title: Characterization of the consequences of YidC depletion on the inner membrane proteome of E. coli using 2D blue native/SDS-PAGE.
abstract: In the bacterium Escherichia coli, the essential inner membrane protein (IMP) YidC assists in the biogenesis of IMPs and IMP complexes. Our current ideas about the function of YidC are based on targeted approaches using only a handful of model IMPs. Proteome-wide approaches are required to further our understanding of the significance of YidC and to find new YidC substrates. Here, using two-dimensional blue native/SDS-PAGE methodology that is suitable for comparative analysis, we have characterized the consequences of YidC depletion for the steady-state levels and oligomeric state of the constituents of the inner membrane proteome. Our analysis showed that (i) YidC depletion reduces the levels of a variety of complexes without changing their composition, (ii) the levels of IMPs containing only soluble domains smaller than 100 amino acids are likely to be reduced upon YidC depletion, whereas the levels of IMPs with at least one soluble domain larger than 100 amino acids do not, and (iii) the levels of a number of proteins with established or putative chaperone activity (HflC, HflK, PpiD, OppA, GroEL and DnaK) are strongly increased in the inner membrane fraction upon YidC depletion. In the absence of YidC, these proteins may assist the folding of sizeable soluble domains of IMPs, thereby supporting their folding and oligomeric assembly. In conclusion, our analysis identifies many new IMPs/IMP complexes that depend on YidC for their biogenesis, responses that accompany depletion of YidC and an IMP characteristic that is associated with YidC dependence.
authors.affiliation: Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
authors.forename: David
authors.initials: D
authors.lastname: Wickström
authors.forename: Samuel
authors.initials: S
authors.lastname: Wagner
authors.forename: Per
authors.initials: P
authors.lastname: Simonsson
authors.forename: Ovidiu
authors.initials: O
authors.lastname: Pop
authors.forename: Louise
authors.initials: L
authors.lastname: Baars
authors.forename: A Jimmy
authors.initials: AJ
authors.lastname: Ytterberg
authors.forename: Klaas J
authors.initials: KJ
authors.lastname: van Wijk
authors.forename: Joen
authors.initials: J
authors.lastname: Luirink
authors.forename: Jan-Willem L
authors.initials: JW
authors.lastname: de Gier
mesh_terms: D049069:ATP-Dependent Proteases / Q000378:metabolism; D002462:Cell Membrane / Q000378:metabolism*; D015180:Electrophoresis, Gel, Two-Dimensional; D004591:Electrophoresis, Polyacrylamide Gel; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D017353:Gene Deletion; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism*; D026901:Membrane Transport Proteins / Q000235:genetics / Q000378:metabolism*; D010455:Peptides / Q000378:metabolism; D011485:Protein Binding; D020543:Proteome / Q000032:analysis*; D018271:Signal Recognition Particle; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: D029968:Escherichia coli Proteins; C512893:HflC protein, E coli; C512891:HflK protein, E coli; D008565:Membrane Proteins; D026901:Membrane Transport Proteins; D010455:Peptides; D020543:Proteome; C511296:QmcA protein, E coli; D018271:Signal Recognition Particle; C412443:YIDC protein, E coli; D049069:ATP-Dependent Proteases; C513383:FtsH protein, E coli