1
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Montoya MR, Quanrud GM, Mei L, Moñtano JL, Hong C, Genereux JC. Factors affecting protein recovery during Hsp40 affinity profiling. Anal Bioanal Chem 2024; 416:4249-4260. [PMID: 38850318 PMCID: PMC11271386 DOI: 10.1007/s00216-024-05362-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 04/30/2024] [Accepted: 05/22/2024] [Indexed: 06/10/2024]
Abstract
The identification and quantification of misfolded proteins from complex mixtures is important for biological characterization and disease diagnosis, but remains a major bioanalytical challenge. We have developed Hsp40 Affinity Profiling as a bioanalytical approach to profile protein stability in response to cellular stress. In this assay, we ectopically introduce the Hsp40 FlagDNAJB8H31Q into cells and use quantitative proteomics to determine how protein affinity for DNAJB8 changes in the presence of cellular stress, without regard for native clients. Herein, we evaluate potential approaches to improve the performance of this bioanalytical assay. We find that although intracellular crosslinking increases recovery of protein interactors, this is not enough to overcome the relative drop in DNAJB8 recovery. While the J-domain promotes Hsp70 association, it does not affect the yield of protein association with DNAJB8 under basal conditions. By contrast, crosslinking and J-domain ablation both substantially increase relative protein interactor recovery with the structurally distinct Class B Hsp40 DNAJB1 but are completely compensated by poorer yield of DNAJB1 itself. Cellular thermal stress promotes increased affinity between DNAJB8H31Q and interacting proteins, as expected for interactions driven by recognition of misfolded proteins. DNAJB8WT does not demonstrate such a property, suggesting that under stress misfolded proteins are handed off to Hsp70. Hence, we find that DNAJB8H31Q is still our most effective recognition element for the recovery of destabilized client proteins following cellular stress.
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Affiliation(s)
- Maureen R Montoya
- Department of Chemistry, University of California, 501 Big Springs Rd, Riverside, CA, 92521, USA
| | - Guy M Quanrud
- Department of Chemistry, University of California, 501 Big Springs Rd, Riverside, CA, 92521, USA
| | - Liangyong Mei
- Department of Chemistry, University of North Florida, Jacksonville, FL, USA
| | - José L Moñtano
- Department of Chemistry, University of California, 501 Big Springs Rd, Riverside, CA, 92521, USA
| | - Caleb Hong
- Department of Chemistry, University of California, 501 Big Springs Rd, Riverside, CA, 92521, USA
| | - Joseph C Genereux
- Department of Chemistry, University of California, 501 Big Springs Rd, Riverside, CA, 92521, USA.
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2
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Taefehshokr N, Lac A, Vrieze AM, Dickson BH, Guo PN, Jung C, Blythe EN, Fink C, Aktar A, Dikeakos JD, Dekaban GA, Heit B. SARS-CoV-2 NSP5 antagonizes MHC II expression by subverting histone deacetylase 2. J Cell Sci 2024; 137:jcs262172. [PMID: 38682259 PMCID: PMC11166459 DOI: 10.1242/jcs.262172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 04/17/2024] [Indexed: 05/01/2024] Open
Abstract
SARS-CoV-2 interferes with antigen presentation by downregulating major histocompatibility complex (MHC) II on antigen-presenting cells, but the mechanism mediating this process is unelucidated. Herein, analysis of protein and gene expression in human antigen-presenting cells reveals that MHC II is downregulated by the SARS-CoV-2 main protease, NSP5. This suppression of MHC II expression occurs via decreased expression of the MHC II regulatory protein CIITA. CIITA downregulation is independent of the proteolytic activity of NSP5, and rather, NSP5 delivers HDAC2 to the transcription factor IRF3 at an IRF-binding site within the CIITA promoter. Here, HDAC2 deacetylates and inactivates the CIITA promoter. This loss of CIITA expression prevents further expression of MHC II, with this suppression alleviated by ectopic expression of CIITA or knockdown of HDAC2. These results identify a mechanism by which SARS-CoV-2 limits MHC II expression, thereby delaying or weakening the subsequent adaptive immune response.
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Affiliation(s)
- Nima Taefehshokr
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Alex Lac
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Angela M. Vrieze
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Brandon H. Dickson
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Peter N. Guo
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Catherine Jung
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Eoin N. Blythe
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Corby Fink
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Amena Aktar
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Jimmy D. Dikeakos
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Gregory A. Dekaban
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Bryan Heit
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
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3
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Ochiai K, Shima H, Tamahara T, Sugie N, Funayama R, Nakayama K, Kurosaki T, Igarashi K. Accelerated plasma-cell differentiation in Bach2-deficient mouse B cells is caused by altered IRF4 functions. EMBO J 2024; 43:1947-1964. [PMID: 38605225 PMCID: PMC11099079 DOI: 10.1038/s44318-024-00077-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/19/2024] [Accepted: 02/24/2024] [Indexed: 04/13/2024] Open
Abstract
Transcription factors BACH2 and IRF4 are both essential for antibody class-switch recombination (CSR) in activated B lymphocytes, while they oppositely regulate the differentiation of plasma cells (PCs). Here, we investigated how BACH2 and IRF4 interact during CSR and plasma-cell differentiation. We found that BACH2 organizes heterochromatin formation of target gene loci in mouse splenic B cells, including targets of IRF4 activation such as Aicda, an inducer of CSR, and Prdm1, a master plasma-cell regulator. Release of these gene loci from heterochromatin in response to B-cell receptor stimulation was coupled to AKT-mTOR pathway activation. In Bach2-deficient B cells, PC genes' activation depended on IRF4 protein accumulation, without an increase in Irf4 mRNA. Mechanistically, a PU.1-IRF4 heterodimer in activated B cells promoted BACH2 function by inducing gene expression of Bach2 and Pten, a negative regulator of AKT signaling. Elevated AKT activity in Bach2-deficient B cells resulted in IRF4 protein accumulation. Thus, BACH2 and IRF4 mutually modulate the activity of each other, and BACH2 inhibits PC differentiation by both the repression of PC genes and the restriction of IRF4 protein accumulation.
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Affiliation(s)
- Kyoko Ochiai
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, 980-8575, Japan.
| | - Hiroki Shima
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, 980-8575, Japan
| | - Toru Tamahara
- Division of Community Oral Health Science, Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-machi 2-1, Sendai, 980-8573, Japan
| | - Nao Sugie
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, 980-8575, Japan
| | - Ryo Funayama
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, 980-8575, Japan
| | - Keiko Nakayama
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, 980-8575, Japan
| | - Tomohiro Kurosaki
- Laboratory of Lymphocyte Differentiation, Immunology Frontier Research Center, Osaka University, Osaka, 565-0871, Japan
- Laboratory for Lymhocyte Differentiation, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, 230-0045, Japan
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, 980-8575, Japan.
- Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, 980-8575, Japan.
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4
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Zhang T, Li S, Tan YA, Na JH, Chen Z, Damle P, Chen X, Choi S, Mishra B, Wang D, Grossman SR, Jiang X, Li Y, Chen YT, Xiang JZ, Du YCN. Bcl-xL is translocated to the nucleus via CtBP2 to epigenetically promote metastasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538373. [PMID: 37163116 PMCID: PMC10168309 DOI: 10.1101/2023.04.26.538373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Besides its mitochondria-based anti-apoptotic role, Bcl-xL also travels to the nucleus to promote cancer metastasis by upregulating global histone H3 trimethyl Lys4 (H3K4me3) and TGFβ transcription. How Bcl-xL is translocated into the nucleus and how nuclear Bcl-xL regulates H3K4me3 modification are not understood. Here, we report that C-terminal Binding Protein 2 (CtBP2) binds Bcl-xL via its N-terminus and translocates Bcl-xL into the nucleus. Knockdown of CtBP2 by shRNA decreases the nuclear portion of Bcl-xL and reverses Bcl-xL-induced cell migration and metastasis in mouse models. Furthermore, knockout of CtBP2 suppresses Bcl-xL transcription. The binding between Bcl-xL and CtBP2 is required for their interaction with MLL1, a histone H3K4 methyltransferase. Pharmacologic inhibition of MLL1 enzymatic activity reverses Bcl-xL-induced H3K4me3 and TGFβ mRNA upregulation as well as cell invasion. Moreover, cleavage under targets and release using nuclease (CUT&RUN) coupled with next generation sequencing reveals that H3K4me3 modifications are particularly enriched in the promotor region of genes encoding TGFβ and its signaling pathway in the cancer cells overexpressing Bcl-xL. Altogether, the metastatic function of Bcl-xL is mediated by its interaction with CtBP2 and MLL1.
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Affiliation(s)
- Tiantian Zhang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sha Li
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Yingcai Adrian Tan
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY 10065, USA
| | - Joseph HyungJoon Na
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Zhengming Chen
- Division of Biostatistics, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY 10065, USA
| | - Priyadarshan Damle
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Xiang Chen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Soyoung Choi
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Bikash Mishra
- Immunology & Microbial Pathogenesis Graduate Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Dunrui Wang
- Laboratory of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steven R. Grossman
- USC Norris Comprehensive Cancer Center and Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Xuejun Jiang
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yi Li
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yao-Tseng Chen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jenny Z. Xiang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY 10065, USA
| | - Yi-Chieh Nancy Du
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
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5
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Jäverfelt S, Hellsén G, Kaji I, Goldenring JR, Pelaseyed T. The MYO1B and MYO5B motor proteins and the SNX27 sorting nexin regulate membrane mucin MUC17 trafficking in enterocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.530313. [PMID: 36945389 PMCID: PMC10028800 DOI: 10.1101/2023.03.06.530313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
A dense glycocalyx, composed of the megaDalton-sized membrane mucin MUC17, coats the microvilli in the apical brush border of transporting intestinal epithelial cells, called enterocytes. The establishment of the MUC17-based glycocalyx in the mouse small intestine occurs at the critical suckling-weaning transition. The enterocytic glycocalyx extends 1 µm into the intestinal lumen and prevents the gut bacteria from directly attaching to the enterocytes. To date, the mechanism behind apical targeting of MUC17 to the brush border remains unknown. Here, we show that the actin-based motor proteins MYO1B and MYO5B, and the sorting nexin SNX27 regulate the intracellular trafficking of MUC17 in enterocytes. We demonstrate that MUC17 turnover at the brush border is slow and controlled by MYO1B and SNX27. Furthermore, we report that MYO1B regulates MUC17 protein levels in enterocytes, whereas MYO5B specifically governs MUC17 levels at the brush border. Together, our results extend our understanding of the intracellular trafficking of membrane mucins and provide mechanistic insights into how defective trafficking pathways render enterocytes sensitive to bacterial invasion.
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6
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Tan Y, Yao L, Gamliel A, Nair SJ, Taylor H, Ohgi K, Aggarwal AK, Rosenfeld MG. Signal-induced enhancer activation requires Ku70 to read topoisomerase1-DNA covalent complexes. Nat Struct Mol Biol 2023; 30:148-158. [PMID: 36747093 PMCID: PMC9935399 DOI: 10.1038/s41594-022-00883-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 10/27/2022] [Indexed: 02/08/2023]
Abstract
Enhancer activation serves as the main mechanism regulating signal-dependent transcriptional programs, ensuring cellular plasticity, yet central questions persist regarding their mechanism of activation. Here, by successfully mapping topoisomerase I-DNA covalent complexes genome-wide, we find that most, if not all, acutely activated enhancers, including those induced by 17β-estradiol, dihydrotestosterone, tumor necrosis factor alpha and neuronal depolarization, are hotspots for topoisomerase I-DNA covalent complexes, functioning as epigenomic signatures read by the classic DNA damage sensor protein, Ku70. Ku70 in turn nucleates a heterochromatin protein 1 gamma (HP1γ)-mediator subunit Med26 complex to facilitate acute, but not chronic, transcriptional activation programs. Together, our data uncover a broad, unappreciated transcriptional code, required for most, if not all, acute signal-dependent enhancer activation events in both mitotic and postmitotic cells.
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Affiliation(s)
- Yuliang Tan
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Lu Yao
- Familial and Hereditary Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
| | - Amir Gamliel
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sreejith J Nair
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Oncology Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, USA
| | - Havilah Taylor
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kenny Ohgi
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Aneel K Aggarwal
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael G Rosenfeld
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
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7
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Shan B, Horton EC, Xu SC, Huntington KE, Kawano DK, Mendoza CL, Lin L, Stafford CM, Allen ED, Huang J, Nakahara H, Greenstein LE, Hille MB. Dephosphorylation of Y228 and Y217 and phosphorylation of Y335 in p120 catenin activate convergent extension during zebrafish gastrulation. Dev Dyn 2022; 251:1934-1951. [PMID: 35996230 DOI: 10.1002/dvdy.524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 04/15/2022] [Accepted: 05/26/2022] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND The cadherin-associated protein p120 catenin regulates convergent extension through interactions with cadherin proteins, Cdc42, and Rac1, as we previously showed in zebrafish (Danio rerio). Phosphorylation of p120 catenin changes the nature of its activity in vitro but is virtually unexplored in embryos. We used our previously developed antisense RNA splice-site morpholino targeted to endogenous p120 catenin-δ1 to cause defects in axis elongation probing the functions of three p120 catenin tyrosine-phosphorylation sites in gastrulating zebrafish embryos. RESULTS The morpholino-induced defects were rescued by co-injections with mouse p120 catenin-δ1-3A mRNAs mutated at residues Y228 and Y217 to a non-phosphorylatable phenylalanine (F) or mutated at residue Y335 to a phosphomimetic glutamic acid (E). Co-injection of the complementary mutations Y228E, Y217E, or Y335F mRNAs partially rescued embryos whereas dual mutation to Y228E-Y217E blocked rescue. Immunopurification showed Y228F mutant proteins preferentially interacted with Rac1, potentially promoting cell migration. In contrast, the phosphomimetic Y228E preferentially interacted with E-cadherin increasing adhesion. Both Y228F and Y335F strongly bind VAV2. CONCLUSIONS p120 catenin serves dual roles during gastrulation of zebrafish. Phosphorylation and dephosphorylation of tyrosine residues Y217, Y228, and Y335 precisely balance cell adhesion and cell migration to facilitate somite compaction and axis elongation.
