Otal number of GFP-TRPML1-stained structures in a section and multiplied by 100. The graphs show the average from sections of at least eight different cells, with at least twenty GFP-TRPML1stained structures per cell.Results Identification of TRPML1 KDM5A-IN-1 interactors by Immunoprecipitation and Mass SpectrometryOur first approach for identifying TRPML1 interactors was immunoprecipitation combined with Mass Spectrometry. We immunoprecipitated GFP-TRPML1 or Derlin-1-GFP (an integral membrane protein found in the LY-2409021 web endoplasmic reticulum and endosomes) from stably expressing RAW264.7 clones in the absence of Ca2+ and then used Mass Spectrometry to identify proteins in each immunoprecipitate [19,34]. Proteins that coimmunoprecipitated with GFP-TRPML1 but not Derlin-1-GFP were considered potential TRPML1-specific interactors (Table S2). While this approach allowed us to eliminate many nonspecific interactors, the complexity of each sample imposes some limits on this stringency by detection failures. For example, some proteins that we characterized as candidates may actually be nonspecific interactors that escaped detection in the Derlin-1-GFPStrategy for Identifying Candidate TRPML1 InteractorsWe chose seven proteins identified by Immunoprecipitation/ Mass Spectrometry list and six proteins identified from the SUYTH screen to validate as TRPML1 candidate interactors with additional assays (highlighted in yellow in Tables S2 and S3). In addition, because we had identified the small GTPases Rac2 and Cdc42 by Immunoprecipitation/Mass Spectrometry, we tested two other closely related family members, Rac1 and RhoG (Table S2). Furthermore, we tested two Phosphatidylinositol 4-Phosphate 5-Kinase type I-beta (P5KT1) homologous proteins that are encoded by different genes, BAA13031 on chromosome 3 (a 11967625 truncated form encoding the first 366 amino acids of this protein was identified by the SU-YTH screen; Table S3) and NP_032872 on chromosome 19. We amplified by Polymerase Chain reaction (PCR) full-length mouse cDNAs corresponding to these proteins and used GatewayProteins That Interact with TRPMLFigure 2. Immunoprecipitation Tests 
of Candidate Interactors. Plasmids expressing GFP (control) or murine GFP-TRPML1 protein were cotransfected with plasmids expressing V5 fusions to candidate interactors into HeLa cells. Anti-GFP immunoprecipitation was performed on lysates. Left panels are Western blots that show total expression in lysates and right panels are Western blots of immunoprecipitates (IP). Red lettering indicates lanes exhibiting co-immunoprecipitation with GFP-TRPML1. The top left, boxed panel shows a typical pattern of GFP-TRPML1 bands: PR = processed/cleaved; FL = full-length; OG = oligomer. doi:10.1371/journal.pone.0056780.gProteins That Interact with TRPMLTable 1. TRPML1 Interactions Summary.IP (2Ca2+) 2 ++* 2 2 + +/2 2 2 ++ ++ 2 + ++ 2 2Protein PEA-15 STOML1 DNAJ HOM NDKA Rac2 Cdc42 Rac1 RhoG NP9 ERGIC P5KT1 (BAA) P5KT1 (NP) YIF1 BAE PMP2 PEXSplit-Ub YTH +/2 2 2 ++ ++ ++ + 2 + + ND 2 + + ++ ++Co-localization + ++ 2 2 ++ ++ 2 ++ ++ 2 2 2 2 + 2Qualitative assessment of interactions. Plus signs indicate interaction; minus signs indicate lack of interaction. Immunoprecipitation interaction strength was based on length of time before anti-V5 band appeared (anti-GFP bands appeared with 1 second of film exposure). Asterisk indicates that endogenous mouse STOML1 co-immunoprecipitates with GFP-TRPML1 in murine RAW264.7 macrophages. Split-Ubiquitin Yeast Two-Hy.Otal number of GFP-TRPML1-stained structures in a section and multiplied by 100. The graphs show the average from sections of at least eight different cells, with at least twenty GFP-TRPML1stained structures per cell.Results Identification of TRPML1 Interactors by Immunoprecipitation and Mass SpectrometryOur first approach for identifying TRPML1 interactors was immunoprecipitation combined with Mass Spectrometry. We immunoprecipitated GFP-TRPML1 or Derlin-1-GFP (an integral membrane protein found in the endoplasmic reticulum and endosomes) from stably expressing RAW264.7 clones in the absence of Ca2+ and then used Mass Spectrometry to identify proteins in each immunoprecipitate [19,34]. Proteins that coimmunoprecipitated with GFP-TRPML1 but not Derlin-1-GFP were considered potential TRPML1-specific interactors (Table S2). While this approach allowed us to eliminate many nonspecific interactors, the complexity of each sample imposes some limits on this stringency by detection failures. For example, some proteins that we characterized as candidates may actually be nonspecific interactors that escaped detection in the Derlin-1-GFPStrategy for Identifying Candidate TRPML1 InteractorsWe chose seven proteins identified by Immunoprecipitation/ Mass Spectrometry list and six proteins identified from the SUYTH screen to validate as TRPML1 candidate interactors with additional assays (highlighted in yellow in Tables S2 and S3). In addition, because we had identified the small GTPases Rac2 and Cdc42 by Immunoprecipitation/Mass Spectrometry, we tested two other closely related family members, Rac1 and RhoG (Table S2). Furthermore, we tested two Phosphatidylinositol 4-Phosphate 5-Kinase type I-beta (P5KT1) homologous proteins that are encoded by different genes, BAA13031 on chromosome 3 (a 11967625 truncated form encoding the first 366 amino acids of this protein 
was identified by the SU-YTH screen; Table S3) and NP_032872 on chromosome 19. We amplified by Polymerase Chain reaction (PCR) full-length mouse cDNAs corresponding to these proteins and used GatewayProteins That Interact with TRPMLFigure 2. Immunoprecipitation Tests of Candidate Interactors. Plasmids expressing GFP (control) or murine GFP-TRPML1 protein were cotransfected with plasmids expressing V5 fusions to candidate interactors into HeLa cells. Anti-GFP immunoprecipitation was performed on lysates. Left panels are Western blots that show total expression in lysates and right panels are Western blots of immunoprecipitates (IP). Red lettering indicates lanes exhibiting co-immunoprecipitation with GFP-TRPML1. The top left, boxed panel shows a typical pattern of GFP-TRPML1 bands: PR = processed/cleaved; FL = full-length; OG = oligomer. doi:10.1371/journal.pone.0056780.gProteins That Interact with TRPMLTable 1. TRPML1 Interactions Summary.IP (2Ca2+) 2 ++* 2 2 + +/2 2 2 ++ ++ 2 + ++ 2 2Protein PEA-15 STOML1 DNAJ HOM NDKA Rac2 Cdc42 Rac1 RhoG NP9 ERGIC P5KT1 (BAA) P5KT1 (NP) YIF1 BAE PMP2 PEXSplit-Ub YTH +/2 2 2 ++ ++ ++ + 2 + + ND 2 + + ++ ++Co-localization + ++ 2 2 ++ ++ 2 ++ ++ 2 2 2 2 + 2Qualitative assessment of interactions. Plus signs indicate interaction; minus signs indicate lack of interaction. Immunoprecipitation interaction strength was based on length of time before anti-V5 band appeared (anti-GFP bands appeared with 1 second of film exposure). Asterisk indicates that endogenous mouse STOML1 co-immunoprecipitates with GFP-TRPML1 in murine RAW264.7 macrophages. Split-Ubiquitin Yeast Two-Hy.
