Bcl2-associated Athanogene 3 Interactome Analysis Reveals a New Role in Modulating Proteasome Activity*

Bcl2-associated athanogene 3 (BAG3), a member of the BAG family of co-chaperones, plays a critical role in regulating apoptosis, development, cell motility, autophagy, and tumor metastasis and in mediating cell adaptive responses to stressful stimuli. BAG3 carries a BAG domain, a WW domain, and a proline-rich repeat (PXXP), all of which mediate binding to different partners. To elucidate BAG3's interaction network at the molecular level, we employed quantitative immunoprecipitation combined with knockdown and human proteome microarrays to comprehensively profile the BAG3 interactome in humans. We identified a total of 382 BAG3-interacting proteins with diverse functions, including transferase activity, nucleic acid binding, transcription factors, proteases, and chaperones, suggesting that BAG3 is a critical regulator of diverse cellular functions. In addition, we characterized interactions between BAG3 and some of its newly identified partners in greater detail. In particular, bioinformatic analysis revealed that the BAG3 interactome is strongly enriched in proteins functioning within the proteasome-ubiquitination process and that compose the proteasome complex itself, suggesting that a critical biological function of BAG3 is associated with the proteasome. Functional studies demonstrated that BAG3 indeed interacts with the proteasome and modulates its activity, sustaining cell survival and underlying resistance to therapy through the down-modulation of apoptosis. Taken as a whole, this study expands our knowledge of the BAG3 interactome, provides a valuable resource for understanding how BAG3 affects different cellular functions, and demonstrates that biologically relevant data can be harvested using this kind of integrated approach.

[1]  Yan Wu,et al.  Quantitative Quality Control in Microarray Experiments and the Application in Data Filtering, Normalization and False Positive Rate Prediction , 2003, Bioinform..

[2]  Lan Huang,et al.  An Integrated Mass Spectrometry-based Proteomic Approach , 2006, Molecular & Cellular Proteomics.

[3]  V. Strom,et al.  What's in the "pure" prosody? , 1996, Proceeding of Fourth International Conference on Spoken Language Processing. ICSLP '96.

[4]  M. Bogyo,et al.  A proteolytic system that compensates for loss of proteasome function , 1998, Nature.

[5]  S. Lindquist,et al.  Inhibiting the transcription factor HSF1 as an anticancer strategy. , 2009, Expert opinion on therapeutic targets.

[6]  Shu-juan Guo,et al.  Protein microarrays for systems biology , 2011, Acta biochimica et biophysica Sinica.

[7]  B. Penke,et al.  Protein array based interactome analysis of amyloid-β indicates an inhibition of protein translation. , 2011, Journal of proteome research.

[8]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[9]  Bao-qin Liu,et al.  Proteasome inhibitor MG132 induces BAG3 expression through activation of heat shock factor 1 , 2009, Journal of cellular physiology.

[10]  V. de Laurenzi,et al.  BAG3: a multifaceted protein that regulates major cell pathways , 2011, Cell Death and Disease.

[11]  L. Bi,et al.  Proteomic analysis of multiple myeloma: Current status and future perspectives , 2011, Proteomics. Clinical applications.

[12]  M. Merville,et al.  BCL-3 Degradation Involves Its Polyubiquitination through a FBW7-independent Pathway and Its Binding to the Proteasome Subunit PSMB1* , 2010, The Journal of Biological Chemistry.

[13]  D. Sawyer,et al.  Heat shock proteins in cancer: chaperones of tumorigenesis. , 2006, Trends in biochemical sciences.

[14]  Y. Guan,et al.  Transcriptional upregulation of BAG3 upon proteasome inhibition. , 2008, Biochemical and biophysical research communications.

[15]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[16]  Monica H. Elliott,et al.  Current trends in quantitative proteomics. , 2009, Journal of mass spectrometry : JMS.

[17]  T. Reinheckel,et al.  Proteolysis in Cultured Liver Epithelial Cells during Oxidative Stress , 1995, The Journal of Biological Chemistry.

[18]  Lan Huang,et al.  Oxidative Stress-Mediated Regulation of Proteasome Complexes* , 2011, Molecular & Cellular Proteomics.

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

[20]  Toshio Kitazawa,et al.  BAG3 and Hsc70 Interact With Actin Capping Protein CapZ to Maintain Myofibrillar Integrity Under Mechanical Stress , 2010, Circulation research.

[21]  C. Kyratsous,et al.  The co-chaperone BAG3 regulates Herpes Simplex Virus replication , 2008, Proceedings of the National Academy of Sciences.