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Affiliation(s)
- Botao Shan
- Department of Biology, University of Washington, Seattle, Washington, USA.,Tulane University School of Medicine, New Orleans, LA, USA
| | - Emma C Horton
- Department of Biology, University of Washington, Seattle, Washington, USA.,Developmental and Stem Cell Biology Program, University of California San Francisco, San Francisco, CA, USA
| | - Shan C Xu
- Department of Biology, University of Washington, Seattle, Washington, USA.,New York University Stern Business School, New York, NY, USA
| | - Kelsey E Huntington
- Department of Biology, University of Washington, Seattle, Washington, USA.,Pathobiology Graduate Program, Division of Biology and Medicine, The Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Dane K Kawano
- Department of Biology, University of Washington, Seattle, Washington, USA.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Clemence L Mendoza
- Department of Biology, University of Washington, Seattle, Washington, USA.,VA Portland Health Care System, Portland, OR, USA
| | - Laura Lin
- Department of Biology, University of Washington, Seattle, Washington, USA.,Touro University California College of Osteopathic Medicine, Vallejo, CA, USA
| | | | - Emili D Allen
- Department of Biology, University of Washington, Seattle, Washington, USA.,Adaptive Biotechnologies Corp, Seattle, WA, USA
| | - Joyce Huang
- Department of Biology, University of Washington, Seattle, Washington, USA.,Department of Bioengineering, University of California at Los Angeles, Los Angeles, CA, USA
| | - Hiroko Nakahara
- Department of Biology, University of Washington, Seattle, Washington, USA
| | - Lewis E Greenstein
- Department of Biology, University of Washington, Seattle, Washington, USA.,Department of Medical Entomology, Champaign, IL, USA
| | - Merrill B Hille
- Department of Biology, University of Washington, Seattle, Washington, USA
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8
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An improved CUT&RUN method for regulation network reconstruction of low abundance transcription factor. Cell Signal 2022; 96:110361. [DOI: 10.1016/j.cellsig.2022.110361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/20/2022]
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9
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Reber S, Jutzi D, Lindsay H, Devoy A, Mechtersheimer J, Levone BR, Domanski M, Bentmann E, Dormann D, Mühlemann O, Barabino SML, Ruepp MD. The phase separation-dependent FUS interactome reveals nuclear and cytoplasmic function of liquid-liquid phase separation. Nucleic Acids Res 2021; 49:7713-7731. [PMID: 34233002 PMCID: PMC8287939 DOI: 10.1093/nar/gkab582] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 06/15/2021] [Accepted: 06/28/2021] [Indexed: 12/13/2022] Open
Abstract
Liquid–liquid phase separation (LLPS) of proteins and RNAs has emerged as the driving force underlying the formation of membrane-less organelles. Such biomolecular condensates have various biological functions and have been linked to disease. The protein Fused in Sarcoma (FUS) undergoes LLPS and mutations in FUS have been causally linked to the motor neuron disease Amyotrophic Lateral Sclerosis (ALS-FUS). LLPS followed by aggregation of cytoplasmic FUS has been proposed to be a crucial disease mechanism. However, it is currently unclear how LLPS impacts the behaviour of FUS in cells, e.g. its interactome. Hence, we developed a method allowing for the purification of LLPS FUS-containing droplets from cell lysates. We observe substantial alterations in the interactome, depending on its biophysical state. While non-LLPS FUS interacts mainly with factors involved in pre-mRNA processing, LLPS FUS predominantly binds to proteins involved in chromatin remodelling and DNA damage repair. Interestingly, also mitochondrial factors are strongly enriched with LLPS FUS, providing a potential explanation for the observed changes in mitochondrial gene expression in mouse models of ALS-FUS. In summary, we present a methodology to investigate the interactomes of phase separating proteins and provide evidence that LLPS shapes the FUS interactome with implications for function and disease.
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Affiliation(s)
- Stefan Reber
- United Kingdom Dementia Research Institute Centre at King's College London, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Daniel Jutzi
- United Kingdom Dementia Research Institute Centre at King's College London, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Helen Lindsay
- Department of Mathematics, École polytechnique fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Anny Devoy
- United Kingdom Dementia Research Institute Centre at King's College London, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Jonas Mechtersheimer
- United Kingdom Dementia Research Institute Centre at King's College London, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Brunno Rocha Levone
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Michal Domanski
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Eva Bentmann
- Biomedical Center (BMC), Cell Biology, Ludwig Maximilians University Munich, Germany
| | - Dorothee Dormann
- Biomedical Center (BMC), Cell Biology, Ludwig Maximilians University Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Silvia M L Barabino
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Marc-David Ruepp
- United Kingdom Dementia Research Institute Centre at King's College London, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
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10
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Ochiai K, Shima H, Ikura T, Franke MC, Sievert EP, Sciammas R, Igarashi K. Protocol for in vitro BCR-mediated plasma cell differentiation and purification of chromatin-associated proteins. STAR Protoc 2021; 2:100633. [PMID: 34258594 PMCID: PMC8255920 DOI: 10.1016/j.xpro.2021.100633] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Molecular-level understanding of plasma cell (PC) differentiation has been modeled using lipopolysaccharide (LPS) stimulation in vitro. However, this system does not involve the B-cell receptor (BCR)-a critical component of B cell biology. Here, we present a protocol for in vitro PC differentiation system dependent on BCR signaling that easily scales up for cell number-demanding applications, including protein complex purification. We describe how to set up this system and detail applications for endogenous complex purification of chromatin-associated proteins. For further details on the use and execution of this protocol, please refer to Sciammas et al. (2011) and Ochiai et al. (2018, 2020).
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Affiliation(s)
- Kyoko Ochiai
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
- Corresponding author
| | - Hiroki Shima
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Tsuyoshi Ikura
- Laboratory of Chromatin Regulatory Network, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Marissa C. Franke
- Center for Immunology and Infectious Diseases, University of California Davis, Davis, CA 95616, USA
| | - Evelyn P. Sievert
- Center for Immunology and Infectious Diseases, University of California Davis, Davis, CA 95616, USA
| | - Roger Sciammas
- Center for Immunology and Infectious Diseases, University of California Davis, Davis, CA 95616, USA
- Corresponding author
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
- Corresponding author
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11
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Husain A, Begum NA, Kobayashi M, Honjo T. Native Co-immunoprecipitation Assay to Identify Interacting Partners of Chromatin-associated Proteins in Mammalian Cells. Bio Protoc 2020; 10:e3837. [PMID: 33659486 DOI: 10.21769/bioprotoc.3837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/24/2020] [Accepted: 09/30/2020] [Indexed: 12/25/2022] Open
Abstract
Protein-protein interactions play key roles in nuclear processes including transcription, replication, DNA damage repair, and recombination. Co-immunoprecipitation (Co-IP) followed by western blot or mass spectrometry is an invaluable approach to identify protein-protein interactions. One of the challenges in the Co-IP of a protein localized to nucleus is the extraction of nuclear proteins from sub-nuclear fractions without losing physiologically relevant protein interactions. Here we describe a protocol for native Co-IP, which was originally used to successfully identify previously known as well novel topoisomerase 1 (TOP1) interacting proteins. In this protocol, we first extracted nuclear proteins by sequentially increasing detergent and salt concentrations, the extracted fractions were then diluted, pooled, and used for Co-IP. This protocol can be used to identify protein-interactome of other chromatin-associated proteins in a variety of mammalian cells.
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Affiliation(s)
- Afzal Husain
- Deptartment of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Nasim A Begum
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Maki Kobayashi
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tasuku Honjo
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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12
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Flavivirus Nonstructural Protein NS5 Dysregulates HSP90 to Broadly Inhibit JAK/STAT Signaling. Cells 2020; 9:cells9040899. [PMID: 32272626 PMCID: PMC7226784 DOI: 10.3390/cells9040899] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/29/2020] [Accepted: 04/01/2020] [Indexed: 12/12/2022] Open
Abstract
Pathogenic flaviviruses antagonize host cell Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling downstream of interferons α/β. Here, we show that flaviviruses inhibit JAK/STAT signaling induced by a wide range of cytokines beyond interferon, including interleukins. This broad inhibition was mapped to viral nonstructural protein 5 (NS5) binding to cellular heat shock protein 90 (HSP90), resulting in reduced Janus kinase-HSP90 interaction and thus destabilization of unchaperoned JAKs (and other kinase clients) of HSP90 during infection by Zika virus, West Nile virus, and Japanese encephalitis virus. Our studies implicate viral dysregulation of HSP90 and the JAK/STAT pathway as a critical determinant of cytokine signaling control during flavivirus infection.
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13
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Buonpane C, Yuan C, Wood D, Ares G, Klonoski SC, Hunter CJ. ROCK1 inhibitor stabilizes E-cadherin and improves barrier function in experimental necrotizing enterocolitis. Am J Physiol Gastrointest Liver Physiol 2020; 318:G781-G792. [PMID: 32090605 PMCID: PMC7191467 DOI: 10.1152/ajpgi.00195.2019] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Necrotizing enterocolitis (NEC) is a devastating gastrointestinal disease of newborns. Although incompletely understood, NEC is associated with intestinal barrier dysfunction. E-cadherin, an adherens junction, is a protein complex integral in maintaining normal barrier homeostasis. Rho-associated protein kinase-1 (ROCK1) is a kinase that regulates the E-cadherin complex, and p120-catenin is a subunit of the E-cadherin complex that has been implicated in stabilizing the cadherin complex at the plasma membrane. We hypothesized that E-cadherin is decreased in NEC and that inhibition of ROCK1 would protect against adherens junction disruption. To investigate this, a multimodal approach was used: In vitro Caco-2 model of NEC (LPS/TNFα), rap pup model (hypoxia + bacteria-containing formula), and human intestinal samples. E-cadherin was decreased in NEC compared with controls, with relocalization from the cell border to an intracellular location. ROCK1 exhibited a time-dependent response to disease, with increased early expression in NEC and decreased expression at later time points and disease severity. Administration of ROCK1 inhibitor (RI) resulted in preservation of E-cadherin expression at the cell border, preservation of intestinal villi on histological examination, and decreased apoptosis. ROCK1 upregulation in NEC led to decreased association of E-cadherin to p120 and increased intestinal permeability. RI helped maintain the stability of the E-cadherin-p120 complex, leading to improved barrier integrity and protection from experimental NEC.NEW & NOTEWORTHY This paper is the first to describe the effect of ROCK1 on E-cadherin expression in the intestinal epithelium and the protective effects of ROCK inhibitor on E-cadherin stability in necrotizing enterocolitis.
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Affiliation(s)
- Christie Buonpane
- 1Division of Pediatric Surgery, Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois
| | - Carrie Yuan
- 2Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Douglas Wood
- 2Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Guillermo Ares
- 1Division of Pediatric Surgery, Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois
| | - Samuel C. Klonoski
- 1Division of Pediatric Surgery, Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois
| | - Catherine J. Hunter
- 3Department of Surgery, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
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14
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Gong Y, Marriott G. Bead-Based Immunocomplex Entrapment Assays for Rapid, Sensitive, and Multiplexed Detection of Disease Biomarkers with Minimal User Intervention. ACS Sens 2020; 5:180-190. [PMID: 31867951 DOI: 10.1021/acssensors.9b01970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Current interest in at-home diagnostic devices derives from their potential to disrupt expensive and time-consuming hospital-based diagnostic practices. Conventional immunoassays are often touted for use in at-home diagnostic devices, although in practice they are slow, labor-intensive and require expensive equipment. Here, we introduce bead-based sensors as alternative biomarker detection platforms for at-home diagnostic devices. The immunocomplex entrapment assay (ICEA), and the related enzyme-linked ICEA (ELICEA) offer enhancements over conventional immunoassays in terms of their speed, and minimal requirements for user intervention and instrumentation. In particular, we designed bead-based sensors to entrap large molecular weight complexes between target molecules and signal-generating immunoconjugates while allowing any unbound conjugates to escape from the bead. Confocal fluorescence microscopy was used to demonstrate the sensitivity, robustness, and reproducibility of the ICEA and ELICEA platforms. For example, we showed the intensity of signals generated by entrapped immunoconjugate complexes correlate linearly with the concentration of target molecule in the sample. We employed ICEA, and ELICEA platforms to detect human forms of immunoglobulins, albumin, and κ light chain (KLC). For example, we used ICEA to detect KLC at 5 μg·mL-1 in urine, which would allow for earlier diagnosis of Bence-Jones disease compared to conventional assays. In addition, we showed bead-entrapped phosphatases (AP) in immunocomplexes generate insoluble, blue-colored dyes from AP-substrates that accumulate in beads and allow for visual and cellphone camera-based detection of IgG to 10 ng·mL-1 within 20 min. Finally, we described ICEA and ELICEA platforms to analyze multiple target proteins within individual beads.
