1
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Holtz AG, Lowe TL, Aoki Y, Kubota Y, Hoffman RM, Clarke SG. Asymmetric and symmetric protein arginine methylation in methionine-addicted human cancer cells. PLoS One 2023; 18:e0296291. [PMID: 38134182 PMCID: PMC10745221 DOI: 10.1371/journal.pone.0296291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The methionine addiction of cancer cells is known as the Hoffman effect. While non-cancer cells in culture can utilize homocysteine in place of methionine for cellular growth, most cancer cells require exogenous methionine for proliferation. It has been suggested that a biochemical basis of this effect is the increased utilization of methionine for S-adenosylmethionine, the major methyl donor for a variety of cellular methyltransferases. Recent studies have pointed to the role of S-adenosylmethionine-dependent protein arginine methyltransferases (PRMTs) in cell proliferation and cancer. To further understand the biochemical basis of the methionine addiction of cancer cells, we compared protein arginine methylation in two previously described isogenic cell lines, a methionine-addicted 143B human osteosarcoma cell line and its less methionine-dependent revertant. Previous work showed that the revertant cells were significantly less malignant than the parental cells. In the present study, we utilized antibodies to detect the asymmetric dimethylarginine (ADMA) and symmetric dimethylarginine (SDMA) products of PRMTs in polypeptides from cellular extracts and purified histone preparations of these cell lines fractionated by SDS-PAGE. Importantly, we observed little to no differences in the banding patterns of ADMA- and SDMA-containing species between the osteosarcoma parental and revertant cell lines. Furthermore, enzymatic activity assays using S-adenosyl-ʟ-[methyl-3H] methionine, recombinantly purified PRMT enzymes, cell lysates, and specific PRMT inhibitors revealed no major differences in radiolabeled polypeptides on SDS-PAGE gels. Taken together, these results suggest that changes in protein arginine methylation may not be major contributors to the Hoffman effect and that other consequences of methionine addiction may be more important in the metastasis and malignancy of osteosarcoma and potentially other cancers.
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Affiliation(s)
- Ashley G Holtz
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Troy L Lowe
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Yusuke Aoki
- AntiCancer, Inc, San Diego, CA, United States of America
- Department of Surgery, University of California, San Diego, La Jolla, CA, United States of America
- Department of Orthopedic Surgery, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Yutaro Kubota
- AntiCancer, Inc, San Diego, CA, United States of America
- Department of Surgery, University of California, San Diego, La Jolla, CA, United States of America
| | - Robert M Hoffman
- AntiCancer, Inc, San Diego, CA, United States of America
- Department of Surgery, University of California, San Diego, La Jolla, CA, United States of America
| | - Steven G Clarke
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States of America
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2
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Yang ML, Lam TT, Kanyo J, Kang I, Zhou ZS, Clarke SG, Mamula MJ. Natural isoaspartyl protein modification of ZAP70 alters T cell responses in lupus. Autoimmunity 2023; 56:2282945. [PMID: 37994408 PMCID: PMC10897934 DOI: 10.1080/08916934.2023.2282945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 11/08/2023] [Indexed: 11/24/2023]
Abstract
Protein posttranslational modifications (PTMs) arise in a number of normal cellular biological pathways and in response to pathology caused by inflammation and/or infection. Indeed, a number of PTMs have been identified and linked to specific autoimmune responses and metabolic pathways. One particular PTM, termed isoaspartyl (isoAsp or isoD) modification, is among the most common spontaneous PTM occurring at physiological pH and temperature. Herein, we demonstrate that isoAsp modifications arise within the ZAP70 protein tyrosine kinase upon T-cell antigen receptor (TCR) engagement. The enzyme protein L-isoaspartate O-methyltransferase (PCMT1, or PIMT, EC 2.1.1.77) evolved to repair isoaspartyl modifications in cells. In this regard, we observe that increased levels of isoAsp modification that arise under oxidative stress are correlated with reduced PIMT activity in patients with systemic lupus erythematosus (SLE). PIMT deficiency leads to T cell hyper-proliferation and hyper-phosphorylation through ZAP70 signaling. We demonstrate that inducing the overexpression of PIMT can correct the hyper-responsive phenotype in lupus T cells. Our studies reveal a phenotypic role of isoAsp modification and phosphorylation of ZAP70 in lupus T cell autoimmunity and provide a potential therapeutic target through the repair of isoAsp modification.
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Affiliation(s)
- Mei-Ling Yang
- Section of Rheumatology, Allergy and Immunology, Department of Internal Medicine, Yale University, New Haven, CT, USA
| | - TuKiet T. Lam
- Keck MS & Proteomics Resource, WM Keck Foundation Biotechnology Resource Laboratory, New Haven, CT, USA
- Department of Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jean Kanyo
- Keck MS & Proteomics Resource, WM Keck Foundation Biotechnology Resource Laboratory, New Haven, CT, USA
| | - Insoo Kang
- Section of Rheumatology, Allergy and Immunology, Department of Internal Medicine, Yale University, New Haven, CT, USA
| | - Zhaohui Sunny Zhou
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Steven G. Clarke
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, CA, USA
| | - Mark J. Mamula
- Section of Rheumatology, Allergy and Immunology, Department of Internal Medicine, Yale University, New Haven, CT, USA
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3
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Feoli A, Iannelli G, Cipriano A, Milite C, Shen L, Wang Z, Hadjikyriacou A, Lowe TL, Safaeipour C, Viviano M, Sarno G, Morretta E, Monti MC, Yang Y, Clarke SG, Cosconati S, Castellano S, Sbardella G. Identification of a Protein Arginine Methyltransferase 7 (PRMT7)/Protein Arginine Methyltransferase 9 (PRMT9) Inhibitor. J Med Chem 2023; 66:13665-13683. [PMID: 37560786 PMCID: PMC10578352 DOI: 10.1021/acs.jmedchem.3c01030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Indexed: 08/11/2023]
Abstract
Less studied than the other protein arginine methyltransferase isoforms, PRMT7 and PRMT9 have recently been identified as important therapeutic targets. Yet, most of their biological roles and functions are still to be defined, as well as the structural requirements that could drive the identification of selective modulators of their activity. We recently described the structural requirements that led to the identification of potent and selective PRMT4 inhibitors spanning both the substrate and the cosubstrate pockets. The reanalysis of the data suggested a PRMT7 preferential binding for shorter derivatives and prompted us to extend these structural studies to PRMT9. Here, we report the identification of the first potent PRMT7/9 inhibitor and its binding mode to the two PRMT enzymes. Label-free quantification mass spectrometry confirmed significant inhibition of PRMT activity in cells. We also report the setup of an effective AlphaLISA assay to screen small molecule inhibitors of PRMT9.
