1
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Zhong X, Peddada N, Moresco JJ, Wang J, Jiang Y, Rios JJ, Moresco EMY, Choi JH, Beutler B. Viable mutations of mouse midnolin suppress B cell malignancies. J Exp Med 2024; 221:e20232132. [PMID: 38625151 PMCID: PMC11022886 DOI: 10.1084/jem.20232132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 02/20/2024] [Accepted: 03/28/2024] [Indexed: 04/17/2024] Open
Abstract
In a genetic screen, we identified two viable missense alleles of the essential gene Midnolin (Midn) that were associated with reductions in peripheral B cells. Causation was confirmed in mice with targeted deletion of four of six MIDN protein isoforms. MIDN was expressed predominantly in lymphocytes where it augmented proteasome activity. We showed that purified MIDN directly stimulated 26S proteasome activity in vitro in a manner dependent on the ubiquitin-like domain and a C-terminal region. MIDN-deficient B cells displayed aberrant activation of the IRE-1/XBP-1 pathway of the unfolded protein response. Partial or complete MIDN deficiency strongly suppressed Eμ-Myc-driven B cell leukemia and the antiapoptotic effects of Eμ-BCL2 on B cells in vivo and induced death of Sp2/0 hybridoma cells in vitro, but only partially impaired normal lymphocyte development. Thus, MIDN is required for proteasome activity in support of normal lymphopoiesis and is essential for malignant B cell proliferation over a broad range of differentiation states.
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Affiliation(s)
- Xue Zhong
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nagesh Peddada
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - James J. Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jianhui Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yiao Jiang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jonathan J. Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Eva Marie Y. Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
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2
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Nguyen TT, Kim TH, Bencosme-Cuevas E, Berry J, Gaithuma ASK, Ansari MA, Kim TK, Tirloni L, Radulovic Z, Moresco JJ, Yates JR, Mulenga A. A tick saliva serpin, IxsS17 inhibits host innate immune system proteases and enhances host colonization by Lyme disease agent. PLoS Pathog 2024; 20:e1012032. [PMID: 38394332 PMCID: PMC10917276 DOI: 10.1371/journal.ppat.1012032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 03/06/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Lyme disease (LD) caused by Borrelia burgdorferi is among the most important human vector borne diseases for which there is no effective prevention method. Identification of tick saliva transmission factors of the LD agent is needed before the highly advocated tick antigen-based vaccine could be developed. We previously reported the highly conserved Ixodes scapularis (Ixs) tick saliva serpin (S) 17 (IxsS17) was highly secreted by B. burgdorferi infected nymphs. Here, we show that IxsS17 promote tick feeding and enhances B. burgdorferi colonization of the host. We show that IxsS17 is not part of a redundant system, and its functional domain reactive center loop (RCL) is 100% conserved in all tick species. Yeast expressed recombinant (r) IxsS17 inhibits effector proteases of inflammation, blood clotting, and complement innate immune systems. Interestingly, differential precipitation analysis revealed novel functional insights that IxsS17 interacts with both effector proteases and regulatory protease inhibitors. For instance, rIxsS17 interacted with blood clotting proteases, fXII, fX, fXII, plasmin, and plasma kallikrein alongside blood clotting regulatory serpins (antithrombin III and heparin cofactor II). Similarly, rIxsS17 interacted with both complement system serine proteases, C1s, C2, and factor I and the regulatory serpin, plasma protease C1 inhibitor. Consistently, we validated that rIxsS17 dose dependently blocked deposition of the complement membrane attack complex via the lectin complement pathway and protected complement sensitive B. burgdorferi from complement-mediated killing. Likewise, co-inoculating C3H/HeN mice with rIxsS17 and B. burgdorferi significantly enhanced colonization of mouse heart and skin organs in a reverse dose dependent manner. Taken together, our data suggests an important role for IxsS17 in tick feeding and B. burgdorferi colonization of the host.
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Affiliation(s)
- Thu-Thuy Nguyen
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Tae Heung Kim
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Emily Bencosme-Cuevas
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Jacquie Berry
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Alex Samuel Kiarie Gaithuma
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Moiz Ashraf Ansari
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Tae Kwon Kim
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Lucas Tirloni
- Tick-Pathogen Transmission Unit, Laboratory of Bacteriology, NIAID, Hamilton, Montana, United States of America
| | - Zeljko Radulovic
- Department of Biology, Stephen F. Austin State University, Nacogdoches, Texas, United States of America
| | - James J. Moresco
- Center for Genetics of Host Defense, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - John R. Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Albert Mulenga
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
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Zhong X, Moresco JJ, Diedrich JK, Pinto AM, SoRelle JA, Wang J, Keller K, Ludwig S, Moresco EMY, Beutler B, Choi JH. Essential role of MFSD1-GLMP-GIMAP5 in lymphocyte survival and liver homeostasis. Proc Natl Acad Sci U S A 2023; 120:e2314429120. [PMID: 38055739 PMCID: PMC10723049 DOI: 10.1073/pnas.2314429120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/07/2023] [Indexed: 12/08/2023] Open
Abstract
We detected ENU-induced alleles of Mfsd1 (encoding the major facilitator superfamily domain containing 1 protein) that caused lymphopenia, splenomegaly, progressive liver pathology, and extramedullary hematopoiesis (EMH). MFSD1 is a lysosomal membrane-bound solute carrier protein with no previously described function in immunity. By proteomic analysis, we identified association between MFSD1 and both GLMP (glycosylated lysosomal membrane protein) and GIMAP5 (GTPase of immunity-associated protein 5). Germline knockout alleles of Mfsd1, Glmp, and Gimap5 each caused lymphopenia, liver pathology, EMH, and lipid deposition in the bone marrow and liver. We found that the interactions of MFSD1 and GLMP with GIMAP5 are essential to maintain normal GIMAP5 expression, which in turn is critical to support lymphocyte development and liver homeostasis that suppresses EMH. These findings identify the protein complex MFSD1-GLMP-GIMAP5 operating in hematopoietic and extrahematopoietic tissues to regulate immunity and liver homeostasis.
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Affiliation(s)
- Xue Zhong
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - James J. Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Jolene K. Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA92037
| | - Antonio M. Pinto
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA92037
| | - Jeffrey A. SoRelle
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Jianhui Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Katie Keller
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Sara Ludwig
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Eva Marie Y. Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX75390
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Zhong X, Peddada N, Wang J, Moresco JJ, Zhan X, Shelton JM, SoRelle JA, Keller K, Lazaro DR, Moresco EMY, Choi JH, Beutler B. OVOL2 sustains postnatal thymic epithelial cell identity. Nat Commun 2023; 14:7786. [PMID: 38012144 PMCID: PMC10682436 DOI: 10.1038/s41467-023-43456-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 11/09/2023] [Indexed: 11/29/2023] Open
Abstract
Distinct pathways and molecules may support embryonic versus postnatal thymic epithelial cell (TEC) development and maintenance. Here, we identify a mechanism by which TEC numbers and function are maintained postnatally. A viable missense allele (C120Y) of Ovol2, expressed ubiquitously or specifically in TECs, results in lymphopenia, in which T cell development is compromised by loss of medullary TECs and dysfunction of cortical TECs. We show that the epithelial identity of TECs is aberrantly subverted towards a mesenchymal state in OVOL2-deficient mice. We demonstrate that OVOL2 inhibits the epigenetic regulatory BRAF-HDAC complex, specifically disrupting RCOR1-LSD1 interaction. This causes inhibition of LSD1-mediated H3K4me2 demethylation, resulting in chromatin accessibility and transcriptional activation of epithelial genes. Thus, OVOL2 controls the epigenetic landscape of TECs to enforce TEC identity. The identification of a non-redundant postnatal mechanism for TEC maintenance offers an entry point to understanding thymic involution, which normally begins in early adulthood.
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Affiliation(s)
- Xue Zhong
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Nagesh Peddada
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Jianhui Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - James J Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Xiaowei Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
- Department of Population and Data Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8821, USA
| | - John M Shelton
- Intermal Medicine-Histopathology Core, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8573, USA
| | - Jeffrey A SoRelle
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-9072, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390-9063, USA
| | - Katie Keller
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Danielle Renee Lazaro
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA.
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA.
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5
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Zhong X, Moresco JJ, Keller K, Lazaro DR, Ely C, Moresco EMY, Beutler B, Choi JH. Essential requirement for IER3IP1 in B cell development. Proc Natl Acad Sci U S A 2023; 120:e2312810120. [PMID: 37934820 PMCID: PMC10655558 DOI: 10.1073/pnas.2312810120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/05/2023] [Indexed: 11/09/2023] Open
Abstract
In a forward genetic screen of mice with N-ethyl-N-nitrosourea-induced mutations for aberrant immune function, we identified animals with low percentages of B220+ cells in the peripheral blood. The causative mutation was in Ier3ip1, encoding immediate early response 3 interacting protein 1 (IER3IP1), an endoplasmic reticulum membrane protein mutated in an autosomal recessive neurodevelopmental disorder termed Microcephaly with simplified gyration, Epilepsy and permanent neonatal Diabetes Syndrome (MEDS) in humans. However, no immune function for IER3IP1 had previously been reported. The viable hypomorphic Ier3ip1 allele uncovered in this study, identical to a reported IER3IP1 variant in a MEDS patient, reveals an essential hematopoietic-intrinsic role for IER3IP1 in B cell development and function. We show that IER3IP1 forms a complex with the Golgi transmembrane protein 167A and limits activation of the unfolded protein response mediated by inositol-requiring enzyme-1α and X-box binding protein 1 in B cells. Our findings suggest that B cell deficiency may be a feature of MEDS.
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Affiliation(s)
- Xue Zhong
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390-8505
| | - James J. Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390-8505
| | - Katie Keller
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390-8505
| | - Danielle Renee Lazaro
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390-8505
| | - Claire Ely
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390-8505
| | - Eva Marie Y. Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390-8505
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390-8505
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390-8505
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX75390
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6
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Pinto AFM, Diedrich JK, Moresco JJ, Yates JR. Differential Precipitation of Proteins: A Simple Protein Fractionation Strategy to Gain Biological Insights with Proteomics. J Am Soc Mass Spectrom 2023; 34:2025-2033. [PMID: 37527410 DOI: 10.1021/jasms.3c00182] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Differential precipitation of proteins (DiffPOP) is a simple technique for fractionating complex protein mixtures. Using stepwise addition of acidified methanol, ten distinct subsets of proteins can be selectively precipitated by centrifugation and identified by mass spectrometry-based proteomics. We have previously shown that the ability of a protein to resist precipitation can be altered by drug binding, which enabled us to identify a novel drug-target interaction. Here, we show that the addition of DiffPOP to a standard LC-MS proteomics workflow results in a three-dimensional separation of peptides that increases protein coverage and peptide identifications. Importantly, DiffPOP reveals solubility differences between proteoforms, potentially providing valuable insights that are typically lost in bottom-up proteomics.
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Affiliation(s)
- Antonio F M Pinto
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - James J Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, California 92037, United States
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
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7
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Song R, McAlpine W, Fond AM, Nair-Gill E, Choi JH, Nyström EEL, Arike L, Field S, Li X, SoRelle JA, Moresco JJ, Moresco EMY, Yates JR, Azadi P, Ni J, Birchenough GMH, Beutler B, Turer EE. Trans-Golgi protein TVP23B regulates host-microbe interactions via Paneth cell homeostasis and Goblet cell glycosylation. Nat Commun 2023; 14:3652. [PMID: 37339972 PMCID: PMC10282085 DOI: 10.1038/s41467-023-39398-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/09/2023] [Indexed: 06/22/2023] Open
Abstract
A key feature in intestinal immunity is the dynamic intestinal barrier, which separates the host from resident and pathogenic microbiota through a mucus gel impregnated with antimicrobial peptides. Using a forward genetic screen, we have found a mutation in Tvp23b, which conferred susceptibility to chemically induced and infectious colitis. Trans-Golgi apparatus membrane protein TVP23 homolog B (TVP23B) is a transmembrane protein conserved from yeast to humans. We found that TVP23B controls the homeostasis of Paneth cells and function of goblet cells, leading to a decrease in antimicrobial peptides and more penetrable mucus layer. TVP23B binds with another Golgi protein, YIPF6, which is similarly critical for intestinal homeostasis. The Golgi proteomes of YIPF6 and TVP23B-deficient colonocytes have a common deficiency of several critical glycosylation enzymes. TVP23B is necessary for the formation of the sterile mucin layer of the intestine and its absence disturbs the balance of host and microbe in vivo.
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Affiliation(s)
- Ran Song
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - William McAlpine
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Aaron M Fond
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
- Department of Internal Medicine, Division of Gastroenterology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Evan Nair-Gill
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Elisabeth E L Nyström
- Institute of Biochemistry, University of Kiel, 24118, Kiel, Schleswig-Holstein, Germany
| | - Liisa Arike
- The Wallenberg Centre for Molecular & Translational Medicine, Department of Medical Biochemistry, Institute of Biomedicine, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Sydney Field
- Department of Internal Medicine, Division of Gastroenterology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Xiaohong Li
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Jeffrey A SoRelle
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - James J Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Josephine Ni
- Department of Internal Medicine, Division of Gastroenterology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - George M H Birchenough
- The Wallenberg Centre for Molecular & Translational Medicine, Department of Medical Biochemistry, Institute of Biomedicine, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Emre E Turer
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA.
- Department of Internal Medicine, Division of Gastroenterology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA.
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8
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Cui H, Diedrich JK, Wu DC, Lim JJ, Nottingham RM, Moresco JJ, Yates JR, Blencowe BJ, Lambowitz AM, Schimmel P. Publisher Correction: Arg-tRNA synthetase links inflammatory metabolism to RNA splicing and nuclear trafficking via SRRM2. Nat Cell Biol 2023:10.1038/s41556-023-01172-2. [PMID: 37237245 DOI: 10.1038/s41556-023-01172-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Haissi Cui
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Douglas C Wu
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX, USA
| | - Justin J Lim
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ryan M Nottingham
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX, USA
| | - James J Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Benjamin J Blencowe
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Alan M Lambowitz
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX, USA.
| | - Paul Schimmel
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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9
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Lee S, Abini-Agbomson S, Perry DS, Goodman A, Rao B, Huang MY, Diedrich JK, Moresco JJ, Yates JR, Armache KJ, Madhani HD. Intrinsic mesoscale properties of a Polycomb protein underpin heterochromatin fidelity. Nat Struct Mol Biol 2023:10.1038/s41594-023-01000-z. [PMID: 37217653 DOI: 10.1038/s41594-023-01000-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/17/2023] [Indexed: 05/24/2023]
Abstract
Little is understood about how the two major types of heterochromatin domains (HP1 and Polycomb) are kept separate. In the yeast Cryptococcus neoformans, the Polycomb-like protein Ccc1 prevents deposition of H3K27me3 at HP1 domains. Here we show that phase separation propensity underpins Ccc1 function. Mutations of the two basic clusters in the intrinsically disordered region or deletion of the coiled-coil dimerization domain alter phase separation behavior of Ccc1 in vitro and have commensurate effects on formation of Ccc1 condensates in vivo, which are enriched for PRC2. Notably, mutations that alter phase separation trigger ectopic H3K27me3 at HP1 domains. Supporting a direct condensate-driven mechanism for fidelity, Ccc1 droplets efficiently concentrate recombinant C. neoformans PRC2 in vitro whereas HP1 droplets do so only weakly. These studies establish a biochemical basis for chromatin regulation in which mesoscale biophysical properties play a key functional role.