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Affiliation(s)
- Yuhui Gong
- Department of Bioengineering, University of California-Berkeley, Berkeley, California 94720, United States
| | - Gerard Marriott
- Department of Bioengineering, University of California-Berkeley, Berkeley, California 94720, United States
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15
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Gallion LA, Anttila MM, Abraham DH, Proctor A, Allbritton NL. Preserving Single Cells in Space and Time for Analytical Assays. Trends Analyt Chem 2020; 122:115723. [PMID: 32153309 PMCID: PMC7061724 DOI: 10.1016/j.trac.2019.115723] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Analytical assays performed within clinical laboratories influence roughly 70% of all medical decisions by facilitating disease detection, diagnosis, and management. Both in clinical and academic research laboratories, single-cell assays permit measurement of cell diversity and identification of rare cells, both of which are important in the understanding of disease pathogenesis. For clinically utility, the single-cell assays must be compatible with the clinical workflow steps of sample collection, sample transportation, pre-analysis processing, and single-cell assay; therefore, it is paramount to preserve cells in a state that resembles that in vivo rather than measuring signaling behaviors initiated in response to stressors such as sample collection and processing. To address these challenges, novel cell fixation (and more broadly, cell preservation) techniques incorporate programmable fixation times, reversible bond formation and cleavage, chemoselective reactions, and improved analyte recovery. These technologies will further the development of individualized, precision therapies for patients to yield improved clinical outcomes.
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Affiliation(s)
- Luke A. Gallion
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Matthew M. Anttila
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - David H. Abraham
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Angela Proctor
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Nancy L. Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
- Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599, USA and North Carolina State University, Raleigh, NC 27695, USA
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16
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Kotrys AV, Cysewski D, Czarnomska SD, Pietras Z, Borowski LS, Dziembowski A, Szczesny RJ. Quantitative proteomics revealed C6orf203/MTRES1 as a factor preventing stress-induced transcription deficiency in human mitochondria. Nucleic Acids Res 2019; 47:7502-7517. [PMID: 31226201 PMCID: PMC6698753 DOI: 10.1093/nar/gkz542] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 06/05/2019] [Accepted: 06/13/2019] [Indexed: 12/18/2022] Open
Abstract
Maintenance of mitochondrial gene expression is crucial for cellular homeostasis. Stress conditions may lead to a temporary reduction of mitochondrial genome copy number, raising the risk of insufficient expression of mitochondrial encoded genes. Little is known how compensatory mechanisms operate to maintain proper mitochondrial transcripts levels upon disturbed transcription and which proteins are involved in them. Here we performed a quantitative proteomic screen to search for proteins that sustain expression of mtDNA under stress conditions. Analysis of stress-induced changes of the human mitochondrial proteome led to the identification of several proteins with poorly defined functions among which we focused on C6orf203, which we named MTRES1 (Mitochondrial Transcription Rescue Factor 1). We found that the level of MTRES1 is elevated in cells under stress and we show that this upregulation of MTRES1 prevents mitochondrial transcript loss under perturbed mitochondrial gene expression. This protective effect depends on the RNA binding activity of MTRES1. Functional analysis revealed that MTRES1 associates with mitochondrial RNA polymerase POLRMT and acts by increasing mitochondrial transcription, without changing the stability of mitochondrial RNAs. We propose that MTRES1 is an example of a protein that protects the cell from mitochondrial RNA loss during stress.
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Affiliation(s)
- Anna V Kotrys
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Dominik Cysewski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Sylwia D Czarnomska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Zbigniew Pietras
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw 02-106, Poland.,Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
| | - Lukasz S Borowski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw 02-106, Poland.,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw 02-106, Poland
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw 02-106, Poland.,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw 02-106, Poland
| | - Roman J Szczesny
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw 02-106, Poland
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17
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Identification of protein-protein and ribonucleoprotein complexes containing Hfq. Sci Rep 2019; 9:14054. [PMID: 31575967 PMCID: PMC6773851 DOI: 10.1038/s41598-019-50562-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 09/06/2019] [Indexed: 11/08/2022] Open
Abstract
Hfq is a RNA-binding protein that plays a pivotal role in the control of gene expression in bacteria by stabilizing sRNAs and facilitating their pairing with multiple target mRNAs. It has already been shown that Hfq, directly or indirectly, interacts with many proteins: RNase E, Rho, poly(A)polymerase, RNA polymerase… In order to detect more Hfq-related protein-protein interactions we have used two approaches, TAP-tag combined with RNase A treatment to access the role of RNA in these complexes, and protein-protein crosslinking, which freezes protein-protein complexes formed in vivo. In addition, we have performed microscale thermophoresis to evaluate the role of RNA in some of the complexes detected and used far-western blotting to confirm some protein-protein interactions. Taken together, the results show unambiguously a direct interaction between Hfq and EF-Tu. However a very large number of the interactions of proteins with Hfq in E. coli involve RNAs. These RNAs together with the interacting protein, may play an active role in the formation of Hfq-containing complexes with previously unforeseen implications for the riboregulatory functions of Hfq.
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18
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Drexler HCA, Vockel M, Polaschegg C, Frye M, Peters K, Vestweber D. Vascular Endothelial Receptor Tyrosine Phosphatase: Identification of Novel Substrates Related to Junctions and a Ternary Complex with EPHB4 and TIE2. Mol Cell Proteomics 2019; 18:2058-2077. [PMID: 31427368 PMCID: PMC6773558 DOI: 10.1074/mcp.ra119.001716] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Indexed: 12/30/2022] Open
Abstract
Vascular endothelial protein tyrosine phosphatase (VE-PTP, PTPRB) is a receptor type phosphatase that is crucial for the regulation of endothelial junctions and blood vessel development. We and others have shown recently that VE-PTP regulates vascular integrity by dephosphorylating substrates that are key players in endothelial junction stability, such as the angiopoietin receptor TIE2, the endothelial adherens junction protein VE-cadherin and the vascular endothelial growth factor receptor VEGFR2. Here, we have systematically searched for novel substrates of VE-PTP in endothelial cells by utilizing two approaches. First, we studied changes in the endothelial phosphoproteome on exposing cells to a highly VE-PTP-specific phosphatase inhibitor followed by affinity isolation and mass-spectrometric analysis of phosphorylated proteins by phosphotyrosine-specific antibodies. Second, we used a substrate trapping mutant of VE-PTP to pull down phosphorylated substrates in combination with SILAC-based quantitative mass spectrometry measurements. We identified a set of substrate candidates of VE-PTP, of which a remarkably large fraction (29%) is related to cell junctions. Several of those were found in both screens and displayed very high connectivity in predicted functional interaction networks. The receptor protein tyrosine kinase EPHB4 was the most prominently phosphorylated protein on VE-PTP inhibition among those VE-PTP targets that were identified by both proteomic approaches. Further analysis revealed that EPHB4 forms a ternary complex with VE-PTP and TIE2 in endothelial cells. VE-PTP controls the phosphorylation of each of these two tyrosine kinase receptors. Despite their simultaneous presence in a ternary complex, stimulating each of the receptors with their own specific ligand did not cross-activate the respective partner receptor. Our systematic approach has led to the identification of novel substrates of VE-PTP, of which many are relevant for the control of cellular junctions further promoting the importance of VE-PTP as a key player of junctional signaling.
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Affiliation(s)
- Hannes C A Drexler
- Bioanalytical Mass Spectrometry, Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149 Münster, Germany.
| | - Matthias Vockel
- Department of Vascular Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149 Münster, Germany; Institute of Human Genetics, University Hospital Münster, 48149 Münster, Germany
| | - Christian Polaschegg
- Department of Vascular Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149 Münster, Germany
| | - Maike Frye
- Department of Vascular Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149 Münster, Germany
| | | | - Dietmar Vestweber
- Department of Vascular Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149 Münster, Germany.
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19
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Lingemann M, McCarty T, Liu X, Buchholz UJ, Surman S, Martin SE, Collins PL, Munir S. The alpha-1 subunit of the Na+,K+-ATPase (ATP1A1) is required for macropinocytic entry of respiratory syncytial virus (RSV) in human respiratory epithelial cells. PLoS Pathog 2019; 15:e1007963. [PMID: 31381610 PMCID: PMC6695199 DOI: 10.1371/journal.ppat.1007963] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/15/2019] [Accepted: 07/05/2019] [Indexed: 01/07/2023] Open
Abstract
Human respiratory syncytial virus (RSV) is the leading viral cause of acute pediatric lower respiratory tract infections worldwide, with no available vaccine or effective antiviral drug. To gain insight into virus-host interactions, we performed a genome-wide siRNA screen. The expression of over 20,000 cellular genes was individually knocked down in human airway epithelial A549 cells, followed by infection with RSV expressing green fluorescent protein (GFP). Knockdown of expression of the cellular ATP1A1 protein, which is the major subunit of the Na+,K+-ATPase of the plasma membrane, had one of the strongest inhibitory effects on GFP expression and viral titer. Inhibition was not observed for vesicular stomatitis virus, indicating that it was RSV-specific rather than a general effect. ATP1A1 formed clusters in the plasma membrane very early following RSV infection, which was independent of replication but dependent on the attachment glycoprotein G. RSV also triggered activation of ATP1A1, resulting in signaling by c-Src-kinase activity that transactivated epidermal growth factor receptor (EGFR) by Tyr845 phosphorylation. ATP1A1 signaling and activation of both c-Src and EGFR were found to be required for efficient RSV uptake. Signaling events downstream of EGFR culminated in the formation of macropinosomes. There was extensive uptake of RSV virions into macropinosomes at the beginning of infection, suggesting that this is a major route of RSV uptake, with fusion presumably occurring in the macropinosomes rather than at the plasma membrane. Important findings were validated in primary human small airway epithelial cells (HSAEC). In A549 cells and HSAEC, RSV uptake could be inhibited by the cardiotonic steroid ouabain and the digitoxigenin derivative PST2238 (rostafuroxin) that bind specifically to the ATP1A1 extracellular domain and block RSV-triggered EGFR Tyr845 phosphorylation. In conclusion, we identified ATP1A1 as a host protein essential for macropinocytic entry of RSV into respiratory epithelial cells, and identified PST2238 as a potential anti-RSV drug. RSV continues to be the most important viral cause of severe bronchiolitis and pneumonia in infants and young children, and also has a substantial impact in the elderly. It is estimated to claim the lives of ~118,000 children under five years of age annually. No vaccine or antiviral drug suitable for general use is available. The involvement of host factors in RSV infection and replication is not well understood, but this knowledge might lead to intervention strategies to prevent infection. Using a genome-wide siRNA screen to knock down the expression of over 20,000 individual cellular genes, we identified ATP1A1, the major subunit of the Na+,K+-ATPase, as an important host protein for RSV entry. We showed that ATP1A1 activation by RSV resulted in transactivation of EGFR by Src-kinase activity, resulting in the uptake of RSV particles into the host cell through macropinocytosis. We also showed that the cardiotonic steroid ouabain and the synthetic digitoxigenin derivative PST2238, which bind specifically to the extracellular domain of ATP1A1, significantly reduced RSV entry. Taken together, we describe a novel ATP1A1-enabled mechanism used by RSV to enter the host cell, and describe candidate antiviral drugs that block this entry.
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Affiliation(s)
- Matthias Lingemann
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Thomas McCarty
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Xueqiao Liu
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ursula J. Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sonja Surman
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Scott E. Martin
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, Rockville, Maryland, United States of America
| | - Peter L. Collins
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Shirin Munir
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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20
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Plate L, Rius B, Nguyen B, Genereux JC, Kelly JW, Wiseman RL. Quantitative Interactome Proteomics Reveals a Molecular Basis for ATF6-Dependent Regulation of a Destabilized Amyloidogenic Protein. Cell Chem Biol 2019; 26:913-925.e4. [PMID: 31105062 DOI: 10.1016/j.chembiol.2019.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/14/2019] [Accepted: 03/31/2019] [Indexed: 12/24/2022]
Abstract
Activation of the unfolded protein response (UPR)-associated transcription factor ATF6 has emerged as a promising strategy to reduce the secretion and subsequent toxic aggregation of destabilized, amyloidogenic proteins implicated in systemic amyloid diseases. However, the molecular mechanism by which ATF6 activation reduces the secretion of amyloidogenic proteins remains poorly defined. We employ a quantitative interactomics platform to define how ATF6 activation reduces secretion of a destabilized, amyloidogenic immunoglobulin light chain (LC) associated with light-chain amyloidosis (AL). Using this platform, we show that ATF6 activation increases the targeting of this destabilized LC to a subset of pro-folding ER proteostasis factors that retains the amyloidogenic LC within the ER, preventing its secretion. Our results define a molecular basis for the ATF6-dependent reduction in destabilized LC secretion and highlight the advantage for targeting this UPR-associated transcription factor to reduce secretion of destabilized, amyloidogenic proteins implicated in AL and related systemic amyloid diseases.