[22]  Zhi-ping Zhang,et al.  Quantitative Proteomics Analysis Reveals BAG3 as a Potential Target To Suppress Severe Acute Respiratory Syndrome Coronavirus Replication , 2010, Journal of Virology.

[23]  Gary D. Bader,et al.  An automated method for finding molecular complexes in large protein interaction networks , 2003, BMC Bioinformatics.

[24]  Sung Kyu Park,et al.  A quantitative analysis software tool for mass spectrometry–based proteomics , 2008, Nature Methods.

[25]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[26]  A. Burlingame,et al.  Comprehensive mass spectrometric analysis of the 20S proteasome complex. , 2005, Methods in enzymology.

[27]  Christian von Mering,et al.  STRING 8—a global view on proteins and their functional interactions in 630 organisms , 2008, Nucleic Acids Res..

[28]  Jun Wan,et al.  Protein Acetylation Microarray Reveals that NuA4 Controls Key Metabolic Target Regulating Gluconeogenesis , 2009, Cell.

[29]  E. Kohn,et al.  Caught in the middle: the role of Bag3 in disease. , 2009, The Biochemical journal.

[30]  J. Buchner,et al.  The heat shock response: life on the verge of death. , 2010, Molecular cell.

[31]  D. Klionsky,et al.  Autophagosome formation: core machinery and adaptations , 2007, Nature Cell Biology.

[32]  E. Kohn,et al.  What's in the 'BAG'?--A functional domain analysis of the BAG-family proteins. , 2002, Cancer letters.

[33]  Heng Zhu,et al.  A proteome chip approach reveals new DNA damage recognition activities in Escherichia coli , 2008, Nature Methods.

[34]  M. Gerstein,et al.  Global Analysis of Protein Activities Using Proteome Chips , 2001, Science.

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

[36]  Tijana Milenkovic,et al.  Characterization of the proteasome interaction network using a QTAX-based tag-team strategy and protein interaction network analysis , 2008, Proceedings of the National Academy of Sciences.

[37]  M. Askenazi,et al.  A QUICK Screen for Lrrk2 Interaction Partners – Leucine-rich Repeat Kinase 2 is Involved in Actin Cytoskeleton Dynamics* , 2010, Molecular & Cellular Proteomics.

[38]  J. Adams,et al.  The proteasome: structure, function, and role in the cell. , 2003, Cancer treatment reviews.

[39]  Jef D. Boeke,et al.  Rapid Identification of Monospecific Monoclonal Antibodies Using a Human Proteome Microarray* , 2012, Molecular & Cellular Proteomics.

[40]  Nan Guo,et al.  PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways , 2006, Nucleic Acids Res..

[41]  B. Striepen,et al.  Autophagy Protein Atg3 is Essential for Maintaining Mitochondrial Integrity and for Normal Intracellular Development of Toxoplasma gondii Tachyzoites , 2011, PLoS pathogens.

[42]  J. Driscoll,et al.  The ubiquitin+proteasome protein degradation pathway as a therapeutic strategy in the treatment of solid tumor malignancies. , 2011, Anti-cancer agents in medicinal chemistry.

[43]  E. Kohn,et al.  CAIR-1/BAG-3 forms an EGF-regulated ternary complex with phospholipase C-gamma and Hsp70/Hsc70. , 2000, Oncogene.

[44]  L. Kay,et al.  Novel proteasome inhibitors to overcome bortezomib resistance. , 2011, Journal of the National Cancer Institute.

[45]  J. Workman,et al.  The proteasome and its regulatory roles in gene expression. , 2011, Biochimica et biophysica acta.

[46]  Heng Zhu,et al.  A functional protein microarray approach to characterizing posttranslational modifications on lysine residues. , 2011, Methods in molecular biology.

[47]  Christian von Mering,et al.  STRING: a database of predicted functional associations between proteins , 2003, Nucleic Acids Res..

[48]  E. Kohn,et al.  CAIR-1/BAG-3 Abrogates Heat Shock Protein-70 Chaperone Complex-mediated Protein Degradation , 2003, Journal of Biological Chemistry.

[49]  Brendan K Faherty,et al.  Optimization and Use of Peptide Mass Measurement Accuracy in Shotgun Proteomics*S , 2006, Molecular & Cellular Proteomics.

[50]  C. Behl BAG3 and friends: Co-chaperones in selective autophagy during aging and disease , 2011, Autophagy.