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Affiliation(s)
- Alessandra Feoli
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Giulia Iannelli
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
- PhD
Program in Drug Discovery and Development, University of Salerno, via Giovanni Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Alessandra Cipriano
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Ciro Milite
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Lei Shen
- Department
of Cancer Genetics and Epigenetics, Beckman
Research Institute, City of Hope National Cancer Center, Duarte, California 91010, United States
| | - Zhihao Wang
- Department
of Cancer Genetics and Epigenetics, Beckman
Research Institute, City of Hope National Cancer Center, Duarte, California 91010, United States
| | - Andrea Hadjikyriacou
- Department
of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
| | - Troy L. Lowe
- Department
of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
| | - Cyrus Safaeipour
- Department
of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
| | - Monica Viviano
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Giuliana Sarno
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
- PhD
Program in Drug Discovery and Development, University of Salerno, via Giovanni Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Elva Morretta
- Department
of Pharmacy, ProteoMass Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Maria Chiara Monti
- Department
of Pharmacy, ProteoMass Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Yanzhong Yang
- Department
of Cancer Genetics and Epigenetics, Beckman
Research Institute, City of Hope National Cancer Center, Duarte, California 91010, United States
| | - Steven G. Clarke
- Department
of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
| | - Sandro Cosconati
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Sabrina Castellano
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Gianluca Sbardella
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
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4
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Bondoc TJ, Lowe TL, Clarke SG. The exquisite specificity of human protein arginine methyltransferase 7 (PRMT7) toward Arg-X-Arg sites. PLoS One 2023; 18:e0285812. [PMID: 37216364 DOI: 10.1371/journal.pone.0285812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/01/2023] [Indexed: 05/24/2023] Open
Abstract
Mammalian protein arginine methyltransferase 7 (PRMT7) has been shown to target substrates with motifs containing two arginine residues separated by one other residue (RXR motifs). In particular, the repression domain of human histone H2B (29-RKRSR-33) has been a key substrate in determining PRMT7 activity. We show that incubating human PRMT7 and [3H]-AdoMet with full-length Xenopus laevis histone H2B, containing the substitutions K30R and R31K (RKRSR to RRKSR), results in greatly reduced methylation activity. Using synthetic peptides, we have now focused on the enzymology behind this specificity. We show for the human and Xenopus peptide sequences 23-37 the difference in activity results from changes in the Vmax rather than the apparent binding affinity of the enzyme for the substrates. We then characterized six additional peptides containing a single arginine or a pair of arginine residues flanked by glycine and lysine residues. We have corroborated previous findings that peptides with an RXR motif have much higher activity than peptides that contain only one Arg residue. We show that these peptides have similar apparent km values but significant differences in their Vmax values. Finally, we have examined the effect of ionic strength on these peptides. We found the inclusion of salt had little effect on the Vmax value but a considerable increase in the apparent km value, suggesting that the inhibitory effect of ionic strength on PRMT7 activity occurs largely by decreasing apparent substrate-enzyme binding affinity. In summary, we find that even subtle substitutions in the RXR recognition motif can dramatically affect PRMT7 catalysis.
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Affiliation(s)
- Timothy J Bondoc
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Troy L Lowe
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
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5
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Aoki Y, Han Q, Tome Y, Yamamoto J, Kubota Y, Masaki N, Obara K, Hamada K, Wang JD, Inubushi S, Bouvet M, Clarke SG, Nishida K, Hoffman RM. Reversion of methionine addiction of osteosarcoma cells to methionine independence results in loss of malignancy, modulation of the epithelial-mesenchymal phenotype and alteration of histone-H3 lysine-methylation. Front Oncol 2022; 12:1009548. [PMID: 36408173 PMCID: PMC9671209 DOI: 10.3389/fonc.2022.1009548] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 08/02/2022] [Accepted: 10/19/2022] [Indexed: 02/01/2024] Open
Abstract
Methionine addiction, a fundamental and general hallmark of cancer, known as the Hoffman Effect, is due to altered use of methionine for increased and aberrant transmethylation reactions. However, the linkage of methionine addiction and malignancy of cancer cells is incompletely understood. An isogenic pair of methionine-addicted parental osteosarcoma cells and their rare methionine-independent revertant cells enabled us to compare them for malignancy, their epithelial-mesenchymal phenotype, and pattern of histone-H3 lysine-methylation. Methionine-independent revertant 143B osteosarcoma cells (143B-R) were selected from methionine-addicted parental cells (143B-P) by their chronic growth in low-methionine culture medium for 4 passages, which was depleted of methionine by recombinant methioninase (rMETase). Cell-migration capacity was compared with a wound-healing assay and invasion capability was compared with a transwell assay in 143B-P and 143B-R cells in vitro. Tumor growth and metastatic potential were compared after orthotopic cell-injection into the tibia bone of nude mice in vivo. Epithelial-mesenchymal phenotypic expression and the status of H3 lysine-methylation were determined with western immunoblotting. 143B-P cells had an IC50 of 0.20 U/ml and 143B-R cells had an IC50 of 0.68 U/ml for treatment with rMETase, demonstrating that 143B-R cells had regained the ability to grow in low methionine conditions. 143B-R cells had reduced cell migration and invasion capability in vitro, formed much smaller tumors than 143B-P cells and lost metastatic potential in vivo, indicating loss of malignancy in 143B-R cells. 143B-R cells showed gain of the epithelial marker, ZO-1 and loss of mesenchymal markers, vimentin, Snail, and Slug and, an increase of histone H3K9me3 and H3K27me3 methylation and a decrease of H3K4me3, H3K36me3, and H3K79me3 methylation, along with their loss of malignancy. These results suggest that shifting the balance in histone methylases might be a way to decrease the malignant potential of cells. The present results demonstrate the rationale to target methionine addiction for improved sarcoma therapy.
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Affiliation(s)
- Yusuke Aoki
- AntiCancer Inc, San Diego, CA, United States
- Department of Surgery, University of California San Diego, La Jolla, CA, United States
- Department of Orthopedic Surgery, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | | | - Yasunori Tome
- Department of Orthopedic Surgery, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Jun Yamamoto
- AntiCancer Inc, San Diego, CA, United States
- Department of Surgery, University of California San Diego, La Jolla, CA, United States
| | - Yutaro Kubota
- AntiCancer Inc, San Diego, CA, United States
- Department of Surgery, University of California San Diego, La Jolla, CA, United States
| | - Noriyuki Masaki
- AntiCancer Inc, San Diego, CA, United States
- Department of Surgery, University of California San Diego, La Jolla, CA, United States
| | - Koya Obara
- AntiCancer Inc, San Diego, CA, United States
- Department of Surgery, University of California San Diego, La Jolla, CA, United States
| | - Kazuyuki Hamada
- AntiCancer Inc, San Diego, CA, United States
- Department of Surgery, University of California San Diego, La Jolla, CA, United States
| | - Justin D. Wang
- School of Medicine, California University of Science and Medicine, Colton, CA, United States
| | | | - Michael Bouvet
- Department of Surgery, University of California San Diego, La Jolla, CA, United States
| | - Steven G. Clarke
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, United States
| | - Kotaro Nishida
- Department of Orthopedic Surgery, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Robert M. Hoffman
- AntiCancer Inc, San Diego, CA, United States
- Department of Surgery, University of California San Diego, La Jolla, CA, United States
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6
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Yang ML, Connolly SE, Gee RJ, Lam TT, Kanyo J, Peng J, Guyer P, Syed F, Tse HM, Clarke SG, Clarke CF, James EA, Speake C, Evans-Molina C, Arvan P, Herold KC, Wen L, Mamula MJ. Carbonyl Posttranslational Modification Associated With Early-Onset Type 1 Diabetes Autoimmunity. Diabetes 2022; 71:1979-1993. [PMID: 35730902 PMCID: PMC9450849 DOI: 10.2337/db21-0989] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 06/15/2022] [Indexed: 11/13/2022]
Abstract
Inflammation and oxidative stress in pancreatic islets amplify the appearance of various posttranslational modifications to self-proteins. In this study, we identified a select group of carbonylated islet proteins arising before the onset of hyperglycemia in NOD mice. Of interest, we identified carbonyl modification of the prolyl-4-hydroxylase β subunit (P4Hb) that is responsible for proinsulin folding and trafficking as an autoantigen in both human and murine type 1 diabetes. We found that carbonylated P4Hb is amplified in stressed islets coincident with decreased glucose-stimulated insulin secretion and altered proinsulin-to-insulin ratios. Autoantibodies against P4Hb were detected in prediabetic NOD mice and in early human type 1 diabetes prior to the onset of anti-insulin autoimmunity. Moreover, we identify autoreactive CD4+ T-cell responses toward carbonyl-P4Hb epitopes in the circulation of patients with type 1 diabetes. Our studies provide mechanistic insight into the pathways of proinsulin metabolism and in creating autoantigenic forms of insulin in type 1 diabetes.
