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The methyltransferase SETD2 couples transcription and splicing by engaging mRNA processing factors through its SHI domain. Nat Commun 2021; 12:1443. [PMID: 33664260 PMCID: PMC7933334 DOI: 10.1038/s41467-021-21663-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 02/04/2021] [Indexed: 12/13/2022] Open
Abstract
Heterogeneous ribonucleoproteins (hnRNPs) are RNA binding molecules that are involved in key processes such as RNA splicing and transcription. One such hnRNP protein, hnRNP L, regulates alternative splicing (AS) by binding to pre-mRNA transcripts. However, it is unclear what factors contribute to hnRNP L-regulated AS events. Using proteomic approaches, we identified several key factors that co-purify with hnRNP L. We demonstrate that one such factor, the histone methyltransferase SETD2, specifically interacts with hnRNP L in vitro and in vivo. This interaction occurs through a previously uncharacterized domain in SETD2, the SETD2-hnRNP Interaction (SHI) domain, the deletion of which, leads to a reduced H3K36me3 deposition. Functionally, SETD2 regulates a subset of hnRNP L-targeted AS events. Our findings demonstrate that SETD2, by interacting with Pol II as well as hnRNP L, can mediate the crosstalk between the transcription and the splicing machinery. The methylation of Histone 3 at Lysine 36 (H3K36) has been implicated in the regulation of transcription and coupled processes such as mRNA splicing. Here the authors show that the histone methyltransferase SETD2 interacts with hnRNP L to mediate the crosstalk between the transcription and splicing machineries.
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152
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Kim TK, Tirloni L, Bencosme-Cuevas E, Kim TH, Diedrich JK, Yates JR, Mulenga A. Borrelia burgdorferi infection modifies protein content in saliva of Ixodes scapularis nymphs. BMC Genomics 2021; 22:152. [PMID: 33663385 PMCID: PMC7930271 DOI: 10.1186/s12864-021-07429-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/08/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Lyme disease (LD) caused by Borrelia burgdorferi is the most prevalent tick-borne disease. There is evidence that vaccines based on tick proteins that promote tick transmission of B. burgdorferi could prevent LD. As Ixodes scapularis nymph tick bites are responsible for most LD cases, this study sought to identify nymph tick saliva proteins associated with B. burgdorferi transmission using LC-MS/MS. Tick saliva was collected using a non-invasive method of stimulating ticks (uninfected and infected: unfed, and every 12 h during feeding through 72 h, and fully-fed) to salivate into 2% pilocarpine-PBS for protein identification using LC-MS/MS. RESULTS We identified a combined 747 tick saliva proteins of uninfected and B. burgdorferi infected ticks that were classified into 25 functional categories: housekeeping-like (48%), unknown function (18%), protease inhibitors (9%), immune-related (6%), proteases (8%), extracellular matrix (7%), and small categories that account for <5% each. Notably, B. burgdorferi infected ticks secreted high number of saliva proteins (n=645) than uninfected ticks (n=376). Counter-intuitively, antimicrobial peptides, which function to block bacterial infection at tick feeding site were suppressed 23-85 folds in B. burgdorferi infected ticks. Similar to glycolysis enzymes being enhanced in mammalian cells exposed to B. burgdorferi : eight of the 10-glycolysis pathway enzymes were secreted at high abundance by B. burgdorferi infected ticks. Of significance, rabbits exposed to B. burgdorferi infected ticks acquired potent immunity that caused 40-60% mortality of B. burgdorferi infected ticks during the second infestation compared to 15-28% for the uninfected. This might be explained by ELISA data that show that high expression levels of immunogenic proteins in B. burgdorferi infected ticks. CONCLUSION Data here suggest that B. burgdorferi infection modified protein content in tick saliva to promote its survival at the tick feeding site. For instance, enzymes; copper/zinc superoxide dismutase that led to production of H2O2 that is toxic to B. burgdorferi were suppressed, while, catalase and thioredoxin that neutralize H2O2, and pyruvate kinase which yields pyruvate that protects Bb from H2O2 killing were enhanced. We conclude data here is an important resource for discovery of effective antigens for a vaccine to prevent LD.
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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
- Department of Diagnostic Medicine and Veterinary Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, 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
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Hamilton, Montana, United States of America
| | - Emily Bencosme-Cuevas
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Tae Heung Kim
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, 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
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Albert Mulenga
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America.
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153
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Acrolein-conjugated proteomics in brains of adult C57BL/6 mice chronically exposed to acrolein and aged APP/PS1 transgenic AD mice. Toxicol Lett 2021; 344:11-17. [PMID: 33675918 DOI: 10.1016/j.toxlet.2021.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 02/09/2021] [Accepted: 03/01/2021] [Indexed: 11/22/2022]
Abstract
Acrolein is a universal contaminant with high nucleophilicity in environment and also an endogenous product from lipid peroxidation or polyamine metabolism. Acrolein can react with nucleophilic amino acids, such as cysteines, lysines and histidines via Michael addition. Also, Schiff base products can be formed between acrolein and free amine of lysines. Accumulating evidences demonstrated that acrolein is involved in many diseases, including Alzheimer's disease (AD). Previously we found that oral exposure of acrolein induced AD-like pathology in rats. Here we investigated the acrolein-conjugated proteins in the hippocampus of acrolein-treated mice (3.0 mg/kg/d by gavage for 4 weeks) and aged APP/PS1 mice (the age of 22 months). Acrolein-conjugated proteins were enriched by an aniline-based aldehyde-directed probe, meta-aminophenylacetylene (m-APA). Combined with a quantitative chemoproteomic strategy, 912 proteins were finally identified. Gene ontology analysis revealed several acrolein affected pathways including glycolysis, tricarboxylic acid (TCA) cycle and carbon metabolism. Acrolein are mainly conjugated with 14-3-3 protein and members of small GTPase family in hippocampus. Taken together, our results provide new evidences for the roles of acrolein in AD.
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154
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Quantitative chemoproteomics reveals O-GlcNAcylation of cystathionine γ-lyase (CSE) represses trophoblast syncytialization. Cell Chem Biol 2021; 28:788-801.e5. [PMID: 33626323 DOI: 10.1016/j.chembiol.2021.01.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 01/08/2021] [Accepted: 01/28/2021] [Indexed: 12/24/2022]
Abstract
Emerging evidence indicates the involvement of O-GlcNAc modification in placental development and pregnant health through mechanisms that are not well understood. Herein, by applying the quantitative O-GlcNAc proteomics, we established a database of O-GlcNAcylated proteins in human placental trophoblasts. Hundreds of proteins that were dynamically O-GlcNAcylated during trophoblast differentiation were identified, among which cystathionine γ-lyase (CSE) exhibited the most significant change. Site-specific analysis by mass spectrometry revealed Ser138 as the core O-GlcNAc site in CSE, and its O-GlcNAcylation promoted the enzymatic activity to produce H2S, which in turn repressed trophoblast differentiation via inhibiting androgen receptor dimerization. Consistently, in preeclamptic placentas, remarkably enhanced CSE O-GlcNAcylation and H2S production were associated with restricted trophoblast differentiation. The findings establish a resource of O-GlcNAc dynamics in human placenta, and provide a deeper insight into the biological significance of O-GlcNAcylation in placental development as well as potential therapeutic targets for the relevant pregnant complications.
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155
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Bamberger C, Pankow S, Martínez-Bartolomé S, Diedrich J, Park R, Yates J. The Host Interactome of Spike Expands the Tropism of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.16.431318. [PMID: 33619478 PMCID: PMC7899442 DOI: 10.1101/2021.02.16.431318] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The SARS-CoV-2 virus causes severe acute respiratory syndrome (COVID-19) and has rapidly created a global pandemic. Patients that survive may face a slow recovery with long lasting side effects that can afflict different organs. SARS-CoV-2 primarily infects epithelial airway cells that express the host entry receptor Angiotensin Converting Enzyme 2 (ACE2) which binds to spike protein trimers on the surface of SARS-CoV-2 virions. However, SARS-CoV-2 can spread to other tissues even though they are negative for ACE2. To gain insight into the molecular constituents that might influence SARS-CoV-2 tropism, we determined which additional host factors engage with the viral spike protein in disease-relevant human bronchial epithelial cells (16HBEo-). We found that spike recruited the extracellular proteins laminin and thrombospondin and was retained in the endoplasmatic reticulum (ER) by the proteins DJB11 and FBX2 which support re-folding or degradation of nascent proteins in the ER. Because emerging mutations of the spike protein potentially impact the virus tropism, we compared the interactome of D614 spike with that of the rapidly spreading G614 mutated spike. More D614 than G614 spike associated with the proteins UGGT1, calnexin, HSP7A and GRP78/BiP which ensure glycosylation and folding of proteins in the ER. In contrast to G614 spike, D614 spike was endoproteolytically cleaved, and the N-terminal S1 domain was degraded in the ER even though C-terminal 'S2 only' proteoforms remained present. D614 spike also bound more laminin than G614 spike, which suggested that extracellular laminins may function as co-factor for an alternative, 'S2 only' dependent virus entry. Because the host interactome determines whether an infection is productive, we developed a novel proteome-based cell type set enrichment analysis (pCtSEA). With pCtSEA we determined that the host interactome of the spike protein may extend the tropism of SARS-CoV-2 beyond mucous epithelia to several different cell types, including macrophages and epithelial cells in the nephron. An 'S2 only' dependent, alternative infection of additional cell types with SARS-CoV-2 may impact vaccination strategies and may provide a molecular explanation for a severe or prolonged progression of disease in select COVID-19 patients.
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Affiliation(s)
- Casimir Bamberger
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Sandra Pankow
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Jolene Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Robin Park
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - John Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
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156
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Luo M, Spradlin JN, Boike L, Tong B, Brittain SM, McKenna JM, Tallarico JA, Schirle M, Maimone TJ, Nomura DK. Chemoproteomics-enabled discovery of covalent RNF114-based degraders that mimic natural product function. Cell Chem Biol 2021; 28:559-566.e15. [PMID: 33513350 DOI: 10.1016/j.chembiol.2021.01.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 12/10/2020] [Accepted: 01/05/2021] [Indexed: 12/26/2022]
Abstract
The translation of functionally active natural products into fully synthetic small-molecule mimetics has remained an important process in medicinal chemistry. We recently discovered that the terpene natural product nimbolide can be utilized as a covalent recruiter of the E3 ubiquitin ligase RNF114 for use in targeted protein degradation-a powerful therapeutic modality within modern-day drug discovery. Using activity-based protein profiling-enabled covalent ligand-screening approaches, here we report the discovery of fully synthetic RNF114-based recruiter molecules that can also be exploited for PROTAC applications, and demonstrate their utility in degrading therapeutically relevant targets, such as BRD4 and BCR-ABL, in cells. The identification of simple and easily manipulated drug-like scaffolds that can mimic the function of a complex natural product is beneficial in further expanding the toolbox of E3 ligase recruiters, an area of great importance in drug discovery and chemical biology.
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Affiliation(s)
- Mai Luo
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Cambridge, MA 02139, USA
| | - Jessica N Spradlin
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Cambridge, MA 02139, USA
| | - Lydia Boike
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Cambridge, MA 02139, USA
| | - Bingqi Tong
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Cambridge, MA 02139, USA
| | - Scott M Brittain
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Cambridge, MA 02139, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Jeffrey M McKenna
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Cambridge, MA 02139, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - John A Tallarico
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Cambridge, MA 02139, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Markus Schirle
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Cambridge, MA 02139, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Thomas J Maimone
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Cambridge, MA 02139, USA.
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Cambridge, MA 02139, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Nutritional Sciences and Toxicology, Univerity of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, Berkeley, CA 94720, USA.
