1
|
Guillotin S, Fulzele A, Vallet A, de Peredo AG, Mouton-Barbosa E, Cestac P, Andrieu S, Burlet-Schiltz O, Delcourt N, Schmidt E. Cerebrospinal fluid proteomic profile of frailty: Results from the PROLIPHYC cohort. Aging Cell 2024:e14168. [PMID: 38698559 DOI: 10.1111/acel.14168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/21/2024] [Accepted: 03/25/2024] [Indexed: 05/05/2024] Open
Abstract
Frailty is a clinical state reflecting a decrease in physiological reserve capacities, known to affect numerous biological pathways and is associated with health issues, including neurodegenerative diseases. However, how global protein expression is affected in the central nervous system in frail subject remains underexplored. In this post hoc cross-sectional biomarker analysis, we included 90 adults (52-85 years) suspected of normal pressure hydrocephalus (NPH) and presenting with markers of neurodegenerative diseases. We investigated the human proteomic profile of cerebrospinal fluid associated with frailty defined by an established cumulated frailty index (FI, average = 0.32), not enriched for neurology clinical features. Using a label-free quantitative proteomic approach, we identified and quantified 999 proteins of which 13 were positively associated with frailty. Pathway analysis with the top positively frailty-associated proteins revealed enrichment for proteins related to inflammation and immune response. Among the 60 proteins negatively associated with frailty, functional pathways enriched included neurogenesis, synaptogenesis and neuronal guidance. We constructed a frailty prediction model using ridge regression with 932 standardized proteins. Our results showed that the "proteomic model" could become an equivalent predictor of FI in order to study chronological age. This study represents the first comprehensive exploration of the proteomic profile of frailty within cerebrospinal fluid. It sheds light on the physiopathology of frailty, particularly highlighting processes of neuroinflammation and inhibition of neurogenesis. Our findings unveil a range of biological mechanisms that are dysregulated in frailty, in NPH subjects at risk of neurodegenerative impairment, offering new perspectives on frailty phenotyping and prediction.
Collapse
Affiliation(s)
- Sophie Guillotin
- Aging-MAINTAIN Research Team, Center for Epidemiology and Research in POPulation Health (CERPOP), University of Toulouse, Toulouse, France
- Poison Control Center, Toulouse University Hospital, Toulouse, France
| | - Amit Fulzele
- Institute of Pharmacology and Structural Biology (IPBS), University of Toulouse, CNRS, University of Toulouse III (Paul Sabatier (UT3), Toulouse, France
| | - Alexandra Vallet
- Biological Tissue and Surface Engineering Department, INSERM U1059 Sainbiose, Ecole Des Mines of Saint-Etienne, Saint-Etienne, France
| | - Anne Gonzalez de Peredo
- Institute of Pharmacology and Structural Biology (IPBS), University of Toulouse, CNRS, University of Toulouse III (Paul Sabatier (UT3), Toulouse, France
| | - Emmanuelle Mouton-Barbosa
- Institute of Pharmacology and Structural Biology (IPBS), University of Toulouse, CNRS, University of Toulouse III (Paul Sabatier (UT3), Toulouse, France
| | - Philippe Cestac
- Aging-MAINTAIN Research Team, Center for Epidemiology and Research in POPulation Health (CERPOP), University of Toulouse, Toulouse, France
- Department of Clinical Pharmacy, Toulouse University Hospital, Toulouse, France
| | - Sandrine Andrieu
- Aging-MAINTAIN Research Team, Center for Epidemiology and Research in POPulation Health (CERPOP), University of Toulouse, Toulouse, France
- Department of Epidemiology and Public Health, Toulouse University Hospital, Toulouse, France
- IHU HealthAge, Toulouse, France
| | - Odile Burlet-Schiltz
- Institute of Pharmacology and Structural Biology (IPBS), University of Toulouse, CNRS, University of Toulouse III (Paul Sabatier (UT3), Toulouse, France
| | - Nicolas Delcourt
- Poison Control Center, Toulouse University Hospital, Toulouse, France
- Toulouse NeuroImaging Center (ToNIC), University of Toulouse, INSERM UPS, Toulouse, France
| | - Eric Schmidt
- Toulouse NeuroImaging Center (ToNIC), University of Toulouse, INSERM UPS, Toulouse, France
- Department of Neurosurgery, Toulouse University Hospital, Toulouse, France
| |
Collapse
|
2
|
Nan Q, Liang H, Mendoza J, Liu L, Fulzele A, Wright A, Bennett EJ, Rasmussen CG, Facette MR. The OPAQUE1/DISCORDIA2 myosin XI is required for phragmoplast guidance during asymmetric cell division in maize. Plant Cell 2023; 35:2678-2693. [PMID: 37017144 PMCID: PMC10291028 DOI: 10.1093/plcell/koad099] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 06/19/2023]
Abstract
Formative asymmetric divisions produce cells with different fates and are critical for development. We show the maize (Zea mays) myosin XI protein, OPAQUE1 (O1), is necessary for asymmetric divisions during maize stomatal development. We analyzed stomatal precursor cells before and during asymmetric division to determine why o1 mutants have abnormal division planes. Cell polarization and nuclear positioning occur normally in the o1 mutant, and the future site of division is correctly specified. The defect in o1 becomes apparent during late cytokinesis, when the phragmoplast forms the nascent cell plate. Initial phragmoplast guidance in o1 is normal; however, as phragmoplast expansion continues o1 phragmoplasts become misguided. To understand how O1 contributes to phragmoplast guidance, we identified O1-interacting proteins. Maize kinesins related to the Arabidopsis thaliana division site markers PHRAGMOPLAST ORIENTING KINESINs (POKs), which are also required for correct phragmoplast guidance, physically interact with O1. We propose that different myosins are important at multiple steps of phragmoplast expansion, and the O1 actin motor and POK-like microtubule motors work together to ensure correct late-stage phragmoplast guidance.