[51]  Heng Zhu,et al.  Applications of protein microarray technology. , 2007, Combinatorial chemistry & high throughput screening.

[52]  L. Holm,et al.  The Pfam protein families database , 2005, Nucleic Acids Res..

[53]  R. Ralhan,et al.  14-3-3 zeta as novel molecular target for cancer therapy , 2012, Expert opinion on therapeutic targets.

[54]  Michael Karin,et al.  Is NF-κB a good target for cancer therapy? Hopes and pitfalls , 2009, Nature Reviews Drug Discovery.

[55]  S. Charette,et al.  Identification of the key structural motifs involved in HspB8/HspB6-Bag3 interaction. , 2009, The Biochemical journal.

[56]  Y. Tsujimoto,et al.  Bis, a Bcl-2-binding protein that synergizes with Bcl-2 in preventing cell death , 1999, Oncogene.

[57]  M. Mann,et al.  Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK) , 2006, Nature Methods.

[58]  B. Monsarrat,et al.  Affinity Purification Strategy to Capture Human Endogenous Proteasome Complexes Diversity and to Identify Proteasome-interacting Proteins*S , 2009, Molecular & Cellular Proteomics.

[59]  S. Carra The stress-inducible HspB8-Bag3 complex induces the eIF2α kinase pathway: Implications for protein quality control and viral factory degradation? , 2009, Autophagy.

[60]  F. Gillardon,et al.  Protein array analysis of oligomerization-induced changes in alpha-synuclein protein–protein interactions points to an interference with Cdc42 effector proteins , 2008, Neuroscience.

[61]  Jaques Reifman,et al.  Categorizing Biases in High-Confidence High-Throughput Protein-Protein Interaction Data Sets* , 2011, Molecular & Cellular Proteomics.

[62]  D. Klionsky,et al.  Eaten alive: a history of macroautophagy , 2010, Nature Cell Biology.

[63]  L. Bi,et al.  QUICK identification and SPR validation of signal transducers and activators of transcription 3 (Stat3) interacting proteins. , 2012, Journal of proteomics.

[64]  M. Karin,et al.  Is NF-kappaB a good target for cancer therapy? Hopes and pitfalls. , 2009 .

[65]  K. Khalili,et al.  BAG3 Expression in Glioblastoma Cells Promotes Accumulation of Ubiquitinated Clients in an Hsp70-dependent Manner* , 2011, The Journal of Biological Chemistry.

[66]  H. Jarrett,et al.  Transcription factor proteomics: identification by a novel gel mobility shift-three-dimensional electrophoresis method coupled with southwestern blot and high-performance liquid chromatography-electrospray-mass spectrometry analysis. , 2011, Journal of chromatography. A.

[67]  J. Sebolt-Leopold,et al.  Targeting the mitogen-activated protein kinase cascade to treat cancer , 2004, Nature Reviews Cancer.

[68]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[69]  H. Kampinga,et al.  HspB8 Participates in Protein Quality Control by a Non-chaperone-like Mechanism That Requires eIF2α Phosphorylation* , 2009, Journal of Biological Chemistry.

[70]  C. Kyratsous,et al.  BAG3, a Host Cochaperone, Facilitates Varicella-Zoster Virus Replication , 2007, Journal of Virology.

[71]  Peipei Ping,et al.  Regulation of Murine Cardiac 20S Proteasomes: Role of Associating Partners , 2006, Circulation research.

[72]  L. Birolo,et al.  The co-chaperone BAG3 interacts with the cytosolic chaperonin CCT: new hints for actin folding. , 2010, The international journal of biochemistry & cell biology.

[73]  F. Hartl,et al.  Protein quality control during aging involves recruitment of the macroautophagy pathway by BAG3 , 2009, The EMBO journal.

[74]  L. Bi,et al.  Identification of novel 14-3-3ζ interacting proteins by quantitative immunoprecipitation combined with knockdown (QUICK). , 2010, Journal of proteome research.

[75]  M. Dickman,et al.  The BAG proteins: a ubiquitous family of chaperone regulators , 2008, Cellular and Molecular Life Sciences.

[76]  E. Solary,et al.  Heat shock proteins: essential proteins for apoptosis regulation , 2008, Journal of cellular and molecular medicine.

[77]  Brad T. Sherman,et al.  Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists , 2008, Nucleic acids research.

[78]  E. Kohn,et al.  CAIR-1/BAG-3 forms an EGF-regulated ternary complex with phospholipase C-γ and Hsp70/Hsc70 , 2000, Oncogene.