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Affiliation(s)
- Mei-Ling Yang
- Section of Rheumatology, Allergy and Immunology, Department of Internal Medicine, Yale University, New Haven, CT
| | - Sean E. Connolly
- Section of Rheumatology, Allergy and Immunology, Department of Internal Medicine, Yale University, New Haven, CT
| | - Renelle J. Gee
- Section of Rheumatology, Allergy and Immunology, Department of Internal Medicine, Yale University, New Haven, CT
| | - TuKiet T. Lam
- Mass Spectrometry & Proteomics Resource, W.M. Keck Foundation Biotechnology Resource Laboratory, New Haven
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Jean Kanyo
- Mass Spectrometry & Proteomics Resource, W.M. Keck Foundation Biotechnology Resource Laboratory, New Haven
| | - Jian Peng
- Section of Endocrinology, Department of Internal Medicine, Yale University, New Haven, CT
| | - Perrin Guyer
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA
| | - Farooq Syed
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
| | - Hubert M. Tse
- Department of Microbiology, Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL
| | - Steven G. Clarke
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA
| | - Catherine F. Clarke
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA
| | - Eddie A. James
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA
| | - Cate Speake
- Center for Interventional Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA
| | - Carmella Evans-Molina
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
| | - Peter Arvan
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Kevan C. Herold
- Section of Endocrinology, Department of Internal Medicine, Yale University, New Haven, CT
- Department of Immunobiology, Yale University, New Haven, CT
| | - Li Wen
- Section of Endocrinology, Department of Internal Medicine, Yale University, New Haven, CT
| | - Mark J. Mamula
- Section of Rheumatology, Allergy and Immunology, Department of Internal Medicine, Yale University, New Haven, CT
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7
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Warmack RA, Pang EZ, Peluso E, Lowenson JD, Ong JY, Torres JZ, Clarke SG. Human Protein-l-isoaspartate O-Methyltransferase Domain-Containing Protein 1 (PCMTD1) Associates with Cullin-RING Ligase Proteins. Biochemistry 2022; 61:879-894. [PMID: 35486881 PMCID: PMC9875861 DOI: 10.1021/acs.biochem.2c00130] [Citation(s) in RCA: 1] [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] [Indexed: 01/27/2023]
Abstract
The spontaneous l-isoaspartate protein modification has been observed to negatively affect protein function. However, this modification can be reversed in many proteins in reactions initiated by the protein-l-isoaspartyl (d-aspartyl) O-methyltransferase (PCMT1). It has been hypothesized that an additional mechanism exists in which l-isoaspartate-damaged proteins are recognized and proteolytically degraded. Herein, we describe the protein-l-isoaspartate O-methyltransferase domain-containing protein 1 (PCMTD1) as a putative E3 ubiquitin ligase substrate adaptor protein. The N-terminal domain of PCMTD1 contains l-isoaspartate and S-adenosylmethionine (AdoMet) binding motifs similar to those in PCMT1. This protein also has a C-terminal domain containing suppressor of cytokine signaling (SOCS) box ubiquitin ligase recruitment motifs found in substrate receptor proteins of the Cullin-RING E3 ubiquitin ligases. We demonstrate specific PCMTD1 binding to the canonical methyltransferase cofactor S-adenosylmethionine (AdoMet). Strikingly, while PCMTD1 is able to bind AdoMet, it does not demonstrate any l-isoaspartyl methyltransferase activity under the conditions tested here. However, this protein is able to associate with the Cullin-RING proteins Elongins B and C and Cul5 in vitro and in human cells. The previously uncharacterized PCMTD1 protein may therefore provide an alternate maintenance pathway for modified proteins in mammalian cells by acting as an E3 ubiquitin ligase adaptor protein.
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Affiliation(s)
- Rebeccah A Warmack
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Eric Z Pang
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Esther Peluso
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Jonathan D Lowenson
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Joseph Y Ong
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Jorge Z Torres
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
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8
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Yamamoto J, Inubushi S, Han Q, Tashiro Y, Sugisawa N, Hamada K, Aoki Y, Miyake K, Matsuyama R, Bouvet M, Clarke SG, Endo I, Hoffman RM. Linkage of methionine addiction, histone lysine hypermethylation, and malignancy. iScience 2022; 25:104162. [PMID: 35434545 PMCID: PMC9010622 DOI: 10.1016/j.isci.2022.104162] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/19/2022] [Accepted: 03/23/2022] [Indexed: 11/25/2022] Open
Abstract
Methionine addiction, found in all types of cancer investigated, is because of the overuse of methionine by cancer cells for excess transmethylation reactions. In the present study, we compared the histone H3 lysine-methylation status and degree of malignancy between methionine-addicted cancer cells and their isogenic methionine-independent revertants, selected by their growth in low concentration of methionine. The methionine-independent revertans can grow on low levels of methionine or independently of exogenous methionine using methionine precursors, as do normal cells. In the methionine-independent revertants, the excess levels of trimethylated histone H3 lysine marks found in the methionine-addicted parental cancer cells were reduced or lost, and their tumorigenicity and experimental metastatic potential in nude mice were also highly reduced. Methionine addiction of cancer is linked with malignancy and hypermethylation of histone H3 lysines. The results of the present study thus provide a unique framework to further understand a fundamental basis of malignancy. Methionine(MET)-independent revertants were selected from MET-addicted cancer cells MET-independent revertants had greatly reduced malignancy MET-independent revertants have lost or reduced methylation of H3 lysine marks MET addiction, malignancy, and hypermethylated H3 lysine marks are linked
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Affiliation(s)
- Jun Yamamoto
- AntiCancer Inc, 7917 Ostrow St, San Diego, CA 92111, USA.,Department of Surgery, University of California, San Diego, 9300 Campus Point Drive #7220, La Jolla, CA 92037-7220, USA.,Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Sachiko Inubushi