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Affiliation(s)
- Sujin Lee
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Stephen Abini-Agbomson
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Daniela S Perry
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Allen Goodman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Beiduo Rao
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Manning Y Huang
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - James J Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Karim-Jean Armache
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
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10
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Koppes EA, Johnson MA, Moresco JJ, Luppi P, Lewis DW, Stolz DB, Diedrich JK, Yates JR, Wek RC, Watkins SC, Gollin SM, Park HJ, Drain P, Nicholls RD. Insulin secretion deficits in a Prader-Willi syndrome β-cell model are associated with a concerted downregulation of multiple endoplasmic reticulum chaperones. PLoS Genet 2023; 19:e1010710. [PMID: 37068109 PMCID: PMC10138222 DOI: 10.1371/journal.pgen.1010710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 04/27/2023] [Accepted: 03/21/2023] [Indexed: 04/18/2023] Open
Abstract
Prader-Willi syndrome (PWS) is a multisystem disorder with neurobehavioral, metabolic, and hormonal phenotypes, caused by loss of expression of a paternally-expressed imprinted gene cluster. Prior evidence from a PWS mouse model identified abnormal pancreatic islet development with retention of aged insulin and deficient insulin secretion. To determine the collective roles of PWS genes in β-cell biology, we used genome-editing to generate isogenic, clonal INS-1 insulinoma lines having 3.16 Mb deletions of the silent, maternal- (control) and active, paternal-allele (PWS). PWS β-cells demonstrated a significant cell autonomous reduction in basal and glucose-stimulated insulin secretion. Further, proteomic analyses revealed reduced levels of cellular and secreted hormones, including all insulin peptides and amylin, concomitant with reduction of at least ten endoplasmic reticulum (ER) chaperones, including GRP78 and GRP94. Critically, differentially expressed genes identified by whole transcriptome studies included reductions in levels of mRNAs encoding these secreted peptides and the group of ER chaperones. In contrast to the dosage compensation previously seen for ER chaperones in Grp78 or Grp94 gene knockouts or knockdown, compensation is precluded by the stress-independent deficiency of ER chaperones in PWS β-cells. Consistent with reduced ER chaperones levels, PWS INS-1 β-cells are more sensitive to ER stress, leading to earlier activation of all three arms of the unfolded protein response. Combined, the findings suggest that a chronic shortage of ER chaperones in PWS β-cells leads to a deficiency of protein folding and/or delay in ER transit of insulin and other cargo. In summary, our results illuminate the pathophysiological basis of pancreatic β-cell hormone deficits in PWS, with evolutionary implications for the multigenic PWS-domain, and indicate that PWS-imprinted genes coordinate concerted regulation of ER chaperone biosynthesis and β-cell secretory pathway function.
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Affiliation(s)
- Erik A Koppes
- Division of Genetic and Genomic Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Marie A Johnson
- Division of Genetic and Genomic Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - James J Moresco
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Patrizia Luppi
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Dale W Lewis
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Donna B Stolz
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Jolene K Diedrich
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - John R Yates
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ronald C Wek
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Simon C Watkins
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Susanne M Gollin
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Hyun Jung Park
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Peter Drain
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Robert D Nicholls
- Division of Genetic and Genomic Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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11
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Cui H, Diedrich JK, Wu DC, Lim JJ, Nottingham RM, Moresco JJ, Yates JR, Blencowe BJ, Lambowitz AM, Schimmel P. Arg-tRNA synthetase links inflammatory metabolism to RNA splicing and nuclear trafficking via SRRM2. Nat Cell Biol 2023; 25:592-603. [PMID: 37059883 DOI: 10.1038/s41556-023-01118-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 02/27/2023] [Indexed: 04/16/2023]
Abstract
Cells respond to perturbations such as inflammation by sensing changes in metabolite levels. Especially prominent is arginine, which has known connections to the inflammatory response. Aminoacyl-tRNA synthetases, enzymes that catalyse the first step of protein synthesis, can also mediate cell signalling. Here we show that depletion of arginine during inflammation decreased levels of nuclear-localized arginyl-tRNA synthetase (ArgRS). Surprisingly, we found that nuclear ArgRS interacts and co-localizes with serine/arginine repetitive matrix protein 2 (SRRM2), a spliceosomal and nuclear speckle protein, and that decreased levels of nuclear ArgRS correlated with changes in condensate-like nuclear trafficking of SRRM2 and splice-site usage in certain genes. These splice-site usage changes cumulated in the synthesis of different protein isoforms that altered cellular metabolism and peptide presentation to immune cells. Our findings uncover a mechanism whereby an aminoacyl-tRNA synthetase cognate to a key amino acid that is metabolically controlled during inflammation modulates the splicing machinery.
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Affiliation(s)
- Haissi Cui
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Douglas C Wu
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX, USA
| | - Justin J Lim
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ryan M Nottingham
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX, USA
| | - James J Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Benjamin J Blencowe
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Alan M Lambowitz
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX, USA.
| | - Paul Schimmel
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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12
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Mulenga A, Radulovic Z, Porter L, Britten TH, Kim TK, Tirloni L, Gaithuma AK, Adeniyi-Ipadeola GO, Dietrich JK, Moresco JJ, Yates JR. Identification and characterization of proteins that form the inner core Ixodes scapularis tick attachment cement layer. Sci Rep 2022; 12:21300. [PMID: 36494396 PMCID: PMC9734129 DOI: 10.1038/s41598-022-24881-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
Ixodes scapularis long-term blood feeding behavior is facilitated by a tick secreted bio adhesive (tick cement) that attaches tick mouthparts to skin tissue and prevents the host from dislodging the attached tick. Understanding tick cement formation is highly sought after as its disruption will prevent tick feeding. This study describes proteins that form the inner core layer of I. scapularis tick cement as disrupting these proteins will likely stop formation of the outer cortical layer. The inner core cement layer completes formation by 24 h of tick attachment. Thus, we used laser-capture microdissection to isolate cement from cryosections of 6 h and 24 h tick attachment sites and to distinguish between early and late inner core cement proteins. LC-MS/MS analysis identified 138 tick cement proteins (TCPs) of which 37 and 35 were unique in cement of 6 and 24 h attached ticks respectively. We grouped TCPs in 14 functional categories: cuticular protein (16%), tick specific proteins of unknown function, cytoskeletal proteins, and enzymes (13% each), enzymes (10%), antioxidant, glycine rich, scaffolding, heat shock, histone, histamine binding, proteases and protease inhibitors, and miscellaneous (3-6% each). Gene ontology analysis confirm that TCPs are enriched for bio adhesive properties. Our data offer insights into tick cement bonding patterns and set the foundation for understanding the molecular basis of I. scapularis tick cement formation.
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Affiliation(s)
- Albert Mulenga
- grid.264756.40000 0004 4687 2082Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX USA
| | - Zeljko Radulovic
- grid.264756.40000 0004 4687 2082Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX USA ,grid.264303.00000 0001 0754 4420Present Address: Department of Biology, Stephen F. Austin State University, Nacogdoches, TX USA
| | - Lindsay Porter
- grid.264756.40000 0004 4687 2082Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX USA ,grid.264303.00000 0001 0754 4420Present Address: Department of Biology, Stephen F. Austin State University, Nacogdoches, TX USA
| | - Taylor Hollman Britten
- grid.264756.40000 0004 4687 2082Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX USA
| | - Tae Kwon Kim
- grid.264756.40000 0004 4687 2082Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX USA ,grid.36567.310000 0001 0737 1259Present Address: Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS USA
| | - Lucas Tirloni
- grid.264756.40000 0004 4687 2082Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX USA ,grid.419681.30000 0001 2164 9667Present Address: Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Hamilton, MT USA
| | - Alex Kiarie Gaithuma
- grid.264756.40000 0004 4687 2082Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX USA
| | - Grace O. Adeniyi-Ipadeola
- grid.264756.40000 0004 4687 2082Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX USA ,grid.39382.330000 0001 2160 926XPresent Address: Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030 USA
| | - Jolene K. Dietrich
- grid.214007.00000000122199231Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA USA ,grid.250671.70000 0001 0662 7144Mass Spectrometry Core, Salk Institute for Biological Studies, La Jolla, CA USA
| | - James J. Moresco
- grid.214007.00000000122199231Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA USA ,grid.267313.20000 0000 9482 7121Present Address: Center for Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX USA
| | - John R. Yates
- grid.214007.00000000122199231Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA USA
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13
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Chen YS, Hou W, Tracy S, Harvey AT, Harjono V, Xu F, Moresco JJ, Yates JR, Zid BM. Rvb1/Rvb2 proteins couple transcription and translation during glucose starvation. eLife 2022; 11:76965. [PMID: 36107469 PMCID: PMC9531950 DOI: 10.7554/elife.76965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
During times of unpredictable stress, organisms must adapt their gene expression to maximize survival. Along with changes in transcription, one conserved means of gene regulation during conditions that quickly repress translation is the formation of cytoplasmic phase-separated mRNP granules such as P-bodies and stress granules. Previously, we identified that distinct steps in gene expression can be coupled during glucose starvation as promoter sequences in the nucleus are able to direct the subcellular localization and translatability of mRNAs in the cytosol. Here, we report that Rvb1 and Rvb2, conserved ATPase proteins implicated as protein assembly chaperones and chromatin remodelers, were enriched at the promoters and mRNAs of genes involved in alternative glucose metabolism pathways that we previously found to be transcriptionally upregulated but translationally downregulated during glucose starvation in yeast. Engineered Rvb1/Rvb2-binding on mRNAs was sufficient to sequester mRNAs into mRNP granules and repress their translation. Additionally, this Rvb tethering to the mRNA drove further transcriptional upregulation of the target genes. Further, we found that depletion of Rvb2 caused decreased alternative glucose metabolism gene mRNA induction, but upregulation of protein synthesis during glucose starvation. Overall, our results point to Rvb1/Rvb2 coupling transcription, mRNA granular localization, and translatability of mRNAs during glucose starvation. This Rvb-mediated rapid gene regulation could potentially serve as an efficient recovery plan for cells after stress removal.
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Affiliation(s)
- Yang S Chen
- Department of Chemistry and Biochemistry, University of California, San Diego
| | - Wanfu Hou
- Department of Chemistry and Biochemistry, University of California, San Diego
| | - Sharon Tracy
- Department of Chemistry and Biochemistry, University of California, San Diego
| | - Alex T Harvey
- Department of Chemistry and Biochemistry, University of California, San Diego
| | - Vince Harjono
- Department of Chemistry and Biochemistry, University of California, San Diego
| | - Fan Xu
- Division of Biological Sciences, University of California, San Diego
| | - James J Moresco
- Department of Chemical Physiology, Scripps Research Institute
| | | | - Brian M Zid
- Department of Chemistry and Biochemistry, University of California San Diego
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14
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Yuan B, Zhou X, Suzuki K, Ramos-Mandujano G, Wang M, Tehseen M, Cortés-Medina LV, Moresco JJ, Dunn S, Hernandez-Benitez R, Hishida T, Kim NY, Andijani MM, Bi C, Ku M, Takahashi Y, Xu J, Qiu J, Huang L, Benner C, Aizawa E, Qu J, Liu GH, Li Z, Yi F, Ghosheh Y, Shao C, Shokhirev M, Comoli P, Frassoni F, Yates JR, Fu XD, Esteban CR, Hamdan S, Izpisua Belmonte JC, Li M. Author Correction: Wiskott-Aldrich syndrome protein forms nuclear condensates and regulates alternative splicing. Nat Commun 2022; 13:5291. [PMID: 36075901 PMCID: PMC9458650 DOI: 10.1038/s41467-022-32875-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Baolei Yuan
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Xuan Zhou
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Keiichiro Suzuki
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.,Institute for Advanced Co-Creation Studies, Graduate School of Engineering Science, Osaka University, Osaka, Japan
| | - Gerardo Ramos-Mandujano
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Mengge Wang
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Muhammad Tehseen
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Lorena V Cortés-Medina
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - James J Moresco
- Department of Cell Biology, Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Sarah Dunn
- The Waitt Advanced Biophotonics Core Facility, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Reyna Hernandez-Benitez
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.,Altos Labs, Inc. 5510 Morehouse Drive, Suite 300, San Diego, CA, 92121, USA
| | - Tomoaki Hishida
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.,Laboratory of Biological Chemistry, School of Pharmaceutical Sciences, Wakayama Medical University, 25-1 Shitibancho, Wakayama, Wakayama, 640-8156, Japan
| | - Na Young Kim
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Manal M Andijani
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Chongwei Bi
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Manching Ku
- Next-generation sequencing core, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Yuta Takahashi
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.,Life Science Center, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Jinna Xu
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Jinsong Qiu
- Department of Cellular & Molecular Medicine, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Ling Huang
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Christopher Benner
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Emi Aizawa
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.,Institute for Advanced Co-Creation Studies, Graduate School of Engineering Science, Osaka University, Osaka, Japan
| | - Jing Qu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhongwei Li
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.,University of Southern California, 1333 San Pablo Street, MMR 618, Los Angeles, CA, 90033, USA
| | - Fei Yi
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.,Ambys Medicines, 131 Oyster Point Blvd. Suite 200, South San Francisco, CA, 94080, USA
| | - Yanal Ghosheh
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Changwei Shao
- Department of Cellular & Molecular Medicine, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Maxim Shokhirev
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Patrizia Comoli
- Pediatric Hematology/Oncology and Cell Factory, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Francesco Frassoni
- Department of Research Laboratories and Director of Center for Stem Cell and Cell Therapy, Instituto G. Gaslini Children Hospital Scientific Institute, 16147, Genova, Italy
| | - John R Yates
- Department of Cell Biology, Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Xiang-Dong Fu
- Department of Cellular & Molecular Medicine, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Concepcion Rodriguez Esteban
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.,Altos Labs, Inc. 5510 Morehouse Drive, Suite 300, San Diego, CA, 92121, USA
| | - Samir Hamdan
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Juan Carlos Izpisua Belmonte
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia. .,Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA. .,Altos Labs, Inc. 5510 Morehouse Drive, Suite 300, San Diego, CA, 92121, USA.
| | - Mo Li
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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15
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Yuan B, Zhou X, Suzuki K, Ramos-Mandujano G, Wang M, Tehseen M, Cortés-Medina LV, Moresco JJ, Dunn S, Hernandez-Benitez R, Hishida T, Kim NY, Andijani MM, Bi C, Ku M, Takahashi Y, Xu J, Qiu J, Huang L, Benner C, Aizawa E, Qu J, Liu GH, Li Z, Yi F, Ghosheh Y, Shao C, Shokhirev M, Comoli P, Frassoni F, Yates JR, Fu XD, Esteban CR, Hamdan S, Li M, Izpisua Belmonte JC. Wiskott-Aldrich syndrome protein forms nuclear condensates and regulates alternative splicing. Nat Commun 2022; 13:3646. [PMID: 35752626 PMCID: PMC9233711 DOI: 10.1038/s41467-022-31220-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 06/06/2022] [Indexed: 11/09/2022] Open
Abstract
The diverse functions of WASP, the deficiency of which causes Wiskott-Aldrich syndrome (WAS), remain poorly defined. We generated three isogenic WAS models using patient induced pluripotent stem cells and genome editing. These models recapitulated WAS phenotypes and revealed that WASP deficiency causes an upregulation of numerous RNA splicing factors and widespread altered splicing. Loss of WASP binding to splicing factor gene promoters frequently leads to aberrant epigenetic activation. WASP interacts with dozens of nuclear speckle constituents and constrains SRSF2 mobility. Using an optogenetic system, we showed that WASP forms phase-separated condensates that encompasses SRSF2, nascent RNA and active Pol II. The role of WASP in gene body condensates is corroborated by ChIPseq and RIPseq. Together our data reveal that WASP is a nexus regulator of RNA splicing that controls the transcription of splicing factors epigenetically and the dynamics of the splicing machinery through liquid-liquid phase separation.