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157
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Schipper S, Wu H, Furdui CM, Poole LB, Delahunty CM, Park R, Yates JR, Becker K, Przyborski JM. Identification of sulfenylation patterns in trophozoite stage Plasmodium falciparum using a non-dimedone based probe. Mol Biochem Parasitol 2021; 242:111362. [PMID: 33513391 DOI: 10.1016/j.molbiopara.2021.111362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/31/2020] [Accepted: 01/18/2021] [Indexed: 10/22/2022]
Abstract
Plasmodium falciparum causes the deadliest form of malaria. Adequate redox control is crucial for this protozoan parasite to overcome oxidative and nitrosative challenges, thus enabling its survival. Sulfenylation is an oxidative post-translational modification, which acts as a molecular on/off switch, regulating protein activity. To obtain a better understanding of which proteins are redox regulated in malaria parasites, we established an optimized affinity capture protocol coupled with mass spectrometry analysis for identification of in vivo sulfenylated proteins. The non-dimedone based probe BCN-Bio1 shows reaction rates over 100-times that of commonly used dimedone-based probes, allowing for a rapid trapping of sulfenylated proteins. Mass spectrometry analysis of BCN-Bio1 labeled proteins revealed the first insight into the Plasmodium falciparum trophozoite sulfenylome, identifying 102 proteins containing 152 sulfenylation sites. Comparison with Plasmodium proteins modified by S-glutathionylation and S-nitrosation showed a high overlap, suggesting a common core of proteins undergoing redox regulation by multiple mechanisms. Furthermore, parasite proteins which were identified as targets for sulfenylation were also identified as being sulfenylated in other organisms, especially proteins of the glycolytic cycle. This study suggests that a number of Plasmodium proteins are subject to redox regulation and it provides a basis for further investigations into the exact structural and biochemical basis of regulation, and a deeper understanding of cross-talk between post-translational modifications.
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Affiliation(s)
- Susanne Schipper
- Department of Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Hanzhi Wu
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Cristina M Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Leslie B Poole
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Claire M Delahunty
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Robin Park
- Department of Chemical Physiology, 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
| | - Katja Becker
- Department of Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Jude M Przyborski
- Department of Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany.
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158
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Zanon P, Pizzato SB, da Rosa RL, Terraciano PB, Moraes JA, Beys-da-Silva WO, Santi L, Yates JR, Passos EP, Barja-Fidalgo C, Guimarães JA, Berger M. Urine proteomic analysis reveals alterations in heme/hemoglobin and aminopeptidase metabolism during Lonomia obliqua venom-induced acute kidney injury. Toxicol Lett 2021; 341:11-22. [PMID: 33472085 DOI: 10.1016/j.toxlet.2021.01.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 12/13/2020] [Accepted: 01/08/2021] [Indexed: 11/29/2022]
Abstract
AIMS Accidental contact with the Lonomia obliqua caterpillar is a common event in southern Brazil. Envenomed victims present consumption coagulopathy, which can evolve to acute kidney injury (AKI). In the present study, we searched for AKI biomarkers and changes in molecular pathway signatures through urine proteomic analysis. METHODOLOGY Male Wistar rats were injected with L. obliqua venom (1.5 mg/kg, via s.c.) or 0.9 % NaCl and distributed into metabolic cages. After 24 h, urine was obtained, and the set of differentially regulated proteins was analyzed by MudPIT technology in an OrbiTRAP mass spectrometer. RESULTS L. obliqua venom leads to an increase in urine output and water and electrolyte excretion and to an increase in the albumin to creatine ratio in urine. The proteomic analysis revealed an up-regulation of tubular injury biomarkers, such as neutrophil-gelatinase associated lipocalin (NGAL) and cystatin C, in urine from envenomed rats. Several components related to the heme scavenging system were up-regulated or exclusively identified in urine from envenomed animals. There was an increase in urinary heme levels and hemoglobin subunits, hemopexin, haptoglobin, and biliverdin reductase. Similarly, kinin- and angiotensin-generating/degrading peptidases, such as kallikreins, neprilysin, plasmin, dipeptidyl peptidase IV, cathepsin D, kininogen, and neutral, basic, glutamyl, and acidic aminopeptidases, were also up-regulated in urine. CONCLUSIONS L. obliqua envenomation induced tubular and glomerular injury, probably involving heme/hemoglobin toxicity and an imbalance in the kinin/angiotensin generating/degrading system.
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Affiliation(s)
- Pamela Zanon
- Laboratório de Bioquímica Farmacológica, Centro de Pesquisa Experimental (CPE), Hospital de Clínicas de Porto Alegre (HCPA-UFRGS), Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Ciências de Saúde: Ginecologia e Obstetrícia (PPGGO), Faculdade de Medicina, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Sabrina Beal Pizzato
- Laboratório de Bioquímica Farmacológica, Centro de Pesquisa Experimental (CPE), Hospital de Clínicas de Porto Alegre (HCPA-UFRGS), Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Ciências de Saúde: Ginecologia e Obstetrícia (PPGGO), Faculdade de Medicina, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Rafael Lopes da Rosa
- Laboratório de Proteômica e Microbiologia Molecular, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Biologia Celular de Molecular (PPGBCM), Centro de Biotecnologia (Cbiot-UFRGS), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Paula Barros Terraciano
- Programa de Pós-Graduação em Ciências de Saúde: Ginecologia e Obstetrícia (PPGGO), Faculdade de Medicina, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Laboratório de Embriologia e Diferenciação Celular, Centro de Pesquisa Experimental (CPE), Hospital de Clínicas de Porto Alegre (HCPA-UFRGS), Porto Alegre, RS, Brazil
| | - João Alfredo Moraes
- Laboratório de Biologia REDOX, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Walter Orlando Beys-da-Silva
- Laboratório de Proteômica e Microbiologia Molecular, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Biologia Celular de Molecular (PPGBCM), Centro de Biotecnologia (Cbiot-UFRGS), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Lucélia Santi
- Laboratório de Proteômica e Microbiologia Molecular, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Biologia Celular de Molecular (PPGBCM), Centro de Biotecnologia (Cbiot-UFRGS), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Jonh R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Eduardo Pandolfi Passos
- Programa de Pós-Graduação em Ciências de Saúde: Ginecologia e Obstetrícia (PPGGO), Faculdade de Medicina, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Laboratório de Embriologia e Diferenciação Celular, Centro de Pesquisa Experimental (CPE), Hospital de Clínicas de Porto Alegre (HCPA-UFRGS), Porto Alegre, RS, Brazil
| | - Christina Barja-Fidalgo
- Laboratório de Farmacologia Celular e Molecular, Departamento de Biologia Celular, IBRAG, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ, Brazil
| | - Jorge Almeida Guimarães
- Laboratório de Bioquímica Farmacológica, Centro de Pesquisa Experimental (CPE), Hospital de Clínicas de Porto Alegre (HCPA-UFRGS), Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Biologia Celular de Molecular (PPGBCM), Centro de Biotecnologia (Cbiot-UFRGS), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Markus Berger
- Laboratório de Bioquímica Farmacológica, Centro de Pesquisa Experimental (CPE), Hospital de Clínicas de Porto Alegre (HCPA-UFRGS), Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Ciências de Saúde: Ginecologia e Obstetrícia (PPGGO), Faculdade de Medicina, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
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159
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Affiliation(s)
- Tobias
P. Wörner
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Tatiana M. Shamorkina
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Joost Snijder
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
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160
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Pan M, Zheng Q, Yu Y, Ai H, Xie Y, Zeng X, Wang C, Liu L, Zhao M. Seesaw conformations of Npl4 in the human p97 complex and the inhibitory mechanism of a disulfiram derivative. Nat Commun 2021; 12:121. [PMID: 33402676 PMCID: PMC7785736 DOI: 10.1038/s41467-020-20359-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/25/2020] [Indexed: 01/29/2023] Open
Abstract
p97, also known as valosin-containing protein (VCP) or Cdc48, plays a central role in cellular protein homeostasis. Human p97 mutations are associated with several neurodegenerative diseases. Targeting p97 and its cofactors is a strategy for cancer drug development. Despite significant structural insights into the fungal homolog Cdc48, little is known about how human p97 interacts with its cofactors. Recently, the anti-alcohol abuse drug disulfiram was found to target cancer through Npl4, a cofactor of p97, but the molecular mechanism remains elusive. Here, using single-particle cryo-electron microscopy (cryo-EM), we uncovered three Npl4 conformational states in complex with human p97 before ATP hydrolysis. The motion of Npl4 results from its zinc finger motifs interacting with the N domain of p97, which is essential for the unfolding activity of p97. In vitro and cell-based assays showed that the disulfiram derivative bis-(diethyldithiocarbamate)-copper (CuET) can bypass the copper transporter system and inhibit the function of p97 in the cytoplasm by releasing cupric ions under oxidative conditions, which disrupt the zinc finger motifs of Npl4, locking the essential conformational switch of the complex.
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Affiliation(s)
- Man Pan
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Qingyun Zheng
- Tsinghua-Peking Center for Life Sciences, Department of Chemistry, Tsinghua University, 100084, Beijing, China
| | - Yuanyuan Yu
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Huasong Ai
- Tsinghua-Peking Center for Life Sciences, Department of Chemistry, Tsinghua University, 100084, Beijing, China
| | - Yuan Xie
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Xin Zeng
- Peking-Tsinghua Center for Life Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871, Beijing, China
| | - Chu Wang
- Peking-Tsinghua Center for Life Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871, Beijing, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Department of Chemistry, Tsinghua University, 100084, Beijing, China.
| | - Minglei Zhao
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.
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161
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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: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [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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162
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Abstract
Mass spectrometry (MS)-based proteomics is currently the most successful approach to measure and compare peptides and proteins in a large variety of biological samples. Modern mass spectrometers, equipped with high-resolution analyzers, provide large amounts of data output. This is the case of shotgun/bottom-up proteomics, which consists in the enzymatic digestion of protein into peptides that are then measured by MS-instruments through a data dependent acquisition (DDA) mode. Dedicated bioinformatic tools and platforms have been developed to face the increasing size and complexity of raw MS data that need to be processed and interpreted for large-scale protein identification and quantification. This chapter illustrates the most popular bioinformatics solution for the analysis of shotgun MS-proteomics data. A general description will be provided on the data preprocessing options and the different search engines available, including practical suggestions on how to optimize the parameters for peptide search, based on hands-on experience.
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Affiliation(s)
- Avinash Yadav
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Federica Marini
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan, Italy.
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163
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Urresti J, Zhang P, Moran-Losada P, Yu NK, Negraes PD, Trujillo CA, Antaki D, Amar M, Chau K, Pramod AB, Diedrich J, Tejwani L, Romero S, Sebat J, Yates III JR, Muotri AR, Iakoucheva LM. Cortical organoids model early brain development disrupted by 16p11.2 copy number variants in autism. Mol Psychiatry 2021; 26:7560-7580. [PMID: 34433918 PMCID: PMC8873019 DOI: 10.1038/s41380-021-01243-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 07/12/2021] [Accepted: 07/20/2021] [Indexed: 11/09/2022]
Abstract
Reciprocal deletion and duplication of the 16p11.2 region is the most common copy number variation (CNV) associated with autism spectrum disorders. We generated cortical organoids from skin fibroblasts of patients with 16p11.2 CNV to investigate impacted neurodevelopmental processes. We show that organoid size recapitulates macrocephaly and microcephaly phenotypes observed in the patients with 16p11.2 deletions and duplications. The CNV dosage affects neuronal maturation, proliferation, and synapse number, in addition to its effect on organoid size. We demonstrate that 16p11.2 CNV alters the ratio of neurons to neural progenitors in organoids during early neurogenesis, with a significant excess of neurons and depletion of neural progenitors observed in deletions. Transcriptomic and proteomic profiling revealed multiple pathways dysregulated by the 16p11.2 CNV, including neuron migration, actin cytoskeleton, ion channel activity, synaptic-related functions, and Wnt signaling. The level of the active form of small GTPase RhoA was increased in both, deletions and duplications. Inhibition of RhoA activity rescued migration deficits, but not neurite outgrowth. This study provides insights into potential neurobiological mechanisms behind the 16p11.2 CNV during neocortical development.