- AntiCancer Inc, 7917 Ostrow St, San Diego, CA 92111, USA.,Department of Surgery, University of California, San Diego, 9300 Campus Point Drive #7220, La Jolla, CA 92037-7220, USA
| | - Qinghong Han
- AntiCancer Inc, 7917 Ostrow St, San Diego, CA 92111, USA
| | - Yoshihiko Tashiro
- AntiCancer Inc, 7917 Ostrow St, San Diego, CA 92111, USA.,Department of Surgery, University of California, San Diego, 9300 Campus Point Drive #7220, La Jolla, CA 92037-7220, USA
| | - Norihiko Sugisawa
- AntiCancer Inc, 7917 Ostrow St, San Diego, CA 92111, USA.,Department of Surgery, University of California, San Diego, 9300 Campus Point Drive #7220, La Jolla, CA 92037-7220, USA
| | - Kazuyuki Hamada
- AntiCancer Inc, 7917 Ostrow St, San Diego, CA 92111, USA.,Department of Surgery, University of California, San Diego, 9300 Campus Point Drive #7220, La Jolla, CA 92037-7220, USA
| | - Yusuke Aoki
- AntiCancer Inc, 7917 Ostrow St, San Diego, CA 92111, USA.,Department of Surgery, University of California, San Diego, 9300 Campus Point Drive #7220, La Jolla, CA 92037-7220, USA
| | - Kentaro Miyake
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Ryusei Matsuyama
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Michael Bouvet
- Department of Surgery, University of California, San Diego, 9300 Campus Point Drive #7220, La Jolla, CA 92037-7220, USA
| | - Steven G Clarke
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Robert M Hoffman
- AntiCancer Inc, 7917 Ostrow St, San Diego, CA 92111, USA.,Department of Surgery, University of California, San Diego, 9300 Campus Point Drive #7220, La Jolla, CA 92037-7220, USA
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9
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Yamamoto J, Aoki Y, Inubushi S, Han Q, Hamada K, Tashiro Y, Miyake K, Matsuyama R, Bouvet M, Clarke SG, Endo I, Hoffman RM. Extent and Instability of Trimethylation of Histone H3 Lysine Increases With Degree of Malignancy and Methionine Addiction. Cancer Genomics Proteomics 2021; 19:12-18. [PMID: 34949655 DOI: 10.21873/cgp.20299] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/23/2021] [Accepted: 11/30/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND/AIM Methionine addiction is a fundamental and general hallmark of cancer, termed the Hoffman effect. Methionine addiction is due to excessive use of and dependence on methionine by cancer cells. In the present report, we correlated the extent of methionine addiction and degree of malignancy with the amount and stability of methylated histone H3 lysine marks. MATERIALS AND METHODS We established low- and high-malignancy variants from a parental human pancreatic-cancer cell line and compared their sensitivity to methionine restriction and histone H3 lysine methylation status. RESULTS A low-malignancy, low-methionine-addiction revertant of the parental pancreatic-cancer cell line had less methylated H3K9me3 and was less sensitive to methionine restriction effected by recombinant methioninase (rMETase) than the parental cell line. A high-malignancy variant of the pancreatic cancer cell line had increased methylated H3K9me3 and was more sensitive to methionine restriction by rMETase with regard to inhibition of proliferation and to instability of histone H3 lysine methylation than the parental cell line. Orthotopic malignancy in nude mice was reduced in the low-methionine-addiction revertant and greater in the high-malignancy variant than in the parental cell line. CONCLUSION The present study indicates that the degree of malignancy is linked to the extent of methionine addiction and the level and instability of trimethylation of histone H3, suggesting these phenomena are linked as a fundamental basis of oncogenic transformation.
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Affiliation(s)
- Jun Yamamoto
- AntiCancer Inc., San Diego, CA, U.S.A.; .,Department of Surgery, University of California, San Diego, La Jolla, CA, U.S.A.,Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yusuke Aoki
- AntiCancer Inc., San Diego, CA, U.S.A.,Department of Surgery, University of California, San Diego, La Jolla, CA, U.S.A
| | - Sachiko Inubushi
- AntiCancer Inc., San Diego, CA, U.S.A.,Department of Surgery, University of California, San Diego, La Jolla, CA, U.S.A
| | | | - Kazuyuki Hamada
- AntiCancer Inc., San Diego, CA, U.S.A.,Department of Surgery, University of California, San Diego, La Jolla, CA, U.S.A
| | - Yoshihiko Tashiro
- AntiCancer Inc., San Diego, CA, U.S.A.,Department of Surgery, University of California, San Diego, La Jolla, CA, U.S.A
| | - Kentaro Miyake
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ryusei Matsuyama
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Michael Bouvet
- Department of Surgery, University of California, San Diego, La Jolla, CA, U.S.A
| | - Steven G Clarke
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, U.S.A
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Japan;
| | - Robert M Hoffman
- AntiCancer Inc., San Diego, CA, U.S.A.; .,Department of Surgery, University of California, San Diego, La Jolla, CA, U.S.A
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10
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Gladyshev VN, Kritchevsky SB, Clarke SG, Cuervo AM, Fiehn O, de Magalhães JP, Mau T, Maes M, Moritz R, Niedernhofer LJ, Van Schaftingen E, Tranah GJ, Walsh K, Yura Y, Zhang B, Cummings SR. Molecular Damage in Aging. Nat Aging 2021; 1:1096-1106. [PMID: 36846190 PMCID: PMC9957516 DOI: 10.1038/s43587-021-00150-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 11/04/2021] [Indexed: 11/09/2022]
Abstract
Cellular metabolism generates molecular damage affecting all levels of biological organization. Accumulation of this damage over time is thought to play a central role in the aging process, but damage manifests in diverse molecular forms complicating its assessment. Insufficient attention has been paid to date to the role of molecular damage in aging-related phenotypes, particularly in humans, in part because of the difficulty in measuring its various forms. Recently, omics approaches have been developed that begin to address this challenge, because they are able to assess a sizeable proportion of age-related damage at the level of small molecules, proteins, RNA, DNA, organelles and cells. This review describes the concept of molecular damage in aging and discusses its diverse aspects from theoretical models to experimental approaches. Measurement of multiple types of damage enables studies of the role of damage in human aging outcomes and lays a foundation for testing interventions to reduce the burden of molecular damage, opening new approaches to slowing aging and reducing its consequences.