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Affiliation(s)
- Baolei Yuan
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Xuan Zhou
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Keiichiro Suzuki
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.,Institute for Advanced Co-Creation Studies, Graduate School of Engineering Science, Osaka University, Osaka, Japan
| | - Gerardo Ramos-Mandujano
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Mengge Wang
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Muhammad Tehseen
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Lorena V Cortés-Medina
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - James J Moresco
- Department of Cell Biology, Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Sarah Dunn
- The Waitt Advanced Biophotonics Core Facility, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Reyna Hernandez-Benitez
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.,Altos Labs, Inc. 5510 Morehouse Drive, Suite 300, San Diego, CA, 92121, USA
| | - Tomoaki Hishida
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.,Laboratory of Biological Chemistry, School of Pharmaceutical Sciences, Wakayama Medical University, 25-1 Shitibancho, Wakayama, Wakayama, 640-8156, Japan
| | - Na Young Kim
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Manal M Andijani
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Chongwei Bi
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Manching Ku
- Next-generation sequencing core, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Yuta Takahashi
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.,Life Science Center, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Jinna Xu
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Jinsong Qiu
- Department of Cellular & Molecular Medicine, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Ling Huang
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Christopher Benner
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Emi Aizawa
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.,Institute for Advanced Co-Creation Studies, Graduate School of Engineering Science, Osaka University, Osaka, Japan
| | - Jing Qu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhongwei Li
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.,University of Southern California, 1333 San Pablo Street, MMR 618, Los Angeles, CA, 90033, USA
| | - Fei Yi
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.,Ambys Medicines, 131 Oyster Point Blvd. Suite 200, South San Francisco, CA, 94080, USA
| | - Yanal Ghosheh
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Changwei Shao
- Department of Cellular & Molecular Medicine, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Maxim Shokhirev
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Patrizia Comoli
- Pediatric Hematology/Oncology and Cell Factory, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Francesco Frassoni
- Department of Research Laboratories and Director of Center for Stem Cell and Cell Therapy, Instituto G. Gaslini Children Hospital Scientific Institute, 16147, Genova, Italy
| | - John R Yates
- Department of Cell Biology, Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Xiang-Dong Fu
- Department of Cellular & Molecular Medicine, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Concepcion Rodriguez Esteban
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.,Altos Labs, Inc. 5510 Morehouse Drive, Suite 300, San Diego, CA, 92121, USA
| | - Samir Hamdan
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Mo Li
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
| | - Juan Carlos Izpisua Belmonte
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia. .,Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA. .,Altos Labs, Inc. 5510 Morehouse Drive, Suite 300, San Diego, CA, 92121, USA.
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16
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Seiler K, Humbert M, Minder P, Mashimo I, Schläfli AM, Krauer D, Federzoni EA, Vu B, Moresco JJ, Yates JR, Sadowski MC, Radpour R, Kaufmann T, Sarry JE, Dengjel J, Tschan MP, Torbett BE. Hexokinase 3 enhances myeloid cell survival via non-glycolytic functions. Cell Death Dis 2022; 13:448. [PMID: 35538058 PMCID: PMC9091226 DOI: 10.1038/s41419-022-04891-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 04/10/2022] [Accepted: 04/28/2022] [Indexed: 12/14/2022]
Abstract
The family of hexokinases (HKs) catalyzes the first step of glycolysis, the ATP-dependent phosphorylation of glucose to glucose-6-phosphate. While HK1 and HK2 are ubiquitously expressed, the less well-studied HK3 is primarily expressed in hematopoietic cells and tissues and is highly upregulated during terminal differentiation of some acute myeloid leukemia (AML) cell line models. Here we show that expression of HK3 is predominantly originating from myeloid cells and that the upregulation of this glycolytic enzyme is not restricted to differentiation of leukemic cells but also occurs during ex vivo myeloid differentiation of healthy CD34+ hematopoietic stem and progenitor cells. Within the hematopoietic system, we show that HK3 is predominantly expressed in cells of myeloid origin. CRISPR/Cas9 mediated gene disruption revealed that loss of HK3 has no effect on glycolytic activity in AML cell lines while knocking out HK2 significantly reduced basal glycolysis and glycolytic capacity. Instead, loss of HK3 but not HK2 led to increased sensitivity to ATRA-induced cell death in AML cell lines. We found that HK3 knockout (HK3-null) AML cells showed an accumulation of reactive oxygen species (ROS) as well as DNA damage during ATRA-induced differentiation. RNA sequencing analysis confirmed pathway enrichment for programmed cell death, oxidative stress, and DNA damage response in HK3-null AML cells. These signatures were confirmed in ATAC sequencing, showing that loss of HK3 leads to changes in chromatin configuration and increases the accessibility of genes involved in apoptosis and stress response. Through isoform-specific pulldowns, we furthermore identified a direct interaction between HK3 and the proapoptotic BCL-2 family member BIM, which has previously been shown to shorten myeloid life span. Our findings provide evidence that HK3 is dispensable for glycolytic activity in AML cells while promoting cell survival, possibly through direct interaction with the BH3-only protein BIM during ATRA-induced neutrophil differentiation.
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Affiliation(s)
- Kristina Seiler
- grid.5734.50000 0001 0726 5157Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland ,grid.5734.50000 0001 0726 5157Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland ,grid.214007.00000000122199231Department of Immunology and Microbiology, Scripps Research, La Jolla, CA USA
| | - Magali Humbert
- grid.5734.50000 0001 0726 5157Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland
| | - Petra Minder
- grid.214007.00000000122199231Department of Immunology and Microbiology, Scripps Research, La Jolla, CA USA
| | - Iris Mashimo
- grid.214007.00000000122199231Department of Immunology and Microbiology, Scripps Research, La Jolla, CA USA
| | - Anna M. Schläfli
- grid.5734.50000 0001 0726 5157Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland
| | - Deborah Krauer
- grid.5734.50000 0001 0726 5157Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland
| | - Elena A. Federzoni
- grid.214007.00000000122199231Department of Immunology and Microbiology, Scripps Research, La Jolla, CA USA
| | - Bich Vu
- grid.8534.a0000 0004 0478 1713Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - James J. Moresco
- grid.214007.00000000122199231Department of Molecular Medicine, Scripps Research, La Jolla, CA USA
| | - John R. Yates
- grid.214007.00000000122199231Department of Molecular Medicine, Scripps Research, La Jolla, CA USA
| | - Martin C. Sadowski
- grid.5734.50000 0001 0726 5157Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland
| | - Ramin Radpour
- grid.411656.10000 0004 0479 0855Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland ,grid.5734.50000 0001 0726 5157Tumor Immunology, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Thomas Kaufmann
- grid.5734.50000 0001 0726 5157Institute of Pharmacology, University of Bern, Bern, Switzerland
| | - Jean-Emmanuel Sarry
- grid.457379.bCentre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France ,grid.411175.70000 0001 1457 2980Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Joern Dengjel
- grid.8534.a0000 0004 0478 1713Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Mario P. Tschan
- grid.5734.50000 0001 0726 5157Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland ,grid.5734.50000 0001 0726 5157Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Bruce E. Torbett
- grid.214007.00000000122199231Department of Immunology and Microbiology, Scripps Research, La Jolla, CA USA ,grid.34477.330000000122986657Department of Pediatrics, School of Medicine, University of Washington, Seattle, WA USA ,grid.240741.40000 0000 9026 4165Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA USA ,Institute for Stem Cell and Regenerative Medicine, Seattle, WA USA
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17
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Freund EC, Sapiro AL, Li Q, Linder S, Moresco JJ, Yates JR, Li JB. Unbiased Identification of trans Regulators of ADAR and A-to-I RNA Editing. Cell Rep 2021; 31:107656. [PMID: 32433965 DOI: 10.1016/j.celrep.2020.107656] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/11/2020] [Accepted: 04/23/2020] [Indexed: 12/20/2022] Open
Abstract
Adenosine-to-inosine RNA editing is catalyzed by adenosine deaminase acting on RNA (ADAR) enzymes that deaminate adenosine to inosine. Although many RNA editing sites are known, few trans regulators have been identified. We perform BioID followed by mass spectrometry to identify trans regulators of ADAR1 and ADAR2 in HeLa and M17 neuroblastoma cells. We identify known and novel ADAR-interacting proteins. Using ENCODE data, we validate and characterize a subset of the novel interactors as global or site-specific RNA editing regulators. Our set of novel trans regulators includes all four members of the DZF-domain-containing family of proteins: ILF3, ILF2, STRBP, and ZFR. We show that these proteins interact with each ADAR and modulate RNA editing levels. We find ILF3 is a broadly influential negative regulator of editing. This work demonstrates the broad roles that RNA binding proteins play in regulating editing levels, and establishes DZF-domain-containing proteins as a group of highly influential RNA editing regulators.
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Affiliation(s)
- Emily C Freund
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Anne L Sapiro
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Qin Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Sandra Linder
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - James J Moresco
- Department of Molecular Medicine, 10550 North Torrey Pines Road, SR302, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Molecular Medicine, 10550 North Torrey Pines Road, SR302, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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18
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Mohieldin AM, Pala R, Beuttler R, Moresco JJ, Yates JR, Nauli SM. Ciliary extracellular vesicles are distinct from the cytosolic extracellular vesicles. J Extracell Vesicles 2021; 10:e12086. [PMID: 33936569 PMCID: PMC8077156 DOI: 10.1002/jev2.12086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 03/25/2021] [Accepted: 04/06/2021] [Indexed: 12/28/2022] Open
Abstract
Extracellular vesicles (EVs) are cell‐derived membrane vesicles that are released into the extracellular space. EVs encapsulate key proteins and mediate intercellular signalling pathways. Recently, primary cilia have been shown to release EVs under fluid‐shear flow, but many proteins encapsulated in these vesicles have never been identified. Primary cilia are ubiquitous mechanosensory organelles that protrude from the apical surface of almost all human cells. Primary cilia also serve as compartments for signalling pathways, and their defects have been associated with a wide range of human genetic diseases called ciliopathies. To better understand the mechanism of ciliopathies, it is imperative to know the distinctive protein profiles of the differently sourced EVs (cilia vs cytosol). Here, we isolated EVs from ciliated wild‐type (WT) and non‐ciliated IFT88 knockout (KO) mouse endothelial cells using fluid‐shear flow followed by a conventional method of EV isolation. EVs isolated from WT and KO exhibited distinctive sizes. Differences in EV protein contents were studied using liquid chromatography with tandem mass spectrometry (LC‐MS‐MS) and proteomic comparative analysis, which allowed us to classify proteins between ciliary EVs and cytosolic EVs derived from WT and KO, respectively. A total of 79 proteins were exclusively expressed in WT EVs, 145 solely in KO EVs, and 524 in both EVs. Our bioinformatics analyses revealed 29% distinct protein classes and 75% distinct signalling pathways between WT and KO EVs. Based on our statistical analyses and in vitro studies, we identified NADPH‐cytochrome P450 reductase (POR), and CD166 antigen (CD166) as potential biomarkers for ciliary and cytosolic EVs, respectively. Our protein‐protein interaction network analysis revealed that POR, but not CD166, interacted with either established or strong ciliopathy gene candidates. This report shows the unique differences between EVs secreted from cilia and the cytosol. These results will be important in advancing our understanding of human genetic diseases.
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Affiliation(s)
- Ashraf M Mohieldin
- Department of Biomedical & Pharmaceutical Sciences Chapman University Irvine California USA.,Department of Medicine University of California Irvine Irvine California USA
| | - Rajasekharreddy Pala
- Department of Biomedical & Pharmaceutical Sciences Chapman University Irvine California USA
| | - Richard Beuttler
- Department of Biomedical & Pharmaceutical Sciences Chapman University Irvine California USA
| | - James J Moresco
- Department of Molecular Medicine The Scripps Research Institute La Jolla California USA
| | - John R Yates
- Department of Molecular Medicine The Scripps Research Institute La Jolla California USA
| | - Surya M Nauli
- Department of Biomedical & Pharmaceutical Sciences Chapman University Irvine California USA.,Department of Medicine University of California Irvine Irvine California USA
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19
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Choi CP, Tay RJ, Starostik MR, Feng S, Moresco JJ, Montgomery BE, Xu E, Hammonds MA, Schatz MC, Montgomery TA, Yates JR, Jacobsen SE, Kim JK. SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans. eLife 2021; 10:e60681. [PMID: 33587037 PMCID: PMC7884074 DOI: 10.7554/elife.60681] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 02/02/2021] [Indexed: 12/29/2022] Open
Abstract
Piwi-interacting RNAs (piRNAs) play essential roles in silencing repetitive elements to promote fertility in metazoans. Studies in worms, flies, and mammals reveal that piRNAs are expressed in a sex-specific manner. However, the mechanisms underlying this sex-specific regulation are unknown. Here we identify SNPC-1.3, a male germline-enriched variant of a conserved subunit of the small nuclear RNA-activating protein complex, as a male-specific piRNA transcription factor in Caenorhabditis elegans. SNPC-1.3 colocalizes with the core piRNA transcription factor, SNPC-4, in nuclear foci of the male germline. Binding of SNPC-1.3 at male piRNA loci drives spermatogenic piRNA transcription and requires SNPC-4. Loss of snpc-1.3 leads to depletion of male piRNAs and defects in male-dependent fertility. Furthermore, TRA-1, a master regulator of sex determination, binds to the snpc-1.3 promoter and represses its expression during oogenesis. Loss of TRA-1 targeting causes ectopic expression of snpc-1.3 and male piRNAs during oogenesis. Thus, sexually dimorphic regulation of snpc-1.3 expression coordinates male and female piRNA expression during germline development.