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Affiliation(s)
- Lars Plate
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MB110, La Jolla, CA 92037, USA; Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bibiana Rius
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MB110, La Jolla, CA 92037, USA
| | - Bianca Nguyen
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MB110, La Jolla, CA 92037, USA
| | - Joseph C Genereux
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MB110, La Jolla, CA 92037, USA; Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeffery W Kelly
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - R Luke Wiseman
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MB110, La Jolla, CA 92037, USA.
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21
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Blackburn JWD, Lau DHC, Liu EY, Ellins J, Vrieze AM, Pawlak EN, Dikeakos JD, Heit B. Soluble CD93 is an apoptotic cell opsonin recognized by α x β 2. Eur J Immunol 2019; 49:600-610. [PMID: 30656676 DOI: 10.1002/eji.201847801] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 12/13/2018] [Accepted: 01/16/2019] [Indexed: 11/11/2022]
Abstract
Efferocytosis is essential for homeostasis and prevention of the inflammatory and autoimmune diseases resulting from apoptotic cell lysis. CD93 is a transmembrane glycoprotein previously implicated in efferocytosis, with mutations in CD93 predisposing patients to efferocytosis-associated diseases. CD93 is a cell surface protein, which is proteolytically shed under inflammatory conditions, but it is unknown how CD93 mediates efferocytosis or whether its efferocytic activity is mediated by the soluble or membrane-bound form. Herein, using cell lines and human monocytes and macrophages, we demonstrate that soluble CD93 (sCD93) potently opsonizes apoptotic cells but not a broad range of microorganisms, whereas membrane-bound CD93 has no phagocytic, efferocytic, or tethering activity. Using mass spectrometry, we identified αx β2 as the receptor that recognizes sCD93, and via deletion mutagenesis determined that sCD93 binds to apoptotic cells via its C-type lectin-like domain and to αx β2 by its EGF-like repeats. The bridging of apoptotic cells to αx β2 markedly enhanced efferocytosis by macrophages and was abrogated by αx β2 knockdown. Combined, these data elucidate the mechanism by which CD93 regulates efferocytosis and identifies a previously unreported opsonin-receptor system utilized by phagocytes for the efferocytic clearance of apoptotic cells.
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Affiliation(s)
- Jack W D Blackburn
- Department of Microbiology and Immunology, Center for Human Immunology, The University of Western Ontario, London, Ontario, Canada
| | - Darius H C Lau
- Department of Microbiology and Immunology, Center for Human Immunology, The University of Western Ontario, London, Ontario, Canada
| | - Elaine Y Liu
- Department of Microbiology and Immunology, Center for Human Immunology, The University of Western Ontario, London, Ontario, Canada
| | - Jessica Ellins
- Department of Microbiology and Immunology, Center for Human Immunology, The University of Western Ontario, London, Ontario, Canada
| | - Angela M Vrieze
- Department of Microbiology and Immunology, Center for Human Immunology, The University of Western Ontario, London, Ontario, Canada
| | - Emily N Pawlak
- Department of Microbiology and Immunology, Center for Human Immunology, The University of Western Ontario, London, Ontario, Canada
| | - Jimmy D Dikeakos
- Department of Microbiology and Immunology, Center for Human Immunology, The University of Western Ontario, London, Ontario, Canada
| | - Bryan Heit
- Department of Microbiology and Immunology, Center for Human Immunology, The University of Western Ontario, London, Ontario, Canada
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22
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Titeca K, Lemmens I, Tavernier J, Eyckerman S. Discovering cellular protein-protein interactions: Technological strategies and opportunities. MASS SPECTROMETRY REVIEWS 2019; 38:79-111. [PMID: 29957823 DOI: 10.1002/mas.21574] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 01/03/2018] [Accepted: 06/04/2018] [Indexed: 05/09/2023]
Abstract
The analysis of protein interaction networks is one of the key challenges in the study of biology. It connects genotypes to phenotypes, and disruption often leads to diseases. Hence, many technologies have been developed to study protein-protein interactions (PPIs) in a cellular context. The expansion of the PPI technology toolbox however complicates the selection of optimal approaches for diverse biological questions. This review gives an overview of the binary and co-complex technologies, with the former evaluating the interaction of two co-expressed genetically tagged proteins, and the latter only needing the expression of a single tagged protein or no tagged proteins at all. Mass spectrometry is crucial for some binary and all co-complex technologies. After the detailed description of the different technologies, the review compares their unique specifications, advantages, disadvantages, and applicability, while highlighting opportunities for further advancements.
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Affiliation(s)
- Kevin Titeca
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Irma Lemmens
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Jan Tavernier
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
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23
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Ruan X, Monjarás Feria J, Hamad M, Valvano MA. Escherichia coli and Pseudomonas aeruginosa lipopolysaccharide O-antigen ligases share similar membrane topology and biochemical properties. Mol Microbiol 2018; 110:95-113. [PMID: 30047569 DOI: 10.1111/mmi.14085] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
WaaL is an inner membrane glycosyltransferase that catalyzes the transfer of O-antigen polysaccharide from its lipid-linked intermediate to a terminal sugar of the lipid A-core oligosaccharide, a conserved step in lipopolysaccharide biosynthesis. Ligation occurs at the periplasmic side of the bacterial cell membrane, suggesting the catalytic region of WaaL faces the periplasm. Establishing the membrane topology of the WaaL protein family will enable understanding its mechanism and exploit it as a potential antimicrobial target. Applying oxidative labeling of native methionine/cysteine residues, we previously validated a topological model for Escherichia coli WaaL, which differs substantially from the reported topology of the Pseudomonas aeruginosa WaaL, derived from the analysis of truncated protein reporter fusions. Here, we examined the topology of intact E. coli and P. aeruginosa WaaL proteins by labeling engineered cysteine residues with the membrane-impermeable sulfhydryl reagent polyethylene glycol maleimide (PEG-Mal). The accessibility of PEG-Mal to targeted engineered cysteine residues in both E. coli and P. aeruginosa WaaL proteins demonstrates that both ligases share similar membrane topology. Further, we also demonstrate that P. aeruginosa WaaL shares similar functional properties with E. coli WaaL and that E. coli WaaL may adopt a functional dimer conformation.
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Affiliation(s)
- Xiang Ruan
- Department of Microbiology and Immunology, University of Western Ontario, London, N6A 5C1, Canada
| | - Julia Monjarás Feria
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, BT9 7BL, United Kingdom
| | - Mohamad Hamad
- Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Miguel A Valvano
- Department of Microbiology and Immunology, University of Western Ontario, London, N6A 5C1, Canada.,Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, BT9 7BL, United Kingdom
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24
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Li J, Shima H, Nishizawa H, Ikeda M, Brydun A, Matsumoto M, Kato H, Saiki Y, Liu L, Watanabe-Matsui M, Iemura K, Tanaka K, Shiraki T, Igarashi K. Phosphorylation of BACH1 switches its function from transcription factor to mitotic chromosome regulator and promotes its interaction with HMMR. Biochem J 2018; 475:981-1002. [PMID: 29459360 DOI: 10.1042/bcj20170520] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 01/31/2018] [Accepted: 02/19/2018] [Indexed: 12/17/2023]
Abstract
The transcription repressor BACH1 performs mutually independent dual roles in transcription regulation and chromosome alignment during mitosis by supporting polar ejection force of mitotic spindle. We now found that the mitotic spindles became oblique relative to the adhesion surface following endogenous BACH1 depletion in HeLa cells. This spindle orientation rearrangement was rescued by re-expression of BACH1 depending on its interactions with HMMR and CRM1, both of which are required for the positioning of mitotic spindle, but independently of its DNA-binding activity. A mass spectrometry analysis of BACH1 complexes in interphase and M phase revealed that BACH1 lost during mitosis interactions with proteins involved in chromatin and gene expression but retained interactions with HMMR and its known partners including CHICA. By analyzing BACH1 modification using stable isotope labeling with amino acids in cell culture, mitosis-specific phosphorylations of BACH1 were observed, and mutations of these residues abolished the activity of BACH1 to restore mitotic spindle orientation in knockdown cells and to interact with HMMR. Detailed histological analysis of Bach1-deficient mice revealed lengthening of the epithelial fold structures of the intestine. These observations suggest that BACH1 performs stabilization of mitotic spindle orientation together with HMMR and CRM1 in mitosis, and that the cell cycle-specific phosphorylation switches the transcriptional and mitotic functions of BACH1.
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Affiliation(s)
- Jie Li
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Hiroki Shima
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
- Center for Regulatory Epigenome and Diseases, Tohoku University, Sendai 980-8575, Japan
| | - Hironari Nishizawa
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Masatoshi Ikeda
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Andrey Brydun
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Mitsuyo Matsumoto
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
- Center for Regulatory Epigenome and Diseases, Tohoku University, Sendai 980-8575, Japan
| | - Hiroki Kato
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Yuriko Saiki
- Department of Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Liang Liu
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Miki Watanabe-Matsui
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
- Restart Postdoctoral Fellow, Japan Society for the Promotion of Science, Tokyo 102-0083, Japan
| | - Kenji Iemura
- Department of Molecular Oncology, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan
| | - Kozo Tanaka
- Department of Molecular Oncology, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan
| | - Takuma Shiraki
- Department of Science and Technology on Food Safety, Faculty of Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawashi 649-6493, Japan
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
- Center for Regulatory Epigenome and Diseases, Tohoku University, Sendai 980-8575, Japan
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25
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Balek L, Nemec P, Konik P, Kunova Bosakova M, Varecha M, Gudernova I, Medalova J, Krakow D, Krejci P. Proteomic analyses of signalling complexes associated with receptor tyrosine kinase identify novel members of fibroblast growth factor receptor 3 interactome. Cell Signal 2018; 42:144-154. [DOI: 10.1016/j.cellsig.2017.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 09/13/2017] [Accepted: 10/05/2017] [Indexed: 01/08/2023]
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26
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Heffernan C, Jain MR, Liu T, Kim H, Barretto K, Li H, Maurel P. Nectin-like 4 Complexes with Choline Transporter-like Protein-1 and Regulates Schwann Cell Choline Homeostasis and Lipid Biogenesis in Vitro. J Biol Chem 2017; 292:4484-4498. [PMID: 28119456 DOI: 10.1074/jbc.m116.747816] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 01/13/2017] [Indexed: 11/06/2022] Open
Abstract
Nectin-like 4 (NECL4, CADM4) is a Schwann cell-specific cell adhesion molecule that promotes axo-glial interactions. In vitro and in vivo studies have shown that NECL4 is necessary for proper peripheral nerve myelination. However, the molecular mechanisms that are regulated by NECL4 and affect peripheral myelination currently remain unclear. We used an in vitro approach to begin identifying some of the mechanisms that could explain NECL4 function. Using mass spectrometry and Western blotting techniques, we have identified choline transporter-like 1 (CTL1) as a putative complexing partner with NECL4. We show that intracellular choline levels are significantly elevated in NECL4-deficient Schwann cells. The analysis of extracellular d9-choline uptake revealed a deficit in the amount of d9-choline found inside NECL4-deficient Schwann cells, suggestive of either reduced transport capabilities or increased metabolization of transported choline. An extensive lipidomic screen of choline derivatives showed that total phosphatidylcholine and phosphatidylinositol (but not diacylglycerol or sphingomyelin) are significantly elevated in NECL4-deficient Schwann cells, particularly specific subspecies of phosphatidylcholine carrying very long polyunsaturated fatty acid chains. Finally, CTL1-deficient Schwann cells are significantly impaired in their ability to myelinate neurites in vitro To our knowledge, this is the first demonstration of a bona fide cell adhesion molecule, NECL4, regulating choline homeostasis and lipid biogenesis. Phosphatidylcholines are major myelin phospholipids, and several phosphorylated phosphatidylinositol species are known to regulate key aspects of peripheral myelination. Furthermore, the biophysical properties imparted to plasma membranes are regulated by fatty acid chain profiles. Therefore, it will be important to translate these in vitro observations to in vivo studies of NECL4 and CTL1-deficient mice.