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Affiliation(s)
- Jorge Urresti
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Pan Zhang
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Patricia Moran-Losada
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Nam-Kyung Yu
- grid.214007.00000000122199231Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA USA
| | - Priscilla D. Negraes
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics/Rady Children’s Hospital San Diego, University of California, San Diego, La Jolla, CA USA
| | - Cleber A. Trujillo
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics/Rady Children’s Hospital San Diego, University of California, San Diego, La Jolla, CA USA
| | - Danny Antaki
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA
| | - Megha Amar
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Kevin Chau
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Akula Bala Pramod
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Jolene Diedrich
- grid.214007.00000000122199231Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA USA
| | - Leon Tejwani
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics/Rady Children’s Hospital San Diego, University of California, San Diego, La Jolla, CA USA
| | - Sarah Romero
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics/Rady Children’s Hospital San Diego, University of California, San Diego, La Jolla, CA USA
| | - Jonathan Sebat
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242University of California San Diego, Beyster Center for Psychiatric Genomics, La Jolla, CA USA
| | - John R. Yates III
- grid.214007.00000000122199231Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA USA
| | - Alysson R. Muotri
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics/Rady Children’s Hospital San Diego, University of California, San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242University of California San Diego, Kavli Institute for Brain and Mind, La Jolla, CA USA ,Center for Academic Research and Training in Anthropogeny (CARTA), La Jolla, CA USA
| | - Lilia M. Iakoucheva
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
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164
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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] [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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165
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Lee J, Oh S, Bhattacharya S, Zhang Y, Florens L, Washburn MP, Workman JL. The plasticity of the pyruvate dehydrogenase complex confers a labile structure that is associated with its catalytic activity. PLoS One 2020; 15:e0243489. [PMID: 33370314 PMCID: PMC7769281 DOI: 10.1371/journal.pone.0243489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/21/2020] [Indexed: 12/04/2022] Open
Abstract
The pyruvate dehydrogenase complex (PDC) is a multienzyme complex that plays a key role in energy metabolism by converting pyruvate to acetyl-CoA. An increase of nuclear PDC has been shown to be correlated with an increase of histone acetylation that requires acetyl-CoA. PDC has been reported to form a ~ 10 MDa macromolecular machine that is proficient in performing sequential catalytic reactions via its three components. In this study, we show that the PDC displays size versatility in an ionic strength-dependent manner using size exclusion chromatography of yeast cell extracts. Biochemical analysis in combination with mass spectrometry indicates that yeast PDC (yPDC) is a salt-labile complex that dissociates into sub-megadalton individual components even under physiological ionic strength. Interestingly, we find that each oligomeric component of yPDC displays a larger size than previously believed. In addition, we show that the mammalian PDC also displays this uncommon characteristic of salt-lability, although it has a somewhat different profile compared to yeast. We show that the activity of yPDC is reduced in higher ionic strength. Our results indicate that the structure of PDC may not always maintain its ~ 10 MDa organization, but is rather variable. We propose that the flexible nature of PDC may allow modulation of its activity.
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Affiliation(s)
- Jaehyoun Lee
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Seunghee Oh
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Saikat Bhattacharya
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Michael P. Washburn
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Jerry L. Workman
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- * E-mail:
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166
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Hark TJ, Rao NR, Castillon C, Basta T, Smukowski S, Bao H, Upadhyay A, Bomba-Warczak E, Nomura T, O'Toole ET, Morgan GP, Ali L, Saito T, Guillermier C, Saido TC, Steinhauser ML, Stowell MHB, Chapman ER, Contractor A, Savas JN. Pulse-Chase Proteomics of the App Knockin Mouse Models of Alzheimer's Disease Reveals that Synaptic Dysfunction Originates in Presynaptic Terminals. Cell Syst 2020; 12:141-158.e9. [PMID: 33326751 DOI: 10.1016/j.cels.2020.11.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 09/23/2020] [Accepted: 11/19/2020] [Indexed: 12/14/2022]
Abstract
Compromised protein homeostasis underlies accumulation of plaques and tangles in Alzheimer's disease (AD). To observe protein turnover at early stages of amyloid beta (Aβ) proteotoxicity, we performed pulse-chase proteomics on mouse brains in three genetic models of AD that knock in alleles of amyloid precursor protein (APP) prior to the accumulation of plaques and during disease progression. At initial stages of Aβ accumulation, the turnover of proteins associated with presynaptic terminals is selectively impaired. Presynaptic proteins with impaired turnover, particularly synaptic vesicle (SV)-associated proteins, have elevated levels, misfold in both a plaque-dependent and -independent manner, and interact with APP and Aβ. Concurrent with elevated levels of SV-associated proteins, we found an enlargement of the SV pool as well as enhancement of presynaptic potentiation. Together, our findings reveal that the presynaptic terminal is particularly vulnerable and represents a critical site for manifestation of initial AD etiology. A record of this paper's transparent peer review process is included in the Supplemental Information.
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Affiliation(s)
- Timothy J Hark
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nalini R Rao
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Charlotte Castillon
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Tamara Basta
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Samuel Smukowski
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Huan Bao
- Department of Neuroscience and Howard Hughes Medical Institute, University of Wisconsin, Madison, WI 53706, USA; Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Arun Upadhyay
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ewa Bomba-Warczak
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Toshihiro Nomura
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Eileen T O'Toole
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Garry P Morgan
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Laith Ali
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Takashi Saito
- Laboratory of Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan; Department of Neurocognitive Science, Institute of Brain Science, Nagoya City University Graduate School of Medical Science, Nagoya, Aichi 467-8601, Japan
| | - Christelle Guillermier
- Center for NanoImaging, Brigham and Women's Hospital and Harvard Medical School, Cambridge, MA 02138, USA
| | - Takaomi C Saido
- Laboratory of Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
| | - Matthew L Steinhauser
- Center for NanoImaging, Brigham and Women's Hospital and Harvard Medical School, Cambridge, MA 02138, USA; Department of Medicine, Divisions of Genetics and Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Michael H B Stowell
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO 80309, USA; Department of Mechanical Engineering, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Edwin R Chapman
- Department of Neuroscience and Howard Hughes Medical Institute, University of Wisconsin, Madison, WI 53706, USA
| | - Anis Contractor
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Neurobiology, Weinberg College of Arts and Sciences, Northwestern University, Chicago, IL 60611, USA
| | - Jeffrey N Savas
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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167
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Jongkamonwiwat N, Ramirez MA, Edassery S, Wong ACY, Yu J, Abbott T, Pak K, Ryan AF, Savas JN. Noise Exposures Causing Hearing Loss Generate Proteotoxic Stress and Activate the Proteostasis Network. Cell Rep 2020; 33:108431. [PMID: 33238128 PMCID: PMC7722268 DOI: 10.1016/j.celrep.2020.108431] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 09/24/2020] [Accepted: 11/04/2020] [Indexed: 12/20/2022] Open
Abstract
Exposure to excessive sound causes noise-induced hearing loss through complex mechanisms and represents a common and unmet neurological condition. We investigate how noise insults affect the cochlea with proteomics and functional assays. Quantitative proteomics reveals that exposure to loud noise causes proteotoxicity. We identify and confirm hundreds of proteins that accumulate, including cytoskeletal proteins, and several nodes of the proteostasis network. Transcriptomic analysis reveals that a subset of the genes encoding these proteins also increases acutely after noise exposure, including numerous proteasome subunits. Global cochlear protein ubiquitylation levels build up after exposure to excess noise, and we map numerous posttranslationally modified lysines residues. Several collagen proteins decrease in abundance, and Col9a1 specifically localizes to pillar cell heads. After two weeks of recovery, the cochlea selectively elevates the abundance of the protein synthesis machinery. We report that overstimulation of the auditory system drives a robust cochlear proteotoxic stress response.
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Affiliation(s)
- Nopporn Jongkamonwiwat
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Miguel A Ramirez
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Seby Edassery
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ann C Y Wong
- Departments of Surgery and Neuroscience, University of California San Diego and Veterans Administration Medical Center, La Jolla, CA 92093, USA; Translational Neuroscience Facility, Department of Physiology, NSW Australia, Sydney, NSW 2052, Australia
| | - Jintao Yu
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Tirzah Abbott
- Northwestern University Atomic and Nanoscale Characterization Experimental (NUANCE) Center, Northwestern University, Evanston, IL 60208, USA
| | - Kwang Pak
- Departments of Surgery and Neuroscience, University of California San Diego and Veterans Administration Medical Center, La Jolla, CA 92093, USA
| | - Allen F Ryan
- Departments of Surgery and Neuroscience, University of California San Diego and Veterans Administration Medical Center, La Jolla, CA 92093, USA
| | - Jeffrey N Savas
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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168
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Ibrahim L, Mesgarzadeh J, Xu I, Powers ET, Wiseman RL, Bollong MJ. Defining the Functional Targets of Cap'n'collar Transcription Factors NRF1, NRF2, and NRF3. Antioxidants (Basel) 2020; 9:E1025. [PMID: 33096892 PMCID: PMC7588902 DOI: 10.3390/antiox9101025] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 12/18/2022] Open
Abstract
The NRF transcription factors NRF1, NRF2, and NRF3, are a subset of Cap'n'collar transcriptional regulators which modulate the expression of genes harboring antioxidant-response element (ARE) sequences within their genomic loci. Despite the emerging physiological importance of NRF family members, the repertoire of their genetic targets remains incompletely defined. Here we use RNA-sequencing-based transcriptional profiling and quantitative proteomics to delineate the overlapping and differential genetic programs effected by the three NRF transcription factors. We then create consensus target gene sets regulated by NRF1, NRF2, and NRF3 and define the integrity of these gene sets for probing NRF activity in mammalian cell culture and human tissues. Together, our data provide a quantitative assessment of how NRF family members sculpt proteomes and transcriptomes, providing a framework to understand the critical physiological importance of NRF transcription factors and to establish pharmacologic approaches for therapeutically activating these transcriptional programs in disease.
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Affiliation(s)
- Lara Ibrahim
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; (L.I.); (J.M.); (I.X.); (R.L.W.)
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA;
| | - Jaleh Mesgarzadeh
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; (L.I.); (J.M.); (I.X.); (R.L.W.)
| | - Ian Xu
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; (L.I.); (J.M.); (I.X.); (R.L.W.)
| | - Evan T. Powers
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA;
| | - R. Luke Wiseman
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; (L.I.); (J.M.); (I.X.); (R.L.W.)
| | - Michael J. Bollong
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA;
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169
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Synapse type-specific proteomic dissection identifies IgSF8 as a hippocampal CA3 microcircuit organizer. Nat Commun 2020; 11:5171. [PMID: 33057002 PMCID: PMC7560607 DOI: 10.1038/s41467-020-18956-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 09/23/2020] [Indexed: 12/20/2022] Open
Abstract
Excitatory and inhibitory neurons are connected into microcircuits that generate circuit output. Central in the hippocampal CA3 microcircuit is the mossy fiber (MF) synapse, which provides powerful direct excitatory input and indirect feedforward inhibition to CA3 pyramidal neurons. Here, we dissect its cell-surface protein (CSP) composition to discover novel regulators of MF synaptic connectivity. Proteomic profiling of isolated MF synaptosomes uncovers a rich CSP composition, including many CSPs without synaptic function and several that are uncharacterized. Cell-surface interactome screening identifies IgSF8 as a neuronal receptor enriched in the MF pathway. Presynaptic Igsf8 deletion impairs MF synaptic architecture and robustly decreases the density of bouton filopodia that provide feedforward inhibition. Consequently, IgSF8 loss impairs excitation/inhibition balance and increases excitability of CA3 pyramidal neurons. Our results provide insight into the CSP landscape and interactome of a specific excitatory synapse and reveal IgSF8 as a critical regulator of CA3 microcircuit connectivity and function. Mossy fiber synapses are key in CA3 microcircuit function. Here, the authors profile the mossy fiber synapse proteome and cell-surface interactome. They uncover a diverse repertoire of cell-surface proteins and identify the receptor IgSF8 as a regulator of CA3 microcircuit connectivity and function.