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Affiliation(s)
- Charlotte P Choi
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Rebecca J Tay
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | | | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California, Los AngelesLos AngelesUnited States
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los AngelesLos AngelesUnited States
| | - James J Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical CenterDallasUnited States
| | | | - Emily Xu
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Maya A Hammonds
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Michael C Schatz
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
- Department of Computer Science, Johns Hopkins UniversityBaltimoreUnited States
| | | | - John R Yates
- Department of Molecular Medicine, The Scripps Research InstituteLa JollaUnited States
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
| | - John K Kim
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
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20
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Tran JR, Paulson DI, Moresco JJ, Adam SA, Yates JR, Goldman RD, Zheng Y. An APEX2 proximity ligation method for mapping interactions with the nuclear lamina. J Cell Biol 2021; 220:e202002129. [PMID: 33306092 PMCID: PMC7737704 DOI: 10.1083/jcb.202002129] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 10/19/2020] [Accepted: 10/29/2020] [Indexed: 01/13/2023] Open
Abstract
The nuclear lamina (NL) is a meshwork found beneath the inner nuclear membrane. The study of the NL is hindered by the insolubility of the meshwork and has driven the development of proximity ligation methods to identify the NL-associated/proximal proteins, RNA, and DNA. To simplify and improve temporal labeling, we fused APEX2 to the NL protein lamin-B1 to map proteins, RNA, and DNA. The identified NL-interacting/proximal RNAs show a long 3' UTR bias, a finding consistent with an observed bias toward longer 3' UTRs in genes deregulated in lamin-null cells. A C-rich motif was identified in these 3' UTR. Our APEX2-based proteomics identifies a C-rich motif binding regulatory protein that exhibits altered localization in lamin-null cells. Finally, we use APEX2 to map lamina-associated domains (LADs) during the cell cycle and uncover short, H3K27me3-rich variable LADs. Thus, the APEX2-based tools presented here permit identification of proteomes, transcriptomes, and genome elements associated with or proximal to the NL.
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Affiliation(s)
- Joseph R. Tran
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD
| | - Danielle I. Paulson
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD
- Horace Mann School, The Bronx, NY
| | - James J. Moresco
- The Scripps Research Institution, Department of Molecular Medicine, La Jolla, CA
| | - Stephen A. Adam
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology, Chicago, IL
| | - John R. Yates
- The Scripps Research Institution, Department of Molecular Medicine, La Jolla, CA
| | - Robert D. Goldman
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology, Chicago, IL
| | - Yixian Zheng
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD
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21
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Chaves DA, Dai H, Li L, Moresco JJ, Oh ME, Conte D, Yates JR, Mello CC, Gu W. The RNA phosphatase PIR-1 regulates endogenous small RNA pathways in C. elegans. Mol Cell 2020; 81:546-557.e5. [PMID: 33378643 DOI: 10.1016/j.molcel.2020.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 11/25/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022]
Abstract
Eukaryotic cells regulate 5'-triphosphorylated RNAs (ppp-RNAs) to promote cellular functions and prevent recognition by antiviral RNA sensors. For example, RNA capping enzymes possess triphosphatase domains that remove the γ phosphates of ppp-RNAs during RNA capping. Members of the closely related PIR-1 (phosphatase that interacts with RNA and ribonucleoprotein particle 1) family of RNA polyphosphatases remove both the β and γ phosphates from ppp-RNAs. Here, we show that C. elegans PIR-1 dephosphorylates ppp-RNAs made by cellular RNA-dependent RNA polymerases (RdRPs) and is required for the maturation of 26G-RNAs, Dicer-dependent small RNAs that regulate thousands of genes during spermatogenesis and embryogenesis. PIR-1 also regulates the CSR-1 22G-RNA pathway and has critical functions in both somatic and germline development. Our findings suggest that PIR-1 modulates both Dicer-dependent and Dicer-independent Argonaute pathways and provide insight into how cells and viruses use a conserved RNA phosphatase to regulate and respond to ppp-RNA species.
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Affiliation(s)
- Daniel A Chaves
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA; Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Hui Dai
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, USA
| | - Lichao Li
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, USA
| | - James J Moresco
- Center for Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX, USA
| | - Myung Eun Oh
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, USA
| | - Darryl Conte
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - John R Yates
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA
| | - Craig C Mello
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA; RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Weifeng Gu
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, USA.
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22
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Chen H, Victor AK, Klein J, Tacer KF, Tai DJ, de Esch C, Nuttle A, Temirov J, Burnett LC, Rosenbaum M, Zhang Y, Ding L, Moresco JJ, Diedrich JK, Yates JR, Tillman HS, Leibel RL, Talkowski ME, Billadeau DD, Reiter LT, Potts PR. Loss of MAGEL2 in Prader-Willi syndrome leads to decreased secretory granule and neuropeptide production. JCI Insight 2020; 5:138576. [PMID: 32879135 PMCID: PMC7526459 DOI: 10.1172/jci.insight.138576] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/22/2020] [Indexed: 12/17/2022] Open
Abstract
Prader-Willi syndrome (PWS) is a developmental disorder caused by loss of maternally imprinted genes on 15q11-q13, including melanoma antigen gene family member L2 (MAGEL2). The clinical phenotypes of PWS suggest impaired hypothalamic neuroendocrine function; however, the exact cellular defects are unknown. Here, we report deficits in secretory granule (SG) abundance and bioactive neuropeptide production upon loss of MAGEL2 in humans and mice. Unbiased proteomic analysis of Magel2pΔ/m+ mice revealed a reduction in components of SG in the hypothalamus that was confirmed in 2 PWS patient-derived neuronal cell models. Mechanistically, we show that proper endosomal trafficking by the MAGEL2-regulated WASH complex is required to prevent aberrant lysosomal degradation of SG proteins and reduction of mature SG abundance. Importantly, loss of MAGEL2 in mice, NGN2-induced neurons, and human patients led to reduced neuropeptide production. Thus, MAGEL2 plays an important role in hypothalamic neuroendocrine function, and cellular defects in this pathway may contribute to PWS disease etiology. Moreover, these findings suggest unanticipated approaches for therapeutic intervention.
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Affiliation(s)
- Helen Chen
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - A Kaitlyn Victor
- Department of Neurology, Department of Pediatrics, and Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Jonathon Klein
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Klementina Fon Tacer
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Derek Jc Tai
- Center for Genomic Medicine, Department of Neurology, Department of Pathology, and Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA.,Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts, USA
| | - Celine de Esch
- Center for Genomic Medicine, Department of Neurology, Department of Pathology, and Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA.,Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts, USA
| | - Alexander Nuttle
- Center for Genomic Medicine, Department of Neurology, Department of Pathology, and Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA.,Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts, USA
| | - Jamshid Temirov
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Lisa C Burnett
- Levo Therapeutics, Inc., Skokie, Illinois, USA.,Division of Molecular Genetics, Department of Pediatrics, and Naomi Berrie Diabetes Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Michael Rosenbaum
- Division of Molecular Genetics, Department of Pediatrics, and Naomi Berrie Diabetes Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Yiying Zhang
- Division of Molecular Genetics, Department of Pediatrics, and Naomi Berrie Diabetes Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Li Ding
- Division of Oncology Research and Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - James J Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Heather S Tillman
- Veterinary Pathology Core, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rudolph L Leibel
- Division of Molecular Genetics, Department of Pediatrics, and Naomi Berrie Diabetes Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Michael E Talkowski
- Center for Genomic Medicine, Department of Neurology, Department of Pathology, and Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA.,Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts, USA
| | - Daniel D Billadeau
- Division of Oncology Research and Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Lawrence T Reiter
- Department of Neurology, Department of Pediatrics, and Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Patrick Ryan Potts
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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23
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Mohieldin AM, Pala R, Sherpa RT, Alanazi M, Alanazi A, Shamloo K, Ahsan A, AbouAlaiwi WA, Moresco JJ, Yates JR, Nauli SM. Proteomic Identification Reveals the Role of Ciliary Extracellular-Like Vesicle in Cardiovascular Function. Adv Sci (Weinh) 2020; 7:1903140. [PMID: 32832346 PMCID: PMC7435257 DOI: 10.1002/advs.201903140] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 04/07/2020] [Indexed: 06/11/2023]
Abstract
Primary cilia are shown to have membrane swelling, also known as ciliary bulbs. However, the role of these structures and their physiological relevance remains unknown. Here, it is reported that a ciliary bulb has extracellular vesicle (EV)-like characteristics. The ciliary extracellular-like vesicle (cELV) has a unique dynamic movement and can be released by mechanical fluid force. To better identify the cELV, differential multidimensional proteomic analyses are performed on the cELV. A database of 172 cELV proteins is generated, and all that examined are confirmed to be in the cELV. Repressing the expression of these proteins in vitro and in vivo inhibits cELV formation. In addition to the randomized heart looping, hydrocephalus, and cystic kidney in fish, compensated heart contractility is observed in both fish and mouse models. Specifically, low circulation of cELV results in hypotension with compensated heart function, left ventricular hypertrophy, cardiac fibrosis, and arrhythmogenic characteristics, which result in a high mortality rate in mice. Furthermore, the overall ejection fraction, stroke volume, and cardiac output are significantly decreased in mice lacking cELV. It is thus proposed that the cELV as a nanocompartment within a primary cilium plays an important role in cardiovascular functions.
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Affiliation(s)
- Ashraf M. Mohieldin
- Department of Biomedical and Pharmaceutical SciencesChapman UniversityIrvineCA92618USA
| | - Rajasekharreddy Pala
- Department of Biomedical and Pharmaceutical SciencesChapman UniversityIrvineCA92618USA
| | - Rinzhin T. Sherpa
- Department of Biomedical and Pharmaceutical SciencesChapman UniversityIrvineCA92618USA
| | - Madhawi Alanazi
- Department of Biomedical and Pharmaceutical SciencesChapman UniversityIrvineCA92618USA
| | - Ashwaq Alanazi
- Department of Biomedical and Pharmaceutical SciencesChapman UniversityIrvineCA92618USA
| | - Kiumars Shamloo
- Department of Biomedical and Pharmaceutical SciencesChapman UniversityIrvineCA92618USA
| | - Amir Ahsan
- Department of Physics, Computer Science and EngineeringChapman UniversityOrangeCA92866USA
| | - Wissam A. AbouAlaiwi
- Department of Pharmacology and Experimental TherapeuticsUniversity of ToledoToledoOH43614USA
| | - James J. Moresco
- Department of Molecular MedicineThe Scripps Research InstituteLa JollaCA92037USA
| | - John R. Yates
- Department of Molecular MedicineThe Scripps Research InstituteLa JollaCA92037USA
| | - Surya M. Nauli
- Department of Biomedical and Pharmaceutical SciencesChapman UniversityIrvineCA92618USA
- Department of MedicineUniversity of California IrvineIrvineCA92868USA
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24
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Chen M, Kuhle B, Diedrich J, Liu Z, Moresco JJ, Yates Iii JR, Pan T, Yang XL. Cross-editing by a tRNA synthetase allows vertebrates to abundantly express mischargeable tRNA without causing mistranslation. Nucleic Acids Res 2020; 48:6445-6457. [PMID: 32484512 PMCID: PMC7337962 DOI: 10.1093/nar/gkaa469] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/19/2020] [Accepted: 05/31/2020] [Indexed: 01/18/2023] Open
Abstract
The accuracy in pairing tRNAs with correct amino acids by aminoacyl-tRNA synthetases (aaRSs) dictates the fidelity of translation. To ensure fidelity, multiple aaRSs developed editing functions that remove a wrong amino acid from tRNA before it reaches the ribosome. However, no specific mechanism within an aaRS is known to handle the scenario where a cognate amino acid is mischarged onto a wrong tRNA, as exemplified by AlaRS mischarging alanine to G4:U69-containing tRNAThr. Here, we report that the mischargeable G4:U69-containing tRNAThr are strictly conserved in vertebrates and are ubiquitously and abundantly expressed in mammalian cells and tissues. Although these tRNAs are efficiently mischarged, no corresponding Thr-to-Ala mistranslation is detectable. Mistranslation is prevented by a robust proofreading activity of ThrRS towards Ala-tRNAThr. Therefore, while wrong amino acids are corrected within an aaRS, a wrong tRNA is handled in trans by an aaRS cognate to the mischarged tRNA species. Interestingly, although Ala-tRNAThr mischarging is not known to occur in bacteria, Escherichia coli ThrRS also possesses robust cross-editing ability. We propose that the cross-editing activity of ThrRS is evolutionarily conserved and that this intrinsic activity allows G4:U69-containing tRNAThr to emerge and be preserved in vertebrates to have alternative functions without compromising translational fidelity.
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Affiliation(s)
- Meirong Chen
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA.,College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Bernhard Kuhle
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jolene Diedrich
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ze Liu
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - James J Moresco
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Yates Iii
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Xiang-Lei Yang
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
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25
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Fuller GG, Han T, Freeberg MA, Moresco JJ, Ghanbari Niaki A, Roach NP, Yates JR, Myong S, Kim JK. RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia. eLife 2020; 9:e48480. [PMID: 32298230 PMCID: PMC7162659 DOI: 10.7554/elife.48480] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 03/31/2020] [Indexed: 12/20/2022] Open
Abstract
In hypoxic stress conditions, glycolysis enzymes assemble into singular cytoplasmic granules called glycolytic (G) bodies. G body formation in yeast correlates with increased glucose consumption and cell survival. However, the physical properties and organizing principles that define G body formation are unclear. We demonstrate that glycolysis enzymes are non-canonical RNA binding proteins, sharing many common mRNA substrates that are also integral constituents of G bodies. Targeting nonspecific endoribonucleases to G bodies reveals that RNA nucleates G body formation and maintains its structural integrity. Consistent with a phase separation mechanism of biogenesis, recruitment of glycolysis enzymes to G bodies relies on multivalent homotypic and heterotypic interactions. Furthermore, G bodies fuse in vivo and are largely insensitive to 1,6-hexanediol, consistent with a hydrogel-like composition. Taken together, our results elucidate the biophysical nature of G bodies and demonstrate that RNA nucleates phase separation of the glycolysis machinery in response to hypoxic stress.
