Ernesto Nakayasu

PROVIDER: MSV000094475 | MassIVE | Fri Apr 05 14:37:00 BST 2024

REPOSITORIES: MassIVE

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Publications

Regulation of bacterial stringent response by an evolutionarily conserved ribosomal protein L11 methylation.

Walukiewicz Hanna E HE Farris Yuliya Y Burnet Meagan C MC Feid Sarah C SC You Youngki Y Kim Hyeyoon H Bank Thomas T Christensen David D Payne Samuel H SH Wolfe Alan J AJ Rao Christopher V CV Nakayasu Ernesto S ES

mBio 20240827 10

Lysine and arginine methylation is an important regulator of enzyme activity and transcription in eukaryotes. However, little is known about this covalent modification in bacteria. In this work, we investigated the role of methylation in bacteria. By reanalyzing a large phyloproteomics data set from 48 bacterial strains representing six phyla, we found that almost a quarter of the bacterial proteome is methylated. Many of these methylated proteins are conserved across diverse bacterial lineages, ...[more]

PMID: 39189746

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