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Affiliation(s)
- Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Stephen B. Kritchevsky
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Steven G. Clarke
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Ana Maria Cuervo
- Department of Development and Molecular Biology, Albert Einstein College of Medicine, New York, NY 10461, USA
- Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California Davis, Davis, CA 95616, USA
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - Theresa Mau
- San Francisco Coordinating Center, California Pacific Medical Center, Research Institute, San Francisco, CA 94143, USA
| | - Michal Maes
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Robert Moritz
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Laura J. Niedernhofer
- Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Emile Van Schaftingen
- De Duve Institute, Université catholique de Louvain, Bruxelles, Belgium
- Walloon Excellence in Life Sciences and Biotechnology (WELBIO), Université catholique de Louvain, Bruxelles, Belgium
| | - Gregory J. Tranah
- San Francisco Coordinating Center, California Pacific Medical Center, Research Institute, San Francisco, CA 94143, USA
| | - Kenneth Walsh
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia-School of Medicine, Charlottesville, VA 22908, USA
| | - Yoshimitsu Yura
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia-School of Medicine, Charlottesville, VA 22908, USA
| | - Bohan Zhang
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Steven R. Cummings
- San Francisco Coordinating Center, California Pacific Medical Center, Research Institute, San Francisco, CA 94143, USA
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11
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Ayer A, Fazakerley DJ, Suarna C, Maghzal GJ, Sheipouri D, Lee KJ, Bradley MC, Fernández-Del-Rio L, Tumanov S, Kong SM, van der Veen JN, Yang A, Ho JWK, Clarke SG, James DE, Dawes IW, Vance DE, Clarke CF, Jacobs RL, Stocker R. Genetic screening reveals phospholipid metabolism as a key regulator of the biosynthesis of the redox-active lipid coenzyme Q. Redox Biol 2021; 46:102127. [PMID: 34521065 PMCID: PMC8435697 DOI: 10.1016/j.redox.2021.102127] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/27/2021] [Accepted: 09/04/2021] [Indexed: 11/30/2022] Open
Abstract
Mitochondrial energy production and function rely on optimal concentrations of the essential redox-active lipid, coenzyme Q (CoQ). CoQ deficiency results in mitochondrial dysfunction associated with increased mitochondrial oxidative stress and a range of pathologies. What drives CoQ deficiency in many of these pathologies is unknown, just as there currently is no effective therapeutic strategy to overcome CoQ deficiency in humans. To date, large-scale studies aimed at systematically interrogating endogenous systems that control CoQ biosynthesis and their potential utility to treat disease have not been carried out. Therefore, we developed a quantitative high-throughput method to determine CoQ concentrations in yeast cells. Applying this method to the Yeast Deletion Collection as a genome-wide screen, 30 genes not known previously to regulate cellular concentrations of CoQ were discovered. In combination with untargeted lipidomics and metabolomics, phosphatidylethanolamine N-methyltransferase (PEMT) deficiency was confirmed as a positive regulator of CoQ synthesis, the first identified to date. Mechanistically, PEMT deficiency alters mitochondrial concentrations of one-carbon metabolites, characterized by an increase in the S-adenosylmethionine to S-adenosylhomocysteine (SAM-to-SAH) ratio that reflects mitochondrial methylation capacity, drives CoQ synthesis, and is associated with a decrease in mitochondrial oxidative stress. The newly described regulatory pathway appears evolutionary conserved, as ablation of PEMT using antisense oligonucleotides increases mitochondrial CoQ in mouse-derived adipocytes that translates to improved glucose utilization by these cells, and protection of mice from high-fat diet-induced insulin resistance. Our studies reveal a previously unrecognized relationship between two spatially distinct lipid pathways with potential implications for the treatment of CoQ deficiencies, mitochondrial oxidative stress/dysfunction, and associated diseases. Mitochondrial CoQ deficiency results in oxidative stress and a range of pathologies The drivers of mitochondrial CoQ deficiency remain largely unknown PEMT deficiency is the first identified positive regulator of mitochondrial CoQ PEMT deficiency increases CoQ by increasing the mitochondrial SAM-to-SAH ratio PEMT deficiency prevents insulin resistance by increasing mitochondrial CoQ
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Affiliation(s)
- Anita Ayer
- Heart Research Institute, The University of Sydney, Sydney, New South Wales, Australia; Victor Chang Cardiac Research Institute, Sydney, Australia
| | - Daniel J Fazakerley
- Charles Perkins Centre, School of Life and Environmental Sciences, Sydney Medical School, The University of Sydney, Sydney, Australia; Metabolic Research Laboratory, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Cacang Suarna
- Heart Research Institute, The University of Sydney, Sydney, New South Wales, Australia; Victor Chang Cardiac Research Institute, Sydney, Australia
| | | | - Diba Sheipouri
- Victor Chang Cardiac Research Institute, Sydney, Australia
| | - Kevin J Lee
- Victor Chang Cardiac Research Institute, Sydney, Australia
| | - Michelle C Bradley
- Department of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, United States
| | - Lucía Fernández-Del-Rio
- Department of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, United States
| | - Sergey Tumanov
- Heart Research Institute, The University of Sydney, Sydney, New South Wales, Australia; Victor Chang Cardiac Research Institute, Sydney, Australia
| | - Stephanie My Kong
- Heart Research Institute, The University of Sydney, Sydney, New South Wales, Australia; Victor Chang Cardiac Research Institute, Sydney, Australia
| | - Jelske N van der Veen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Andrian Yang
- Victor Chang Cardiac Research Institute, Sydney, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, Australia
| | - Joshua W K Ho
- Victor Chang Cardiac Research Institute, Sydney, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, Australia; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China; Laboratory for Data Discovery for Health, Hong Kong Science Park, Hong Kong SAR, China
| | - Steven G Clarke
- Department of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, United States
| | - David E James
- Charles Perkins Centre, School of Life and Environmental Sciences, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Ian W Dawes
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Dennis E Vance
- Department of Biochemistry, University of Alberta, Edmonton, Canada
| | - Catherine F Clarke
- Department of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, United States
| | - René L Jacobs
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Roland Stocker
- Heart Research Institute, The University of Sydney, Sydney, New South Wales, Australia; Victor Chang Cardiac Research Institute, Sydney, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, Australia; School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.
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12
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Soliman R, Cordero-Maldonado ML, Martins TG, Moein M, Conrotte JF, Warmack RA, Skupin A, Crawford AD, Clarke SG, Linster CL. l-Isoaspartyl Methyltransferase Deficiency in Zebrafish Leads to Impaired Calcium Signaling in the Brain. Front Genet 2021; 11:612343. [PMID: 33552132 PMCID: PMC7859441 DOI: 10.3389/fgene.2020.612343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 09/30/2020] [Accepted: 12/21/2020] [Indexed: 11/13/2022] Open
Abstract
Isomerization of l-aspartyl and l-asparaginyl residues to l-isoaspartyl residues is one type of protein damage that can occur under physiological conditions and leads to conformational changes, loss of function, and enhanced protein degradation. Protein l-isoaspartyl methyltransferase (PCMT) is a repair enzyme whose action initiates the reconversion of abnormal l-isoaspartyl residues to normal l-aspartyl residues in proteins. Many lines of evidence support a crucial role for PCMT in the brain, but the mechanisms involved remain poorly understood. Here, we investigated PCMT activity and function in zebrafish, a vertebrate model that is particularly well-suited to analyze brain function using a variety of techniques. We characterized the expression products of the zebrafish PCMT homologous genes pcmt and pcmtl. Both zebrafish proteins showed a robust l-isoaspartyl methyltransferase activity and highest mRNA transcript levels were found in brain and testes. Zebrafish morphant larvae with a knockdown in both the pcmt and pcmtl genes showed pronounced morphological abnormalities, decreased survival, and increased isoaspartyl levels. Interestingly, we identified a profound perturbation of brain calcium homeostasis in these morphants. An abnormal calcium response upon ATP stimulation was also observed in mouse hippocampal HT22 cells knocked out for Pcmt1. This work shows that zebrafish is a promising model to unravel further facets of PCMT function and demonstrates, for the first time in vivo, that PCMT plays a pivotal role in the regulation of calcium fluxes.