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Affiliation(s)
- Gregory G Fuller
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Ting Han
- National Institute of Biological SciencesBeijingChina
| | | | - James J Moresco
- Department of Chemical Physiology, The Scripps Research InstituteLa JollaUnited States
| | | | - Nathan P Roach
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research InstituteLa JollaUnited States
| | - Sua Myong
- Department of Biophysics, Johns Hopkins UniversityBaltimoreUnited States
| | - John K Kim
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
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26
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Yang S, Svensson MND, Harder NHO, Hsieh WC, Santelli E, Kiosses WB, Moresco JJ, Yates JR, King CC, Liu L, Stanford SM, Bottini N. PTPN22 phosphorylation acts as a molecular rheostat for the inhibition of TCR signaling. Sci Signal 2020; 13:13/623/eaaw8130. [PMID: 32184287 DOI: 10.1126/scisignal.aaw8130] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The hematopoietic-specific protein tyrosine phosphatase nonreceptor type 22 (PTPN22) is encoded by a major autoimmunity risk gene. PTPN22 inhibits T cell activation by dephosphorylating substrates involved in proximal T cell receptor (TCR) signaling. Here, we found by mass spectrometry that PTPN22 was phosphorylated at Ser751 by PKCα in Jurkat and primary human T cells activated with phorbol ester/ionomycin or antibodies against CD3/CD28. The phosphorylation of PTPN22 at Ser751 prolonged its half-life by inhibiting K48-linked ubiquitination and impairing recruitment of the phosphatase to the plasma membrane, which is necessary to inhibit proximal TCR signaling. Additionally, the phosphorylation of PTPN22 at Ser751 enhanced the interaction of PTPN22 with the carboxyl-terminal Src kinase (CSK), an interaction that is impaired by the PTPN22 R620W variant associated with autoimmune disease. The phosphorylation of Ser751 did not affect the recruitment of PTPN22 R620W to the plasma membrane but protected this mutant from degradation. Together, out data indicate that phosphorylation at Ser751 mediates a reciprocal regulation of PTPN22 stability versus translocation to TCR signaling complexes by CSK-dependent and CSK-independent mechanisms.
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Affiliation(s)
- Shen Yang
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mattias N D Svensson
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nathaniel H O Harder
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.,Division of Cellular Biology, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Wan-Chen Hsieh
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eugenio Santelli
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - William B Kiosses
- Core Microscopy, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - James J Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Charles C King
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lin Liu
- Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, CA, 92037, USA.,Veterans Affairs San Diego Healthcare System, San Diego, CA 90026, USA
| | - Stephanie M Stanford
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.,Division of Cellular Biology, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Nunzio Bottini
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA. .,Division of Cellular Biology, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
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27
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Kim TK, Tirloni L, Pinto AFM, Diedrich JK, Moresco JJ, Yates JR, da Silva Vaz I, Mulenga A. Time-resolved proteomic profile of Amblyomma americanum tick saliva during feeding. PLoS Negl Trop Dis 2020; 14:e0007758. [PMID: 32049966 PMCID: PMC7041860 DOI: 10.1371/journal.pntd.0007758] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 02/25/2020] [Accepted: 01/03/2020] [Indexed: 12/26/2022] Open
Abstract
Amblyomma americanum ticks transmit more than a third of human tick-borne disease (TBD) agents in the United States. Tick saliva proteins are critical to success of ticks as vectors of TBD agents, and thus might serve as targets in tick antigen-based vaccines to prevent TBD infections. We describe a systems biology approach to identify, by LC-MS/MS, saliva proteins (tick = 1182, rabbit = 335) that A. americanum ticks likely inject into the host every 24 h during the first 8 days of feeding, and towards the end of feeding. Searching against entries in GenBank grouped tick and rabbit proteins into 27 and 25 functional categories. Aside from housekeeping-like proteins, majority of tick saliva proteins belong to the tick-specific (no homology to non-tick organisms: 32%), protease inhibitors (13%), proteases (8%), glycine-rich proteins (6%) and lipocalins (4%) categories. Global secretion dynamics analysis suggests that majority (74%) of proteins in this study are associated with regulating initial tick feeding functions and transmission of pathogens as they are secreted within 24–48 h of tick attachment. Comparative analysis of the A. americanum tick saliva proteome to five other tick saliva proteomes identified 284 conserved tick saliva proteins: we speculate that these regulate critical tick feeding functions and might serve as tick vaccine antigens. We discuss our findings in the context of understanding A. americanum tick feeding physiology as a means through which we can find effective targets for a vaccine against tick feeding. The lone star tick, Amblyomma americanum, is a medically important species in US that transmits 5 of the 16 reported tick-borne disease agents. Most recently, bites of this tick were associated with red meat allergies in humans. Vaccination of animals against tick feeding has been shown to be a sustainable and an effective alternative to current acaricide based tick control method which has several limitations. The pre-requisite to tick vaccine development is to understand the molecular basis of tick feeding physiology. Toward this goal, this study has identified proteins that A. americanum ticks inject into the host at different phases of its feeding cycle. This data set has identified proteins that A. americanum inject into the host within 24–48 h of feeding before it starts to transmit pathogens. Of high importance, we identified 284 proteins that are present in saliva of other tick species, which we suspect regulate important role(s) in tick feeding success and might represent rich source target antigens for a tick vaccine. Overall, this study provides a foundation to understand the molecular mechanisms regulating tick feeding physiology.
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Affiliation(s)
- Tae Kwon Kim
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Lucas Tirloni
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Antônio F. M. Pinto
- Foundation Peptide Biology Lab, Salk Institute for Biological Studies, La Jolla, Californai, United States of America
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jolene K. Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
- Mass Spectrometry Core, Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - James J. Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
- Mass Spectrometry Core, Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - John R. Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Itabajara da Silva Vaz
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Albert Mulenga
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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28
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Sonntag T, Moresco JJ, Yates JR, Montminy M. The KLDpT activation loop motif is critical for MARK kinase activity. PLoS One 2019; 14:e0225727. [PMID: 31794565 PMCID: PMC6890249 DOI: 10.1371/journal.pone.0225727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/11/2019] [Indexed: 11/19/2022] Open
Abstract
MAP/microtubule-affinity regulating kinases (MARK1-4) are members of the AMPK family of Ser/Thr-specific kinases, which phosphorylate substrates at consensus LXRXXSXXXL motifs. Within microtubule-associated proteins, MARKs also mediate phosphorylation of variant KXGS or ζXKXGSXXNΨ motifs, interfering with the ability of tau and MAP2/4 to bind to microtubules. Here we show that, although MARKs and the closely related salt-inducible kinases (SIKs) phosphorylate substrates with consensus AMPK motifs comparably, MARKs are more potent in recognizing variant ζXKXGSXXNΨ motifs on cellular tau. In studies to identify regions of MARKs that confer catalytic activity towards variant sites, we found that the C-terminal kinase associated-1 (KA1) domain in MARK1-3 mediates binding to microtubule-associated proteins CLASP1/2; but this interaction is dispensable for ζXKXGSXXNΨ phosphorylation. Mutational analysis of MARK2 revealed that the N-terminal kinase domain of MARK2 is sufficient for phosphorylation of both consensus and variant ζXKXGSXXNΨ sites. Within this domain, the KLDpT activation loop motif promotes MARK2 activity both intracellularly and in vitro, but has no effect on SIK2 activity. As KLDpT is conserved in all vertebrates MARKs, we conclude that this sequence is crucial for MARK-dependent regulation of cellular polarity.
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Affiliation(s)
- Tim Sonntag
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - James J. Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - John R. Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Marc Montminy
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, California, United States of America
- * E-mail:
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29
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McFall T, Diedrich JK, Mengistu M, Littlechild SL, Paskvan KV, Sisk-Hackworth L, Moresco JJ, Shaw AS, Stites EC. A systems mechanism for KRAS mutant allele-specific responses to targeted therapy. Sci Signal 2019; 12:12/600/eaaw8288. [PMID: 31551296 DOI: 10.1126/scisignal.aaw8288] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cancer treatment decisions are increasingly guided by which specific genes are mutated within each patient's tumor. For example, agents inhibiting the epidermal growth factor receptor (EGFR) benefit many colorectal cancer (CRC) patients, with the general exception of those whose tumor includes a KRAS mutation. However, among the various KRAS mutations, that which encodes the G13D mutant protein (KRASG13D) behaves differently; for unknown reasons, KRASG13D CRC patients benefit from the EGFR-blocking antibody cetuximab. Controversy surrounds this observation, because it contradicts the well-established mechanisms of EGFR signaling with regard to RAS mutations. Here, we identified a systems-level, mechanistic explanation for why KRASG13D cancers respond to EGFR inhibition. A computational model of RAS signaling revealed that the biophysical differences between the three most common KRAS mutants were sufficient to generate different sensitivities to EGFR inhibition. Integrated computation with experimentation then revealed a nonintuitive, mutant-specific dependency of wild-type RAS activation by EGFR that is determined by the interaction strength between KRAS and the tumor suppressor neurofibromin (NF1). KRAS mutants that strongly interacted with and competitively inhibited NF1 drove wild-type RAS activation in an EGFR-independent manner, whereas KRASG13D weakly interacted with and could not competitively inhibit NF1 and, thus, KRASG13D cells remained dependent on EGFR for wild-type RAS activity. Overall, our work demonstrates how systems approaches enable mechanism-based inference in genomic medicine and can help identify patients for selective therapeutic strategies.
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Affiliation(s)
- Thomas McFall
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jolene K Diedrich
- Mass Spectrometry Core for Proteomics and Metabolomics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meron Mengistu
- Department of Research Biology, Genentech, South San Francisco, CA 94080, USA
| | - Stacy L Littlechild
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Kendra V Paskvan
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Laura Sisk-Hackworth
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - James J Moresco
- Mass Spectrometry Core for Proteomics and Metabolomics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Andrey S Shaw
- Department of Research Biology, Genentech, South San Francisco, CA 94080, USA
| | - Edward C Stites
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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30
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Santos MDM, Lima DB, Silva ARF, Kurt LU, Clasen MA, Pinto AFM, Moresco JJ, Yates JR, Aquino P, Barbosa VC, Fischer JSG, Carvalho PC. A quantitation module for isotope-labeled peptides integrated into PatternLab for proteomics. J Proteomics 2019; 202:103371. [PMID: 31034900 DOI: 10.1016/j.jprot.2019.04.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 10/26/2022]
Abstract
We present a new module integrated into the widely adopted PatternLab for proteomics to enable analysis of isotope-labeled peptides produced using dimethyl or SILAC. The accurate quantitation of proteins lies within the heart of proteomics; dimethylation has shown to be reliable, inexpensive, and applicable to any sample type. We validate our algorithm using an M. tuberculosis dataset obtained from two biological conditions; we used three dimethyl labels, one serving as an internal control for labeling a mixture of samples from both biological conditions. This internal control certified the proper functioning of our software. Availability: http://patternlabforproteomics.org, freely available for academic use.
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Affiliation(s)
- Marlon D M Santos
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Brazil.
| | - Diogo B Lima
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Brazil; Mass Spectrometry for Biology Unit, CNRS USR 2000, Institut Pasteur, Paris, France
| | - André R F Silva
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Brazil
| | - Louise U Kurt
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Brazil
| | - Milan A Clasen
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Brazil
| | - Antônio F M Pinto
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - James J Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Priscila Aquino
- Leônidas and Maria Deane Institute, Fiocruz, Amazonas, Brazil
| | - Valmir C Barbosa
- Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juliana S G Fischer
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Brazil
| | - Paulo C Carvalho
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Brazil.
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31
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Alonso AM, Turowski VR, Ruiz DM, Orelo BD, Moresco JJ, Yates JR, Corvi MM. Exploring protein myristoylation in Toxoplasma gondii. Exp Parasitol 2019; 203:8-18. [PMID: 31150653 DOI: 10.1016/j.exppara.2019.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/15/2019] [Accepted: 05/27/2019] [Indexed: 10/26/2022]
Abstract
Toxoplasma gondii is an important human and veterinary pathogen and the causative agent of toxoplasmosis, a potentially severe disease especially in immunocompromised or congenitally infected humans. Current therapeutic compounds are not well-tolerated, present increasing resistance, limited efficacy and require long periods of treatment. On this context, searching for new therapeutic targets is crucial to drug discovery. In this sense, recent works suggest that N-myristoyltransferase (NMT), the enzyme responsible for protein myristoylation that is essential in some parasites, could be the target of new anti-parasitic compounds. However, up to date there is no information on NMT and the extent of this modification in T. gondii. In this work, we decided to explore T. gondii genome in search of elements related with the N-myristoylation process. By a bioinformatics approach it was possible to identify a putative T. gondii NMT (TgNMT). This enzyme that is homologous to other parasitic NMTs, presents activity in vitro, is expressed in both intra- and extracellular parasites and interacts with predicted TgNMT substrates. Additionally, NMT activity seems to be important for the lytic cycle of Toxoplasma gondii. In parallel, an in silico myristoylome predicts 157 proteins to be affected by this modification. Myristoylated proteins would be affecting several metabolic functions with some of them being critical for the life cycle of this parasite. Together, these data indicate that TgNMT could be an interesting target of intervention for the treatment of toxoplasmosis.
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Affiliation(s)
- Andrés M Alonso
- Laboratorio de Bioquímica y Biología Celular de Parásitos, Instituto Tecnológico de Chascomús (INTECH), CONICET, Universidad Nacional de San Martín. Intendente Marino Km 8.2, B7130, Chascomús, Buenos Aires, Argentina
| | - Valeria R Turowski
- Laboratorio de Bioquímica y Biología Celular de Parásitos, Instituto Tecnológico de Chascomús (INTECH), CONICET, Universidad Nacional de San Martín. Intendente Marino Km 8.2, B7130, Chascomús, Buenos Aires, Argentina
| | - Diego M Ruiz
- Laboratorio de Bioquímica y Biología Celular de Parásitos, Instituto Tecnológico de Chascomús (INTECH), CONICET, Universidad Nacional de San Martín. Intendente Marino Km 8.2, B7130, Chascomús, Buenos Aires, Argentina
| | - Barbara D Orelo
- Department of Chemical Physiology, 10550 North Torrey Pines Road, SR11, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - James J Moresco
- Department of Chemical Physiology, 10550 North Torrey Pines Road, SR11, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - John R Yates
- Department of Chemical Physiology, 10550 North Torrey Pines Road, SR11, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - María M Corvi
- Laboratorio de Bioquímica y Biología Celular de Parásitos, Instituto Tecnológico de Chascomús (INTECH), CONICET, Universidad Nacional de San Martín. Intendente Marino Km 8.2, B7130, Chascomús, Buenos Aires, Argentina.