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170
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Mangano K, Florin T, Shao X, Klepacki D, Chelysheva I, Ignatova Z, Gao Y, Mankin AS, Vázquez-Laslop N. Genome-wide effects of the antimicrobial peptide apidaecin on translation termination in bacteria. eLife 2020; 9:e62655. [PMID: 33031031 PMCID: PMC7544508 DOI: 10.7554/elife.62655] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 09/20/2020] [Indexed: 12/16/2022] Open
Abstract
Biochemical studies suggested that the antimicrobial peptide apidaecin (Api) inhibits protein synthesis by binding in the nascent peptide exit tunnel and trapping the release factor associated with a terminating ribosome. The mode of Api action in bacterial cells had remained unknown. Here genome-wide analysis reveals that in bacteria, Api arrests translating ribosomes at stop codons and causes pronounced queuing of the trailing ribosomes. By sequestering the available release factors, Api promotes pervasive stop codon bypass, leading to the expression of proteins with C-terminal extensions. Api-mediated translation arrest leads to the futile activation of the ribosome rescue systems. Understanding the unique mechanism of Api action in living cells may facilitate the development of new medicines and research tools for genome exploration.
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Affiliation(s)
- Kyle Mangano
- Center for Biomolecular Sciences, University of Illinois at ChicagoChicagoUnited States
- Department of Pharmaceutical Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Tanja Florin
- Center for Biomolecular Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Xinhao Shao
- Department of Pharmaceutical Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Dorota Klepacki
- Center for Biomolecular Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Irina Chelysheva
- Institute of Biochemistry and Molecular Biology, University of HamburgHamburgGermany
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of HamburgHamburgGermany
| | - Yu Gao
- Department of Pharmaceutical Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at ChicagoChicagoUnited States
- Department of Pharmaceutical Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at ChicagoChicagoUnited States
- Department of Pharmaceutical Sciences, University of Illinois at ChicagoChicagoUnited States
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171
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Huang L, McClatchy DB, Maher P, Liang Z, Diedrich JK, Soriano-Castell D, Goldberg J, Shokhirev M, Yates JR, Schubert D, Currais A. Intracellular amyloid toxicity induces oxytosis/ferroptosis regulated cell death. Cell Death Dis 2020; 11:828. [PMID: 33024077 PMCID: PMC7538552 DOI: 10.1038/s41419-020-03020-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/04/2020] [Accepted: 09/09/2020] [Indexed: 02/07/2023]
Abstract
Amyloid beta (Aβ) accumulates within neurons in the brains of early stage Alzheimer’s disease (AD) patients. However, the mechanism underlying its toxicity remains unclear. Here, a triple omics approach was used to integrate transcriptomic, proteomic, and metabolomic data collected from a nerve cell model of the toxic intracellular aggregation of Aβ. It was found that intracellular Aβ induces profound changes in the omics landscape of nerve cells that are associated with a pro-inflammatory, metabolic reprogramming that predisposes cells to die via the oxytosis/ferroptosis regulated cell death pathway. Notably, the degenerative process included substantial alterations in glucose metabolism and mitochondrial bioenergetics. Our findings have implications for the understanding of the basic biology of proteotoxicity, aging, and AD as well as for the development of future therapeutic interventions designed to target the oxytosis/ferroptosis regulated cell death pathway in the AD brain.
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Affiliation(s)
- Ling Huang
- The Razavi Newman Integrative Genomics and Bioinformatics Core, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Daniel B McClatchy
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Pamela Maher
- Cellular Neurobiology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Zhibin Liang
- Cellular Neurobiology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - David Soriano-Castell
- Cellular Neurobiology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Joshua Goldberg
- Cellular Neurobiology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Maxim Shokhirev
- The Razavi Newman Integrative Genomics and Bioinformatics Core, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - John R Yates
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - David Schubert
- Cellular Neurobiology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Antonio Currais
- Cellular Neurobiology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA, 92037, USA.
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172
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McClatchy DB, Martínez-Bartolomé S, Gao Y, Lavallée-Adam M, Yates JR. Quantitative analysis of global protein stability rates in tissues. Sci Rep 2020; 10:15983. [PMID: 32994440 PMCID: PMC7524747 DOI: 10.1038/s41598-020-72410-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/28/2020] [Indexed: 02/06/2023] Open
Abstract
Protein degradation is an essential mechanism for maintaining proteostasis in response to internal and external perturbations. Disruption of this process is implicated in many human diseases. We present a new technique, QUAD (Quantification of Azidohomoalanine Degradation), to analyze the global degradation rates in tissues using a non-canonical amino acid and mass spectrometry. QUAD analysis reveals that protein stability varied within tissues, but discernible trends in the data suggest that cellular environment is a major factor dictating stability. Within a tissue, different organelles and protein functions were enriched with different stability patterns. QUAD analysis demonstrated that protein stability is enhanced with age in the brain but not in the liver. Overall, QUAD allows the first global quantitation of protein stability rates in tissues, which will allow new insights and hypotheses in basic and translational research.
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Affiliation(s)
- Daniel B McClatchy
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Yu Gao
- College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Mathieu Lavallée-Adam
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Department of Biochemistry, Microbiology and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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173
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Stein BD, Calzolari D, Hellberg K, Hu YS, He L, Hung CM, Toyama EQ, Ross DS, Lillemeier BF, Cantley LC, Yates JR, Shaw RJ. Quantitative In Vivo Proteomics of Metformin Response in Liver Reveals AMPK-Dependent and -Independent Signaling Networks. Cell Rep 2020; 29:3331-3348.e7. [PMID: 31801093 DOI: 10.1016/j.celrep.2019.10.117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 08/20/2019] [Accepted: 10/28/2019] [Indexed: 12/25/2022] Open
Abstract
Metformin is the front-line treatment for type 2 diabetes worldwide. It acts via effects on glucose and lipid metabolism in metabolic tissues, leading to enhanced insulin sensitivity. Despite significant effort, the molecular basis for metformin response remains poorly understood, with a limited number of specific biochemical pathways studied to date. To broaden our understanding of hepatic metformin response, we combine phospho-protein enrichment in tissue from genetically engineered mice with a quantitative proteomics platform to enable the discovery and quantification of basophilic kinase substrates in vivo. We define proteins whose binding to 14-3-3 are acutely regulated by metformin treatment and/or loss of the serine/threonine kinase, LKB1. Inducible binding of 250 proteins following metformin treatment is observed, 44% of which proteins bind in a manner requiring LKB1. Beyond AMPK, metformin activates protein kinase D and MAPKAPK2 in an LKB1-independent manner, revealing additional kinases that may mediate aspects of metformin response. Deeper analysis uncovered substrates of AMPK in endocytosis and calcium homeostasis.
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Affiliation(s)
- Benjamin D Stein
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Diego Calzolari
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Kristina Hellberg
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Ying S Hu
- Nomis Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Lin He
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Chien-Min Hung
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Erin Q Toyama
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Debbie S Ross
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Björn F Lillemeier
- Nomis Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - John R Yates
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | - Reuben J Shaw
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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174
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Boike L, Cioffi AG, Majewski FC, Co J, Henning NJ, Jones MD, Liu G, McKenna JM, Tallarico JA, Schirle M, Nomura DK. Discovery of a Functional Covalent Ligand Targeting an Intrinsically Disordered Cysteine within MYC. Cell Chem Biol 2020; 28:4-13.e17. [PMID: 32966806 DOI: 10.1016/j.chembiol.2020.09.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 08/14/2020] [Accepted: 09/01/2020] [Indexed: 12/21/2022]
Abstract
MYC is a major oncogenic transcriptional driver of most human cancers that has remained intractable to direct targeting because much of MYC is intrinsically disordered. Here, we have performed a cysteine-reactive covalent ligand screen to identify compounds that could disrupt the binding of MYC to its DNA consensus sequence in vitro and also impair MYC transcriptional activity in situ in cells. We have identified a covalent ligand, EN4, that targets cysteine 171 of MYC within a predicted intrinsically disordered region of the protein. We show that EN4 directly targets MYC in cells, reduces MYC and MAX thermal stability, inhibits MYC transcriptional activity, downregulates multiple MYC transcriptional targets, and impairs tumorigenesis. We also show initial structure-activity relationships of EN4 and identify compounds that show improved potency. Overall, we identify a unique ligandable site within an intrinsically disordered region of MYC that leads to inhibition of MYC transcriptional activity.
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Affiliation(s)
- Lydia Boike
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Alexander G Cioffi
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Felix C Majewski
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Jennifer Co
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Nathaniel J Henning
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Michael D Jones
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Gang Liu
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Jeffrey M McKenna
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - John A Tallarico
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Markus Schirle
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, Berkeley, CA 94720, USA.
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175
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Hoffmann S, Izquierdo HM, Gamba R, Chardon F, Dumont M, Keizer V, Hervé S, McNulty SM, Sullivan BA, Manel N, Fachinetti D. A genetic memory initiates the epigenetic loop necessary to preserve centromere position. EMBO J 2020; 39:e105505. [PMID: 32945564 PMCID: PMC7560200 DOI: 10.15252/embj.2020105505] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 08/10/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022] Open
Abstract
Centromeres are built on repetitive DNA sequences (CenDNA) and a specific chromatin enriched with the histone H3 variant CENP‐A, the epigenetic mark that identifies centromere position. Here, we interrogate the importance of CenDNA in centromere specification by developing a system to rapidly remove and reactivate CENP‐A (CENP‐AOFF/ON). Using this system, we define the temporal cascade of events necessary to maintain centromere position. We unveil that CENP‐B bound to CenDNA provides memory for maintenance on human centromeres by promoting de novo CENP‐A deposition. Indeed, lack of CENP‐B favors neocentromere formation under selective pressure. Occasionally, CENP‐B triggers centromere re‐activation initiated by CENP‐C, but not CENP‐A, recruitment at both ectopic and native centromeres. This is then sufficient to initiate the CENP‐A‐based epigenetic loop. Finally, we identify a population of CENP‐A‐negative, CENP‐B/C‐positive resting CD4+ T cells capable to re‐express and reassembles CENP‐A upon cell cycle entry, demonstrating the physiological importance of the genetic memory.
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Affiliation(s)
| | | | - Riccardo Gamba
- Institut Curie, CNRS, UMR 144, PSL Research University, Paris, France
| | - Florian Chardon
- Institut Curie, CNRS, UMR 144, PSL Research University, Paris, France
| | - Marie Dumont
- Institut Curie, CNRS, UMR 144, PSL Research University, Paris, France
| | - Veer Keizer
- Institut Curie, CNRS, UMR 144, PSL Research University, Paris, France
| | - Solène Hervé
- Institut Curie, CNRS, UMR 144, PSL Research University, Paris, France
| | - Shannon M McNulty
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Beth A Sullivan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Nicolas Manel
- Institut Curie, PSL Research University, INSERM U932, Paris, France
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176
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Gomes FP, Park R, Viana AG, Fernandez-Costa C, Topper E, Kaya A, Memili E, Yates JR, Moura AA. Protein signatures of seminal plasma from bulls with contrasting frozen-thawed sperm viability. Sci Rep 2020; 10:14661. [PMID: 32887897 PMCID: PMC7474054 DOI: 10.1038/s41598-020-71015-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 07/22/2020] [Indexed: 02/07/2023] Open
Abstract
The present study investigated the seminal plasma proteome of Holstein bulls with low (LF; n = 6) and high (HF; n = 8) sperm freezability. The percentage of viable frozen-thawed sperm (%ViableSperm) determined by flow cytometry varied from -2.2 in LF to + 7.8 in HF bulls, as compared to the average %ViableSperm (54.7%) measured in an 860-sire population. Seminal proteins were analyzed by label free mass spectrometry, with the support of statistical and bioinformatics analyses. This approach identified 1,445 proteins, associated with protein folding, cell-cell adhesion, NADH dehydrogenase activity, ATP-binding, proteasome complex, among other processes. There were 338 seminal proteins differentially expressed (p < 0.05) in LF and HF bulls. Based on multivariate analysis, BSP5 and seminal ribonuclease defined the HF phenotype, while spermadhesin-1, gelsolin, tubulins, glyceraldehyde-3-phosphate dehydrogenase, calmodulin, ATP synthase, sperm equatorial segment protein 1, peroxiredoxin-5, secretoglobin family 1D and glucose-6-phosphate isomerase characterized the LF phenotype. Regression models indicated that %ViableSperm of bulls was related to seminal plasma peroxiredoxin-5, spermadhesin-1 and the spermadhesin-1 × BSP5 interaction (R2 = 0.84 and 0.79; p < 0.05). This report is the largest dataset of bovine seminal plasma proteins. Specific proteins of the non-cellular microenvironment of semen are potential markers of sperm cryotolerance.
