Proteomic Plasma Membrane Profiling Reveals an Essential Role for gp96 in the Cell Surface Expression of LDLR Family Members, Including the LDL Receptor and LRP6

The endoplasmic reticulum chaperone gp96 is required for the cell surface expression of a narrow range of proteins, including toll-like receptors (TLRs) and integrins. To identify a more comprehensive repertoire of proteins whose cell surface expression is dependent on gp96, we developed plasma membrane profiling (PMP), a technique that combines SILAC labeling with selective cell surface aminooxy-biotinylation. This approach allowed us to compare the relative abundance of plasma membrane (PM) proteins on gp96-deficient versus gp96-reconstituted murine pre-B cells. Analysis of unfractionated tryptic peptides initially identified 113 PM proteins, which extended to 706 PM proteins using peptide prefractionation. We confirmed a requirement for gp96 in the cell surface expression of certain TLRs and integrins and found a marked decrease in cell surface expression of four members of the extended LDL receptor family (LDLR, LRP6, Sorl1 and LRP8) in the absence of gp96. Other novel gp96 client proteins included CD180/Ly86, important in the B-cell response to lipopolysaccharide. We highlight common structural motifs in these client proteins that may be recognized by gp96, including the beta-propeller and leucine-rich repeat. This study therefore identifies the extended LDL receptor family as an important new family of proteins whose cell surface expression is regulated by gp96.

[1]  J. Zempleni,et al.  Biotinylation is a natural, albeit rare, modification of human histones. , 2011, Molecular genetics and metabolism.

[2]  Aleksandra Stojanovic,et al.  Heat-shock protein gp96/grp94 is an essential chaperone for the platelet glycoprotein Ib-IX-V complex. , 2011, Blood.

[3]  Zhihua Liu,et al.  S100A14 Stimulates Cell Proliferation and Induces Cell Apoptosis at Different Concentrations via Receptor for Advanced Glycation End Products (RAGE) , 2011, PloS one.

[4]  M. Mann,et al.  Andromeda: a peptide search engine integrated into the MaxQuant environment. , 2011, Journal of proteome research.

[5]  Jan Albert Kuivenhoven,et al.  Genetic variant of the scavenger receptor BI in humans. , 2011, The New England journal of medicine.

[6]  M. Weekes,et al.  Comparative analysis of techniques to purify plasma membrane proteins. , 2010, Journal of biomolecular techniques : JBT.

[7]  B. Hao,et al.  Folding of Toll-like receptors by the HSP90 paralogue gp96 requires a substrate-specific cochaperone , 2010, Nature communications.

[8]  Devin Dersh,et al.  GRP94 in ER quality control and stress responses. , 2010, Seminars in cell & developmental biology.

[9]  S. Bloor,et al.  Endoplasmic reticulum chaperone gp96 is essential for infection with vesicular stomatitis virus , 2010, Proceedings of the National Academy of Sciences.

[10]  Matthew M. Staron,et al.  gp96, an endoplasmic reticulum master chaperone for integrins and Toll-like receptors, selectively regulates early T and B lymphopoiesis. , 2010, Blood.

[11]  Catherine A Makarewich,et al.  Glucose regulated protein 94 is required for muscle differentiation through its control of the autocrine production of insulin-like growth factors. , 2010, Biochimica et biophysica acta.

[12]  B. Hao,et al.  TLRs and Integrins Bond-Independent Chaperone Function for HSP 90 b 1 , HSPC 4 ) and Retains Disulfide ( grp 94 , Mammalian Heat Shock Protein gp 96 Glycoprotein 93 Is an Ortholog of Drosophila , 2009 .

[13]  Donald Gullberg,et al.  Integrins , 2009, Cell and Tissue Research.

[14]  G. Bu,et al.  Cooperative Folding and Ligand-binding Properties of LRP6 β-Propeller Domains* , 2009, Journal of Biological Chemistry.

[15]  P. Lehner,et al.  Stable Isotope Labeling by Amino Acids in Cell Culture and Differential Plasma Membrane Proteome Quantitation Identify New Substrates for the MARCH9 Transmembrane E3 Ligase , 2009, Molecular & Cellular Proteomics.

[16]  M. Mann,et al.  Universal sample preparation method for proteome analysis , 2009, Nature Methods.

[17]  Ruedi Aebersold,et al.  Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins , 2009, Nature Biotechnology.

[18]  O. Ostrovsky,et al.  The chaperone activity of GRP94 toward insulin-like growth factor II is necessary for the stress response to serum deprivation. , 2009, Molecular biology of the cell.

[19]  T. Ramya,et al.  High-efficiency labeling of sialylated glycoproteins on living cells , 2009, Nature Methods.

[20]  Ronald T Raines,et al.  Hydrolytic stability of hydrazones and oximes. , 2008, Angewandte Chemie.

[21]  B. Doble,et al.  Prevention of Amino Acid Conversion in SILAC Experiments with Embryonic Stem Cells * , 2008, Molecular & Cellular Proteomics.

[22]  Zihai Li,et al.  Endoplasmic reticulum HSP90b1 (gp96, grp94) optimizes B-cell function via chaperoning integrin and TLR but not immunoglobulin. , 2008, Blood.