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Affiliation(s)
- Corey Heffernan
- From the Department of Biological Sciences, Rutgers, the State University of New Jersey, Newark, New Jersey 07102-1814 and
| | - Mohit R Jain
- the Center for Advanced Proteomics Research, New Jersey Medical School, Newark, New Jersey 07103
| | - Tong Liu
- the Center for Advanced Proteomics Research, New Jersey Medical School, Newark, New Jersey 07103
| | - Hyosung Kim
- From the Department of Biological Sciences, Rutgers, the State University of New Jersey, Newark, New Jersey 07102-1814 and
| | - Kevin Barretto
- From the Department of Biological Sciences, Rutgers, the State University of New Jersey, Newark, New Jersey 07102-1814 and
| | - Hong Li
- the Center for Advanced Proteomics Research, New Jersey Medical School, Newark, New Jersey 07103
| | - Patrice Maurel
- From the Department of Biological Sciences, Rutgers, the State University of New Jersey, Newark, New Jersey 07102-1814 and
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27
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Yin C, Kim Y, Argintaru D, Heit B. Rab17 mediates differential antigen sorting following efferocytosis and phagocytosis. Cell Death Dis 2016; 7:e2529. [PMID: 28005073 PMCID: PMC5261003 DOI: 10.1038/cddis.2016.431] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/17/2016] [Accepted: 11/18/2016] [Indexed: 12/29/2022]
Abstract
Macrophages engulf and destroy pathogens (phagocytosis) and apoptotic cells (efferocytosis), and can subsequently initiate adaptive immune responses by presenting antigens derived from engulfed materials. Both phagocytosis and efferocytosis share a common degradative pathway in which the target is engulfed into a membrane-bound vesicle, respectively, termed the phagosome and efferosome, where they are degraded by sequential fusion with endosomes and lysosomes. Despite this shared maturation pathway, macrophages are immunogenic following phagocytosis but not efferocytosis, indicating that differential processing or trafficking of antigens must occur. Mass spectrometry and immunofluorescence microscopy of efferosomes and phagosomes in macrophages demonstrated that efferosomes lacked the proteins required for antigen presentation and instead recruited the recycling regulator Rab17. As a result, degraded materials from efferosomes bypassed the MHC class II loading compartment via the recycling endosome - a process not observed in phagosomes. Combined, these results indicate that macrophages prevent presentation of apoptotic cell-derived antigens by preferentially trafficking efferocytosed, but not phagocytosed, materials away from the MHC class II loading compartment via the recycling endosome pathway.
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Affiliation(s)
- Charles Yin
- Department of Microbiology and Immunology and The Centre for Human Immunology, The University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON, Canada N6A 5C1
| | - Yohan Kim
- Department of Microbiology and Immunology and The Centre for Human Immunology, The University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON, Canada N6A 5C1
| | - Dean Argintaru
- Department of Microbiology and Immunology and The Centre for Human Immunology, The University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON, Canada N6A 5C1
| | - Bryan Heit
- Department of Microbiology and Immunology and The Centre for Human Immunology, The University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON, Canada N6A 5C1
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28
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Zumthor JP, Cernikova L, Rout S, Kaech A, Faso C, Hehl AB. Static Clathrin Assemblies at the Peripheral Vacuole-Plasma Membrane Interface of the Parasitic Protozoan Giardia lamblia. PLoS Pathog 2016; 12:e1005756. [PMID: 27438602 PMCID: PMC4954726 DOI: 10.1371/journal.ppat.1005756] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/18/2016] [Indexed: 11/19/2022] Open
Abstract
Giardia lamblia is a parasitic protozoan that infects a wide range of vertebrate hosts including humans. Trophozoites are non-invasive but associate tightly with the enterocyte surface of the small intestine. This narrow ecological specialization entailed extensive morphological and functional adaptations during host-parasite co-evolution, including a distinctly polarized array of endocytic organelles termed peripheral vacuoles (PVs), which are confined to the dorsal cortical region exposed to the gut lumen and are in close proximity to the plasma membrane (PM). Here, we investigated the molecular consequences of these adaptations on the Giardia endocytic machinery and membrane coat complexes. Despite the absence of canonical clathrin coated vesicles in electron microscopy, Giardia possesses conserved PV-associated clathrin heavy chain (GlCHC), dynamin-related protein (GlDRP), and assembly polypeptide complex 2 (AP2) subunits, suggesting a novel function for GlCHC and its adaptors. We found that, in contrast to GFP-tagged AP2 subunits and DRP, CHC::GFP reporters have no detectable turnover in living cells, indicating fundamental differences in recruitment to the membrane and disassembly compared to previously characterized clathrin coats. Histochemical localization in electron tomography showed that these long-lived GlCHC assemblies localized at distinctive approximations between the plasma and PV membrane. A detailed protein interactome of GlCHC revealed all of the conserved factors in addition to novel or highly diverged proteins, including a putative clathrin light chain and lipid-binding proteins. Taken together, our data provide strong evidence for giardial CHC as a component of highly stable assemblies at PV-PM junctions that likely have a central role in organizing continuities between the PM and PV membranes for controlled sampling of the fluid environment. This suggests a novel function for CHC in Giardia and the extent of molecular remodeling of endocytosis in this species. In canonical clathrin mediated endocytosis (CME) models, the concerted action of ca. 50 proteins mediates the uptake of extracellular components. The key player in this process is clathrin which coats transport intermediates called clathrin coated vesicles (CCV). The intestinal parasite Giardia lamblia has undergone extensive remodeling during colonization of the mammalian duodenum. Here, we report on unique features of this parasite’s endocytic system, consisting of fixed peripheral vacuoles (PV) in close proximity to the exposed plasma membrane (PM), with no discernible CCVs. Using state-of-the-art imaging strategies, we show that the surface of Giardia trophozoites is pock-marked with PM invaginations reaching to the underlying PV membrane. Co-immunoprecipitation and analysis of protein dynamics reveal that, in line with the absence of CCVs, giardial clathrin assemblies have no dynamic behavior. CHC still remains associated to AP2 and dynamin, both conserved dynamic CME components, and to a newly identified putative clathrin light chain. The emerging model calls for giardial clathrin organized into static cores surrounded by dynamic interaction partners, and most likely involved in the regulation of fusion between the PM and the PVs in a “kiss-and-flush”-like mechanism. This suggests that Giardia harbors a conceptually novel function for clathrin in endocytosis, which might be a consequence of host-parasite co-evolution.
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Affiliation(s)
| | - Lenka Cernikova
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
| | - Samuel Rout
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
| | - Andres Kaech
- Center for Microscopy and Image Analysis, University of Zurich, Zurich, Switzerland
| | - Carmen Faso
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
- * E-mail: (CF); (ABH)
| | - Adrian B. Hehl
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
- * E-mail: (CF); (ABH)
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29
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David-Morrison G, Xu Z, Rui YN, Charng WL, Jaiswal M, Yamamoto S, Xiong B, Zhang K, Sandoval H, Duraine L, Zuo Z, Zhang S, Bellen HJ. WAC Regulates mTOR Activity by Acting as an Adaptor for the TTT and Pontin/Reptin Complexes. Dev Cell 2016; 36:139-51. [PMID: 26812014 DOI: 10.1016/j.devcel.2015.12.019] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 10/16/2015] [Accepted: 12/18/2015] [Indexed: 01/09/2023]
Abstract
The ability to sense energy status is crucial in the regulation of metabolism via the mechanistic Target of Rapamycin Complex 1 (mTORC1). The assembly of the TTT-Pontin/Reptin complex is responsive to changes in energy status. Under energy-sufficient conditions, the TTT-Pontin/Reptin complex promotes mTORC1 dimerization and mTORC1-Rag interaction, which are critical for mTORC1 activation. We show that WAC is a regulator of energy-mediated mTORC1 activity. In a Drosophila screen designed to isolate mutations that cause neuronal dysfunction, we identified wacky, the homolog of WAC. Loss of Wacky leads to neurodegeneration, defective mTOR activity, and increased autophagy. Wacky and WAC have conserved physical interactions with mTOR and its regulators, including Pontin and Reptin, which bind to the TTT complex to regulate energy-dependent activation of mTORC1. WAC promotes the interaction between TTT and Pontin/Reptin in an energy-dependent manner, thereby promoting mTORC1 activity by facilitating mTORC1 dimerization and mTORC1-Rag interaction.
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Affiliation(s)
| | - Zhen Xu
- The Brown Foundation Institute of Molecular Medicine, The University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - Yan-Ning Rui
- The Brown Foundation Institute of Molecular Medicine, The University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - Wu-Lin Charng
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Manish Jaiswal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Bo Xiong
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ke Zhang
- Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hector Sandoval
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lita Duraine
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhongyuan Zuo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sheng Zhang
- The Brown Foundation Institute of Molecular Medicine, The University of Texas Medical School at Houston, Houston, TX 77030, USA; Department of Neurobiology and Anatomy, The University of Texas Medical School at Houston, Houston, TX 77030, USA; Programs in Human and Molecular Genetics and Neuroscience, The Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX 77030, USA.
| | - Hugo J Bellen
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.
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30
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Mesén-Ramírez P, Reinsch F, Blancke Soares A, Bergmann B, Ullrich AK, Tenzer S, Spielmann T. Stable Translocation Intermediates Jam Global Protein Export in Plasmodium falciparum Parasites and Link the PTEX Component EXP2 with Translocation Activity. PLoS Pathog 2016; 12:e1005618. [PMID: 27168322 PMCID: PMC4864081 DOI: 10.1371/journal.ppat.1005618] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 04/17/2016] [Indexed: 11/25/2022] Open
Abstract
Protein export is central for the survival and virulence of intracellular P. falciparum blood stage parasites. To reach the host cell, exported proteins cross the parasite plasma membrane (PPM) and the parasite-enclosing parasitophorous vacuole membrane (PVM), a process that requires unfolding, suggestive of protein translocation. Components of a proposed translocon at the PVM termed PTEX are essential in this phase of export but translocation activity has not been shown for the complex and questions have been raised about its proposed membrane pore component EXP2 for which no functional data is available in P. falciparum. It is also unclear how PTEX mediates trafficking of both, soluble as well as transmembrane proteins. Taking advantage of conditionally foldable domains, we here dissected the translocation events in the parasite periphery, showing that two successive translocation steps are needed for the export of transmembrane proteins, one at the PPM and one at the PVM. Our data provide evidence that, depending on the length of the C-terminus of the exported substrate, these steps occur by transient interaction of the PPM and PVM translocon, similar to the situation for protein transport across the mitochondrial membranes. Remarkably, we obtained constructs of exported proteins that remained arrested in the process of being translocated across the PVM. This clogged the translocation pore, prevented the export of all types of exported proteins and, as a result, inhibited parasite growth. The substrates stuck in translocation were found in a complex with the proposed PTEX membrane pore component EXP2, suggesting a role of this protein in translocation. These data for the first time provide evidence for EXP2 to be part of a translocating entity, suggesting that PTEX has translocation activity and provide a mechanistic framework for the transport of soluble as well as transmembrane proteins from the parasite boundary into the host cell. P. falciparum parasites, the deadliest agent of human malaria, develop within erythrocytes where they are surrounded by a parasitophorous vacuolar membrane (PVM). To ensure intracellular survival, the parasite exports a large repertoire of proteins into the host cell. Exported proteins require unfolding for trafficking across the membrane boundaries separating the parasite from the erythrocyte, typical for transport by protein translocating membrane channels. Here, we dissected the sequence of translocation events at the parasite boundary using substrates that can be conditionally arrested at translocation steps. We for the first time obtained exported proteins arrested in the process of being translocated across the PVM. This jammed the translocons for all other types of exported proteins and inhibited parasite growth. The constructs stuck in translocation were in a complex with EXP2, a component of a complex known to be essential for protein export that is termed PTEX. Our work links the need for unfolding and the function of this complex in export, giving experimental evidence that PTEX indeed is a translocon. Conditionally unfoldable domains have been instrumental in unravelling transport processes across membranes and here resolve the transport steps the different kinds of exported proteins require to reach the P. falciparum-infected host cell.
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Affiliation(s)
- Paolo Mesén-Ramírez
- Bernhard Nocht Institute for Tropical Medicine, Parasitology section, Hamburg, Germany
| | - Ferdinand Reinsch
- Bernhard Nocht Institute for Tropical Medicine, Parasitology section, Hamburg, Germany
| | | | - Bärbel Bergmann
- Bernhard Nocht Institute for Tropical Medicine, Parasitology section, Hamburg, Germany
| | - Ann-Katrin Ullrich
- Bernhard Nocht Institute for Tropical Medicine, Parasitology section, Hamburg, Germany
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Tobias Spielmann
- Bernhard Nocht Institute for Tropical Medicine, Parasitology section, Hamburg, Germany
- * E-mail:
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31
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Chromatin remodeller SMARCA4 recruits topoisomerase 1 and suppresses transcription-associated genomic instability. Nat Commun 2016; 7:10549. [PMID: 26842758 PMCID: PMC4742980 DOI: 10.1038/ncomms10549] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/25/2015] [Indexed: 02/07/2023] Open
Abstract
Topoisomerase 1, an enzyme that relieves superhelical tension, is implicated in transcription-associated mutagenesis and genome instability-associated with neurodegenerative diseases as well as activation-induced cytidine deaminase. From proteomic analysis of TOP1-associated proteins, we identify SMARCA4, an ATP-dependent chromatin remodeller; FACT, a histone chaperone; and H3K4me3, a transcriptionally active chromatin marker. Here we show that SMARCA4 knockdown in a B-cell line decreases TOP1 recruitment to chromatin, and leads to increases in Igh/c-Myc chromosomal translocations, variable and switch region mutations and negative superhelicity, all of which are also observed in response to TOP1 knockdown. In contrast, FACT knockdown inhibits association of TOP1 with H3K4me3, and severely reduces DNA cleavage and Igh/c-Myc translocations, without significant effect on TOP1 recruitment to chromatin. We thus propose that SMARCA4 is involved in the TOP1 recruitment to general chromatin, whereas FACT is required for TOP1 binding to H3K4me3 at non-B DNA containing chromatin for the site-specific cleavage. Topoisomerase 1 (TOP1) relieves superhelical tension when DNA strands are unwound during transcription. Here, Husain et al. report that SMARCA4, an ATP-dependent chromatin remodeller, is associated with TOP1 and suppresses transcription-associated genomic instability.