Collapse
Affiliation(s)
- Qiong Nan
- Department of Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Hong Liang
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Janette Mendoza
- Department of Botany, University of New Mexico, Albuquerque, NM 87131, USA
| | - Le Liu
- Department of Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Amit Fulzele
- Division of Biological Sciences, University of California, Riverside, CA 92093, USA
| | - Amanda Wright
- Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
| | - Eric J Bennett
- Division of Biological Sciences, University of California, Riverside, CA 92093, USA
| | - Carolyn G Rasmussen
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Michelle R Facette
- Department of Biology, University of Massachusetts, Amherst, MA 01003, USA
| |
Collapse
|
3
|
Bhaduri S, Aguayo A, Ohno Y, Proietto M, Jung J, Wang I, Kandel R, Singh N, Ibrahim I, Fulzele A, Bennett EJ, Kihara A, Neal SE. An ERAD-independent role for rhomboid pseudoprotease Dfm1 in mediating sphingolipid homeostasis. EMBO J 2023; 42:e112275. [PMID: 36350249 PMCID: PMC9929635 DOI: 10.15252/embj.2022112275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/20/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Nearly one-third of nascent proteins are initially targeted to the endoplasmic reticulum (ER), where they are correctly folded and assembled before being delivered to their final cellular destinations. To prevent the accumulation of misfolded membrane proteins, ER-associated degradation (ERAD) removes these client proteins from the ER membrane to the cytosol in a process known as retrotranslocation. Our previous work demonstrated that rhomboid pseudoprotease Dfm1 is involved in the retrotranslocation of ubiquitinated membrane integral ERAD substrates. Herein, we found that Dfm1 associates with the SPOTS complex, which is composed of serine palmitoyltransferase (SPT) enzymes and accessory components that are critical for catalyzing the first rate-limiting step of the sphingolipid biosynthesis pathway. Furthermore, Dfm1 employs an ERAD-independent role for facilitating the ER export and endosome- and Golgi-associated degradation (EGAD) of Orm2, which is a major antagonist of SPT activity. Given that the accumulation of human Orm2 homologs, ORMDLs, is associated with various pathologies, our study serves as a molecular foothold for understanding how dysregulation of sphingolipid metabolism leads to various diseases.
Collapse
Affiliation(s)
- Satarupa Bhaduri
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Analine Aguayo
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Yusuke Ohno
- Laboratory of Biochemistry, Faculty of Pharmaceutical SciencesHokkaido UniversitySapporoJapan
| | - Marco Proietto
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Jasmine Jung
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Isabel Wang
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Rachel Kandel
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Narinderbir Singh
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Ikran Ibrahim
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Amit Fulzele
- Present address:
Institute of Molecular BiologyMainzGermany
| | - Eric J Bennett
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Akio Kihara
- Laboratory of Biochemistry, Faculty of Pharmaceutical SciencesHokkaido UniversitySapporoJapan
| | - Sonya E Neal
- Department of Cell and Developmental Biology, School of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| |
Collapse
|
4
|
Banta KL, Xu X, Chitre AS, Au-Yeung A, Takahashi C, O'Gorman WE, Wu TD, Mittman S, Cubas R, Comps-Agrar L, Fulzele A, Bennett EJ, Grogan JL, Hui E, Chiang EY, Mellman I. Mechanistic convergence of the TIGIT and PD-1 inhibitory pathways necessitates co-blockade to optimize anti-tumor CD8 + T cell responses. Immunity 2022; 55:512-526.e9. [PMID: 35263569 PMCID: PMC9287124 DOI: 10.1016/j.immuni.2022.02.005] [Citation(s) in RCA: 102] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 12/01/2021] [Accepted: 02/07/2022] [Indexed: 02/07/2023]
Abstract
Dual blockade of the PD-1 and TIGIT coinhibitory receptors on T cells shows promising early results in cancer patients. Here, we studied the mechanisms whereby PD-1 and/or TIGIT blockade modulate anti-tumor CD8+ T cells. Although PD-1 and TIGIT are thought to regulate different costimulatory receptors (CD28 and CD226), effectiveness of PD-1 or TIGIT inhibition in preclinical tumor models was reduced in the absence of CD226. CD226 expression associated with clinical benefit in patients with non-small cell lung carcinoma (NSCLC) treated with anti-PD-L1 antibody atezolizumab. CD226 and CD28 were co-expressed on NSCLC infiltrating CD8+ T cells poised for expansion. Mechanistically, PD-1 inhibited phosphorylation of both CD226 and CD28 via its ITIM-containing intracellular domain (ICD); TIGIT's ICD was dispensable, with TIGIT restricting CD226 co-stimulation by blocking interaction with their common ligand PVR (CD155). Thus, full restoration of CD226 signaling, and optimal anti-tumor CD8+ T cell responses, requires blockade of TIGIT and PD-1, providing a mechanistic rationale for combinatorial targeting in the clinic.