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Kachaev ZM, Lebedeva LA, Shaposhnikov AV, Moresco JJ, Yates JR, Schedl P, Shidlovskii YV. Paip2 cooperates with Cbp80 at an active promoter and participates in RNA Polymerase II phosphorylation in Drosophila. FEBS Lett 2019; 593:1102-1112. [PMID: 31001806 DOI: 10.1002/1873-3468.13391] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/28/2019] [Accepted: 04/09/2019] [Indexed: 01/01/2023]
Abstract
The Paip2 protein is a factor regulating mRNA translation and stability in the cytoplasm. It has also been found in the nuclei of several cell types in Drosophila. Here, we aim to elucidate the functions of Paip2 in the cell nucleus. We find that nuclear Paip2 is a component of an ~300-kDa protein complex. Paip2 interacts with mRNA capping factor and factors of RNA polymerase II (Pol II) transcription initiation and early elongation. Paip2 functionally cooperates with the Cbp80 subunit of the cap-binding complex, with both proteins ensuring proper Pol II C-terminal domain (CTD) Ser5 phosphorylation at the promoter. Thus, Paip2 is a novel player at the stage of mRNA capping and early Pol II elongation.
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Affiliation(s)
- Zaur M Kachaev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Lyubov A Lebedeva
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - James J Moresco
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Paul Schedl
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.,Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Yulii V Shidlovskii
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.,I.M. Sechenov First Moscow State Medical University, Russia
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Cho Y, Tachibana S, Hazen BC, Moresco JJ, Yates JR, Kok B, Saez E, Ross RS, Russell AP, Kralli A. Perm1 regulates CaMKII activation and shapes skeletal muscle responses to endurance exercise training. Mol Metab 2019; 23:88-97. [PMID: 30862473 PMCID: PMC6480336 DOI: 10.1016/j.molmet.2019.02.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/15/2019] [Accepted: 02/24/2019] [Indexed: 12/14/2022] Open
Abstract
Objective Endurance exercise training remodels skeletal muscle, leading to increased mitochondrial content and oxidative capacity. How exercise entrains skeletal muscle signaling pathways to induce adaptive responses remains unclear. In past studies, we identified Perm1 (PGC-1 and ERR induced regulator, muscle 1) as an exercise-induced gene and showed that Perm1 overexpression elicits similar muscle adaptations as endurance exercise training. The mechanism of action and the role of Perm1 in exercise-induced responses are not known. In this study, we aimed to determine the pathway by which Perm1 acts as well as the importance of Perm1 for acute and long-term responses to exercise. Methods We performed immunoprecipitation and mass spectrometry to identify Perm1 associated proteins, and validated Perm1 interactions with the Ca2+/calmodulin-dependent protein kinase II (CaMKII). We also knocked down Perm1 expression in gastrocnemius muscles of mice via AAV-mediated delivery of shRNA and assessed the impact of reduced Perm1 expression on both acute molecular responses to a single treadmill exercise bout and long-term adaptive responses to four weeks of voluntary wheel running training. Finally, we asked whether Perm1 levels are modulated by diet or diseases affecting skeletal muscle function. Results We show that Perm1 associates with skeletal muscle CaMKII and promotes CaMKII activation. In response to an acute exercise bout, muscles with a knock down of Perm1 showed defects in the activation of CaMKII and p38 MAPK and blunted induction of regulators of oxidative metabolism. Following four weeks of voluntary training, Perm1 knockdown muscles had attenuated mitochondrial biogenesis. Finally, we found that Perm1 expression is reduced in diet-induced obese mice and in muscular dystrophy patients and mouse models. Conclusions Our findings identify Perm1 as a muscle-specific regulator of exercise-induced signaling and Perm1 levels as tuners of the skeletal muscle response to exercise. The decreased Perm1 levels in states of obesity or muscle disease suggest that Perm1 may link pathological states to inefficient exercise responses. Perm1 interacts with CaMKII and activates the CaMKII-MEF2 pathway. Perm1 is important for CaMKII activation and PGC-1α induction by an exercise bout. In endurance training, Perm1 impacts muscle oxidative metabolism pathway responses. Skeletal muscle levels of Perm1 are reduced in obesity and muscular dystrophy.
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Affiliation(s)
- Yoshitake Cho
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, 92037, USA; Division of Cardiology, Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Shizuko Tachibana
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, 92037, USA; Division of Cardiology, Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Bethany C Hazen
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - James J Moresco
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, 92037, USA; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, 92037, USA; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Bernard Kok
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, 92037, USA; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Enrique Saez
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, 92037, USA; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Robert S Ross
- Division of Cardiology, Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Aaron P Russell
- Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia
| | - Anastasia Kralli
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, 92037, USA; Department of Physiology, Johns Hopkins University, Baltimore, MD, 21205, USA.
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Burke JE, Longhurst AD, Merkurjev D, Sales-Lee J, Rao B, Moresco JJ, Yates JR, Li JJ, Madhani HD. Spliceosome Profiling Visualizes Operations of a Dynamic RNP at Nucleotide Resolution. Cell 2019; 173:1014-1030.e17. [PMID: 29727661 DOI: 10.1016/j.cell.2018.03.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/19/2018] [Accepted: 03/07/2018] [Indexed: 11/28/2022]
Abstract
Tools to understand how the spliceosome functions in vivo have lagged behind advances in the structural biology of the spliceosome. Here, methods are described to globally profile spliceosome-bound pre-mRNA, intermediates, and spliced mRNA at nucleotide resolution. These tools are applied to three yeast species that span 600 million years of evolution. The sensitivity of the approach enables the detection of canonical and non-canonical events, including interrupted, recursive, and nested splicing. This application of statistical modeling uncovers independent roles for the size and position of the intron and the number of introns per transcript in substrate progression through the two catalytic stages. These include species-specific inputs suggestive of spliceosome-transcriptome coevolution. Further investigations reveal the ATP-dependent discard of numerous endogenous substrates after spliceosome assembly in vivo and connect this discard to intron retention, a form of splicing regulation. Spliceosome profiling is a quantitative, generalizable global technology used to investigate an RNP central to eukaryotic gene expression.
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Affiliation(s)
- Jordan E Burke
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Adam D Longhurst
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daria Merkurjev
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jade Sales-Lee
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Beiduo Rao
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James J Moresco
- Department of Molecular Medicine, the Scripps Research Institute, La Jolla, CA, USA
| | - John R Yates
- Department of Molecular Medicine, the Scripps Research Institute, La Jolla, CA, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA.
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Sonntag T, Ostojić J, Vaughan JM, Moresco JJ, Yoon YS, Yates JR, Montminy M. Mitogenic Signals Stimulate the CREB Coactivator CRTC3 through PP2A Recruitment. iScience 2018; 11:134-145. [PMID: 30611118 PMCID: PMC6317279 DOI: 10.1016/j.isci.2018.12.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/12/2018] [Accepted: 12/13/2018] [Indexed: 11/18/2022] Open
Abstract
The second messenger 3',5'-cyclic adenosine monophosphate (cAMP) stimulates gene expression via the cAMP-regulated transcriptional coactivator (CRTC) family of cAMP response element-binding protein coactivators. In the basal state, CRTCs are phosphorylated by salt-inducible kinases (SIKs) and sequestered in the cytoplasm by 14-3-3 proteins. cAMP signaling inhibits the SIKs, leading to CRTC dephosphorylation and nuclear translocation. Here we show that although all CRTCs are regulated by SIKs, their interactions with Ser/Thr-specific protein phosphatases are distinct. CRTC1 and CRTC2 associate selectively with the calcium-dependent phosphatase calcineurin, whereas CRTC3 interacts with B55 PP2A holoenzymes via a conserved PP2A-binding region (amino acids 380-401). CRTC3-PP2A complex formation was induced by phosphorylation of CRTC3 at S391, facilitating the subsequent activation of CRTC3 by dephosphorylation at 14-3-3 binding sites. As stimulation of mitogenic pathways promoted S391 phosphorylation via the activation of ERKs and CDKs, our results demonstrate how a ubiquitous phosphatase enables cross talk between growth factor and cAMP signaling pathways at the level of a transcriptional coactivator.
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Affiliation(s)
- Tim Sonntag
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jelena Ostojić
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Joan M Vaughan
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - James J Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Young-Sil Yoon
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Marc Montminy
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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36
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Ziegler YS, Moresco JJ, Tu PG, Yates JR, Nardulli AM. Proteomic analysis identifies highly expressed plasma membrane proteins for detection and therapeutic targeting of specific breast cancer subtypes. Clin Proteomics 2018; 15:30. [PMID: 30250408 PMCID: PMC6145347 DOI: 10.1186/s12014-018-9206-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 09/14/2018] [Indexed: 01/14/2023] Open
Abstract
In recent years, there has been an emphasis on personalizing breast cancer treatment in order to avoid the debilitating side effects caused by broad-spectrum chemotherapeutic drug treatment. Development of personalized medicine requires the identification of proteins that are expressed by individual tumors. Herein, we reveal the identity of plasma membrane proteins that are overexpressed in estrogen receptor α-positive, HER2-positive, and triple negative breast cancer cells. The proteins we identified are involved in maintaining protein structure, intracellular homeostasis, and cellular architecture; enhancing cell proliferation and invasion; and influencing cell migration. These proteins may be useful for breast cancer detection and/or treatment.
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Affiliation(s)
- Yvonne S Ziegler
- 1Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - James J Moresco
- 2Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA USA
| | - Patricia G Tu
- 2Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA USA
| | - John R Yates
- 2Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA USA
| | - Ann M Nardulli
- 1Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL USA
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37
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Louka P, Vasudevan KK, Guha M, Joachimiak E, Wloga D, Tomasi RFX, Baroud CN, Dupuis-Williams P, Galati DF, Pearson CG, Rice LM, Moresco JJ, Yates JR, Jiang YY, Lechtreck K, Dentler W, Gaertig J. Proteins that control the geometry of microtubules at the ends of cilia. J Cell Biol 2018; 217:4298-4313. [PMID: 30217954 PMCID: PMC6279374 DOI: 10.1083/jcb.201804141] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/25/2018] [Accepted: 08/31/2018] [Indexed: 11/22/2022] Open
Abstract
Louka et al. describe three conserved proteins that regulate the positions of microtubule ends near the tips of cilia. Mutations in two of these proteins cause a brain malformation, Joubert syndrome. Thus, microtubule ends in cilia may play a role in the pathology of Joubert syndrome. Cilia, essential motile and sensory organelles, have several compartments: the basal body, transition zone, and the middle and distal axoneme segments. The distal segment accommodates key functions, including cilium assembly and sensory activities. While the middle segment contains doublet microtubules (incomplete B-tubules fused to complete A-tubules), the distal segment contains only A-tubule extensions, and its existence requires coordination of microtubule length at the nanometer scale. We show that three conserved proteins, two of which are mutated in the ciliopathy Joubert syndrome, determine the geometry of the distal segment, by controlling the positions of specific microtubule ends. FAP256/CEP104 promotes A-tubule elongation. CHE-12/Crescerin and ARMC9 act as positive and negative regulators of B-tubule length, respectively. We show that defects in the distal segment dimensions are associated with motile and sensory deficiencies of cilia. Our observations suggest that abnormalities in distal segment organization cause a subset of Joubert syndrome cases.
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Affiliation(s)
- Panagiota Louka
- Department of Cellular Biology, University of Georgia, Athens, GA
| | | | - Mayukh Guha
- Department of Cellular Biology, University of Georgia, Athens, GA
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Raphaël F-X Tomasi
- Department of Mechanics, LadHyX, Ecole Polytechnique-Centre National de la Recherche Scientifique, Palaiseau, France
| | - Charles N Baroud
- Department of Mechanics, LadHyX, Ecole Polytechnique-Centre National de la Recherche Scientifique, Palaiseau, France
| | - Pascale Dupuis-Williams
- UMR-S1174 Institut National de la Santé et de la Recherche Médicale, Université Paris-Sud, Bat 443, Orsay, France.,École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris, Paris, France
| | - Domenico F Galati
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Chad G Pearson
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Luke M Rice
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - James J Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA
| | - Yu-Yang Jiang
- Department of Cellular Biology, University of Georgia, Athens, GA
| | - Karl Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA
| | - William Dentler
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS
| | - Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens, GA
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38
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González DP, Lamb HV, Partida D, Wilson ZT, Harrison MC, Prieto JA, Moresco JJ, Diedrich JK, Yates JR, Olson SK. CBD-1 organizes two independent complexes required for eggshell vitelline layer formation and egg activation in C. elegans. Dev Biol 2018; 442:288-300. [PMID: 30120927 DOI: 10.1016/j.ydbio.2018.08.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/04/2018] [Accepted: 08/09/2018] [Indexed: 10/28/2022]
Abstract
Metazoan eggs have a specialized coat of extracellular matrix that aids in sperm-egg recognition. The coat is rapidly remodeled after fertilization to prevent polyspermy and establish a more permanent barrier to protect the developing embryo. In nematodes, this coat is called the vitelline layer, which is remodeled into the outermost layer of a rigid and impermeable eggshell. We have identified three key components of the vitelline layer structural scaffold - PERM-2, PERM-4 and CBD-1, the first such proteins to be described in the nematode C. elegans. CBD-1 tethered PERM-2 and PERM-4 to the nascent vitelline layer via two N-terminal chitin-binding domains. After fertilization, all three proteins redistributed from the zygote surface to the outer eggshell. Depletion of PERM-2 and PERM-4 from the scaffold led to a porous vitelline layer that permitted soluble factors to leak through the eggshell and resulted in embryonic death. In addition to its role in vitelline layer assembly, CBD-1 is also known to anchor a protein complex required for fertilization and egg activation (EGG-1-5/CHS-1/MBK-2). We found the PERM complex and EGG complex to be functionally independent, and structurally organized through distinct domains of CBD-1. CBD-1 is thus a multifaceted regulator that promotes distinct aspects of vitelline layer assembly and egg activation. In sum, our findings characterize the first vitelline layer components in nematodes, and provide a foundation through which to explore both conserved and species-specific strategies used by animals to build protective barriers following fertilization.
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Affiliation(s)
- Delfina P González
- Department of Biology and Program in Molecular Biology, Pomona College, Claremont, CA 91711, USA
| | - Helen V Lamb
- Department of Biology and Program in Molecular Biology, Pomona College, Claremont, CA 91711, USA
| | - Diana Partida
- Department of Biology and Program in Molecular Biology, Pomona College, Claremont, CA 91711, USA
| | - Zachary T Wilson
- Department of Biology and Program in Molecular Biology, Pomona College, Claremont, CA 91711, USA
| | - Marie-Claire Harrison
- Department of Biology and Program in Molecular Biology, Pomona College, Claremont, CA 91711, USA
| | - Julián A Prieto
- Department of Biology and Program in Molecular Biology, Pomona College, Claremont, CA 91711, USA
| | - James J Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sara K Olson
- Department of Biology and Program in Molecular Biology, Pomona College, Claremont, CA 91711, USA.