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32
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Tanaka H, Muto A, Shima H, Katoh Y, Sax N, Tajima S, Brydun A, Ikura T, Yoshizawa N, Masai H, Hoshikawa Y, Noda T, Nio M, Ochiai K, Igarashi K. Epigenetic Regulation of the Blimp-1 Gene (Prdm1) in B Cells Involves Bach2 and Histone Deacetylase 3. J Biol Chem 2016; 291:6316-30. [PMID: 26786103 DOI: 10.1074/jbc.m116.713842] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Indexed: 11/06/2022] Open
Abstract
B lymphocyte-induced maturation protein 1 (Blimp-1) encoded by Prdm1 is a master regulator of plasma cell differentiation. The transcription factor Bach2 represses Blimp-1 expression in B cells to stall terminal differentiation, by which it supports reactions such as class switch recombination of the antibody genes. We found that histones H3 and H4 around the Prdm1 intron 5 Maf recognition element were acetylated at higher levels in X63/0 plasma cells expressing Blimp-1 than in BAL17 mature B cells lacking its expression. Conversely, methylation of H3-K9 was lower in X63/0 cells than BAL17 cells. Purification of the Bach2 complex in BAL17 cells revealed its interaction with histone deacetylase 3 (HDAC3), nuclear co-repressors NCoR1 and NCoR2, transducin β-like 1X-linked (Tbl1x), and RAP1-interacting factor homolog (Rif1). Chromatin immunoprecipitation confirmed the binding of HDAC3 and Rif1 to the Prdm1 locus. Reduction of HDAC3 or NCoR1 expression by RNA interference in B cells resulted in an increased Prdm1 mRNA expression. Bach2 is suggested to cooperate with HDAC3-containing co-repressor complexes in B cells to regulate the stage-specific expression of Prdm1 by writing epigenetic modifications at the Prdm1 locus.
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Affiliation(s)
- Hiromu Tanaka
- From the Department of Biochemistry and the Department of Pediatric Surgery, Tohoku University Graduate School of Medicine, Seiryo-machi 1-1, Sendai 980-0874
| | - Akihiko Muto
- From the Department of Biochemistry and CREST, Japan Science and Technology Agency, Seiryo-machi 2-1, Sendai 980-8575
| | - Hiroki Shima
- From the Department of Biochemistry and CREST, Japan Science and Technology Agency, Seiryo-machi 2-1, Sendai 980-8575
| | - Yasutake Katoh
- From the Department of Biochemistry and Center for Regulatory Epigenome and Diseases,Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575
| | - Nicolas Sax
- From the Department of Biochemistry and CREST, Japan Science and Technology Agency, Seiryo-machi 2-1, Sendai 980-8575
| | | | | | - Tsuyoshi Ikura
- the Radiation Biology Center, Kyoto University, Kyoto 606-8501
| | - Naoko Yoshizawa
- Tokyo Metropolitan Institute of Medical Sciences, Kamikitazawa 1-6, Tokyo 156-8506, and
| | - Hisao Masai
- Tokyo Metropolitan Institute of Medical Sciences, Kamikitazawa 1-6, Tokyo 156-8506, and
| | - Yutaka Hoshikawa
- the Japanese Foundation for Cancer Research, Cancer Institute, Ariake 3-10-6, Tokyo 135-8550, Japan
| | - Tetsuo Noda
- the Japanese Foundation for Cancer Research, Cancer Institute, Ariake 3-10-6, Tokyo 135-8550, Japan
| | - Masaki Nio
- the Department of Pediatric Surgery, Tohoku University Graduate School of Medicine, Seiryo-machi 1-1, Sendai 980-0874
| | - Kyoko Ochiai
- From the Department of Biochemistry and CREST, Japan Science and Technology Agency, Seiryo-machi 2-1, Sendai 980-8575
| | - Kazuhiko Igarashi
- From the Department of Biochemistry and CREST, Japan Science and Technology Agency, Seiryo-machi 2-1, Sendai 980-8575, Center for Regulatory Epigenome and Diseases,Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575,
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Uchida T, Tamaki Y, Ayaki T, Shodai A, Kaji S, Morimura T, Banno Y, Nishitsuji K, Sakashita N, Maki T, Yamashita H, Ito H, Takahashi R, Urushitani M. CUL2-mediated clearance of misfolded TDP-43 is paradoxically affected by VHL in oligodendrocytes in ALS. Sci Rep 2016; 6:19118. [PMID: 26751167 PMCID: PMC4707540 DOI: 10.1038/srep19118] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 12/04/2015] [Indexed: 12/28/2022] Open
Abstract
The molecular machinery responsible for cytosolic accumulation of misfolded TDP-43 in amyotrophic lateral sclerosis (ALS) remains elusive. Here we identified a cullin-2 (CUL2) RING complex as a novel ubiquitin ligase for fragmented forms of TDP-43. The von Hippel Lindau protein (VHL), a substrate binding component of the complex, preferentially recognized misfolded TDP-43 at Glu246 in RNA-recognition motif 2. Recombinant full-length TDP-43 was structurally fragile and readily cleaved, suggesting that misfolded TDP-43 is cleared by VHL/CUL2 in a step-wise manner via fragmentation. Surprisingly, excess VHL stabilized and led to inclusion formation of TDP-43, as well as mutant SOD1, at the juxtanuclear protein quality control center. Moreover, TDP-43 knockdown elevated VHL expression in cultured cells, implying an aberrant interaction between VHL and mislocalized TDP-43 in ALS. Finally, cytoplasmic inclusions especially in oligodendrocytes in ALS spinal cords were immunoreactive to both phosphorylated TDP-43 and VHL. Thus, our results suggest that an imbalance in VHL and CUL2 may underlie oligodendrocyte dysfunction in ALS, and highlight CUL2 E3 ligase emerges as a novel therapeutic potential for ALS.
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Affiliation(s)
- Tsukasa Uchida
- Department of Neurology, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, 606-8507 Japan
| | - Yoshitaka Tamaki
- Department of Neurology, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, 606-8507 Japan
| | - Takashi Ayaki
- Department of Neurology, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, 606-8507 Japan
| | - Akemi Shodai
- Department of Neurology, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, 606-8507 Japan
| | - Seiji Kaji
- Department of Neurology, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, 606-8507 Japan
| | - Toshifumi Morimura
- Molecular Neuroscience Research Center, Shiga University of Medical Science, Seta-Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Yoshinori Banno
- Molecular Neuroscience Research Center, Shiga University of Medical Science, Seta-Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Kazuchika Nishitsuji
- Department of Molecular Pathology, Tokushima University, 2-24 Shinkuracho, Tokushima, Tokushima Prefecture 770-0855, Japan
| | - Naomi Sakashita
- Department of Molecular Pathology, Tokushima University, 2-24 Shinkuracho, Tokushima, Tokushima Prefecture 770-0855, Japan
| | - Takakuni Maki
- Department of Neurology, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, 606-8507 Japan
| | - Hirofumi Yamashita
- Department of Neurology, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, 606-8507 Japan
| | - Hidefumi Ito
- Department of Neurology, Wakayama Medical University, 811-1 Kimiidera, Wakayama, Wakayama Prefecture 641-8509, Japan
| | - Ryosuke Takahashi
- Department of Neurology, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, 606-8507 Japan
| | - Makoto Urushitani
- Department of Neurology, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, 606-8507 Japan
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MCLIP Detection of Novel Protein–Protein Interactions at the Nuclear Envelope. Methods Enzymol 2016; 569:503-15. [DOI: 10.1016/bs.mie.2015.08.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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Helferich AM, Ruf WP, Grozdanov V, Freischmidt A, Feiler MS, Zondler L, Ludolph AC, McLean PJ, Weishaupt JH, Danzer KM. α-synuclein interacts with SOD1 and promotes its oligomerization. Mol Neurodegener 2015; 10:66. [PMID: 26643113 PMCID: PMC4672499 DOI: 10.1186/s13024-015-0062-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/24/2015] [Indexed: 12/15/2022] Open
Abstract
Background Parkinson’s disease (PD) and amyotrophic lateral sclerosis (ALS) are both neurodegenerative diseases leading to impaired execution of movement. α-Synuclein plays a central role in the pathogenesis of PD whereas Cu, Zn superoxide dismutase (SOD1) is a key player in a subset of familial ALS cases. Under pathological conditions both α-synuclein and SOD1 form oligomers and fibrils. In this study we investigated the possible molecular interaction of α-synuclein and SOD1 and its functional and pathological relevance. Results Using a protein-fragment complementation approach and co-IP, we found that α-synuclein and SOD1 physically interact in living cells, human erythrocytes and mouse brain tissue. Additionally, our data show that disease related mutations in α-synuclein (A30P, A53T) and SOD1 (G85R, G93A) modify the binding of α-synuclein to SOD1. Notably, α-synuclein accelerates SOD1 oligomerization independent of SOD1 activity. Conclusion This study provides evidence for a novel interaction of α-synuclein and SOD1 that might be relevant for neurodegenerative diseases. Electronic supplementary material The online version of this article (doi:10.1186/s13024-015-0062-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anika M Helferich
- Department of Neurology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Wolfgang P Ruf
- Department of Neurology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Veselin Grozdanov
- Department of Neurology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Axel Freischmidt
- Department of Neurology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Marisa S Feiler
- Department of Neurology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Lisa Zondler
- Department of Neurology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Albert C Ludolph
- Department of Neurology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | | | - Jochen H Weishaupt
- Department of Neurology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Karin M Danzer
- Department of Neurology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
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Yang J, Wagner SA, Beli P. Illuminating Spatial and Temporal Organization of Protein Interaction Networks by Mass Spectrometry-Based Proteomics. Front Genet 2015; 6:344. [PMID: 26648978 PMCID: PMC4665136 DOI: 10.3389/fgene.2015.00344] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 11/20/2015] [Indexed: 11/13/2022] Open
Abstract
Protein–protein interactions are at the core of all cellular functions and dynamic alterations in protein interactions regulate cellular signaling. In the last decade, mass spectrometry (MS)-based proteomics has delivered unprecedented insights into human protein interaction networks. Affinity purification-MS (AP-MS) has been extensively employed for focused and high-throughput studies of steady state protein–protein interactions. Future challenges remain in mapping transient protein interactions after cellular perturbations as well as in resolving the spatial organization of protein interaction networks. AP-MS can be combined with quantitative proteomics approaches to determine the relative abundance of purified proteins in different conditions, thereby enabling the identification of transient protein interactions. In addition to affinity purification, methods based on protein co-fractionation have been combined with quantitative MS to map transient protein interactions during cellular signaling. More recently, approaches based on proximity tagging that preserve the spatial dimension of protein interaction networks have been introduced. Here, we provide an overview of MS-based methods for analyzing protein–protein interactions with a focus on approaches that aim to dissect the temporal and spatial aspects of protein interaction networks.
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Affiliation(s)
- Jiwen Yang
- Institute of Molecular Biology , Mainz, Germany
| | - Sebastian A Wagner
- Department of Medicine, Hematology and Oncology, Goethe University , Frankfurt, Germany
| | - Petra Beli
- Institute of Molecular Biology , Mainz, Germany
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Scoville DW, Cyphert HA, Liao L, Xu J, Reynolds A, Guo S, Stein R. MLL3 and MLL4 Methyltransferases Bind to the MAFA and MAFB Transcription Factors to Regulate Islet β-Cell Function. Diabetes 2015; 64:3772-83. [PMID: 26180087 PMCID: PMC4613979 DOI: 10.2337/db15-0281] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 07/03/2015] [Indexed: 12/19/2022]
Abstract
Insulin produced by islet β-cells plays a critical role in glucose homeostasis, with type 1 and type 2 diabetes both resulting from inactivation and/or loss of this cell population. Islet-enriched transcription factors regulate β-cell formation and function, yet little is known about the molecules recruited to mediate control. An unbiased in-cell biochemical and mass spectrometry strategy was used to isolate MafA transcription factor-binding proteins. Among the many coregulators identified were all of the subunits of the mixed-lineage leukemia 3 (Mll3) and 4 (Mll4) complexes, with histone 3 lysine 4 methyltransferases strongly associated with gene activation. MafA was bound to the ∼1.5 MDa Mll3 and Mll4 complexes in size-fractionated β-cell extracts. Likewise, closely related human MAFB, which is important to β-cell formation and coproduced with MAFA in adult human islet β-cells, bound MLL3 and MLL4 complexes. Knockdown of NCOA6, a core subunit of these methyltransferases, reduced expression of a subset of MAFA and MAFB target genes in mouse and human β-cell lines. In contrast, a broader effect on MafA/MafB gene activation was observed in mice lacking NCoA6 in islet β-cells. We propose that MLL3 and MLL4 are broadly required for controlling MAFA and MAFB transactivation during development and postnatally.