Collapse
Affiliation(s)
- Karl L Banta
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Xiaozheng Xu
- Section of Cell & Developmental Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | | | - Amelia Au-Yeung
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | | | | | - Thomas D Wu
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Rafael Cubas
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Amit Fulzele
- Section of Cell & Developmental Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Eric J Bennett
- Section of Cell & Developmental Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jane L Grogan
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Enfu Hui
- Section of Cell & Developmental Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Eugene Y Chiang
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Ira Mellman
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| |
Collapse
|
5
|
Markmiller S, Sathe S, Server KL, Nguyen TB, Fulzele A, Cody N, Javaherian A, Broski S, Finkbeiner S, Bennett EJ, Lécuyer E, Yeo GW. Persistent mRNA localization defects and cell death in ALS neurons caused by transient cellular stress. Cell Rep 2021; 36:109685. [PMID: 34496257 DOI: 10.1016/j.celrep.2021.109685] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 07/19/2021] [Accepted: 08/17/2021] [Indexed: 12/15/2022] Open
Abstract
Persistent cytoplasmic aggregates containing RNA binding proteins (RBPs) are central to the pathogenesis of late-onset neurodegenerative disorders such as amyotrophic lateral sclerosis (ALS). These aggregates share components, molecular mechanisms, and cellular protein quality control pathways with stress-induced RNA granules (SGs). Here, we assess the impact of stress on the global mRNA localization landscape of human pluripotent stem cell-derived motor neurons (PSC-MNs) using subcellular fractionation with RNA sequencing and proteomics. Transient stress disrupts subcellular RNA and protein distributions, alters the RNA binding profile of SG- and ALS-relevant RBPs and recapitulates disease-associated molecular changes such as aberrant splicing of STMN2. Although neurotypical PSC-MNs re-establish a normal subcellular localization landscape upon recovery from stress, cells harboring ALS-linked mutations are intransigent and display a delayed-onset increase in neuronal cell death. Our results highlight subcellular molecular distributions as predictive features and underscore the utility of cellular stress as a paradigm to study ALS-relevant mechanisms.
Collapse
Affiliation(s)
- Sebastian Markmiller
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, 92039, USA
| | - Shashank Sathe
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, 92039, USA
| | - Kari L Server
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, 92039, USA
| | - Thai B Nguyen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, 92039, USA
| | - Amit Fulzele
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Neal Cody
- Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada
| | - Ashkan Javaherian
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA; Taube/Koret Center for Neurodegenerative Disease Research, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Sara Broski
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA; Taube/Koret Center for Neurodegenerative Disease Research, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Steven Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA; Taube/Koret Center for Neurodegenerative Disease Research, Gladstone Institutes, San Francisco, CA 94158, USA; Departments of Neurology and Physiology, University of California-San Francisco, San Francisco, CA 94158, USA
| | - Eric J Bennett
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eric Lécuyer
- Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada; Division of Experimental Medicine, McGill University, Montréal, QC H3A 1A3, Canada
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, 92039, USA.
| |
Collapse
|
6
|
Sundaramoorthy E, Ryan AP, Fulzele A, Leonard M, Daugherty MD, Bennett EJ. Ribosome quality control activity potentiates vaccinia virus protein synthesis during infection. J Cell Sci 2021; 134:259243. [PMID: 33912921 PMCID: PMC8106952 DOI: 10.1242/jcs.257188] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/12/2021] [Indexed: 12/21/2022] Open
Abstract
Viral infection both activates stress signaling pathways and redistributes ribosomes away from host mRNAs to translate viral mRNAs. The intricacies of this ribosome shuffle from host to viral mRNAs are poorly understood. Here, we uncover a role for the ribosome-associated quality control (RQC) factor ZNF598 during vaccinia virus mRNA translation. ZNF598 acts on collided ribosomes to ubiquitylate 40S subunit proteins uS10 (RPS20) and eS10 (RPS10), initiating RQC-dependent nascent chain degradation and ribosome recycling. We show that vaccinia infection enhances uS10 ubiquitylation, indicating an increased burden on RQC pathways during viral propagation. Consistent with an increased RQC demand, we demonstrate that vaccinia virus replication is impaired in cells that either lack ZNF598 or express a ubiquitylation-deficient version of uS10. Using SILAC-based proteomics and concurrent RNA-seq analysis, we determine that translation, but not transcription of vaccinia virus mRNAs is compromised in cells with deficient RQC activity. Additionally, vaccinia virus infection reduces cellular RQC activity, suggesting that co-option of ZNF598 by vaccinia virus plays a critical role in translational reprogramming that is needed for optimal viral propagation. Summary: The ribosome-associated quality control factor ZNF598, which senses ribosome collisions, is a host factor necessary for vaccinia viral protein synthesis.