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Affiliation(s)
- Remon Soliman
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Teresa G Martins
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Mahsa Moein
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jean-François Conrotte
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rebeccah A Warmack
- Department of Chemistry and Biochemistry, The Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.,University of California, San Diego, La Jolla, CA, United States
| | - Alexander D Crawford
- Department of Preclinical Sciences and Pathology, Norwegian University of Life Sciences, Oslo, Norway.,Institute for Orphan Drug Discovery, Bremer Innovations- und Technologiezentrum, Bremen, Germany
| | - Steven G Clarke
- Department of Chemistry and Biochemistry, The Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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13
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Lowe TL, Vernon A, Clarke SG. Protein Arginine Methyltransferase 7 (PRMT7): A Human Enzyme Often Overexpressed in Cancer is Most Active Under Non‐physiological Conditions. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.05667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Troy L. Lowe
- Department of Chemistry and Biochemistry and the Molecular Biology Institute UCLA Los Angeles CA 90095-1569
| | - Annabel Vernon
- Department of Chemistry and Biochemistry and the Molecular Biology Institute UCLA Los Angeles CA 90095-1569
| | - Steven G. Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute UCLA Los Angeles CA 90095-1569
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14
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White JT, Cato T, Deramchi N, Gabunilas J, Roy KR, Wang C, Chanfreau GF, Clarke SG. Protein Methylation and Translation: Role of Lysine Modification on the Function of Yeast Elongation Factor 1A. Biochemistry 2019; 58:4997-5010. [PMID: 31738538 DOI: 10.1021/acs.biochem.9b00818] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To date, 12 protein lysine methyltransferases that modify translational elongation factors and ribosomal proteins (Efm1-7 and Rkm 1-5) have been identified in the yeast Saccharomyces cerevisiae. Of these 12, five (Efm1 and Efm4-7) appear to be specific to elongation factor 1A (EF1A), the protein responsible for bringing aminoacyl-tRNAs to the ribosome. In S. cerevisiae, the functional implications of lysine methylation in translation are mostly unknown. In this work, we assessed the physiological impact of disrupting EF1A methylation in a strain where four of the most conserved methylated lysine sites are mutated to arginine residues and in strains lacking either four or five of the Efm lysine methyltransferases specific to EF1A. We found that loss of EF1A methylation was not lethal but resulted in reduced growth rates, particularly under caffeine and rapamycin stress conditions, suggesting EF1A interacts with the TORC1 pathway, as well as altered sensitivities to ribosomal inhibitors. We also detected reduced cellular levels of the EF1A protein, which surprisingly was not reflected in its stability in vivo. We present evidence that these Efm methyltransferases appear to be largely devoted to the modification of EF1A, finding no evidence of the methylation of other substrates in the yeast cell. This work starts to illuminate why one protein can need five different methyltransferases for its functions and highlights the resilience of yeast to alterations in their posttranslational modifications.
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Affiliation(s)
- Jonelle T White
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Tieranee Cato
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Neil Deramchi
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Jason Gabunilas
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Kevin R Roy
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Charles Wang
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Guillaume F Chanfreau
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
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15
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Warmack RA, Boyer DR, Zee CT, Richards LS, Sawaya MR, Cascio D, Gonen T, Eisenberg DS, Clarke SG. Structure of amyloid-β (20-34) with Alzheimer's-associated isomerization at Asp23 reveals a distinct protofilament interface. Nat Commun 2019; 10:3357. [PMID: 31350392 PMCID: PMC6659688 DOI: 10.1038/s41467-019-11183-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 06/24/2019] [Indexed: 02/07/2023] Open
Abstract
Amyloid-β (Aβ) harbors numerous posttranslational modifications (PTMs) that may affect Alzheimer's disease (AD) pathogenesis. Here we present the 1.1 Å resolution MicroED structure of an Aβ 20-34 fibril with and without the disease-associated PTM, L-isoaspartate, at position 23 (L-isoAsp23). Both wild-type and L-isoAsp23 protofilaments adopt β-helix-like folds with tightly packed cores, resembling the cores of full-length fibrillar Aβ structures, and both self-associate through two distinct interfaces. One of these is a unique Aβ interface strengthened by the isoaspartyl modification. Powder diffraction patterns suggest a similar structure may be adopted by protofilaments of an analogous segment containing the heritable Iowa mutation, Asp23Asn. Consistent with its early onset phenotype in patients, Asp23Asn accelerates aggregation of Aβ 20-34, as does the L-isoAsp23 modification. These structures suggest that the enhanced amyloidogenicity of the modified Aβ segments may also reduce the concentration required to achieve nucleation and therefore help spur the pathogenesis of AD.
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Affiliation(s)
- Rebeccah A Warmack
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1569, USA
| | - David R Boyer
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1569, USA
| | - Chih-Te Zee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1569, USA
| | - Logan S Richards
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1569, USA
| | - Michael R Sawaya
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1569, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095-1570, USA.,UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, CA, 90095-1570, USA
| | - Duilio Cascio
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1569, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095-1570, USA.,UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, CA, 90095-1570, USA
| | - Tamir Gonen
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095-1570, USA.,Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095-1570, USA.,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1737, USA.,Department of Physiology, University of California, Los Angeles, Los Angeles, CA, 90095-1751, USA
| | - David S Eisenberg
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1569, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095-1570, USA.,UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, CA, 90095-1570, USA.,Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095-1570, USA.,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1737, USA
| | - Steven G Clarke
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1569, USA. .,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095-1570, USA.
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16
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Warmack RA, Boyer DR, Zee CT, Richards LS, Sawaya MR, Cascio D, Gonen T, Eisenberg DS, Clarke SG. Visualization of the core of a modified Amyloid-β polymorph with MicroED. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s010876731909617x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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17
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Warmack RA, Shawa H, Liu K, Lopez K, Loo JA, Horwitz J, Clarke SG. The l-isoaspartate modification within protein fragments in the aging lens can promote protein aggregation. J Biol Chem 2019; 294:12203-12219. [PMID: 31239355 DOI: 10.1074/jbc.ra119.009052] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 04/25/2019] [Revised: 06/05/2019] [Indexed: 01/15/2023] Open
Abstract
Transparency in the lens is accomplished by the dense packing and short-range order interactions of the crystallin proteins in fiber cells lacking organelles. These features are accompanied by a lack of protein turnover, leaving lens proteins susceptible to a number of damaging modifications and aggregation. The loss of lens transparency is attributed in part to such aggregation during aging. Among the damaging post-translational modifications that accumulate in long-lived proteins, isomerization at aspartate residues has been shown to be extensive throughout the crystallins. In this study of the human lens, we localize the accumulation of l-isoaspartate within water-soluble protein extracts primarily to crystallin peptides in high-molecular weight aggregates and show with MS that these peptides are from a variety of crystallins. To investigate the consequences of aspartate isomerization, we investigated two αA crystallin peptides 52LFRTVLDSGISEVR65 and 89VQDDFVEIH98, identified within this study, with the l-isoaspartate modification introduced at Asp58 and Asp91, respectively. Importantly, whereas both peptides modestly increase protein precipitation, the native 52LFRTVLDSGISEVR65 peptide shows higher aggregation propensity. In contrast, the introduction of l-isoaspartate within a previously identified anti-chaperone peptide from water-insoluble aggregates, αA crystallin 66SDRDKFVIFL(isoAsp)VKHF80, results in enhanced amyloid formation in vitro The modification of this peptide also increases aggregation of the lens chaperone αB crystallin. These findings may represent multiple pathways within the lens wherein the isomerization of aspartate residues in crystallin peptides differentially results in peptides associating with water-soluble or water-insoluble aggregates. Here the eye lens serves as a model for the cleavage and modification of long-lived proteins within other aging tissues.