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Affiliation(s)
- David W Scoville
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN
| | - Holly A Cyphert
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
| | - Lan Liao
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Jianming Xu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Al Reynolds
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN
| | - Shuangli Guo
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
| | - Roland Stein
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
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Galloway JR, Bethea M, Liu Y, Underwood R, Mobley JA, Hunter CS. SSBP3 Interacts With Islet-1 and Ldb1 to Impact Pancreatic β-Cell Target Genes. Mol Endocrinol 2015; 29:1774-86. [PMID: 26495868 DOI: 10.1210/me.2015-1165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Islet-1 (Isl1) is a Lin11, Isl1, Mec3 (LIM)-homeodomain transcription factor important for pancreatic islet cell development, maturation, and function, which largely requires interaction with the LIM domain-binding protein 1 (Ldb1) coregulator. In other tissues, Ldb1 and Isl1 interact with additional factors to mediate target gene transcription, yet few protein partners are known in β-cells. Therefore, we hypothesize that Ldb1 and Isl1 participate in larger regulatory complexes to impact β-cell gene expression. To test this, we used cross-linked immunoprecipitation and mass spectrometry to identify interacting proteins from mouse β-cells. Proteomic datasets revealed numerous interacting candidates, including a member of the single-stranded DNA-binding protein (SSBP) coregulator family, SSBP3. SSBPs potentiate LIM transcription factor complex activity and stability in other tissues. However, nothing was known of SSBP3 interaction, expression, or activity in β-cells. Our analyses confirmed that SSBP3 interacts with Ldb1 and Isl1 in β-cell lines and in mouse and human islets and demonstrated SSBP3 coexpression with Ldb1 and Isl1 pancreas tissue. Furthermore, β-cell line SSBP3 knockdown imparted mRNA deficiencies similar to those observed upon Ldb1 reduction in vitro or in vivo. This appears to be (at least) due to SSBP3 occupancy of known Ldb1-Isl1 target promoters, including MafA and Glp1r. This study collectively demonstrates that SSBP3 is a critical component of Ldb1-Isl1 regulatory complexes, required for expression of critical β-cell target genes.
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Affiliation(s)
- Jamie R Galloway
- Department of Medicine (J.R.G., M.B., Y.L., R.U., C.S.H.), Division of Endocrinology, Diabetes and Metabolism, and Comprehensive Diabetes Center, and Department of Surgery (J.A.M.), University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Maigen Bethea
- Department of Medicine (J.R.G., M.B., Y.L., R.U., C.S.H.), Division of Endocrinology, Diabetes and Metabolism, and Comprehensive Diabetes Center, and Department of Surgery (J.A.M.), University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Yanping Liu
- Department of Medicine (J.R.G., M.B., Y.L., R.U., C.S.H.), Division of Endocrinology, Diabetes and Metabolism, and Comprehensive Diabetes Center, and Department of Surgery (J.A.M.), University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Rachel Underwood
- Department of Medicine (J.R.G., M.B., Y.L., R.U., C.S.H.), Division of Endocrinology, Diabetes and Metabolism, and Comprehensive Diabetes Center, and Department of Surgery (J.A.M.), University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - James A Mobley
- Department of Medicine (J.R.G., M.B., Y.L., R.U., C.S.H.), Division of Endocrinology, Diabetes and Metabolism, and Comprehensive Diabetes Center, and Department of Surgery (J.A.M.), University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Chad S Hunter
- Department of Medicine (J.R.G., M.B., Y.L., R.U., C.S.H.), Division of Endocrinology, Diabetes and Metabolism, and Comprehensive Diabetes Center, and Department of Surgery (J.A.M.), University of Alabama at Birmingham, Birmingham, Alabama 35294
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Yuzefovych Y, Blasczyk R, Huyton T. Oncogenic acidic nuclear phosphoproteins ANP32C/D are novel clients of heat shock protein 90. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:2338-48. [DOI: 10.1016/j.bbamcr.2015.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 06/17/2015] [Accepted: 06/19/2015] [Indexed: 11/27/2022]
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Kourtidis A, Ngok SP, Pulimeno P, Feathers RW, Carpio LR, Baker TR, Carr JM, Yan IK, Borges S, Perez EA, Storz P, Copland JA, Patel T, Thompson EA, Citi S, Anastasiadis PZ. Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity. Nat Cell Biol 2015; 17:1145-57. [PMID: 26302406 PMCID: PMC4975377 DOI: 10.1038/ncb3227] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 07/20/2015] [Indexed: 12/11/2022]
Abstract
E-cadherin and p120 catenin (p120) are essential for epithelial homeostasis, but can also exert pro-tumorigenic activities. Here, we resolve this apparent paradox by identifying two spatially and functionally distinct junctional complexes in non-transformed polarized epithelial cells: one growth suppressing at the apical zonula adherens (ZA), defined by the p120 partner PLEKHA7 and a non-nuclear subset of the core microprocessor components DROSHA and DGCR8, and one growth promoting at basolateral areas of cell-cell contact containing tyrosine-phosphorylated p120 and active Src. Recruitment of DROSHA and DGCR8 to the ZA is PLEKHA7 dependent. The PLEKHA7-microprocessor complex co-precipitates with primary microRNAs (pri-miRNAs) and possesses pri-miRNA processing activity. PLEKHA7 regulates the levels of select miRNAs, in particular processing of miR-30b, to suppress expression of cell transforming markers promoted by the basolateral complex, including SNAI1, MYC and CCND1. Our work identifies a mechanism through which adhesion complexes regulate cellular behaviour and reveals their surprising association with the microprocessor.
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Affiliation(s)
- Antonis Kourtidis
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, 4500 San Pablo Road, Jacksonville, Florida 32224, USA
| | - Siu P. Ngok
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, 4500 San Pablo Road, Jacksonville, Florida 32224, USA
| | - Pamela Pulimeno
- Department of Molecular Biology, University of Geneva, 30 quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland
| | - Ryan W. Feathers
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, 4500 San Pablo Road, Jacksonville, Florida 32224, USA
| | - Lomeli R. Carpio
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, 4500 San Pablo Road, Jacksonville, Florida 32224, USA
| | - Tiffany R. Baker
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, 4500 San Pablo Road, Jacksonville, Florida 32224, USA
| | - Jennifer M. Carr
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, 4500 San Pablo Road, Jacksonville, Florida 32224, USA
| | - Irene K. Yan
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, 4500 San Pablo Road, Jacksonville, Florida 32224, USA
| | - Sahra Borges
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, 4500 San Pablo Road, Jacksonville, Florida 32224, USA
| | - Edith A. Perez
- Division of Hematology/Oncology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, Florida 32224, USA
| | - Peter Storz
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, 4500 San Pablo Road, Jacksonville, Florida 32224, USA
| | - John A. Copland
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, 4500 San Pablo Road, Jacksonville, Florida 32224, USA
| | - Tushar Patel
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, 4500 San Pablo Road, Jacksonville, Florida 32224, USA
| | - E. Aubrey Thompson
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, 4500 San Pablo Road, Jacksonville, Florida 32224, USA
| | - Sandra Citi
- Department of Cell Biology and Institute of Genetics and Genomics of Geneva, University of Geneva, 30 quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland
| | - Panos Z. Anastasiadis
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, 4500 San Pablo Road, Jacksonville, Florida 32224, USA
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Papke CL, Tsunezumi J, Ringuette LJ, Nagaoka H, Terajima M, Yamashiro Y, Urquhart G, Yamauchi M, Davis EC, Yanagisawa H. Loss of fibulin-4 disrupts collagen synthesis and maturation: implications for pathology resulting from EFEMP2 mutations. Hum Mol Genet 2015. [PMID: 26220971 DOI: 10.1093/hmg/ddv308] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Homozygous recessive mutations in either EFEMP2 (encoding fibulin-4) or FBLN5 (encoding fibulin-5), critical genes for elastogenesis, lead to autosomal recessive cutis laxa types 1B and 1A, respectively. Previously, fibulin-4 was shown to bind lysyl oxidase (LOX), an elastin/collagen cross-linking enzyme, in vitro. Consistently, reported defects in humans with EFEMP2 mutations are more severe and broad in range than those due to FBLN5 mutations and encompass both elastin-rich and collagen-rich tissues. However, the underlying disease mechanism in EFEMP2 mutations has not been fully addressed. Here, we show that fibulin-4 is important for the integrity of aortic collagen in addition to elastin. Smooth muscle-specific Efemp2 loss in mouse (termed SMKO) resulted in altered fibrillar collagen localization with larger, poorly organized fibrils. LOX activity was decreased in Efemp2-null cells, and collagen cross-linking was diminished in SMKO aortas; however, elastin cross-linking was unaffected and the level of mature LOX was maintained to that of wild-type aortas. Proteomic screening identified multiple proteins involved in procollagen processing and maturation as potential fibulin-4-binding partners. We showed that fibulin-4 binds procollagen C-endopeptidase enhancer 1 (Pcolce), which enhances proteolytic cleavage of the procollagen C-terminal propeptide during procollagen processing. Interestingly, however, procollagen cleavage was not affected by the presence or absence of fibulin-4 in vitro. Thus, our data indicate that fibulin-4 serves as a potential scaffolding protein during collagen maturation in the extracellular space. Analysis of collagen in other tissues affected by fibulin-4 loss should further increase our understanding of underlying pathologic mechanisms in patients with EFEMP2 mutations.
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Affiliation(s)
- Christina L Papke
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jun Tsunezumi
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Léa-Jeanne Ringuette
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
| | - Hideaki Nagaoka
- NC Oral Health Institute, University of North Carolina, Chapel Hill, NC 27599, USA and
| | - Masahiko Terajima
- NC Oral Health Institute, University of North Carolina, Chapel Hill, NC 27599, USA and
| | - Yoshito Yamashiro
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA, Life Science Center, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Greg Urquhart
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mitsuo Yamauchi
- NC Oral Health Institute, University of North Carolina, Chapel Hill, NC 27599, USA and
| | - Elaine C Davis
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
| | - Hiromi Yanagisawa
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA, Life Science Center, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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Bernaudo F, Monteleone F, Mesuraca M, Krishnan S, Chiarella E, Scicchitano S, Cuda G, Morrone G, Bond HM, Gaspari M. Validation of a novel shotgun proteomic workflow for the discovery of protein-protein interactions: focus on ZNF521. J Proteome Res 2015; 14:1888-99. [PMID: 25774781 DOI: 10.1021/pr501288h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The study of protein-protein interactions is increasingly relying on mass spectrometry (MS). The classical approach of separating immunoprecipitated proteins by SDS-PAGE followed by in-gel digestion is long and labor-intensive. Besides, it is difficult to integrate it with most quantitative MS-based workflows, except for stable isotopic labeling of amino acids in cell culture (SILAC). This work describes a fast, flexible and quantitative workflow for the discovery of novel protein-protein interactions. A cleavable cross-linker, dithiobis[succinimidyl propionate] (DSP), is utilized to stabilize protein complexes before immunoprecipitation. Protein complex detachment from the antibody is achieved by limited proteolysis. Finally, protein quantitation is performed via (18)O labeling. The workflow has been optimized concerning (i) DSP concentration and (ii) incubation times for limited proteolysis, using the stem cell-associated transcription cofactor ZNF521 as a model target. The interaction of ZNF521 with the core components of the nuclear remodelling and histone deacetylase (NuRD) complex, already reported in the literature, was confirmed. Additionally, interactions with newly discovered molecular partners of potentially relevant functional role, such as ZNF423, Spt16, Spt5, were discovered and validated by Western blotting.
