Characterization of the consequences of YidC depletion on the inner membrane proteome of E. coli using 2D blue native/SDS-PAGE

D. Wickstrom, S. Wagner, P. Simonsson, O. Pop, L Baars, A.J. Ytterberg, K.J. van Wijk, J. Luirink, J.W. de Gier

Research output: Contribution to JournalArticleAcademicpeer-review

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. © 2011 Elsevier Ltd. All rights reserved.
Original languageEnglish
Pages (from-to)124-35
JournalJournal of Molecular Biology
Volume409
DOIs
Publication statusPublished - 2011

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Native Polyacrylamide Gel Electrophoresis
Inosine Monophosphate
Proteome
Polyacrylamide Gel Electrophoresis
Escherichia coli
Membranes
Membrane Proteins
Amino Acids
Proteins
Bacteria

Bibliographical note

1089-8638 Wickstrom, David Wagner, Samuel Simonsson, Per Pop, Ovidiu Baars, Louise Ytterberg, A Jimmy van Wijk, Klaas J Luirink, Joen de Gier, Jan-Willem L 5R01GM081827-03/GM/NIGMS NIH HHS/United States Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't England J Mol Biol. 2011 Jun 3;409(2):124-35. doi: 10.1016/j.jmb.2011.03.068. Epub 2011 Apr 8.

Cite this

Wickstrom, D. ; Wagner, S. ; Simonsson, P. ; Pop, O. ; Baars, L ; Ytterberg, A.J. ; van Wijk, K.J. ; Luirink, J. ; de Gier, J.W. / Characterization of the consequences of YidC depletion on the inner membrane proteome of E. coli using 2D blue native/SDS-PAGE. In: Journal of Molecular Biology. 2011 ; Vol. 409. pp. 124-35.
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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. {\circledC} 2011 Elsevier Ltd. All rights reserved.",
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Characterization of the consequences of YidC depletion on the inner membrane proteome of E. coli using 2D blue native/SDS-PAGE. / Wickstrom, D.; Wagner, S.; Simonsson, P.; Pop, O.; Baars, L; Ytterberg, A.J.; van Wijk, K.J.; Luirink, J.; de Gier, J.W.

In: Journal of Molecular Biology, Vol. 409, 2011, p. 124-35.

Research output: Contribution to JournalArticleAcademicpeer-review

TY - JOUR

T1 - Characterization of the consequences of YidC depletion on the inner membrane proteome of E. coli using 2D blue native/SDS-PAGE

AU - Wickstrom, D.

AU - Wagner, S.

AU - Simonsson, P.

AU - Pop, O.

AU - Baars, L

AU - Ytterberg, A.J.

AU - van Wijk, K.J.

AU - Luirink, J.

AU - de Gier, J.W.

N1 - 1089-8638 Wickstrom, David Wagner, Samuel Simonsson, Per Pop, Ovidiu Baars, Louise Ytterberg, A Jimmy van Wijk, Klaas J Luirink, Joen de Gier, Jan-Willem L 5R01GM081827-03/GM/NIGMS NIH HHS/United States Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't England J Mol Biol. 2011 Jun 3;409(2):124-35. doi: 10.1016/j.jmb.2011.03.068. Epub 2011 Apr 8.

PY - 2011

Y1 - 2011

N2 - 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. © 2011 Elsevier Ltd. All rights reserved.

AB - 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. © 2011 Elsevier Ltd. All rights reserved.

U2 - 10.1016/j.jmb.2011.03.068

DO - 10.1016/j.jmb.2011.03.068

M3 - Article

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EP - 135

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

SN - 0022-2836

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