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Affiliation(s)
- Rebeccah A Warmack
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095; Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Harrison Shawa
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095; Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Kate Liu
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095; Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Katia Lopez
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095; Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095; Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Joseph Horwitz
- Molecular Biology Institute, UCLA, Los Angeles, California 90095; Jules Stein Eye Institute, UCLA, Los Angeles, California 90095
| | - Steven G Clarke
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095; Molecular Biology Institute, UCLA, Los Angeles, California 90095.
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18
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Jain K, Clarke SG. PRMT7 as a unique member of the protein arginine methyltransferase family: A review. Arch Biochem Biophys 2019; 665:36-45. [PMID: 30802433 DOI: 10.1016/j.abb.2019.02.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/16/2019] [Accepted: 02/18/2019] [Indexed: 12/14/2022]
Abstract
Protein arginine methyltransferases (PRMTs) are found in a wide variety of eukaryotic organisms and can regulate gene expression, DNA repair, RNA splicing, and stem cell biology. In mammalian cells, nine genes encode a family of sequence-related enzymes; six of these PRMTs catalyze the formation of ω-asymmetric dimethyl derivatives, two catalyze ω-symmetric dimethyl derivatives, and only one (PRMT7) solely catalyzes ω-monomethylarginine formation. Purified recombinant PRMT7 displays a number of unique enzymatic properties including a substrate preference for arginine residues in R-X-R motifs with additional flanking basic amino acid residues and a temperature optimum well below 37 °C. Evidence has been presented for crosstalk between PRMT7 and PRMT5, where methylation of a histone H4 peptide at R17, a PRMT7 substrate, may activate PRMT5 for methylation of R3. Defects in muscle stem cells (satellite cells) and immune cells are found in mouse Prmt7 homozygous knockouts, while humans lacking PRMT7 are characterized by significant intellectual developmental delays, hypotonia, and facial dysmorphisms. The overexpression of the PRMT7 gene has been correlated with cancer metastasis in humans. Current research challenges include identifying cellular factors that control PRMT7 expression and activity, identifying the physiological substrates of PRMT7, and determining the effect of methylation on these substrates.
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Affiliation(s)
- Kanishk Jain
- Lineberger Comprehensive Cancer Center and Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, 27599, USA
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA.
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Abstract
SIGNIFICANCE Various autoimmune syndromes are characterized by abnormalities found at the level of tissues and cells, as well as by microenvironmental influences, such as reactive oxygen species (ROS), that alter intracellular metabolism and protein expression. Moreover, the convergence of genetic, epigenetic, and even environmental influences can result in B and T lymphocyte autoimmunity and tissue pathology. Recent Advances: This review describes how oxidative stress to cells and tissues may alter post-translational protein modifications, both directly and indirectly, as well as potentially lead to aberrant gene expression. For example, it has been clearly observed in many systems how oxidative stress directly amplifies carbonyl protein modifications. However, ROS also lead to a number of nonenzymatic spontaneous modifications including deamidation and isoaspartate modification as well as to enzyme-mediated citrullination of self-proteins. ROS have direct effects on DNA methylation, leading to influences in gene expression, chromosome inactivation, and the silencing of genetic elements. Finally, ROS can alter many other cellular pathways, including the initiation of apoptosis and NETosis, triggering the release of modified intracellular autoantigens. CRITICAL ISSUES This review will detail specific post-translational protein modifications, the pathways that control autoimmunity to modified self-proteins, and how products of ROS may be important biomarkers of tissue pathogenesis. FUTURE DIRECTIONS A clear understanding of the many pathways affected by ROS will lead to potential therapeutic manipulations to alter the onset and/or progression of autoimmune disease.
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Affiliation(s)
- Mei-Ling Yang
- 1 Section of Rheumatology, Yale University School of Medicine , New Haven, Connecticut.,2 Department of Internal Medicine, Yale University School of Medicine , New Haven, Connecticut
| | - Hester A Doyle
- 1 Section of Rheumatology, Yale University School of Medicine , New Haven, Connecticut.,2 Department of Internal Medicine, Yale University School of Medicine , New Haven, Connecticut
| | - Steven G Clarke
- 3 Department of Chemistry and Biochemistry, University of California , Los Angeles, Los Angeles, California
| | - Kevan C Herold
- 2 Department of Internal Medicine, Yale University School of Medicine , New Haven, Connecticut.,4 Department of Immunobiology, Yale University School of Medicine , New Haven, Connecticut
| | - Mark J Mamula
- 1 Section of Rheumatology, Yale University School of Medicine , New Haven, Connecticut.,2 Department of Internal Medicine, Yale University School of Medicine , New Haven, Connecticut
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20
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Abstract
Cellular physiology depends on the alteration of protein structures by covalent modification reactions. Using a combination of bioinformatic, genetic, biochemical, and mass spectrometric approaches, it has been possible to probe ribosomal proteins from the yeast Saccharomyces cerevisiae for post-translationally methylated amino acid residues and for the enzymes that catalyze these modifications. These efforts have resulted in the identification and characterization of the first protein histidine methyltransferase, the first N-terminal protein methyltransferase, two unusual types of protein arginine methyltransferases, and a new type of cysteine methylation. Two of these enzymes may modify their substrates during ribosomal assembly because the final methylated histidine and arginine residues are buried deep within the ribosome with contacts only with RNA. Two of these modifications occur broadly in eukaryotes, including humans, whereas the others demonstrate a more limited phylogenetic range. Analysis of strains where the methyltransferase genes are deleted has given insight into the physiological roles of these modifications. These reactions described here add diversity to the modifications that generate the typical methylated lysine and arginine residues previously described in histones and other proteins.