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Affiliation(s)
- Francesca Bernaudo
- †Department of Experimental and Clinical Medicine, Laboratory of Molecular Haematopoiesis and Stem Cell Biology, University Magna Graecia, Catanzaro 88100, Italy
| | - Francesca Monteleone
- ‡Department of Experimental and Clinical Medicine, Proteomics@UMG, University Magna Graecia, Catanzaro 88100, Italy
| | - Maria Mesuraca
- †Department of Experimental and Clinical Medicine, Laboratory of Molecular Haematopoiesis and Stem Cell Biology, University Magna Graecia, Catanzaro 88100, Italy
| | - Shibu Krishnan
- ‡Department of Experimental and Clinical Medicine, Proteomics@UMG, University Magna Graecia, Catanzaro 88100, Italy
| | - Emanuela Chiarella
- †Department of Experimental and Clinical Medicine, Laboratory of Molecular Haematopoiesis and Stem Cell Biology, University Magna Graecia, Catanzaro 88100, Italy
| | - Stefania Scicchitano
- †Department of Experimental and Clinical Medicine, Laboratory of Molecular Haematopoiesis and Stem Cell Biology, University Magna Graecia, Catanzaro 88100, Italy
| | - Giovanni Cuda
- ‡Department of Experimental and Clinical Medicine, Proteomics@UMG, University Magna Graecia, Catanzaro 88100, Italy
| | - Giovanni Morrone
- †Department of Experimental and Clinical Medicine, Laboratory of Molecular Haematopoiesis and Stem Cell Biology, University Magna Graecia, Catanzaro 88100, Italy
| | - Heather M Bond
- †Department of Experimental and Clinical Medicine, Laboratory of Molecular Haematopoiesis and Stem Cell Biology, University Magna Graecia, Catanzaro 88100, Italy
| | - Marco Gaspari
- ‡Department of Experimental and Clinical Medicine, Proteomics@UMG, University Magna Graecia, Catanzaro 88100, Italy
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McKenna B, Guo M, Reynolds A, Hara M, Stein R. Dynamic recruitment of functionally distinct Swi/Snf chromatin remodeling complexes modulates Pdx1 activity in islet β cells. Cell Rep 2015; 10:2032-42. [PMID: 25801033 DOI: 10.1016/j.celrep.2015.02.054] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 01/21/2015] [Accepted: 02/23/2015] [Indexed: 02/03/2023] Open
Abstract
Pdx1 is a transcription factor of fundamental importance to pancreas formation and adult islet β cell function. However, little is known about the positive- and negative-acting coregulators recruited to mediate transcriptional control. Here, we isolated numerous Pdx1-interacting factors possessing a wide range of cellular functions linked with this protein, including, but not limited to, coregulators associated with transcriptional activation and repression, DNA damage response, and DNA replication. Because chromatin remodeling activities are essential to developmental lineage decisions and adult cell function, our analysis focused on investigating the influence of the Swi/Snf chromatin remodeler on Pdx1 action. The two mutually exclusive and indispensable Swi/Snf core ATPase subunits, Brg1 and Brm, distinctly affected target gene expression in β cells. Furthermore, physiological and pathophysiological conditions dynamically regulated Pdx1 binding to these Swi/Snf complexes in vivo. We discuss how context-dependent recruitment of coregulatory complexes by Pdx1 could impact pancreas cell development and adult islet β cell activity.
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Affiliation(s)
- Brian McKenna
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Min Guo
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Albert Reynolds
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Manami Hara
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Roland Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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Raman D, Sai J, Hawkins O, Richmond A. Adaptor protein2 (AP2) orchestrates CXCR2-mediated cell migration. Traffic 2014; 15:451-69. [PMID: 24450359 DOI: 10.1111/tra.12154] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 01/16/2014] [Accepted: 01/22/2014] [Indexed: 12/14/2022]
Abstract
The chemokine receptor CXCR2 is vital for inflammation, wound healing, angiogenesis, cancer progression and metastasis. Adaptor protein 2 (AP2), a clathrin binding heterotetrameric protein comprised of α, β2, μ2 and σ2 subunits, facilitates clathrin-mediated endocytosis. Mutation of the LLKIL motif in the CXCR2 carboxyl-terminal domain (CTD) results in loss of AP2 binding to the receptor and loss of ligand-mediated receptor internalization and chemotaxis. AP2 knockdown also results in diminished ligand-mediated CXCR2 internalization, polarization and chemotaxis. Using knockdown/rescue approaches with AP2-μ2 mutants, the binding domains were characterized in reference to CXCR2 internalization and chemotaxis. When in an open conformation, μ2 Patch 1 and Patch 2 domains bind tightly to membrane PIP2 phospholipids. When AP2-μ2, is replaced with μ2 mutated in Patch 1 and/or Patch 2 domains, ligand-mediated receptor binding and internalization are not lost. However, chemotaxis requires AP2-μ2 Patch 1, but not Patch 2. AP2-σ2 has been demonstrated to bind dileucine motifs to facilitate internalization. Expression of AP2-σ2 V88D and V98S dominant negative mutants resulted in loss of CXCR2 mediated chemotaxis. Thus, AP2 binding to both membrane phosphatidylinositol phospholipids and dileucine motifs is crucial for directional migration or chemotaxis. Moreover, AP2-mediated receptor internalization can be dissociated from AP2-mediated chemotaxis.
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Affiliation(s)
- Dayanidhi Raman
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN, 37212, USA; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
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45
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Jafferali MH, Vijayaraghavan B, Figueroa RA, Crafoord E, Gudise S, Larsson VJ, Hallberg E. MCLIP, an effective method to detect interactions of transmembrane proteins of the nuclear envelope in live cells. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2399-403. [DOI: 10.1016/j.bbamem.2014.06.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 06/09/2014] [Accepted: 06/10/2014] [Indexed: 10/25/2022]
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A mass spectrometry view of stable and transient protein interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 806:263-82. [PMID: 24952186 DOI: 10.1007/978-3-319-06068-2_11] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Through an impressive range of dynamic interactions, proteins succeed to carry out the majority of functions in a cell. These temporally and spatially regulated interactions provide the means through which one single protein can perform diverse functions and modulate different cellular pathways. Understanding the identity and nature of these interactions is therefore critical for defining protein functions and their contribution to health and disease processes. Here, we provide an overview of workflows that incorporate immunoaffinity purifications and quantitative mass spectrometry (frequently abbreviated as IP-MS or AP-MS) for characterizing protein-protein interactions. We discuss experimental aspects that should be considered when optimizing the isolation of a protein complex. As the presence of nonspecific associations is a concern in these experiments, we discuss the common sources of nonspecific interactions and present label-free and metabolic labeling mass spectrometry-based methods that can help determine the specificity of interactions. The effective regulation of cellular pathways and the rapid reaction to various environmental stresses rely on the formation of stable, transient, and fast-exchanging protein-protein interactions. While determining the exact nature of an interaction remains challenging, we review cross-linking and metabolic labeling approaches that can help address this important aspect of characterizing protein interactions and macromolecular assemblies.
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Winslow AR, Moussaud S, Zhu L, Post KL, Post KL, Dickson DW, Berezovska O, McLean PJ. Convergence of pathology in dementia with Lewy bodies and Alzheimer's disease: a role for the novel interaction of alpha-synuclein and presenilin 1 in disease. Brain 2014; 137:1958-70. [PMID: 24860142 PMCID: PMC4065023 DOI: 10.1093/brain/awu119] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 03/03/2014] [Accepted: 04/02/2014] [Indexed: 12/13/2022] Open
Abstract
A growing number of PSEN1 mutations have been associated with dementia with Lewy bodies and familial Alzheimer's disease with concomitant α-synuclein pathology. The objective of this study was to determine if PSEN1 plays a direct role in the development of α-synuclein pathology in these diseases. Using mass spectrometry, immunoelectron microscopy and fluorescence lifetime image microscopy based on Forster resonance energy transfer (FLIM-FRET) we identified α-synuclein as a novel interactor of PSEN1 in wild-type mouse brain tissue. The interaction of α-synuclein with PSEN1 was detected in post-mortem brain tissue from cognitively normal cases and was significantly increased in tissue from cases with dementia with Lewy bodies and familial Alzheimer's disease associated with known PSEN1 mutations. We confirmed an increased interaction of PSEN1 and α-synuclein in cell lines expressing well characterized familial Alzheimer's disease PSEN1 mutations, L166P and delta exon 9, and demonstrated that PSEN1 mutations associate with increased membrane association and accumulation of α-synuclein. Our data provides evidence of a molecular interaction of PSEN1 and α-synuclein that may explain the clinical and pathophysiological overlap seen in synucleinopathies, including Parkinson's disease, dementia with Lewy bodies, and some forms of Alzheimer's disease.
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Affiliation(s)
- Ashley R Winslow
- 1 MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Simon Moussaud
- 2 Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Liya Zhu
- 1 MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | | | - Katherine L Post
- 1 MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Dennis W Dickson
- 2 Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Oksana Berezovska
- 1 MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Pamela J McLean
- 2 Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
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Tsai CY, Larson CA, Safaei R, Howell SB. Molecular modulation of the copper and cisplatin transport function of CTR1 and its interaction with IRS-4. Biochem Pharmacol 2014; 90:379-87. [PMID: 24967972 DOI: 10.1016/j.bcp.2014.06.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 06/16/2014] [Accepted: 06/17/2014] [Indexed: 01/29/2023]
Abstract
The copper influx transporter CTR1 is also a major influx transporter for cisplatin (cDDP) in tumor cells. It influences the cytotoxicity of cDDP both in vivo and in vitro. Whereas Cu triggers internalization of CTR1 from the plasma membrane, cDDP does not. To investigate the mechanisms of these effects, myc-tagged forms of wild type hCTR1 and variants in which Y103 was converted to alanine, C189 was converted to serine, or the K178/K179 dilysine motif was converted to alanines were re-expressed in mouse embryo cells in which both alleles of CTR1 had been knocked out and also in HEK293T cells. The Y103A mutation and to a lesser extent the C189S mutation reduced internalization of CTR1 induced by Cu while the K178A/K179A had little effect. Both Y103 and C189 were required for Cu and cDDP transport whereas the K178/K179 motif was not. While Y103 lies in an YXXM motif that, when phosphorylated, is a potential docking site for phosphatidylinositol 3-kinase and other proteins involved in endocytosis, Western blot analysis of immunoprecipitated myc-CTR1, and proteomic analysis of peptides derived from CTR1, failed to identify any basal or Cu-induced phosphorylation. However, proteomic analysis did identify an interaction of CTR1 with IRS-4 and this was confirmed by co-immunoprecipitation from HEK cells expressing either FLAG-CTR1 or myc-CTR1. The interaction was greater in the Y103A-expressing cells. We conclude that Y103 is required for the internalization of hCTR1 in response to Cu, that this occurs by a mechanism other than phosphorylation and that mutation of Y103 modulates the interaction with IRS-4.
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Affiliation(s)
- Cheng-Yu Tsai
- Moores Cancer Center, University of California, San Diego, 3855 Health Sciences Drive, Mail Code 0819, La Jolla, CA 92093-0819, USA.
| | - Christopher A Larson
- Moores Cancer Center, University of California, San Diego, 3855 Health Sciences Drive, Mail Code 0819, La Jolla, CA 92093-0819, USA.
| | - Roohangiz Safaei
- Moores Cancer Center, University of California, San Diego, 3855 Health Sciences Drive, Mail Code 0819, La Jolla, CA 92093-0819, USA
| | - Stephen B Howell
- Moores Cancer Center, University of California, San Diego, 3855 Health Sciences Drive, Mail Code 0819, La Jolla, CA 92093-0819, USA; Department of Medicine, University of California, San Diego, 3855 Health Sciences Drive, Mail Code 0819, La Jolla, CA 92093-0819, USA.
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Bhatia V, Barroso SI, García-Rubio ML, Tumini E, Herrera-Moyano E, Aguilera A. BRCA2 prevents R-loop accumulation and associates with TREX-2 mRNA export factor PCID2. Nature 2014; 511:362-5. [DOI: 10.1038/nature13374] [Citation(s) in RCA: 359] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 04/08/2014] [Indexed: 12/23/2022]
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50
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Wang DDH, Guo XE, Modrek AS, Chen CF, Chen PL, Lee WH. Helicase SUV3, polynucleotide phosphorylase, and mitochondrial polyadenylation polymerase form a transient complex to modulate mitochondrial mRNA polyadenylated tail lengths in response to energetic changes. J Biol Chem 2014; 289:16727-35. [PMID: 24770417 DOI: 10.1074/jbc.m113.536540] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mammalian mitochondrial mRNA (mt-mRNA) transcripts are polyadenylated at the 3' end with different lengths. The SUV3·PNPase complex and mtPAP have been shown to degrade and polyadenylate mt mRNA, respectively. How these two opposite actions are coordinated to modulate mt-mRNA poly(A) lengths is of interest to pursue. Here, we demonstrated that a fraction of the SUV3·PNPase complex interacts with mitochondrial polyadenylation polymerase (mtPAP) under low mitochondrial matrix inorganic phosphate (Pi) conditions. In vitro binding experiments using purified proteins suggested that SUV3 binds to mtPAP through the N-terminal region around amino acids 100-104, distinctive from the C-terminal region around amino acids 510-514 of SUV3 for PNPase binding. mtPAP does not interact with PNPase directly, and SUV3 served as a bridge capable of simultaneously binding with mtPAP and PNPase. The complex consists of a SUV3 dimer, a mtPAP dimer, and a PNPase trimer, based on the molecular sizing experiments. Mechanistically, SUV3 provides a robust single strand RNA binding domain to enhance the polyadenylation activity of mtPAP. Furthermore, purified SUV3·PNPase·mtPAP complex is capable of lengthening or shortening the RNA poly(A) tail lengths in low or high Pi/ATP ratios, respectively. Consistently, the poly(A) tail lengths of mt-mRNA transcripts can be lengthened or shortened by altering the mitochondrial matrix Pi levels via selective inhibition of the electron transport chain or ATP synthase, respectively. Taken together, these results suggested that SUV3·PNPase·mtPAP form a transient complex to modulate mt-mRNA poly(A) tail lengths in response to cellular energy changes.
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Affiliation(s)
- Dennis Ding-Hwa Wang
- From the Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California 92697 and
| | - Xuning Emily Guo
- From the Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California 92697 and
| | - Aram Sandaldjian Modrek
- From the Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California 92697 and
| | - Chi-Fen Chen
- From the Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California 92697 and
| | - Phang-Lang Chen
- From the Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California 92697 and
| | - Wen-Hwa Lee
- From the Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California 92697 and the Graduate Institute of Clinical Medical Science, China Medical University, Taichung 40402, Taiwan
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