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Richard P, Ogami K, Chen Y, Feng S, Moresco JJ, Yates JR, Manley JL. NRDE-2, the human homolog of fission yeast Nrl1, prevents DNA damage accumulation in human cells. RNA Biol 2018; 15:868-876. [PMID: 29902117 DOI: 10.1080/15476286.2018.1467180] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The RNA helicase Mtr4 is a versatile protein that is a crucial component of several distinct RNA surveillance complexes. Here we describe a novel complex that contains Mtr4, but has a role distinct from any of those previously described. We found that Mtr4 association with the human homolog of fission yeast Nrl1, NRDE-2, defines a novel function for Mtr4 in the DNA damage response pathway. We provide biochemical evidence that Mtr4 and NRDE-2 are part of the same complex and show that both proteins play a role in the DNA damage response by maintaining low DNA double-strand break levels. Importantly, the DNA damage response function of the Mtr4/NRDE-2 complex does not depend on the formation of R loops. We show however that NRDE-2 and Mtr4 can affect R-loop signals at a subset of distinct genes, possibly regulating their expression. Our work not only expands the wide range of Mtr4 functions, but also elucidates an important role of the less characterized human NRDE-2 protein.
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Affiliation(s)
- Patricia Richard
- a Department of Biological Sciences , Columbia University , New York , NY , USA
| | - Koichi Ogami
- a Department of Biological Sciences , Columbia University , New York , NY , USA.,b Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences , Nagoya City University , Nagoya , Japan
| | - Yaqiong Chen
- a Department of Biological Sciences , Columbia University , New York , NY , USA
| | - Shuang Feng
- a Department of Biological Sciences , Columbia University , New York , NY , USA
| | - James J Moresco
- c Department of Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA
| | - John R Yates
- c Department of Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA
| | - James L Manley
- a Department of Biological Sciences , Columbia University , New York , NY , USA
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40
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Mutlu B, Chen HM, Moresco JJ, Orelo BD, Yang B, Gaspar JM, Keppler-Ross S, Yates JR, Hall DH, Maine EM, Mango SE. Regulated nuclear accumulation of a histone methyltransferase times the onset of heterochromatin formation in C. elegans embryos. Sci Adv 2018; 4:eaat6224. [PMID: 30140741 PMCID: PMC6105299 DOI: 10.1126/sciadv.aat6224] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 07/18/2018] [Indexed: 05/19/2023]
Abstract
Heterochromatin formation during early embryogenesis is timed precisely, but how this process is regulated remains elusive. We report the discovery of a histone methyltransferase complex whose nuclear accumulation and activation establish the onset of heterochromatin formation in Caenorhabditis elegans embryos. We find that the inception of heterochromatin generation coincides with the accumulation of the histone H3 lysine 9 (H3K9) methyltransferase MET-2 (SETDB) into nuclear hubs. The absence of MET-2 results in delayed and disturbed heterochromatin formation, whereas accelerated nuclear localization of the methyltransferase leads to precocious H3K9 methylation. We identify two factors that bind to and function with MET-2: LIN-65, which resembles activating transcription factor 7-interacting protein (ATF7IP) and localizes MET-2 into nuclear hubs, and ARLE-14, which is orthologous to adenosine 5'-diphosphate-ribosylation factor-like 14 effector protein (ARL14EP) and promotes stable association of MET-2 with chromatin. These data reveal that nuclear accumulation of MET-2 in conjunction with LIN-65 and ARLE-14 regulates timing of heterochromatin domains during embryogenesis.
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Affiliation(s)
- Beste Mutlu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Huei-Mei Chen
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - James J. Moresco
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, San Diego, CA 92037, USA
| | - Barbara D. Orelo
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, San Diego, CA 92037, USA
| | - Bing Yang
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA
| | - John M. Gaspar
- Informatics Group, Faculty of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Sabine Keppler-Ross
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, San Diego, CA 92037, USA
| | - David H. Hall
- Center for C. elegans Anatomy, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Eleanor M. Maine
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA
| | - Susan E. Mango
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Corresponding author.
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41
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Vo MN, Terrey M, Lee JW, Roy B, Moresco JJ, Sun L, Fu H, Liu Q, Weber TG, Yates JR, Fredrick K, Schimmel P, Ackerman SL. Publisher Correction: ANKRD16 prevents neuron loss caused by an editing-defective tRNA synthetase. Nature 2018; 560:E35. [PMID: 29925958 DOI: 10.1038/s41586-018-0271-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the Fig. 3b western blot of this Article, 'Myc-AlaRS' in row one should have been 'Myc-AAD Aars', 'AlaRS' in row two should have been 'Aars' and 'ANKRD16' in row four should have been 'Ankrd16'. In Fig. 4f, 'ANKRD16' and 'ANKRD16(3xR)' should have been 'Ankrd16' and 'Ankrd163xR; and in Fig. 3c the position of the molecular mass markers had shifted. These figures have been corrected online, and see Supplementary Information to the accompanying Amendment for the original figure.
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Affiliation(s)
- My-Nuong Vo
- The Skaggs Institute for Chemical Biology, Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA
| | - Markus Terrey
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA.,Section of Neurobiology, University of California San Diego, La Jolla, CA, USA.,Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA.,The Jackson Laboratory, Bar Harbor, ME, USA
| | - Jeong Woong Lee
- The Jackson Laboratory, Bar Harbor, ME, USA.,Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Bappaditya Roy
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - James J Moresco
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA, USA.,Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Litao Sun
- The Skaggs Institute for Chemical Biology, Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA
| | - Hongjun Fu
- The Jackson Laboratory, Bar Harbor, ME, USA.,Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA.,Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Qi Liu
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA.,Sharklet Technologies, Aurora, CO, USA
| | | | - John R Yates
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA, USA
| | - Kurt Fredrick
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Paul Schimmel
- The Skaggs Institute for Chemical Biology, Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA. .,The Scripps Research Institute, Jupiter, FL, USA.
| | - Susan L Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA. .,Section of Neurobiology, University of California San Diego, La Jolla, CA, USA. .,Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA. .,The Jackson Laboratory, Bar Harbor, ME, USA.
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42
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Nishimura N, Tsuchiya W, Moresco JJ, Hayashi Y, Satoh K, Kaiwa N, Irisa T, Kinoshita T, Schroeder JI, Yates JR, Hirayama T, Yamazaki T. Control of seed dormancy and germination by DOG1-AHG1 PP2C phosphatase complex via binding to heme. Nat Commun 2018; 9:2132. [PMID: 29875377 PMCID: PMC5989226 DOI: 10.1038/s41467-018-04437-9] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 05/01/2018] [Indexed: 12/23/2022] Open
Abstract
Abscisic acid (ABA) regulates abiotic stress and developmental responses including regulation of seed dormancy to prevent seeds from germinating under unfavorable environmental conditions. ABA HYPERSENSITIVE GERMINATION1 (AHG1) encoding a type 2C protein phosphatase (PP2C) is a central negative regulator of ABA response in germination; however, the molecular function and regulation of AHG1 remain elusive. Here we report that AHG1 interacts with DELAY OF GERMINATION1 (DOG1), which is a pivotal positive regulator in seed dormancy. DOG1 acts upstream of AHG1 and impairs the PP2C activity of AHG1 in vitro. Furthermore, DOG1 has the ability to bind heme. Binding of DOG1 to AHG1 and heme are independent processes, but both are essential for DOG1 function in vivo. Our study demonstrates that AHG1 and DOG1 constitute an important regulatory system for seed dormancy and germination by integrating multiple environmental signals, in parallel with the PYL/RCAR ABA receptor-mediated regulatory system. The hormone abscisic acid (ABA) prevents seeds from germination when conditions are not suitable. Here the authors show that DOG1, a positive regulator of germination, impairs ABA signaling via genetic and physical interactions with the AHG1 phosphatase and that DOG1 binding to heme is required for this activity.
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Affiliation(s)
- Noriyuki Nishimura
- Radiation Breeding Division, Institute of Crop Science, National Agriculture and Food Research Organization, 2425 Kamimurata, Hitachiohmiya, Ibaraki, 319-2293, Japan. .,Division of Basic Research, Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
| | - Wataru Tsuchiya
- Structural Biology Team, Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | - James J Moresco
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Yuki Hayashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Kouji Satoh
- Radiation Breeding Division, Institute of Crop Science, National Agriculture and Food Research Organization, 2425 Kamimurata, Hitachiohmiya, Ibaraki, 319-2293, Japan
| | - Nahomi Kaiwa
- Radiation Breeding Division, Institute of Crop Science, National Agriculture and Food Research Organization, 2425 Kamimurata, Hitachiohmiya, Ibaraki, 319-2293, Japan
| | - Tomoko Irisa
- Radiation Breeding Division, Institute of Crop Science, National Agriculture and Food Research Organization, 2425 Kamimurata, Hitachiohmiya, Ibaraki, 319-2293, Japan
| | - Toshinori Kinoshita
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan.,Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Julian I Schroeder
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0116, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Takashi Hirayama
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Toshimasa Yamazaki
- Structural Biology Team, Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
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43
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Xu M, Moresco JJ, Chang M, Mukim A, Smith D, Diedrich JK, Yates JR, Jones KA. SHMT2 and the BRCC36/BRISC deubiquitinase regulate HIV-1 Tat K63-ubiquitylation and destruction by autophagy. PLoS Pathog 2018; 14:e1007071. [PMID: 29791506 PMCID: PMC5988312 DOI: 10.1371/journal.ppat.1007071] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 06/05/2018] [Accepted: 05/02/2018] [Indexed: 12/21/2022] Open
Abstract
HIV-1 Tat is a key regulator of viral transcription, however little is known about the mechanisms that control its turnover in T cells. Here we use a novel proteomics technique, called DiffPOP, to identify the molecular target of JIB-04, a small molecule compound that potently and selectively blocks HIV-1 Tat expression, transactivation, and virus replication in T cell lines. Mass-spectrometry analysis of whole-cell extracts from 2D10 Jurkat T cells revealed that JIB-04 targets Serine Hydroxymethyltransferase 2 (SHMT2), a regulator of glycine biosynthesis and an adaptor for the BRCC36 K63Ub-specific deubiquitinase in the BRISC complex. Importantly, knockdown of SHMT1,2 or BRCC36, or exposure of cells to JIB-04, strongly increased Tat K63Ub-dependent destruction via autophagy. Moreover, point mutation of multiple lysines in Tat, or knockdown of BRCC36 or SHMT1,2, was sufficient to prevent destruction of Tat by JIB-04. We conclude that HIV-1 Tat levels are regulated through K63Ub-selective autophagy mediated through SHMT1,2 and the BRCC36 deubiquitinase.
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Affiliation(s)
- Muyu Xu
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, United States of America
| | - James J. Moresco
- Mass Spectrometry Core for Proteomics and Metabolomics, The Salk Institute for Biological Studies, La Jolla, CA, United States of America
| | - Max Chang
- Razavi Newman Integrative Genomics and Bioinformatics Core, The Salk Institute for Biological Studies, La Jolla, CA, United States of America
| | - Amey Mukim
- Division of Infectious Diseases, University of California San Diego School of Medicine, La Jolla, CA, United States of America
| | - Davey Smith
- Division of Infectious Diseases, University of California San Diego School of Medicine, La Jolla, CA, United States of America
| | - Jolene K. Diedrich
- Mass Spectrometry Core for Proteomics and Metabolomics, The Salk Institute for Biological Studies, La Jolla, CA, United States of America
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, United States of America
| | - John R. Yates
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, United States of America
| | - Katherine A. Jones
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, United States of America
- * E-mail:
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44
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Vo MN, Terrey M, Lee JW, Roy B, Moresco JJ, Sun L, Fu H, Liu Q, Weber TG, Yates JR, Fredrick K, Schimmel P, Ackerman SL. ANKRD16 prevents neuron loss caused by an editing-defective tRNA synthetase. Nature 2018; 557:510-515. [PMID: 29769718 PMCID: PMC5973781 DOI: 10.1038/s41586-018-0137-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 04/09/2018] [Indexed: 11/29/2022]
Abstract
Editing domains of aminoacyl tRNA synthetases correct tRNA charging errors to maintain translational fidelity. A mutation in the editing domain of alanyl tRNA synthetase (AlaRS) in Aarssti mutant mice resulted in an increased production of serine-mischarged tRNAAla and degeneration of cerebellar Purkinje cells. By positional cloning, we identified Ankrd16, which acts epistatically with the Aarssti mutation to attenuate neurodegeneration. ANKRD16, a vertebrate-specific, ankyrin repeat-containing protein, binds directly to the catalytic domain of AlaRS. Serine misactivated by AlaRS is captured by lysine side chains of ANKRD16, preventing the charging of serine adenylates to tRNAAla and precluding serine misincorporation in nascent peptides. Deletion of Ankrd16 in the Aarssti/sti brain causes widespread protein aggregation and neuron loss. These results identify a novel amino acid-accepting co-regulator of tRNA synthetase editing as a new layer of the machinery essential for preventing severe pathologies that arise from defects in editing.
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Affiliation(s)
- My-Nuong Vo
- The Skaggs Institute for Chemical Biology, Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA
| | - Markus Terrey
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA.,Section of Neurobiology, University of California San Diego, La Jolla, CA, USA.,Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA.,The Jackson Laboratory, Bar Harbor, ME, USA
| | - Jeong Woong Lee
- The Jackson Laboratory, Bar Harbor, ME, USA.,Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Bappaditya Roy
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - James J Moresco
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA, USA.,Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Litao Sun
- The Skaggs Institute for Chemical Biology, Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA
| | - Hongjun Fu
- The Jackson Laboratory, Bar Harbor, ME, USA.,Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA.,Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Qi Liu
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA.,Sharklet Technologies, Aurora, CO, USA
| | | | - John R Yates
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA, USA
| | - Kurt Fredrick
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Paul Schimmel
- The Skaggs Institute for Chemical Biology, Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA. .,The Scripps Research Institute, Jupiter, FL, USA.
| | - Susan L Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA. .,Section of Neurobiology, University of California San Diego, La Jolla, CA, USA. .,Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA. .,The Jackson Laboratory, Bar Harbor, ME, USA.
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45
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Frankel EB, Shankar R, Moresco JJ, Yates JR, Volkmann N, Audhya A. Ist1 regulates ESCRT-III assembly and function during multivesicular endosome biogenesis in Caenorhabditis elegans embryos. Nat Commun 2017; 8:1439. [PMID: 29129923 PMCID: PMC5682282 DOI: 10.1038/s41467-017-01636-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 10/03/2017] [Indexed: 12/23/2022] Open
Abstract
Degradation of most integral membrane proteins is directed by the endosomal sorting complex required for transport (ESCRT) machinery, which selectively targets ubiquitin-modified cargoes into intralumenal vesicles (ILVs) within multivesicular endosomes (MVEs). To better understand the mechanisms underlying ESCRT-mediated formation of ILVs, we exploited the rapid, de novo biogenesis of MVEs during the oocyte-to-embryo transition in C. elegans. In contrast to previous models suggesting that ILVs form individually, we demonstrate that they remain tethered to one another subsequent to internalization, arguing that they bud continuously from stable subdomains. In addition, we show that membrane bending and ILV formation are directed specifically by the ESCRT-III complex in vivo in a manner regulated by Ist1, which promotes ESCRT-III assembly and inhibits the incorporation of upstream ESCRT components into ILVs. Our findings underscore essential actions for ESCRT-III in membrane remodeling, cargo selection, and cargo retention, which act repetitively to maximize the rate of ILV formation.
