title: Proteome-wide identification of mycobacterial pupylation targets.
abstract: Mycobacteria use a unique system for covalently modifying proteins based on the conjugation of a small protein, referred to as prokaryotic ubiquitin-like protein (PUP). In this study, we report a proteome-wide analysis of endogenous pupylation targets in the model organism Mycobacterium smegmatis. On affinity capture, a total of 243 candidate pupylation targets were identified by two complementary proteomics approaches. For 41 of these protein targets, direct evidence for a total of 48 lysine-mediated pupylation acceptor sites was obtained by collision-induced dissociation spectra. For the majority of these pupylation targets (38 of 41), orthologous genes are found in the M. tuberculosis genome. Interestingly, approximately half of these proteins are involved in intermediary metabolism and respiration pathways. A considerable fraction of the remaining targets are involved in lipid metabolism, information pathways, and virulence, detoxification and adaptation. Approximately one-third of the genes encoding these targets are located in seven gene clusters, indicating functional linkages of mycobacterial pupylation targets. A comparison of the pupylome under different cell culture conditions indicates that substrate targeting for pupylation is rather dynamic.
authors.affiliation: EMBL-Hamburg Unit, European Molecular Biology Laboratory, Hamburg, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Poulsen
authors.forename: Yusuf
authors.initials: Y
authors.lastname: Akhter
authors.forename: Amy Hye-Won
authors.initials: AH
authors.lastname: Jeon
authors.forename: Gerold
authors.initials: G
authors.lastname: Schmitt-Ulms
authors.forename: Helmut E
authors.initials: HE
authors.lastname: Meyer
authors.forename: Anja
authors.initials: A
authors.lastname: Stefanski
authors.forename: Kai
authors.initials: K
authors.lastname: Stühler
authors.forename: Matthias
authors.initials: M
authors.lastname: Wilmanns
authors.forename: Young-Hwa
authors.initials: YH
authors.lastname: Song
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D002853:Chromatography, Liquid; D004591:Electrophoresis, Polyacrylamide Gel; D013058:Mass Spectrometry; D005810:Multigene Family; D020102:Mycobacterium smegmatis / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D025941:Protein Interaction Mapping / Q000379:methods; D020543:Proteome / Q000378:metabolism; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014452:Ubiquitins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D020543:Proteome; D014452:Ubiquitins