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Affiliation(s)
| | - Robin Park
- The Scripps Research Institute, La Jolla, CA, USA
| | | | | | | | | | | | - John R Yates
- The Scripps Research Institute, La Jolla, CA, USA.
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177
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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] [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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178
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Adams MK, Banks CAS, Thornton JL, Kempf CG, Zhang Y, Miah S, Hao Y, Sardiu ME, Killer M, Hattem GL, Murray A, Katt ML, Florens L, Washburn MP. Differential Complex Formation via Paralogs in the Human Sin3 Protein Interaction Network. Mol Cell Proteomics 2020; 19:1468-1484. [PMID: 32467258 PMCID: PMC8143632 DOI: 10.1074/mcp.ra120.002078] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Indexed: 01/09/2023] Open
Abstract
Despite the continued analysis of HDAC inhibitors in clinical trials, the heterogeneous nature of the protein complexes they target limits our understanding of the beneficial and off-target effects associated with their application. Among the many HDAC protein complexes found within the cell, Sin3 complexes are conserved from yeast to humans and likely play important roles as regulators of transcriptional activity. The presence of two Sin3 paralogs in humans, SIN3A and SIN3B, may result in a heterogeneous population of Sin3 complexes and contributes to our poor understanding of the functional attributes of these complexes. Here, we profile the interaction networks of SIN3A and SIN3B to gain insight into complex composition and organization. In accordance with existing data, we show that Sin3 paralog identity influences complex composition. Additionally, chemical cross-linking MS identifies domains that mediate interactions between Sin3 proteins and binding partners. The characterization of rare SIN3B proteoforms provides additional evidence for the existence of conserved and divergent elements within human Sin3 proteins. Together, these findings shed light on both the shared and divergent properties of human Sin3 proteins and highlight the heterogeneous nature of the complexes they organize.
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Affiliation(s)
- Mark K Adams
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | | | - Janet L Thornton
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | | | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Sayem Miah
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Yan Hao
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Mihaela E Sardiu
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Maxime Killer
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Gaye L Hattem
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Alexis Murray
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Maria L Katt
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, Missouri, USA; Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA.
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179
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Kirak O, Ke E, Yang KY, Schwarz A, Plate L, Nham A, Abadejos JR, Valencia A, Wiseman RL, Lui KO, Ku M. Premature Activation of Immune Transcription Programs in Autoimmune-Predisposed Mouse Embryonic Stem Cells and Blastocysts. Int J Mol Sci 2020; 21:ijms21165743. [PMID: 32796510 PMCID: PMC7460978 DOI: 10.3390/ijms21165743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/27/2020] [Accepted: 08/07/2020] [Indexed: 11/17/2022] Open
Abstract
Autoimmune diabetes is a complex multifactorial disease with genetic and environmental factors playing pivotal roles. While many genes associated with the risk of diabetes have been identified to date, the mechanisms by which external triggers contribute to the genetic predisposition remain unclear. Here, we derived embryonic stem (ES) cell lines from diabetes-prone non-obese diabetic (NOD) and healthy C57BL/6 (B6) mice. While overall pluripotency markers were indistinguishable between newly derived NOD and B6 ES cells, we discovered several differentially expressed genes that normally are not expressed in ES cells. Several genes that reside in previously identified insulin-dependent diabetics (Idd) genomic regions were up-regulated in NOD ES cells. Gene set enrichment analysis showed that different groups of genes associated with immune functions are differentially expressed in NOD. Transcriptomic analysis of NOD blastocysts validated several differentially overexpressed Idd genes compared to B6. Genome-wide mapping of active histone modifications using ChIP-Seq supports active expression as the promoters and enhancers of activated genes are also marked by active histone modifications. We have also found that NOD ES cells secrete more inflammatory cytokines. Our data suggest that the known genetic predisposition of NOD to autoimmune diabetes leads to epigenetic instability of several Idd regions.
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Affiliation(s)
- Oktay Kirak
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; (A.S.); (A.N.); (J.R.A.); (A.V.)
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, Medical Center—University of Freiburg, Mathildenstraße 1, 79106 Freiburg, Germany
- Correspondence: (O.K.); (M.K.)
| | - Eugene Ke
- Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA;
| | - Kevin Y. Yang
- Department of Chemical Pathology and Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China; (K.Y.Y.); (K.O.L.)
| | - Anna Schwarz
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; (A.S.); (A.N.); (J.R.A.); (A.V.)
| | - Lars Plate
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; (L.P.); (R.L.W.)
| | - Amy Nham
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; (A.S.); (A.N.); (J.R.A.); (A.V.)
| | - Justin R. Abadejos
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; (A.S.); (A.N.); (J.R.A.); (A.V.)
| | - Anna Valencia
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; (A.S.); (A.N.); (J.R.A.); (A.V.)
| | - R. Luke Wiseman
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; (L.P.); (R.L.W.)
| | - Kathy O. Lui
- Department of Chemical Pathology and Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China; (K.Y.Y.); (K.O.L.)
| | - Manching Ku
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, Medical Center—University of Freiburg, Mathildenstraße 1, 79106 Freiburg, Germany
- Correspondence: (O.K.); (M.K.)
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180
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Fernández-Costa C, Martínez-Bartolomé S, McClatchy DB, Saviola AJ, Yu NK, Yates JR. Impact of the Identification Strategy on the Reproducibility of the DDA and DIA Results. J Proteome Res 2020; 19:3153-3161. [PMID: 32510229 PMCID: PMC7898222 DOI: 10.1021/acs.jproteome.0c00153] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Data-independent acquisition (DIA) is a promising technique for the proteomic analysis of complex protein samples. A number of studies have claimed that DIA experiments are more reproducible than data-dependent acquisition (DDA), but these claims are unsubstantiated since different data analysis methods are used in the two methods. Data analysis in most DIA workflows depends on spectral library searches, whereas DDA typically employs sequence database searches. In this study, we examined the reproducibility of the DIA and DDA results using both sequence database and spectral library search. The comparison was first performed using a cell lysate and then extended to an interactome study. Protein overlap among the technical replicates in both DDA and DIA experiments was 30% higher with library-based identifications than with sequence database identifications. The reproducibility of quantification was also improved with library search compared to database search, with the mean of the coefficient of variation decreasing more than 30% and a reduction in the number of missing values of more than 35%. Our results show that regardless of the acquisition method, higher identification and quantification reproducibility is observed when library search was used.
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Affiliation(s)
- Carolina Fernández-Costa
- Departments of Molecular Medicine & Neurobiology, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Daniel B. McClatchy
- Departments of Molecular Medicine & Neurobiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Anthony J. Saviola
- Departments of Molecular Medicine & Neurobiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nam-Kyung Yu
- Departments of Molecular Medicine & Neurobiology, The Scripps Research Institute, La Jolla, CA, USA
| | - John R. Yates
- Departments of Molecular Medicine & Neurobiology, The Scripps Research Institute, La Jolla, CA, USA
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181
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Kim TK, Tirloni L, Berger M, Diedrich JK, Yates JR, Termignoni C, da Silva Vaz I, Mulenga A. Amblyomma americanum serpin 41 (AAS41) inhibits inflammation by targeting chymase and chymotrypsin. Int J Biol Macromol 2020; 156:1007-1021. [PMID: 32320803 PMCID: PMC11005088 DOI: 10.1016/j.ijbiomac.2020.04.088] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/09/2020] [Accepted: 04/12/2020] [Indexed: 01/01/2023]
Abstract
Ticks inject serine protease inhibitors (serpins) into their feeding sites to evade serine protease-mediated host defenses against tick-feeding. This study describes two highly identitical (97%) but functionally different Amblyomma americanum tick saliva serpins (AAS41 and 46) that are secreted at the inception of tick-feeding. We show that AAS41, which encodes a leucine at the P1 site inhibits inflammation system proteases: chymase (SI = 3.23, Ka = 5.6 ± 3.7X103M-1 s-1) and α-chymotrypsin (SI = 3.18, Ka = 1.6 ± 4.1X104M-1 s-1), while AAS46, which encodes threonine has no inhibitory activity. Similary, rAAS41 inhibits rMCP-1 purified from rat peritonuem derived mast cells. Consistently, rAAS41 inhibits chymase-mediated inflammation induced by compound 48/80 in rat paw edema and vascular permeability models. Native AAS41/46 proteins are among tick saliva immunogens that provoke anti-tick immunity in repeatedly infested animals as revealed by specific reactivity with tick immune sera. Of significance, native AAS41/46 play critical tick-feeding functions in that RNAi-mediated silencing caused ticks to ingest significantly less blood. Importantly, monospecific antibodies to rAAS41 blocked inhibitory functions of rAAS41, suggesting potential for design of vaccine antigens that provokes immunity to neutralize functions of this protein at the tick-feeding site. We discuss our findings with reference to tick-feeding physiology and discovery of effective tick vaccine antigens.
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Affiliation(s)
- Tae Kwon Kim
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, USA
| | - Lucas Tirloni
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, USA; Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Markus Berger
- Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Jolene K Diedrich
- Foundation Peptide Biology Lab, Salk Institute for Biological Studies, La Jolla, CA, USA; 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
| | - Carlos Termignoni
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Itabajara da Silva Vaz
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Albert Mulenga
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, USA.
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182
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Vaisar T, Hu JH, Airhart N, Fox K, Heinecke J, Nicosia RF, Kohler T, Potter ZE, Simon GM, Dix MM, Cravatt BF, Gharib SA, Dichek DA. Parallel Murine and Human Plaque Proteomics Reveals Pathways of Plaque Rupture. Circ Res 2020; 127:997-1022. [PMID: 32762496 PMCID: PMC7508285 DOI: 10.1161/circresaha.120.317295] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
RATIONALE Plaque rupture is the proximate cause of most myocardial infarctions and many strokes. However, the molecular mechanisms that precipitate plaque rupture are unknown. OBJECTIVE By applying proteomic and bioinformatic approaches in mouse models of protease-induced plaque rupture and in ruptured human plaques, we aimed to illuminate biochemical pathways through which proteolysis causes plaque rupture and identify substrates that are cleaved in ruptured plaques. METHODS AND RESULTS We performed shotgun proteomics analyses of aortas of transgenic mice with macrophage-specific overexpression of urokinase (SR-uPA+/0 mice) and of SR-uPA+/0 bone marrow transplant recipients, and we used bioinformatic tools to evaluate protein abundance and functional category enrichment in these aortas. In parallel, we performed shotgun proteomics and bioinformatics studies on extracts of ruptured and stable areas of freshly harvested human carotid plaques. We also applied a separate protein-analysis method (protein topography and migration analysis platform) to attempt to identify substrates and proteolytic fragments in mouse and human plaque extracts. Approximately 10% of extracted aortic proteins were reproducibly altered in SR-uPA+/0 aortas. Proteases, inflammatory signaling molecules, as well as proteins involved with cell adhesion, the cytoskeleton, and apoptosis, were increased. ECM (Extracellular matrix) proteins, including basement-membrane proteins, were decreased. Approximately 40% of proteins were altered in ruptured versus stable areas of human carotid plaques, including many of the same functional categories that were altered in SR-uPA+/0 aortas. Collagens were minimally altered in SR-uPA+/0 aortas and ruptured human plaques; however, several basement-membrane proteins were reduced in both SR-uPA+/0 aortas and ruptured human plaques. Protein topography and migration analysis platform did not detect robust increases in proteolytic fragments of ECM proteins in either setting. CONCLUSIONS Parallel studies of SR-uPA+/0 mouse aortas and human plaques identify mechanisms that connect proteolysis with plaque rupture, including inflammation, basement-membrane protein loss, and apoptosis. Basement-membrane protein loss is a prominent feature of ruptured human plaques, suggesting a major role for basement-membrane proteins in maintaining plaque stability.