Collapse
Affiliation(s)
- Elayanambi Sundaramoorthy
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Andrew P Ryan
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Amit Fulzele
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Marilyn Leonard
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Matthew D Daugherty
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eric J Bennett
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
7
|
Kuhikar R, Khan N, Khare SP, Fulzele A, Melinkeri S, Kale V, Limaye L. Neutrophils generated in vitro from hematopoietic stem cells isolated from apheresis samples and umbilical cord blood form neutrophil extracellular traps. Stem Cell Res 2020; 50:102150. [PMID: 33450673 DOI: 10.1016/j.scr.2020.102150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 11/05/2020] [Accepted: 12/27/2020] [Indexed: 11/22/2022] Open
Abstract
Neutrophils release neutrophil extracellular traps (NET) comprising of decondensed chromatin that immobilizes and kills pathogens. In vitro generation of neutrophils on a large scale from hematopoietic stem cells (HSCs) may be a useful strategy for treating neutropenic patients in future, though it is not in clinical practice yet. Microbial infections lead to major cause of morbidity and mortality in these patients. Despite the importance of NET in preventing infection, efficacy of in vitro-generated neutrophils from HSCs to form NET is not tested. We show that functional neutrophils could be generated in vitro from HSCs/MNCs isolated from umbilical cord blood (UCB) and apheresis-derived peripheral blood (APBL). Neutrophils generated from UCB showed properties comparable to those isolated from peripheral blood. We also show that isolation of HSCs is not absolutely essential for in vitro neutrophil generation. Further, we show that neutrophils generated from HSCs express PADI4 enzyme and their NET-forming ability is comparable to peripheral blood neutrophils. Taken together, our data show that fully functional neutrophils can be generated in vitro from HSCs. NET-forming ability of in vitro-generated neutrophils is an important parameter to determine their functionality and thus, should be studied along with other standard functional assays.
Collapse
Affiliation(s)
- Rutuja Kuhikar
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Pune 411007, India
| | - Nikhat Khan
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Pune 411007, India
| | - Satyajeet P Khare
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune 412115, India
| | - Amit Fulzele
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093, USA
| | - Sameer Melinkeri
- Blood and Marrow Transplant Unit, Deenanath Mangeshkar Hospital, Erandawne, Pune 411004, India
| | - Vaijayanti Kale
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Pune 411007, India; Symbiosis Centre for Stem Cell Research, Symbiosis School of Biological Sciences, Symbiosis Knowledge Village, Lavale, Pune 412115, India
| | - Lalita Limaye
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Pune 411007, India.
| |
Collapse
|
8
|
Sinha NK, Ordureau A, Best K, Saba JA, Zinshteyn B, Sundaramoorthy E, Fulzele A, Garshott DM, Denk T, Thoms M, Paulo JA, Harper JW, Bennett EJ, Beckmann R, Green R. EDF1 coordinates cellular responses to ribosome collisions. eLife 2020; 9:e58828. [PMID: 32744497 PMCID: PMC7486125 DOI: 10.7554/elife.58828] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/02/2020] [Indexed: 12/11/2022] Open
Abstract
Translation of aberrant mRNAs induces ribosomal collisions, thereby triggering pathways for mRNA and nascent peptide degradation and ribosomal rescue. Here we use sucrose gradient fractionation combined with quantitative proteomics to systematically identify proteins associated with collided ribosomes. This approach identified Endothelial differentiation-related factor 1 (EDF1) as a novel protein recruited to collided ribosomes during translational distress. Cryo-electron microscopic analyses of EDF1 and its yeast homolog Mbf1 revealed a conserved 40S ribosomal subunit binding site at the mRNA entry channel near the collision interface. EDF1 recruits the translational repressors GIGYF2 and EIF4E2 to collided ribosomes to initiate a negative-feedback loop that prevents new ribosomes from translating defective mRNAs. Further, EDF1 regulates an immediate-early transcriptional response to ribosomal collisions. Our results uncover mechanisms through which EDF1 coordinates multiple responses of the ribosome-mediated quality control pathway and provide novel insights into the intersection of ribosome-mediated quality control with global transcriptional regulation.
Collapse
Affiliation(s)
- Niladri K Sinha
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Alban Ordureau
- Department of Cell Biology, Blavatnik Institute of Harvard Medical SchoolBostonUnited States
| | - Katharina Best
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - James A Saba
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Boris Zinshteyn
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Elayanambi Sundaramoorthy
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | - Amit Fulzele
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | - Danielle M Garshott
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | - Timo Denk
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Matthias Thoms
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute of Harvard Medical SchoolBostonUnited States
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute of Harvard Medical SchoolBostonUnited States
| | - Eric J Bennett
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | - Roland Beckmann
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Rachel Green
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| |
Collapse
|
9
|
Lin SJH, Fulzele A, Cohen LB, Bennett EJ, Wasserman SA. Bombardier Enables Delivery of Short-Form Bomanins in the Drosophila Toll Response. Front Immunol 2020; 10:3040. [PMID: 31998316 PMCID: PMC6965162 DOI: 10.3389/fimmu.2019.03040] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/11/2019] [Indexed: 01/17/2023] Open
Abstract
Toll mediates a robust and effective innate immune response across vertebrates and invertebrates. In Drosophila melanogaster, activation of Toll by systemic infection drives the accumulation of a rich repertoire of immune effectors in hemolymph, including the recently characterized Bomanins, as well as the classical antimicrobial peptides (AMPs). Here we report the functional characterization of a Toll-induced hemolymph protein encoded by the bombardier (CG18067) gene. Using the CRISPR/Cas9 system to generate a precise deletion of the bombardier transcriptional unit, we found that Bombardier is required for Toll-mediated defense against fungi and Gram-positive bacteria. Assaying cell-free hemolymph, we found that the Bomanin-dependent candidacidal activity is also dependent on Bombardier, but is independent of the antifungal AMPs Drosomycin and Metchnikowin. Using mass spectrometry, we demonstrated that deletion of bombardier results in the specific absence of short-form Bomanins from hemolymph. In addition, flies lacking Bombardier exhibited a defect in pathogen tolerance that we trace to an aberrant condition triggered by Toll activation. These results lead us to a model in which the presence of Bombardier in wild-type flies enables the proper folding, secretion, or intermolecular associations of short-form Bomanins, and the absence of Bombardier disrupts one or more of these steps, resulting in defects in both immune resistance and tolerance.