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Affiliation(s)
- E B Frankel
- Department of Biomolecular Chemistry, University of Wisconsin-Madison School of Medicine and Public Health, 440 Henry Mall, Madison, WI, 53706, USA
| | - Raakhee Shankar
- Department of Biomolecular Chemistry, University of Wisconsin-Madison School of Medicine and Public Health, 440 Henry Mall, Madison, WI, 53706, USA
| | - James J Moresco
- The Scripps Research Institute, 10550 North Torrey Pines Rd., Department of Chemical Physiology, La Jolla, CA, 92037, USA
| | - John R Yates
- The Scripps Research Institute, 10550 North Torrey Pines Rd., Department of Chemical Physiology, La Jolla, CA, 92037, USA
| | - Niels Volkmann
- Bioinformatics and Structural Biology Program, Sanford-Burnham Medical Research Institute, 10901N Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Anjon Audhya
- Department of Biomolecular Chemistry, University of Wisconsin-Madison School of Medicine and Public Health, 440 Henry Mall, Madison, WI, 53706, USA.
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46
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Chaves DFS, Carvalho PC, Brasili E, Rogero MM, Hassimotto NA, Diedrich JK, Moresco JJ, Yates JR, Lajolo FM. Proteomic Analysis of Peripheral Blood Mononuclear Cells after a High-Fat, High-Carbohydrate Meal with Orange Juice. J Proteome Res 2017; 16:4086-4092. [DOI: 10.1021/acs.jproteome.7b00476] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Daniela F. S. Chaves
- Department of Food Science and Experimental Nutrition, School of
Pharmaceutical Sciences, University of São Paulo, São
Paulo 03178-200, Brazil
- Food Research Center (FoRC), CEPID-FAPESP, Research Innovation and Dissemination Centers São Paulo Research Foundation, São Paulo 05468-140, Brazil
| | - Paulo C. Carvalho
- Laboratory
for Proteomics and Protein Engineering, Carlos Chagas Institute, Fiocruz, Paraná 81310-020, Brazil
| | - Elisa Brasili
- Department of Food Science and Experimental Nutrition, School of
Pharmaceutical Sciences, University of São Paulo, São
Paulo 03178-200, Brazil
- Food Research Center (FoRC), CEPID-FAPESP, Research Innovation and Dissemination Centers São Paulo Research Foundation, São Paulo 05468-140, Brazil
| | - Marcelo M. Rogero
- Food Research Center (FoRC), CEPID-FAPESP, Research Innovation and Dissemination Centers São Paulo Research Foundation, São Paulo 05468-140, Brazil
- Department of Nutrition, School of Public
Health, University of São Paulo, São Paulo 03178-200, Brazil
| | - Neuza A. Hassimotto
- Department of Food Science and Experimental Nutrition, School of
Pharmaceutical Sciences, University of São Paulo, São
Paulo 03178-200, Brazil
- Food Research Center (FoRC), CEPID-FAPESP, Research Innovation and Dissemination Centers São Paulo Research Foundation, São Paulo 05468-140, Brazil
| | - Jolene K. Diedrich
- Department of Chemical Physiology, The Scripps Research Institute, San Diego, California 92121, United States
| | - James J. Moresco
- Department of Chemical Physiology, The Scripps Research Institute, San Diego, California 92121, United States
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, San Diego, California 92121, United States
| | - Franco M. Lajolo
- Department of Food Science and Experimental Nutrition, School of
Pharmaceutical Sciences, University of São Paulo, São
Paulo 03178-200, Brazil
- Food Research Center (FoRC), CEPID-FAPESP, Research Innovation and Dissemination Centers São Paulo Research Foundation, São Paulo 05468-140, Brazil
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Jin M, Fuller GG, Han T, Yao Y, Alessi AF, Freeberg MA, Roach N, Moresco JJ, Karnovsky A, Baba M, Yates JR, Gitler AD, Inoki K, Klionsky DJ, Kim JK. Glycolytic Enzymes Coalesce in G Bodies under Hypoxic Stress. Cell Rep 2017; 20:895-908. [PMID: 28746874 PMCID: PMC5586494 DOI: 10.1016/j.celrep.2017.06.082] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/12/2017] [Accepted: 06/27/2017] [Indexed: 12/15/2022] Open
Abstract
Glycolysis is upregulated under conditions such as hypoxia and high energy demand to promote cell proliferation, although the mechanism remains poorly understood. We find that hypoxia in Saccharomyces cerevisiae induces concentration of glycolytic enzymes, including the Pfk2p subunit of the rate-limiting phosphofructokinase, into a single, non-membrane-bound granule termed the "glycolytic body" or "G body." A yeast kinome screen identifies the yeast ortholog of AMP-activated protein kinase, Snf1p, as necessary for G-body formation. Many G-body components identified by proteomics are required for G-body integrity. Cells incapable of forming G bodies in hypoxia display abnormal cell division and produce inviable daughter cells. Conversely, cells with G bodies show increased glucose consumption and decreased levels of glycolytic intermediates. Importantly, G bodies form in human hepatocarcinoma cells in hypoxia. Together, our results suggest that G body formation is a conserved, adaptive response to increase glycolytic output during hypoxia or tumorigenesis.
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Affiliation(s)
- Meiyan Jin
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | | | - Ting Han
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Yao Yao
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Amelia F Alessi
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Mallory A Freeberg
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 USA
| | | | - James J Moresco
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Alla Karnovsky
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Misuzu Baba
- Research Institute for Science and Technology, Kogakuin University, Hachioji, Tokyo 192-0015 Japan
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Ken Inoki
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,Department of Molecular and Integrative Physiology and the Division of Nephrology in the Department of Internal Medicine
| | - Daniel J Klionsky
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109 USA,corresponding authors: John K Kim, Ph.D., Department of Biology, Johns Hopkins University, 3400 N Charles Street, Baltimore, MD, 21218-2683, . Daniel J Klionsky, Ph.D., Life Sciences Institute, Department of Molecular, Cellular and Developmental Biology, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216,
| | - John K Kim
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,corresponding authors: John K Kim, Ph.D., Department of Biology, Johns Hopkins University, 3400 N Charles Street, Baltimore, MD, 21218-2683, . Daniel J Klionsky, Ph.D., Life Sciences Institute, Department of Molecular, Cellular and Developmental Biology, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216,
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48
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Lomaev D, Mikhailova A, Erokhin M, Shaposhnikov AV, Moresco JJ, Blokhina T, Wolle D, Aoki T, Ryabykh V, Yates JR, Shidlovskii YV, Georgiev P, Schedl P, Chetverina D. The GAGA factor regulatory network: Identification of GAGA factor associated proteins. PLoS One 2017; 12:e0173602. [PMID: 28296955 PMCID: PMC5351981 DOI: 10.1371/journal.pone.0173602] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 02/23/2017] [Indexed: 11/24/2022] Open
Abstract
The Drosophila GAGA factor (GAF) has an extraordinarily diverse set of functions that include the activation and silencing of gene expression, nucleosome organization and remodeling, higher order chromosome architecture and mitosis. One hypothesis that could account for these diverse activities is that GAF is able to interact with partners that have specific and dedicated functions. To test this possibility we used affinity purification coupled with high throughput mass spectrometry to identify GAF associated partners. Consistent with this hypothesis the GAF interacting network includes a large collection of factors and complexes that have been implicated in many different aspects of gene activity, chromosome structure and function. Moreover, we show that GAF interactions with a small subset of partners is direct; however for many others the interactions could be indirect, and depend upon intermediates that serve to diversify the functional capabilities of the GAF protein.
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Affiliation(s)
- Dmitry Lomaev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna Mikhailova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maksim Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - James J. Moresco
- Department of Chemical Physiology, SR302B, The Scripps Research Institute, La Jolla, California, United States of America
| | - Tatiana Blokhina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Daniel Wolle
- Department of Molecular Biology Princeton University, Princeton, NJ, United States of America
| | - Tsutomu Aoki
- Department of Molecular Biology Princeton University, Princeton, NJ, United States of America
| | - Vladimir Ryabykh
- Institute of Animal Physiology, Biochemistry and Nutrition, Borovsk, Russia
| | - John R. Yates
- Department of Chemical Physiology, SR302B, The Scripps Research Institute, La Jolla, California, United States of America
| | | | - Pavel Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- * E-mail: (DC); (PS); (PG)
| | - Paul Schedl
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Department of Molecular Biology Princeton University, Princeton, NJ, United States of America
- * E-mail: (DC); (PS); (PG)
| | - Darya Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- * E-mail: (DC); (PS); (PG)
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49
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Sonntag T, Moresco JJ, Vaughan JM, Matsumura S, Yates JR, Montminy M. Analysis of a cAMP regulated coactivator family reveals an alternative phosphorylation motif for AMPK family members. PLoS One 2017; 12:e0173013. [PMID: 28235073 PMCID: PMC5325614 DOI: 10.1371/journal.pone.0173013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/13/2017] [Indexed: 11/24/2022] Open
Abstract
The second messenger cAMP stimulates cellular gene expression via the PKA-mediated phosphorylation of the transcription factor CREB and through dephosphorylation of the cAMP-responsive transcriptional coactivators (CRTCs). Under basal conditions, CRTCs are phosphorylated by members of the AMPK family of Ser/Thr kinases and sequestered in the cytoplasm via a phosphorylation-dependent association with 14-3-3 proteins. Increases in cAMP promote the dephosphorylation and nuclear translocation of CRTCs, where they bind to CREB and stimulate relevant target genes. Although they share considerable sequence homology, members of the CRTC family exert non-overlapping effects on cellular gene expression through as yet unidentified mechanisms. Here we show that the three CRTCs exhibit distinct patterns of 14-3-3 binding at three conserved sites corresponding to S70, S171, and S275 (in CRTC2). S171 functions as the gatekeeper site for 14-3-3 binding; it acts cooperatively with S275 in stabilizing this interaction following its phosphorylation by the cAMP-responsive SIK and the cAMP-nonresponsive MARK kinases. Although S171 contains a consensus recognition site for phosphorylation by AMPK family members, S70 and S275 carry variant motifs (MNTGGS275LPDL), lacking basic residues that are otherwise critical for SIK/MARK recognition as well as 14-3-3 binding. Correspondingly, the activity of these motifs differs between CRTC family members. As the variant (SLPDL) motif is present and apparently phosphorylated in other mammalian proteins, our studies suggest that the regulation of cellular targets by AMPK family members is more extensive than previously appreciated.
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Affiliation(s)
- Tim Sonntag
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - James J. Moresco
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Joan M. Vaughan
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Shigenobu Matsumura
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, Japan
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Marc Montminy
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, California, United States of America
- * E-mail:
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50
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Shan CM, Wang J, Xu K, Chen H, Yue JX, Andrews S, Moresco JJ, Yates JR, Nagy PL, Tong L, Jia S. A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading. eLife 2016; 5. [PMID: 27648579 PMCID: PMC5030085 DOI: 10.7554/elife.17903] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/22/2016] [Indexed: 01/07/2023] Open
Abstract
Histone lysine-to-methionine (K-to-M) mutations are associated with multiple cancers, and they function in a dominant fashion to block the methylation of corresponding lysines on wild type histones. However, their mechanisms of function are controversial. Here we show that in fission yeast, introducing the K9M mutation into one of the three histone H3 genes dominantly blocks H3K9 methylation on wild type H3 across the genome. In addition, H3K9M enhances the interaction of histone H3 tail with the H3K9 methyltransferase Clr4 in a SAM (S-adenosyl-methionine)-dependent manner, and Clr4 is trapped at nucleation sites to prevent its spreading and the formation of large heterochromatin domains. We further determined the crystal structure of an H3K9M peptide in complex with human H3K9 methyltransferase G9a and SAM, which reveales that the methionine side chain had enhanced van der Waals interactions with G9a. Therefore, our results provide a detailed mechanism by which H3K9M regulates H3K9 methylation. DOI:http://dx.doi.org/10.7554/eLife.17903.001 Cells switch their genes on or off in order to respond to changes in their environment. A group of proteins called histones are partly responsible for regulating gene activity. Like all proteins, histones are made from smaller building blocks called amino acids. Enzymes can chemically modify specific amino acids in histone proteins, which allows the histones to switch nearby genes on or off. One of these modifications is called methylation, and the methylation of specific “lysine” amino acids in histone proteins regulates gene activity in different ways. Previous research has shown that, in certain types of cancer cells, lysines that can be methylated are often replaced with another amino acid, a methionine. These substitutions stop the histones from correctly controlling the activity of nearby genes because methionine cannot be methylated like lysine. Additionally, even if only a small number of histones have methionine in place of lysine, this change can have a widespread effect because the few histones with the methionine can block other histones from being methylated too. However, previous studies did not provide a clear mechanism for why this is the case. In the fission yeast Schizosaccharomyces pombe an enzyme called Clr4 methylates a histone protein at a lysine named H3K9. Now, Shan, Wang, Xu et al. show that substituting this lysine with a methionine (referred to as H3K9M) stops the widespread methylation of histones by trapping the Clr4 enzyme. Specifically, Clr4 becomes stuck to the H3K9M histones, and is therefore unable to modify any other histones. Shan et al. went on to carry out a more detailed study of the structure of H3K9M attached to another enzyme called G9a. This enzyme is found in human cells and is similarly inhibited by H3K9M. This investigation identified additional chemical interactions that explain why Clr4 and G9a become trapped by the H3K9M histone but not by normal histones. Future studies are needed to explore whether other altered histones are able to trap enzymes in the way that H3K9M traps Clr4 and G9a. In addition, this work could eventually lead to new cancer therapies. DOI:http://dx.doi.org/10.7554/eLife.17903.002
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Affiliation(s)
- Chun-Min Shan
- Department of Biological Sciences, Columbia University, New York, United States
| | - Jiyong Wang
- Department of Biological Sciences, Columbia University, New York, United States
| | - Ke Xu
- Department of Biological Sciences, Columbia University, New York, United States
| | - Huijie Chen
- Department of Pathology, Columbia University, New York, United States
| | - Jia-Xing Yue
- Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS UMR 7284, INSERM U1081, Nice, France
| | - Stuart Andrews
- Department of Pathology, Columbia University, New York, United States
| | - James J Moresco
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - John R Yates
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - Peter L Nagy
- Department of Pathology, Columbia University, New York, United States
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, United States
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, United States
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