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Affiliation(s)
- Tomáš Vaisar
- Departments of Medicine (T.V., J.H.H., N.A., K.F., J.H., S.A.G., D.A.D.), University of Washington, Seattle
| | - Jie H Hu
- Departments of Medicine (T.V., J.H.H., N.A., K.F., J.H., S.A.G., D.A.D.), University of Washington, Seattle
| | - Nathan Airhart
- Departments of Medicine (T.V., J.H.H., N.A., K.F., J.H., S.A.G., D.A.D.), University of Washington, Seattle
| | - Kate Fox
- Departments of Medicine (T.V., J.H.H., N.A., K.F., J.H., S.A.G., D.A.D.), University of Washington, Seattle
| | - Jay Heinecke
- Departments of Medicine (T.V., J.H.H., N.A., K.F., J.H., S.A.G., D.A.D.), University of Washington, Seattle
| | - Roberto F Nicosia
- Departments of Pathology and Laboratory Medicine (D.A.D., R.F.N.), University of Washington, Seattle.,Departments of Pathology and Laboratory Medicine (R.F.N.), VA Puget Sound Health Care System, Seattle, WA
| | - Ted Kohler
- Departments of Surgery (T.K.), University of Washington, Seattle.,Departments of Surgery (T.K.), VA Puget Sound Health Care System, Seattle, WA
| | - Zachary E Potter
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA (Z.E.P., M.M.D., B.F.C.)
| | | | - Melissa M Dix
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA (Z.E.P., M.M.D., B.F.C.)
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA (Z.E.P., M.M.D., B.F.C.)
| | - Sina A Gharib
- Departments of Medicine (T.V., J.H.H., N.A., K.F., J.H., S.A.G., D.A.D.), University of Washington, Seattle
| | - David A Dichek
- Departments of Medicine (T.V., J.H.H., N.A., K.F., J.H., S.A.G., D.A.D.), University of Washington, Seattle.,Departments of Pathology and Laboratory Medicine (D.A.D., R.F.N.), University of Washington, Seattle
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183
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Integrated analysis of sialotranscriptome and sialoproteome of the brown dog tick Rhipicephalus sanguineus (s.l.): Insights into gene expression during blood feeding. J Proteomics 2020; 229:103899. [PMID: 32673754 DOI: 10.1016/j.jprot.2020.103899] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/30/2020] [Accepted: 07/08/2020] [Indexed: 02/08/2023]
Abstract
Tick salivary glands secrete a complex saliva into their hosts which modulates vertebrate hemostasis, immunity and tissue repair mechanisms. Transcriptomic studies revealed a large number of transcripts coding for structural and secreted protein products in a single tick species. These transcripts are organized in several large families according to their products. Not all transcripts are expressed at the same time, transcription profile switches at intervals, characterizing the phenomenon of "sialome switching". In this work, using transcriptomic and proteomic analysis we explored the sialome of Rhipicephalus sanguineus (s.l.) adult female ticks feeding on a rabbit. The correlations between transcriptional and translational results in the different groups were evaluated, confirming the "sialome switching" and validating the idea that the expression switch may serve as a mechanism of escape from the host immunity. Recombination breakpoints were identified in lipocalin and metalloprotease families, indicating this mechanism could be a possible source of diversity in the tick sialome. Another remarkable observation was the identification of host-derived proteins as a component of tick salivary gland content. These results and disclosed sequences contribute to our understanding of tick feeding biology, to the development of novel anti-tick methods, and to the discovery of novel pharmacologically active products. SIGNIFICANCE: Ticks are a burden by themselves to humans and animals, and vectors of viral, bacterial, protozoal and helminthic diseases. Their saliva has anti-clotting, anti-platelet, vasodilatory and immunomodulatory activities that allows successful feeding and pathogen transmission. Previous transcriptomic studies indicate ticks to have over one thousand transcripts coding for secreted salivary proteins. These transcripts code for proteins of diverse families, but not all are transcribed simultaneously, but rather transiently, in a succession. Here we explored the salivary transcriptome and proteome of the brown dog tick, Rhipicephalus sanguineus. A protein database of over 20 thousand sequences was "de novo" assembled from over 600 million nucleotide reads, from where over two thousand polypeptides were identified by mass spectrometry. The proteomic data was shown to vary in time with the transcription profiles, validating the idea that the expression switch may serve as a mechanism of escape from the host immunity. Analysis of the transcripts coding for lipocalin and metalloproteases indicate their genes to contain signals of breakpoint recombination suggesting a new mechanism responsible for the large diversity in tick salivary proteins. These results and the disclosed sequences contribute to our understanding of the success ticks enjoy as ectoparasites, to the development of novel anti-tick methods, and to the discovery of novel pharmacologically active products.
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184
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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] [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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185
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Kim H, Kim D, Kim J, Lee HY, Park D, Kang H, Matsuda K, Sterky FH, Yuzaki M, Kim JY, Choi SY, Ko J, Um JW. Calsyntenin-3 interacts with both α- and β-neurexins in the regulation of excitatory synaptic innervation in specific Schaffer collateral pathways. J Biol Chem 2020; 295:9244-9262. [PMID: 32434929 PMCID: PMC7335786 DOI: 10.1074/jbc.ra120.013077] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/15/2020] [Indexed: 12/13/2022] Open
Abstract
Calsyntenin-3 (Clstn3) is a postsynaptic adhesion molecule that induces presynaptic differentiation via presynaptic neurexins (Nrxns), but whether Nrxns directly bind to Clstn3 has been a matter of debate. Here, using LC-MS/MS-based protein analysis, confocal microscopy, RNAscope assays, and electrophysiological recordings, we show that β-Nrxns directly interact via their LNS domain with Clstn3 and Clstn3 cadherin domains. Expression of splice site 4 (SS4) insert-positive β-Nrxn variants, but not insert-negative variants, reversed the impaired Clstn3 synaptogenic activity observed in Nrxn-deficient neurons. Consistently, Clstn3 selectively formed complexes with SS4-positive Nrxns in vivo Neuron-specific Clstn3 deletion caused significant reductions in number of excitatory synaptic inputs. Moreover, expression of Clstn3 cadherin domains in CA1 neurons of Clstn3 conditional knockout mice rescued structural deficits in excitatory synapses, especially within the stratum radiatum layer. Collectively, our results suggest that Clstn3 links to SS4-positive Nrxns to induce presynaptic differentiation and orchestrate excitatory synapse development in specific hippocampal neural circuits, including Schaffer collateral afferents.
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Affiliation(s)
- Hyeonho Kim
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Hyeonpoong-Eup, Dalseong-gun, Daegu, Korea
| | - Dongwook Kim
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Hyeonpoong-Eup, Dalseong-gun, Daegu, Korea
| | - Jinhu Kim
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Hyeonpoong-Eup, Dalseong-gun, Daegu, Korea
| | - Hee-Yoon Lee
- Department of Neuroscience and Physiology, Dental Research Institute, School of Dentistry, Seoul National University, Seoul, Korea
| | - Dongseok Park
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Hyeonpoong-Eup, Dalseong-gun, Daegu, Korea
| | - Hyeyeon Kang
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Hyeonpoong-Eup, Dalseong-gun, Daegu, Korea
| | - Keiko Matsuda
- Department of Physiology, School of Medicine, Keio University, Tokyo, Japan
| | - Fredrik H Sterky
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden; Department of Laboratory Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Michisuke Yuzaki
- Department of Physiology, School of Medicine, Keio University, Tokyo, Japan
| | - Jin Young Kim
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Chungbuk, Korea
| | - Se-Young Choi
- Department of Neuroscience and Physiology, Dental Research Institute, School of Dentistry, Seoul National University, Seoul, Korea
| | - Jaewon Ko
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Hyeonpoong-Eup, Dalseong-gun, Daegu, Korea.
| | - Ji Won Um
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Hyeonpoong-Eup, Dalseong-gun, Daegu, Korea; Core Protein Resources Center, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Hyeonpoong-Eup, Dalseong-Gun, Daegu, Korea.
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186
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Sas-Chen A, Thomas JM, Matzov D, Taoka M, Nance KD, Nir R, Bryson KM, Shachar R, Liman GLS, Burkhart BW, Gamage ST, Nobe Y, Briney CA, Levy MJ, Fuchs RT, Robb GB, Hartmann J, Sharma S, Lin Q, Florens L, Washburn MP, Isobe T, Santangelo TJ, Shalev-Benami M, Meier JL, Schwartz S. Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping. Nature 2020; 583:638-643. [PMID: 32555463 PMCID: PMC8130014 DOI: 10.1038/s41586-020-2418-2] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 03/26/2020] [Indexed: 12/14/2022]
Abstract
N4-acetylcytidine (ac4C) is an ancient and highly conserved RNA modification that is present on tRNA and rRNA and has recently been investigated in eukaryotic mRNA1-3. However, the distribution, dynamics and functions of cytidine acetylation have yet to be fully elucidated. Here we report ac4C-seq, a chemical genomic method for the transcriptome-wide quantitative mapping of ac4C at single-nucleotide resolution. In human and yeast mRNAs, ac4C sites are not detected but can be induced-at a conserved sequence motif-via the ectopic overexpression of eukaryotic acetyltransferase complexes. By contrast, cross-evolutionary profiling revealed unprecedented levels of ac4C across hundreds of residues in rRNA, tRNA, non-coding RNA and mRNA from hyperthermophilic archaea. Ac4C is markedly induced in response to increases in temperature, and acetyltransferase-deficient archaeal strains exhibit temperature-dependent growth defects. Visualization of wild-type and acetyltransferase-deficient archaeal ribosomes by cryo-electron microscopy provided structural insights into the temperature-dependent distribution of ac4C and its potential thermoadaptive role. Our studies quantitatively define the ac4C landscape, providing a technical and conceptual foundation for elucidating the role of this modification in biology and disease4-6.
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Affiliation(s)
- Aldema Sas-Chen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Justin M Thomas
- National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Donna Matzov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Kellie D Nance
- National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Ronit Nir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Keri M Bryson
- National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Ran Shachar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Geraldy L S Liman
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Brett W Burkhart
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Yuko Nobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Chloe A Briney
- National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | | | - Ryan T Fuchs
- RNA Research Division, New England Biolabs, Inc, Ipswich, MA, USA
| | - G Brett Robb
- RNA Research Division, New England Biolabs, Inc, Ipswich, MA, USA
| | - Jesse Hartmann
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sunny Sharma
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Qishan Lin
- RNA Epitranscriptomics and Proteomics Resource, University at Albany, Albany, NY, USA
| | | | | | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Thomas J Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Moran Shalev-Benami
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Jordan L Meier
- National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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187
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Isobe Y, Okumura M, McGregor LM, Brittain SM, Jones MD, Liang X, White R, Forrester W, McKenna JM, Tallarico JA, Schirle M, Maimone TJ, Nomura DK. Manumycin polyketides act as molecular glues between UBR7 and P53. Nat Chem Biol 2020; 16:1189-1198. [PMID: 32572277 PMCID: PMC7572527 DOI: 10.1038/s41589-020-0557-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 04/29/2020] [Indexed: 12/16/2022]
Abstract
Molecular glues are an intriguing therapeutic modality that harness small-molecules to induce interactions between proteins that typically do not interact. However, such molecules are rare and have been discovered fortuitously, thus limiting their potential as a general strategy for therapeutic intervention. We postulated that natural products bearing one or more electrophilic sites may be an unexplored source of new molecular glues, potentially acting through multi-covalent attachment. Using chemoproteomic platforms, we show that members of the manumycin family of polyketides, which bear multiple potentially reactive sites, target C374 of the putative E3 ligase UBR7 in breast cancer cells and engage in molecular glue interactions with the neo-substrate tumor-suppressor TP53, leading to p53 transcriptional activation and cell death. Our results reveal a novel anti-cancer mechanism of this natural product family and highlight the potential for combining chemoproteomics and multi-covalent natural products for the discovery of new molecular glues.