Collapse
Affiliation(s)
- Samuel J H Lin
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States
| | - Amit Fulzele
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States
| | - Lianne B Cohen
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States
| | - Eric J Bennett
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States
| | - Steven A Wasserman
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States
| |
Collapse
|
10
|
Markmiller S, Fulzele A, Higgins R, Leonard M, Yeo GW, Bennett EJ. Active Protein Neddylation or Ubiquitylation Is Dispensable for Stress Granule Dynamics. Cell Rep 2019; 27:1356-1363.e3. [PMID: 31042464 PMCID: PMC6508666 DOI: 10.1016/j.celrep.2019.04.015] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 02/26/2019] [Accepted: 04/02/2019] [Indexed: 12/17/2022] Open
Abstract
Stress granule (SG) formation is frequently accompanied by ubiquitin proteasome system (UPS) impairment and ubiquitylated protein accumulation. SGs, ubiquitin, and UPS components co-localize, but the relationship between the ubiquitin pathway and SGs has not been systematically characterized. We utilize pharmacological inhibition of either the ubiquitin- or NEDD8-activating enzyme (UAE or NAE) to probe whether active ubiquitylation or neddylation modulate SG dynamics. We show that UAE inhibition results in rapid loss of global protein ubiquitylation using ubiquitin-specific proteomics. Critically, inhibiting neither UAE nor NAE significantly affected SG formation or disassembly, indicating that active protein ubiquitylation or neddylation is dispensable for SG dynamics. Using antibodies with varying preference for free ubiquitin or polyubiquitin and fluorescently tagged ubiquitin variants in combination with UAE inhibition, we show that SGs co-localize primarily with unconjugated ubiquitin rather than polyubiquitylated proteins. These findings clarify the role of ubiquitin in SG biology and suggest that free ubiquitin may alter SG protein interactions.
Collapse
Affiliation(s)
- Sebastian Markmiller
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Amit Fulzele
- Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Reneé Higgins
- Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Marilyn Leonard
- Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Eric J Bennett
- Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
11
|
Deota S, Rathnachalam S, Namrata K, Boob M, Fulzele A, Radhika S, Ganguli S, Balaji C, Kaypee S, Vishwakarma KK, Kundu TK, Bhandari R, Gonzalez de Peredo A, Mishra M, Venkatramani R, Kolthur-Seetharam U. Allosteric Regulation of Cyclin-B Binding by the Charge State of Catalytic Lysine in CDK1 Is Essential for Cell-Cycle Progression. J Mol Biol 2019; 431:2127-2142. [PMID: 30974121 DOI: 10.1016/j.jmb.2019.04.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 04/03/2019] [Accepted: 04/03/2019] [Indexed: 01/19/2023]
Abstract
Cyclin-dependent kinase 1 (CDK1) is essential for cell-cycle progression. While dependence of CDK activity on cyclin levels is well established, molecular mechanisms that regulate their binding are less understood. Here, we report for the first time that CDK1:cyclin-B binding is not default but rather determined by the evolutionarily conserved catalytic residue, lysine-33 in CDK1. We demonstrate that the charge state of this lysine allosterically remodels the CDK1:cyclin-B interface. Cell cycle-dependent acetylation of lysine-33 or its mutation to glutamine, which mimics acetylation, abrogates cyclin-B binding. Using biochemical approaches and atomistic molecular dynamics simulations, we have uncovered both short-range and long-range effects of perturbing the charged state of the catalytic lysine, which lead to inhibition of kinase activity. Specifically, although loss of the charge state of catalytic lysine did not impact ATP binding significantly, it altered its orientation in the active site. In addition, the catalytic lysine also acts as an intra-molecular electrostatic tether at the active site to orient structural elements interfacing with cyclin-B. Physiologically, opposing activities of SIRT1 and P300 regulate acetylation and thus control the charge state of lysine-33. Importantly, cells expressing acetylation mimic mutant of Cdc2/CDK1 in yeast are arrested in G2 and fail to divide, indicating the requirement of the deacetylated state of the catalytic lysine for cell division. Thus, by illustrating the molecular role of the catalytic lysine and cell cycle-dependent deacetylation as a determinant of CDK1:cyclin-B interaction, our results redefine the current model of CDK1 activation and cell-cycle progression.
Collapse
Affiliation(s)
- Shaunak Deota
- Department of Biological Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Sivasudhan Rathnachalam
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Kanojia Namrata
- Department of Biological Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Mayank Boob
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Amit Fulzele
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Toulouse 31400, France
| | - S Radhika
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Shubhra Ganguli
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad 500039, India; Graduate Studies, Manipal Academy of Higher Education, Manipal 576104, India
| | - Chinthapalli Balaji
- Department of Biological Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Stephanie Kaypee
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru 560064, India
| | - Krishna Kant Vishwakarma
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Tapas Kumar Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru 560064, India
| | - Rashna Bhandari
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad 500039, India
| | | | - Mithilesh Mishra
- Department of Biological Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India.
| | - Ullas Kolthur-Seetharam
- Department of Biological Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai 400005, India.