[23]  P. McEwan,et al.  The leucine-rich repeat structure , 2008, Cellular and Molecular Life Sciences.

[24]  David L. Smith,et al.  Signal processing by its coil zipper domain activates IKKγ , 2008, Proceedings of the National Academy of Sciences.

[25]  Matthias Mann,et al.  In-depth Analysis of the Adipocyte Proteome by Mass Spectrometry and Bioinformatics*S , 2007, Molecular & Cellular Proteomics.

[26]  S. Blacklow,et al.  Requirement for natively unstructured regions of mesoderm development candidate 2 in promoting low-density lipoprotein receptor-related protein 6 maturation. , 2007, Biochemistry.

[27]  A. Soutar,et al.  Mechanisms of Disease: genetic causes of familial hypercholesterolemia , 2007, Nature Clinical Practice Cardiovascular Medicine.

[28]  P. Srivastava,et al.  Heat shock protein gp96 is a master chaperone for toll-like receptors and is important in the innate function of macrophages. , 2007, Immunity.

[29]  C. Harding.  gp96 leads the way for toll-like receptors. , 2007, Immunity.

[30]  K. Lunetta,et al.  The neuronal sortilin-related receptor SORL1 is genetically associated with Alzheimer disease , 2007, Nature Genetics.

[31]  K. Miyake,et al.  MD1 Expression Regulates Development of Regulatory T Cells , 2006, The Journal of Immunology.

[32]  Songping Liang,et al.  Integration of a two-phase partition method into proteomics research on rat liver plasma membrane proteins. , 2006, Journal of proteome research.

[33]  Wenyan Lu,et al.  Mesd binds to mature LDL-receptor-related protein-6 and antagonizes ligand binding , 2005, Journal of Cell Science.

[34]  Martin Kuiper,et al.  BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks , 2005, Bioinform..

[35]  Hyesung Jeon,et al.  Structure and physiologic function of the low-density lipoprotein receptor. , 2005, Annual review of biochemistry.

[36]  A. Sonnenberg,et al.  Integrins control motile strategy through a Rho–cofilin pathway , 2005, The Journal of cell biology.

[37]  R. Nusse,et al.  The Wnt signaling pathway in development and disease. , 2004, Annual review of cell and developmental biology.

[38]  Eberhard Durr,et al.  Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture , 2004, Nature Biotechnology.

[39]  R. Mann,et al.  Boca‐dependent maturation of β‐propeller/EGF modules in low‐density lipoprotein receptor proteins , 2004, The EMBO journal.

[40]  C. Quattrocchi,et al.  Reelin Promotes Hippocampal Dendrite Development through the VLDLR/ApoER2-Dab1 Pathway , 2004, Neuron.

[41]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[42]  J. Herz,et al.  LDL Receptor‐Related Proteins in Neurodevelopment , 2003, Traffic.

[43]  R. Mann,et al.  Boca, an Endoplasmic Reticulum Protein Required for Wingless Signaling and Trafficking of LDL Receptor Family Members in Drosophila , 2003, Cell.

[44]  J. Hsieh,et al.  Mesd Encodes an LRP5/6 Chaperone Essential for Specification of Mouse Embryonic Polarity , 2003, Cell.

[45]  B. Seed,et al.  Endoplasmic reticulum chaperone gp96 is required for innate immunity but not cell viability , 2001, Nature Cell Biology.

[46]  Y. Poirier,et al.  Analysis of the alternative pathways for the beta-oxidation of unsaturated fatty acids using transgenic plants synthesizing polyhydroxyalkanoates in peroxisomes. , 2000, Plant physiology.

[47]  K. Rajewsky,et al.  The Toll-like Receptor Protein Rp105 Regulates Lipopolysaccharide Signaling in B Cells , 2000, The Journal of experimental medicine.

[48]  K. Miyake,et al.  Mouse MD-1, a molecule that is physically associated with RP105 and positively regulates its expression. , 1998, Journal of immunology.

[49]  P Bork,et al.  Structure and distribution of modules in extracellular proteins , 1996, Quarterly Reviews of Biophysics.

[50]  K. Miyake,et al.  RP105, a novel B cell surface molecule implicated in B cell activation, is a member of the leucine-rich repeat protein family. , 1995, Journal of immunology.

[51]  Y. Argon,et al.  Sequential interaction of the chaperones BiP and GRP94 with immunoglobulin chains in the endoplasmic reticulum , 1994, Nature.

[52]  J. Hermes,et al.  Human cytoplasmic 3-hydroxy-3-methylglutaryl coenzyme A synthase: expression, purification, and characterization of recombinant wild-type and Cys129 mutant enzymes. , 1994, Archives of biochemistry and biophysics.

[53]  T. Springer,et al.  Primary structure of the leukocyte function-associated molecule-1 alpha subunit: an integrin with an embedded domain defining a protein superfamily , 1989, The Journal of cell biology.

[54]  Jürgen Cox,et al.  A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics , 2009, Nature Protocols.

[55]  Jing Gao,et al.  Integrating and annotating the interactome using the MiMI plugin for cytoscape , 2009, Bioinform..

[56]  C. Eyers.  Universal sample preparation method for proteome analysis , 2009 .

[57]  M. Mann,et al.  Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips , 2007, Nature Protocols.