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Affiliation(s)
- Yosuke Isobe
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
| | - Mikiko Okumura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
| | - Lynn M McGregor
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Michael D Jones
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Xiaoyou Liang
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Ross White
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
| | | | - Jeffrey M McKenna
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.,Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - John A Tallarico
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.,Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Markus Schirle
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.,Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Thomas J Maimone
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA. .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA. .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA. .,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA. .,Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA. .,Innovative Genomics Institute, Berkeley, CA, USA.
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188
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Proteomics Profiling of KAIMRC1 in Comparison to MDA-MB231 and MCF-7. Int J Mol Sci 2020; 21:ijms21124328. [PMID: 32570693 PMCID: PMC7352455 DOI: 10.3390/ijms21124328] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/05/2020] [Accepted: 03/24/2020] [Indexed: 12/30/2022] Open
Abstract
Proteomics characterization of KAIMRC1 cell line, a naturally immortalized breast cancer cells, is described in comparison to MCF-7 and MDA-MB-231 breast cancer cells. Quantitative proteomics analysis using the tandem mass tag (TMT)-labeled technique in conjunction with the phosphopeptide enrichment method was used to perform comparative profiling of proteins and phosphoproteins in the three cell lines. In total, 673 proteins and 33 Phosphoproteins were differentially expressed among these cell lines. These proteins are involved in several key cellular pathways that include DNA replication and repair, splicing machinery, amino acid metabolism, cellular energy, and estrogen signaling pathway. Many of the differentially expressed proteins are associated with different types of tumors including breast cancer. For validation, 4 highly significant expressed proteins including S-methyl-5'-thioadenosine phosphorylase (MTAP), BTB/POZ domain-containing protein (KCTD12), Poly (ADP-ribose) polymerase 1 (PARP 1), and Prelamin-A/C were subjected to western blotting, and the results were consistent with proteomics analysis. Unlike MCF-7 and MDA-MB-231, KAIMRC1 showed different phospho- and non-phosphoproteomic phenotypes which make it a potential model to study breast cancer.
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189
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NAP1-RELATED PROTEIN1 and 2 negatively regulate H2A.Z abundance in chromatin in Arabidopsis. Nat Commun 2020; 11:2887. [PMID: 32513971 PMCID: PMC7280298 DOI: 10.1038/s41467-020-16691-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 05/20/2020] [Indexed: 12/22/2022] Open
Abstract
In eukaryotes, DNA wraps around histones to form nucleosomes, which are compacted into chromatin. DNA-templated processes, including transcription, require chromatin disassembly and reassembly mediated by histone chaperones. Additionally, distinct histone variants can replace core histones to regulate chromatin structure and function. Although replacement of H2A with the evolutionarily conserved H2A.Z via the SWR1 histone chaperone complex has been extensively studied, in plants little is known about how a reduction of H2A.Z levels can be achieved. Here, we show that NRP proteins cause a decrease of H2A.Z-containing nucleosomes in Arabidopsis under standard growing conditions. nrp1-1 nrp2-2 double mutants show an over-accumulation of H2A.Z genome-wide, especially at heterochromatic regions normally H2A.Z-depleted in wild-type plants. Our work suggests that NRP proteins regulate gene expression by counteracting SWR1, thereby preventing excessive accumulation of H2A.Z. The histone variant H2A.Z is deposited by the SWR1 complex to replace H2A in Arabidopsis, but the mechanism of H2A.Z removal is unclear. Here, the authors show that NRP proteins can regulate gene expression by counteracting SWR1 and prevent excessive accumulation of H2A.Z.
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190
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Ancient MAPK ERK7 is regulated by an unusual inhibitory scaffold required for Toxoplasma apical complex biogenesis. Proc Natl Acad Sci U S A 2020; 117:12164-12173. [PMID: 32409604 PMCID: PMC7275706 DOI: 10.1073/pnas.1921245117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Apicomplexan parasites include organisms that cause widespread and devastating human diseases such as malaria, cryptosporidiosis, and toxoplasmosis. These parasites are named for a structure, called the “apical complex,” that organizes their invasion and secretory machinery. We found that two proteins, apical cap protein 9 (AC9) and an enzyme called ERK7, work together to facilitate apical complex assembly. Intriguingly, ERK7 is an ancient molecule that is found throughout Eukaryota, though its regulation and function are poorly understood. AC9 is a scaffold that concentrates ERK7 at the base of the developing apical complex. In addition, AC9 binding likely confers substrate selectivity upon ERK7. This simple competitive regulatory model may be a powerful but largely overlooked mechanism throughout biology. Apicomplexan parasites use a specialized cilium structure called the apical complex to organize their secretory organelles and invasion machinery. The apical complex is integrally associated with both the parasite plasma membrane and an intermediate filament cytoskeleton called the inner-membrane complex (IMC). While the apical complex is essential to the parasitic lifestyle, little is known about the regulation of apical complex biogenesis. Here, we identify AC9 (apical cap protein 9), a largely intrinsically disordered component of the Toxoplasma gondii IMC, as essential for apical complex development, and therefore for host cell invasion and egress. Parasites lacking AC9 fail to successfully assemble the tubulin-rich core of their apical complex, called the conoid. We use proximity biotinylation to identify the AC9 interaction network, which includes the kinase extracellular signal-regulated kinase 7 (ERK7). Like AC9, ERK7 is required for apical complex biogenesis. We demonstrate that AC9 directly binds ERK7 through a conserved C-terminal motif and that this interaction is essential for ERK7 localization and function at the apical cap. The crystal structure of the ERK7–AC9 complex reveals that AC9 is not only a scaffold but also inhibits ERK7 through an unusual set of contacts that displaces nucleotide from the kinase active site. ERK7 is an ancient and autoactivating member of the mitogen-activated kinase (MAPK) family and its regulation is poorly understood in all organisms. We propose that AC9 dually regulates ERK7 by scaffolding and concentrating it at its site of action while maintaining it in an “off” state until the specific binding of a true substrate.
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191
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Cheng LC, Baboo S, Lindsay C, Brusman L, Martinez-Bartolomé S, Tapia O, Zhang X, Yates JR, Gerace L. Identification of new transmembrane proteins concentrated at the nuclear envelope using organellar proteomics of mesenchymal cells. Nucleus 2020; 10:126-143. [PMID: 31142202 PMCID: PMC6550788 DOI: 10.1080/19491034.2019.1618175] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The double membrane nuclear envelope (NE), which is contiguous with the ER, contains nuclear pore complexes (NPCs) – the channels for nucleocytoplasmic transport, and the nuclear lamina (NL) – a scaffold for NE and chromatin organization. Since numerous human diseases linked to NE proteins occur in mesenchyme-derived cells, we used proteomics to characterize NE and other subcellular fractions isolated from mesenchymal stem cells and from adipocytes and myocytes. Based on spectral abundance, we calculated enrichment scores for proteins in the NE fractions. We demonstrated by quantitative immunofluorescence microscopy that five little-characterized proteins with high enrichment scores are substantially concentrated at the NE, with Itprip exposed at the outer nuclear membrane, Smpd4 enriched at the NPC, and Mfsd10, Tmx4, and Arl6ip6 likely residing in the inner nuclear membrane. These proteins provide new focal points for studying the functions of the NE. Moreover, our datasets provide a resource for evaluating additional potential NE proteins.
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Affiliation(s)
- Li-Chun Cheng
- a Department of Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA
| | - Sabyasachi Baboo
- a Department of Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA
| | - Cory Lindsay
- a Department of Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA
| | - Liza Brusman
- a Department of Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA
| | | | - Olga Tapia
- a Department of Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA
| | - Xi Zhang
- a Department of Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA
| | - John R Yates
- a Department of Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA
| | - Larry Gerace
- a Department of Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA
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192
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Thompson AJ, Cao L, Ma Y, Wang X, Diedrich JK, Kikuchi C, Willis S, Worth C, McBride R, Yates JR, Paulson JC. Human Influenza Virus Hemagglutinins Contain Conserved Oligomannose N-Linked Glycans Allowing Potent Neutralization by Lectins. Cell Host Microbe 2020; 27:725-735.e5. [PMID: 32298658 PMCID: PMC7158820 DOI: 10.1016/j.chom.2020.03.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/13/2020] [Accepted: 03/17/2020] [Indexed: 12/12/2022]
Abstract
Hemagglutinins (HAs) from human influenza viruses adapt to bind α2-6-linked sialosides, overcoming a receptor-defined species barrier distinct from the α2-3 specificity of avian virus progenitors. Additionally, human-adapted HAs gain glycosylation sites over time, although their biological function is poorly defined. Using quantitative glycomic analysis, we show that HAs from human pandemic viruses exhibit significant proportions of high-mannose type N-linked glycans throughout the head domain. By contrast, poorly adapted avian-origin HAs contain predominately complex-type glycans, which have greater structural diversity. Although oligomannose levels vary, they are present in all tested recombinant HAs and whole viruses and can be specifically targeted for universal detection. The positions of high-mannose glycosites on the HA of human H1N1 and H3N2 strains are conserved. Additionally, high-mannose-binding lectins possess a broad capacity to neutralize and prevent infection with contemporary H3N2 strains. These findings reveal the biological significance of HA glycosylation and therapeutic potential of targeting these structures.
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Affiliation(s)
- Andrew J Thompson
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Liwei Cao
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Yuanhui Ma
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Xiaoning Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Chika Kikuchi
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Shelby Willis
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Charli Worth
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Ryan McBride
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - James C Paulson
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA; Department of Immunology & Microbiology, Scripps Research, La Jolla, CA 92037, USA.
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193
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Choi H, Simpson D, Wang D, Prescott M, Pitsillides AA, Dudhia J, Clegg PD, Ping P, Thorpe CT. Heterogeneity of proteome dynamics between connective tissue phases of adult tendon. eLife 2020; 9:e55262. [PMID: 32393437 PMCID: PMC7217697 DOI: 10.7554/elife.55262] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/16/2020] [Indexed: 12/29/2022] Open
Abstract
Maintenance of connective tissue integrity is fundamental to sustain function, requiring protein turnover to repair damaged tissue. However, connective tissue proteome dynamics remain largely undefined, as do differences in turnover rates of individual proteins in the collagen and glycoprotein phases of connective tissue extracellular matrix (ECM). Here, we investigate proteome dynamics in the collagen and glycoprotein phases of connective tissues by exploiting the spatially distinct fascicular (collagen-rich) and interfascicular (glycoprotein-rich) ECM phases of tendon. Using isotope labelling, mass spectrometry and bioinformatics, we calculate turnover rates of individual proteins within rat Achilles tendon and its ECM phases. Our results demonstrate complex proteome dynamics in tendon, with ~1000 fold differences in protein turnover rates, and overall faster protein turnover within the glycoprotein-rich interfascicular matrix compared to the collagen-rich fascicular matrix. These data provide insights into the complexity of proteome dynamics in tendon, likely required to maintain tissue homeostasis.