| |
Collapse
|
12
|
Markmiller S, Soltanieh S, Server KL, Mak R, Jin W, Fang MY, Luo EC, Krach F, Yang D, Sen A, Fulzele A, Wozniak JM, Gonzalez DJ, Kankel MW, Gao FB, Bennett EJ, Lécuyer E, Yeo GW. Context-Dependent and Disease-Specific Diversity in Protein Interactions within Stress Granules. Cell 2019; 172:590-604.e13. [PMID: 29373831 DOI: 10.1016/j.cell.2017.12.032] [Citation(s) in RCA: 529] [Impact Index Per Article: 105.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 10/04/2017] [Accepted: 12/19/2017] [Indexed: 12/14/2022]
Abstract
Stress granules (SGs) are transient ribonucleoprotein (RNP) aggregates that form during cellular stress and are increasingly implicated in human neurodegeneration. To study the proteome and compositional diversity of SGs in different cell types and in the context of neurodegeneration-linked mutations, we used ascorbate peroxidase (APEX) proximity labeling, mass spectrometry, and immunofluorescence to identify ∼150 previously unknown human SG components. A highly integrated, pre-existing SG protein interaction network in unstressed cells facilitates rapid coalescence into larger SGs. Approximately 20% of SG diversity is stress or cell-type dependent, with neuronal SGs displaying a particularly complex repertoire of proteins enriched in chaperones and autophagy factors. Strengthening the link between SGs and neurodegeneration, we demonstrate aberrant dynamics, composition, and subcellular distribution of SGs in cells from amyotrophic lateral sclerosis (ALS) patients. Using three Drosophila ALS/FTD models, we identify SG-associated modifiers of neurotoxicity in vivo. Altogether, our results highlight SG proteins as central to understanding and ultimately targeting neurodegeneration.
Collapse
Affiliation(s)
- Sebastian Markmiller
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92039, USA
| | - Sahar Soltanieh
- Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada
| | - Kari L Server
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92039, USA
| | - Raymond Mak
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wenhao Jin
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Mark Y Fang
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92039, USA
| | - En-Ching Luo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92039, USA
| | - Florian Krach
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92039, USA
| | - Dejun Yang
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Anindya Sen
- Neuromuscular & Movement Disorders, Biogen, Cambridge, MA 02142, USA
| | - Amit Fulzele
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jacob M Wozniak
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mark W Kankel
- Neuromuscular & Movement Disorders, Biogen, Cambridge, MA 02142, USA
| | - Fen-Biao Gao
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Eric J Bennett
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eric Lécuyer
- Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada; Division of Experimental Medicine, McGill University, Montréal, QC H3A 1A3, Canada
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92039, USA; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore; Molecular Engineering Laboratory, A(∗)STAR, Singapore 138673, Singapore.
| |
Collapse
|
13
|
Markmiller S, Soltanieh S, Server KL, Mak R, Jin W, Fang MY, Luo E, Yeo GW, Krach F, Yang D, Sen A, Fulzele A, Wozniak JM, Gonzalez DJ, Kankel MW, Gao F, Bennett EJ, Lécuyer E. Context‐dependent and Disease‐specific Diversity in Stress Granules Formed from Pre‐existing Protein Interactions. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.252.3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sebastian Markmiller
- Stem Cell ProgramUCSDLa JollaCA
- Dept. of Cellular and Molecular Med.UCSDLa JollaCA
- Inst. for Genomic Med.UCSDLa JollaCA
| | | | - Kari L. Server
- Stem Cell ProgramUCSDLa JollaCA
- Dept. of Cellular and Molecular Med.UCSDLa JollaCA
- Inst. for Genomic Med.UCSDLa JollaCA
| | | | - Wenhao Jin
- Dept. of PhysiologyYong Loo Lin Sch. of Med.Nat'l. Univ. of SingaporeSingapore
| | - Mark Y. Fang
- Stem Cell ProgramUCSDLa JollaCA
- Dept. of Cellular and Molecular Med.UCSDLa JollaCA
- Inst. for Genomic Med.UCSDLa JollaCA
| | - En‐Ching Luo
- Stem Cell ProgramUCSDLa JollaCA
- Dept. of Cellular and Molecular Med.UCSDLa JollaCA
- Inst. for Genomic Med.UCSDLa JollaCA
| | - Gene W. Yeo
- Stem Cell ProgramUCSDLa JollaCA
- Dept. of Cellular and Molecular Med.UCSDLa JollaCA
- Dept. of PhysiologyYong Loo Lin Sch. of Med.Nat'l. Univ. of SingaporeSingaporeSingapore
- Molecular Engineering Lab.A*STARSingaporeSingapore
- Inst. for Genomic Med.UCSDLa JollaCA
| | - Florian Krach
- Stem Cell ProgramUCSDLa JollaCA
- Dept. of Cellular and Molecular Med.UCSDLa JollaCA
- Inst. for Genomic Med.UCSDLa JollaCA
| | - Dejun Yang
- Dept. of NeurologyUniv. of Mass. Med. Sch.WorcesterMA
| | - Anindya Sen
- Neurodegeneration and RepairBiogenCambridgeMA
| | | | - Jacob M. Wozniak
- Skaggs Sch. of Pharmacy and Pharmaceutical Sciences, UCSDLa JollaCA
- Dept. of PharmacologyUCSDLa JollaCA
| | - David J. Gonzalez
- Skaggs Sch. of Pharmacy and Pharmaceutical Sciences, UCSDLa JollaCA
- Dept. of PharmacologyUCSDLa JollaCA
| | | | - Fen‐Biao Gao
- Dept. of NeurologyUniv. of Mass. Med. Sch.WorcesterMA
| | | | - Eric Lécuyer
- Dept. de Biochimie et Médecine MoléculaireUniv. de MontréalMontréalQCCanada
- Div. of Experimental Med.McGill Univ.MontréalQCCanada
- Inst. de Recherches Cliniques de MontréalMontréalQCCanada
| |
Collapse
|
14
|
Abstract
