Determination of phosphorylation sites in the DivIVA cytoskeletal protein of Streptomyces coelicolor by targeted LC-MS/MS

Gerhard Saalbach, Antje M. Hempel, Marielle Vigouroux, Klas Flärdh, Mark J. Buttner, Michael J. Naldrett

Research output: Contribution to journalArticle

10 Scopus citations

Abstract

The filamentous bacterium Streptomyces coelicolor modulates polar growth and branching by phosphorylating the cytoskeletal protein DivIVA. Previous MALDI-TOF analysis of DivIVA showed that a large 7.2 kDa tryptic peptide was multiply phosphorylated. To aid localization of the phosphorylation sites, we introduced additional tryptic cleavage sites into DivIVA, and the resulting phosphopeptides were analyzed by LC-MS/MS. Phosphopeptide isomers could be separated chromatographically, but because of overlapping elution and spectrum quality, site assignment by standard software tools was ambiguous. Because fragment ions carrying the phosphate group are essential for confident localization, large numbers of spectra were collected using targeted LC-MS/MS, and a special script was developed for plotting the elution of site-determining fragments from those spectra under the XIC of the parent ions. Where multiple phosphopeptide isomers were present, the elution of the site-determining y-ions perfectly coincided with the elution of the corresponding phosphopeptide isomer. This method represents a useful tool for user inspection of spectra derived from phosphopeptide isomers and significantly increases confidence when defining phosphorylation sites. In this way, we show that DivIVA is phosphorylated in vivo on five sites in the C-terminal part of the protein (T304, S309, S338, S344, and S355). The data have been deposited to the ProteomeXchange Consortium with identifier PXD000095.

Original languageEnglish (US)
Pages (from-to)4187-4192
Number of pages6
JournalJournal of proteome research
Volume12
Issue number9
DOIs
StatePublished - Sep 6 2013

Keywords

  • Ascore
  • DivIVA
  • ScaffoldPTM
  • phosphopeptides
  • phosphorylation site localization
  • targeted LC-MS/MS

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

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