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Affiliation(s)
- Howard Choi
- Department of Physiology and Medicine, David Geffen School of Medicine, UCLALos AngelesUnited States
| | - Deborah Simpson
- Centre for Proteome Research, Biosciences Building, Institute of Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
| | - Ding Wang
- Department of Physiology and Medicine, David Geffen School of Medicine, UCLALos AngelesUnited States
| | - Mark Prescott
- Centre for Proteome Research, Biosciences Building, Institute of Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
| | - Andrew A Pitsillides
- Department of Comparative Biomedical Sciences, Royal Veterinary CollegeLondonUnited Kingdom
| | - Jayesh Dudhia
- Department of Clinical Sciences and Services, Royal Veterinary CollegeHatfieldUnited Kingdom
| | - Peter D Clegg
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of LiverpoolLiverpoolUnited Kingdom
| | - Peipei Ping
- Department of Physiology and Medicine, David Geffen School of Medicine, UCLALos AngelesUnited States
| | - Chavaunne T Thorpe
- Department of Comparative Biomedical Sciences, Royal Veterinary CollegeLondonUnited Kingdom
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194
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Widmeier E, Yu S, Nag A, Chung YW, Nakayama M, Fernández-Del-Río L, Hugo H, Schapiro D, Buerger F, Choi WI, Helmstädter M, Kim JW, Ryu JH, Lee MG, Clarke CF, Hildebrandt F, Gee HY. ADCK4 Deficiency Destabilizes the Coenzyme Q Complex, Which Is Rescued by 2,4-Dihydroxybenzoic Acid Treatment. J Am Soc Nephrol 2020; 31:1191-1211. [PMID: 32381600 DOI: 10.1681/asn.2019070756] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 02/22/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Mutations in ADCK4 (aarF domain containing kinase 4) generally manifest as steroid-resistant nephrotic syndrome and induce coenzyme Q10 (CoQ10) deficiency. However, the molecular mechanisms underlying steroid-resistant nephrotic syndrome resulting from ADCK4 mutations are not well understood, largely because the function of ADCK4 remains unknown. METHODS To elucidate the ADCK4's function in podocytes, we generated a podocyte-specific, Adck4-knockout mouse model and a human podocyte cell line featuring knockout of ADCK4. These knockout mice and podocytes were then treated with 2,4-dihydroxybenzoic acid (2,4-diHB), a CoQ10 precursor analogue, or with a vehicle only. We also performed proteomic mass spectrometry analysis to further elucidate ADCK4's function. RESULTS Absence of Adck4 in mouse podocytes caused FSGS and albuminuria, recapitulating features of nephrotic syndrome caused by ADCK4 mutations. In vitro studies revealed that ADCK4-knockout podocytes had significantly reduced CoQ10 concentration, respiratory chain activity, and mitochondrial potential, and subsequently displayed an increase in the number of dysmorphic mitochondria. However, treatment of 3-month-old knockout mice or ADCK4-knockout cells with 2,4-diHB prevented the development of renal dysfunction and reversed mitochondrial dysfunction in podocytes. Moreover, ADCK4 interacted with mitochondrial proteins such as COQ5, as well as cytoplasmic proteins such as myosin and heat shock proteins. Thus, ADCK4 knockout decreased the COQ complex level, but overexpression of ADCK4 in ADCK4-knockout podocytes transfected with wild-type ADCK4 rescued the COQ5 level. CONCLUSIONS Our study shows that ADCK4 is required for CoQ10 biosynthesis and mitochondrial function in podocytes, and suggests that ADCK4 in podocytes stabilizes proteins in complex Q in podocytes. Our study also suggests a potential treatment strategy for nephrotic syndrome resulting from ADCK4 mutations.
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Affiliation(s)
- Eugen Widmeier
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.,Renal Division, Department of Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Seyoung Yu
- Departments of Pharmacology, Yonsei University College of Medicine, Seoul, Korea .,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Anish Nag
- Department of Chemistry and Biochemistry, Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California
| | - Youn Wook Chung
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Makiko Nakayama
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lucía Fernández-Del-Río
- Department of Chemistry and Biochemistry, Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California
| | - Hannah Hugo
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - David Schapiro
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Florian Buerger
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Won-Il Choi
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Martin Helmstädter
- Renal Division, Department of Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jae-Woo Kim
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea.,Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, Korea
| | - Ji-Hwan Ryu
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea.,Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Min Goo Lee
- Departments of Pharmacology, Yonsei University College of Medicine, Seoul, Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Catherine F Clarke
- Department of Chemistry and Biochemistry, Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Heon Yung Gee
- Departments of Pharmacology, Yonsei University College of Medicine, Seoul, Korea .,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
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195
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Wang Y, Zhou Y, Xiao X, Zheng J, Zhou H. Metaproteomics: A strategy to study the taxonomy and functionality of the gut microbiota. J Proteomics 2020; 219:103737. [DOI: 10.1016/j.jprot.2020.103737] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/07/2020] [Accepted: 03/10/2020] [Indexed: 12/15/2022]
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196
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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] [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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197
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Reid MS, Kern DM, Brohawn SG. Cryo-EM structure of the potassium-chloride cotransporter KCC4 in lipid nanodiscs. eLife 2020; 9:e52505. [PMID: 32286222 PMCID: PMC7200160 DOI: 10.7554/elife.52505] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 04/12/2020] [Indexed: 01/24/2023] Open
Abstract
Cation-chloride-cotransporters (CCCs) catalyze transport of Cl- with K+ and/or Na+across cellular membranes. CCCs play roles in cellular volume regulation, neural development and function, audition, regulation of blood pressure, and renal function. CCCs are targets of clinically important drugs including loop diuretics and their disruption has been implicated in pathophysiology including epilepsy, hearing loss, and the genetic disorders Andermann, Gitelman, and Bartter syndromes. Here we present the structure of a CCC, the Mus musculus K+-Cl- cotransporter (KCC) KCC4, in lipid nanodiscs determined by cryo-EM. The structure, captured in an inside-open conformation, reveals the architecture of KCCs including an extracellular domain poised to regulate transport activity through an outer gate. We identify binding sites for substrate K+ and Cl- ions, demonstrate the importance of key coordinating residues for transporter activity, and provide a structural explanation for varied substrate specificity and ion transport ratio among CCCs. These results provide mechanistic insight into the function and regulation of a physiologically important transporter family.
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Affiliation(s)
- Michelle S Reid
- Department of Molecular and Cell Biology, University of California BerkeleyBerkeleyUnited States
- Helen Wills Neuroscience Institute, University of California BerkeleyBerkeleyUnited States
| | - David M Kern
- Department of Molecular and Cell Biology, University of California BerkeleyBerkeleyUnited States
- Helen Wills Neuroscience Institute, University of California BerkeleyBerkeleyUnited States
| | - Stephen Graf Brohawn
- Department of Molecular and Cell Biology, University of California BerkeleyBerkeleyUnited States
- Helen Wills Neuroscience Institute, University of California BerkeleyBerkeleyUnited States
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198
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Park DE, Cheng J, McGrath JP, Lim MY, Cushman C, Swanson SK, Tillgren ML, Paulo JA, Gokhale PC, Florens L, Washburn MP, Trojer P, DeCaprio JA. Merkel cell polyomavirus activates LSD1-mediated blockade of non-canonical BAF to regulate transformation and tumorigenesis. Nat Cell Biol 2020; 22:603-615. [PMID: 32284543 PMCID: PMC7336275 DOI: 10.1038/s41556-020-0503-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 03/04/2020] [Indexed: 12/12/2022]
Abstract
Merkel cell carcinoma (MCC), a neuroendocrine cancer of the skin, is caused by integration of Merkel cell polyomavirus (MCV) and persistent expression of Large T antigen (LT) and Small T antigen (ST). We report that ST in complex with MYCL and the EP400 complex activates expression of LSD1 (KDM1A), RCOR2, and INSM1 to repress gene expression by the lineage transcription factor ATOH1. LSD1 inhibition reduces growth of MCC in vitro and in vivo. Through a forward-genetics CRISPR-Cas9 screen, we identified an antagonistic relationship between LSD1 and the non-canonical BAF (ncBAF) chromatin remodeling complex. Changes in gene expression and chromatin accessibility caused by LSD1 inhibition could be partially rescued by BRD9 inhibition, revealing that LSD1 and ncBAF antagonistically regulate an overlapping set of genes. Our work provides mechanistic insight into the dependence of MCC on LSD1 and a tumor suppressor role for ncBAF in cancer.
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Affiliation(s)
- Donglim Esther Park
- Program in Virology, Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jingwei Cheng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Matthew Y Lim
- Program in Virology, Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, USA.,Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Camille Cushman
- Program in Virology, Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Michelle L Tillgren
- Experimental Therapeutics Core, Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Prafulla C Gokhale
- Experimental Therapeutics Core, Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, MO, USA.,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | | | - James A DeCaprio
- Program in Virology, Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, USA. .,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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199
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Mei L, Montoya MR, Quanrud GM, Tran M, Villa-Sharma A, Huang M, Genereux JC. Bait Correlation Improves Interactor Identification by Tandem Mass Tag-Affinity Purification-Mass Spectrometry. J Proteome Res 2020; 19:1565-1573. [PMID: 32138514 DOI: 10.1021/acs.jproteome.9b00825] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The quantitative multiplexing capacity of isobaric tandem mass tags (TMT) has increased the throughput of affinity purification mass spectrometry (AP-MS) to characterize protein interaction networks of immunoprecipitated bait proteins. However, variable bait levels between replicates can convolute interactor identification. We compared the Student's t-test and Pearson's R correlation as methods to generate t-statistics and assessed the significance of interactors following TMT-AP-MS. Using a simple linear model of protein recovery in immunoprecipitates to simulate reporter ion ratio distributions, we found that correlation-derived t-statistics protect against bait variance while robustly controlling type I errors (false positives). We experimentally determined the performance of these two approaches for determining t-statistics under two experimental conditions: irreversible prey association to the Hsp40 mutant DNAJB8H31Q followed by stringent washing, and reversible association to 14-3-3ζ with gentle washing. Correlation-derived t-statistics performed at least as well as Student's t-statistics for each sample and with substantial improvement in performance for experiments with high bait-level variance. Deliberately varying bait levels over a large range fails to improve selectivity but does increase the robustness between runs. The use of correlation-derived t-statistics should improve identification of interactors using TMT-AP-MS. Data are available via ProteomeXchange with identifier PXD016613.
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Affiliation(s)
- Liangyong Mei
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Maureen R Montoya
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Guy M Quanrud
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Minh Tran
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Athena Villa-Sharma
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Ming Huang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
| | - Joseph C Genereux
- Department of Chemistry, University of California, Riverside, California 92521, United States.,Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
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200
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Levy MJ, Montgomery DC, Sardiu ME, Montano JL, Bergholtz SE, Nance KD, Thorpe AL, Fox SD, Lin Q, Andresson T, Florens L, Washburn MP, Meier JL. A Systems Chemoproteomic Analysis of Acyl-CoA/Protein Interaction Networks. Cell Chem Biol 2020; 27:322-333.e5. [PMID: 31836350 PMCID: PMC8237707 DOI: 10.1016/j.chembiol.2019.11.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/22/2019] [Accepted: 11/19/2019] [Indexed: 12/18/2022]
Abstract
Acyl-coenzyme A (CoA)/protein interactions are essential for life. Despite this importance, their global scope and selectivity remains undefined. Here, we describe CATNIP (CoA/AcetylTraNsferase Interaction Profiling), a chemoproteomic platform for the high-throughput analysis of acyl-CoA/protein interactions in endogenous proteomes. First, we apply CATNIP to identify acetyl-CoA-binding proteins through unbiased clustering of competitive dose-response data. Next, we use this method to profile the selectivity of acyl-CoA/protein interactions, leading to the identification of specific acyl-CoA engagement signatures. Finally, we apply systems-level analyses to assess the features of protein networks that may interact with acyl-CoAs, and use a strategy for high-confidence proteomic annotation of acetyl-CoA-binding proteins to identify a site of non-enzymatic acylation in the NAT10 acetyltransferase domain that is likely driven by acyl-CoA binding. Overall, our studies illustrate how chemoproteomics and systems biology can be integrated to understand the roles of acyl-CoA metabolism in biology and disease.
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Affiliation(s)
- Michaella J Levy
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - David C Montgomery
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Mihaela E Sardiu
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jose L Montano
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Sarah E Bergholtz
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Kellie D Nance
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Abigail L Thorpe
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Stephen D Fox
- Laboratory of Proteomics and Analytical Technologies, Leidos, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Qishan Lin
- RNA Epitranscriptomics & Proteomics Resource, University of Albany, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Thorkell Andresson
- Laboratory of Proteomics and Analytical Technologies, Leidos, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
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