Protein ubiquitylation is one of the most prevalent posttranslational modifications (PTM) within cells. Ubiquitin modification of target lysine residues typically marks substrates for proteasome-dependent degradation. However, ubiquitylation can also alter protein function through modulation of protein complexes, localization, or activity, without impacting protein turnover. Taken together, ubiquitylation imparts critical regulatory control over nearly every cellular, physiological, and pathophysiological process. Affinity purification techniques coupled with quantitative mass spectrometry have been robust tools to identify PTMs on endogenous proteins. A peptide antibody-based affinity approach has been successfully utilized to enrich for and identify endogenously ubiquitylated proteins. These antibodies recognize the Lys-ϵ-Gly-Gly (diGLY) remnant that is generated following trypsin digestion of ubiquitylated proteins, and these peptides can then be identified by standard mass spectrometry approaches. This technique has led to the identification of >50,000 ubiquitylation sites in human cells and quantitative information about how many of these sites are altered upon exposure to diverse proteotoxic stressors. In addition, the diGLY proteomics approach has led to the identification of specific ubiquitin ligase targets. Here we provide a detailed method to interrogate the ubiquitin-modified proteome from any eukaryotic organism or tissue.
Collapse
Affiliation(s)
- Amit Fulzele
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Eric J Bennett
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
15
|
Deota S, Chattopadhyay T, Ramachandran D, Armstrong E, Camacho B, Maniyadath B, Fulzele A, Gonzalez-de-Peredo A, Denu JM, Kolthur-Seetharam U. Identification of a Tissue-Restricted Isoform of SIRT1 Defines a Regulatory Domain that Encodes Specificity. Cell Rep 2017; 18:3069-3077. [PMID: 28355560 DOI: 10.1016/j.celrep.2017.03.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 01/26/2017] [Accepted: 03/01/2017] [Indexed: 11/26/2022] Open
Abstract
The conserved NAD+-dependent deacylase SIRT1 plays pivotal, sometimes contrasting, roles in diverse physiological and pathophysiological conditions. In this study, we uncover a tissue-restricted isoform of SIRT1 (SIRT1-ΔE2) that lacks exon 2 (E2). Candidate-based screening of SIRT1 substrates demonstrated that the domain encoded by this exon plays a key role in specifying SIRT1 protein-protein interactions. The E2 domain of SIRT1 was both necessary and sufficient for PGC1α binding, enhanced interaction with p53, and thus downstream functions. Since SIRT1-FL and SIRT1-ΔE2 were found to have similar intrinsic catalytic activities, we propose that the E2 domain tethers specific substrate proteins. Given the absence of SIRT1-ΔE2 in liver, our findings provide insight into the role of the E2 domain in specifying "metabolic functions" of SIRT1-FL. Identification of SIRT1-ΔE2 and the conserved specificity domain will enhance our understanding of SIRT1 and guide the development of therapeutic interventions.
Collapse
Affiliation(s)
- Shaunak Deota
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Tandrika Chattopadhyay
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Deepti Ramachandran
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Eric Armstrong
- Wisconsin Institute for Discovery and Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, UW-Madison, Madison, WI 53715, USA
| | - Beatriz Camacho
- Wisconsin Institute for Discovery and Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, UW-Madison, Madison, WI 53715, USA
| | - Babukrishna Maniyadath
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Amit Fulzele
- Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS - UMR 5089, Toulouse 31077, France
| | - Anne Gonzalez-de-Peredo
- Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS - UMR 5089, Toulouse 31077, France
| | - John M Denu
- Wisconsin Institute for Discovery and Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, UW-Madison, Madison, WI 53715, USA
| | - Ullas Kolthur-Seetharam
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India.
| |
Collapse
|
16
|
Fulzele A, Malgundkar SA, Govekar RB, Patil A, Kane SV, Chaturvedi P, D'Cruz AK, Zingde SM. Proteomic profile of keratins in cancer of the gingivo buccal complex: consolidating insights for clinical applications. J Proteomics 2013; 91:242-58. [PMID: 23876858 DOI: 10.1016/j.jprot.2013.07.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 06/27/2013] [Accepted: 07/07/2013] [Indexed: 12/18/2022]
Abstract
UNLABELLED Keratins play a major role in several cellular functions. Each tissue type expresses a specific set of keratins. The immense potential of keratins as diagnostic and prognostic markers for different cancers is emerging. Oral cancer is the fifteenth most common cancer worldwide. However, comprehensive information on the profile of keratins in the oral cavity is not available. Several independent reports have identified keratins using antibody based techniques which have pitfalls due to the cross reactivity of the antibodies to this set of very homologous proteins. A few recent proteomic studies have reported the identification of keratins in head and neck cancer. Majority of the studies have used tissues from the head and neck region without specifying subsites. This study reports the analysis of enriched preparations of keratins from cancer of the gingivo buccal complex (GBC) using MS, 2DE, WB, silver staining of 2DE gels and IHC. Our study reveals the absence of K4 and K13 and presence of K14, K16, and K17, in cancers of the GBC and combination of these expression patterns in the cut margins. This report also shows that K13 is glycosylated. This well characterized profile of keratins may have potential to be used in clinics. BIOLOGICAL SIGNIFICANCE In recent years the immense potential of keratins as diagnostic and prognostic markers for different cancers is emerging. However, comprehensive information on the profile of keratins in the oral cavity is not available. Several independent reports have identified keratins using only antibody based techniques which have pitfalls due to the cross reactivity of the antibodies to this set of very homologous proteins. This study reports the analysis of enriched preparations of keratins from a subsite of the oral cavity, the gingivo buccal complex (GBC) using mass spectrometry, 2DE, western blotting, silver staining of 2DE gels and IHC. The proteomic analysis shows the absence of K4 and K13 and presence of K14, K16, and K17 in cancers of the GBC and combination of these expression patterns in the cut margins. This well characterized profile of keratins from the gingivo buccal complex provides defined markers which may have potential to be used in the clinics.
Collapse
Affiliation(s)
- Amit Fulzele
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi-Mumbai, 410210, India
| | | | | | | | | | | | | | | |
Collapse
|
17
|
Fulzele A, Malgundkar SA, Govekar RB, D'Cruz AK, Chaturvedi P, Patil A, Kane SV, Zingde SM. Keratins in oral cancer: necessity of mass spectrometry for validation of antibody based identifications. J Proteomics 2012; 75:2404-16. [PMID: 22387131 DOI: 10.1016/j.jprot.2012.02.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 01/31/2012] [Accepted: 02/15/2012] [Indexed: 11/30/2022]
Abstract
Keratins are intermediate filament family proteins which are predominantly expressed in the epithelial cells. Most of the studies which evaluate the status of keratins in clinical samples of the oral cavity are based on the identification of their presence and localization by immunohistochemistry using monoclonal antibodies. It is very well known that many monoclonal/polyclonal antibodies show cross-reactivity with the other closely related or non-related proteins. This cross-reactivity might be the result of epitope similarity, but it is not always necessary. Therefore studies done with only antibody based techniques can mislead interpretation unless they are validated with additional techniques like mass-spectrometry. In this investigation we have evaluated the status of keratin 18 in cancer of buccal mucosa using 1DE, 2DE and western blotting with monoclonal antibody to keratin 18. The patterns emerging showed aberrant as well as differential expression of K18 in adjacent normal versus tumor tissue samples of buccal mucosa. Mass spectrometry analysis of the immunodetected spots however revealed that it is keratin 13. Thus this study emphasizes the necessity of validation of antibody based findings when dealing with proteins of a large family having similarity/homology in amino acid sequence.
Collapse
Affiliation(s)
- Amit Fulzele
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi-Mumbai, 410210, India
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Singh G, Singhal RK, Malav RK, Fulzele A, Prakash A, Afzal M, Panakkal JP. A comparative study on dissolution rate of sintered (Th-U)O 2 pellets in by microwave and conventional heating. Anal Methods 2011; 3:622-627. [PMID: 32938082 DOI: 10.1039/c0ay00630k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
ThO2 with approximately 3% 233UO2 is the proposed fuel for the Advanced Heavy Water Reactor (AHWR) and characterized as a mixed oxide (MOX) fuel. Due to the existence of a single oxidation state, quantitative dissolution of MOX samples like (Th-U)O2 and (Th-Pu)O2 is a challenging task for any analytical chemist. However, dissolution is a pre-requisite for complete characterization of the fuel. The present paper describes a detailed study carried out on the comparison of dissolution of sintered (Th-U)O2 mixed oxide pellets, in 16 M HNO3 using microwave and conventional heating techniques, under reflux conditions. The study was carried out with variation of parameters such as concentration of HF and UO2 substitution in the MOX solid solution. The concentration of dissolved U and Th was determined by modified Davies and Gray potentiometric titration and Th-EDTA complexometric titration using xylenol orange as the titration end point indicator respectively. Experimental results clearly indicate that the microwave heating assisted dissolution rate is 2 to 3 times higher than the conventional infrared heating assisted dissolution rate, for sintered pellets. The concentration of HF is a critical parameter, an excess leads to precipitation of insoluble ThF4. The concentration of HF was optimized to 0.025 M. Experimental results also clearly show that at this concentration of HF in 16 M HNO3, a higher substitution of UO2 in MOX solid solution also facilitates the dissolution process. Different trace metal impurities were determined in the MOX samples after dissolving by microwave and infra red heating techniques and it was observed that the results are comparable.
Collapse
Affiliation(s)
- G Singh
- Advanced Fuel Fabrication Facility, BARC, Tarapur, 401502, India.
| | - R K Singhal
- Advanced Fuel Fabrication Facility, BARC, Tarapur, 401502, India.
- Analytical Chemistry Division BARC, Mumbai, 400084, India
| | - R K Malav
- Advanced Fuel Fabrication Facility, BARC, Tarapur, 401502, India.
| | - A Fulzele
- Advanced Fuel Fabrication Facility, BARC, Tarapur, 401502, India.
| | - A Prakash
- Advanced Fuel Fabrication Facility, BARC, Tarapur, 401502, India.
| | - Md Afzal
- Advanced Fuel Fabrication Facility, BARC, Tarapur, 401502, India.
| | - J P Panakkal
- Advanced Fuel Fabrication Facility, BARC, Tarapur, 401502, India.
| |
Collapse
|