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Affiliation(s)
- Steven G Clarke
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California 90095
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21
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Clarke SG. What can protein methylation tell us about histones, ribosomes, translation factors and the biology of cancer and aging? FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.473.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Steven G. Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology InstituteUCLALos AngelesCA
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22
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Roher AE, Kokjohn TA, Clarke SG, Sierks MR, Maarouf CL, Serrano GE, Sabbagh MS, Beach TG. APP/Aβ structural diversity and Alzheimer's disease pathogenesis. Neurochem Int 2017; 110:1-13. [PMID: 28811267 PMCID: PMC5688956 DOI: 10.1016/j.neuint.2017.08.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/25/2017] [Accepted: 08/11/2017] [Indexed: 02/01/2023]
Abstract
The amyloid cascade hypothesis of Alzheimer's disease (AD) proposes amyloid- β (Aβ) is a chief pathological element of dementia. AD therapies have targeted monomeric and oligomeric Aβ 1-40 and 1-42 peptides. However, alternative APP proteolytic processing produces a complex roster of Aβ species. In addition, Aβ peptides are subject to extensive posttranslational modification (PTM). We propose that amplified production of some APP/Aβ species, perhaps exacerbated by differential gene expression and reduced peptide degradation, creates a diverse spectrum of modified species which disrupt brain homeostasis and accelerate AD neurodegeneration. We surveyed the literature to catalog Aβ PTM including species with isoAsp at positions 7 and 23 which may phenocopy the Tottori and Iowa Aβ mutations that result in early onset AD. We speculate that accumulation of these alterations induce changes in secondary and tertiary structure of Aβ that favor increased toxicity, and seeding and propagation in sporadic AD. Additionally, amyloid-β peptides with a pyroglutamate modification at position 3 and oxidation of Met35 make up a substantial portion of sporadic AD amyloid deposits. The intrinsic physical properties of these species, including resistance to degradation, an enhanced aggregation rate, increased neurotoxicity, and association with behavioral deficits, suggest their emergence is linked to dementia. The generation of specific 3D-molecular conformations of Aβ impart unique biophysical properties and a capacity to seed the prion-like global transmission of amyloid through the brain. The accumulation of rogue Aβ ultimately contributes to the destruction of vascular walls, neurons and glial cells culminating in dementia. A systematic examination of Aβ PTM and the analysis of the toxicity that they induced may help create essential biomarkers to more precisely stage AD pathology, design countermeasures and gauge the impacts of interventions.
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Affiliation(s)
- Alex E Roher
- Division of Neurobiology, Barrow Neurological Institute, Phoenix, AZ 85013, USA; Division of Clinical Education, Midwestern University, Glendale, AZ 85308, USA.
| | - Tyler A Kokjohn
- Department of Microbiology, Midwestern University, Glendale, AZ 85308, USA
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles CA 90095-1569, USA
| | - Michael R Sierks
- Department of Chemical Engineering, Arizona State University, Tempe, AZ 85287-6106, USA
| | - Chera L Maarouf
- Laboratory of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Geidy E Serrano
- Laboratory of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Marwan S Sabbagh
- Alzheimer's and Memory Disorders Division, Barrow Neurological Institute, Phoenix, AZ 85013, USA
| | - Thomas G Beach
- Laboratory of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ 85351, USA
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Hadjikyriacou A, Clarke SG. Caenorhabditis elegans PRMT-7 and PRMT-9 Are Evolutionarily Conserved Protein Arginine Methyltransferases with Distinct Substrate Specificities. Biochemistry 2017; 56:2612-2626. [PMID: 28441492 DOI: 10.1021/acs.biochem.7b00283] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Caenorhabditis elegans protein arginine methyltransferases PRMT-7 and PRMT-9 are two evolutionarily conserved enzymes, with distinct orthologs in plants, invertebrates, and vertebrates. Biochemical characterization of these two enzymes reveals that they share much in common with their mammalian orthologs. C. elegans PRMT-7 produces only monomethylarginine (MMA) and preferentially methylates R-X-R motifs in a broad collection of substrates, including human histone peptides and RG-rich peptides. In addition, the activity of the PRMT-7 enzyme is dependent on temperature, the presence of metal ions, and the reducing agent dithiothreitol. C. elegans PRMT-7 has a substrate specificity and a substrate preference different from those of mammalian PRMT7, and the available X-ray crystal structures of the PRMT7 orthologs show differences in active site architecture. C. elegans PRMT-9, on the other hand, produces symmetric dimethylarginine and MMA on SFTB-2, the conserved C. elegans ortholog of human RNA splicing factor SF3B2, indicating a possible role in the regulation of nematode splicing. In contrast to PRMT-7, C. elegans PRMT-9 appears to be biochemically indistinguishable from its human ortholog.
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Affiliation(s)
- Andrea Hadjikyriacou
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles , 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles , 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
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Kafková L, Debler EW, Fisk JC, Jain K, Clarke SG, Read LK. The Major Protein Arginine Methyltransferase in Trypanosoma brucei Functions as an Enzyme-Prozyme Complex. J Biol Chem 2016; 292:2089-2100. [PMID: 27998975 DOI: 10.1074/jbc.m116.757112] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [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: 09/05/2016] [Revised: 12/14/2016] [Indexed: 11/06/2022] Open
Abstract
Prozymes are catalytically inactive enzyme paralogs that dramatically stimulate the function of weakly active enzymes through complex formation. The two prozymes described to date reside in the polyamine biosynthesis pathway of the human parasite Trypanosoma brucei, an early branching eukaryote that lacks transcriptional regulation and regulates its proteome through posttranscriptional and posttranslational means. Arginine methylation is a common posttranslational modification in eukaryotes catalyzed by protein arginine methyltransferases (PRMTs) that are typically thought to function as homodimers. We demonstrate that a major T. brucei PRMT, TbPRMT1, functions as a heterotetrameric enzyme-prozyme pair. The inactive PRMT paralog, TbPRMT1PRO, is essential for catalytic activity of the TbPRMT1ENZ subunit. Mutational analysis definitively demonstrates that TbPRMT1ENZ is the cofactor-binding subunit and carries all catalytic activity of the complex. Our results are the first demonstration of an obligate heteromeric PRMT, and they suggest that enzyme-prozyme organization is expanded in trypanosomes as a posttranslational means of enzyme regulation.
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Affiliation(s)
- Lucie Kafková
- From the Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, and Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14214
| | - Erik W Debler
- the Laboratory of Cell Biology, The Rockefeller University, New York, New York 10065, and
| | - John C Fisk
- From the Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, and Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14214
| | - Kanishk Jain
- the Department of Chemistry and Biochemistry and The Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Steven G Clarke
- the Department of Chemistry and Biochemistry and The Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Laurie K Read
- From the Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, and Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14214,
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25
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Caslavka Zempel KE, Vashisht AA, Barshop WD, Wohlschlegel JA, Clarke SG. Determining the Mitochondrial Methyl Proteome in Saccharomyces cerevisiae using Heavy Methyl SILAC. J Proteome Res 2016; 15:4436-4451. [PMID: 27696855 DOI: 10.1021/acs.jproteome.6b00521] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Methylation is a common and abundant post-translational modification. High-throughput proteomic investigations have reported many methylation sites from complex mixtures of proteins. The lack of consistency between parallel studies, resulting from both false positives and missed identifications, suggests problems with both over-reporting and under-reporting methylation sites. However, isotope labeling can be used effectively to address the issue of false-positives, and fractionation of proteins can increase the probability of identifying methylation sites in lower abundance. Here we have adapted heavy methyl SILAC to analyze fractions of the budding yeast Saccharomyces cerevisiae under respiratory conditions to allow for the production of mitochondria, an organelle whose proteins are often overlooked in larger methyl proteome studies. We have found 12 methylation sites on 11 mitochondrial proteins as well as an additional 14 methylation sites on 9 proteins that are nonmitochondrial. Of these methylation sites, 20 sites have not been previously reported. This study represents the first characterization of the yeast mitochondrial methyl proteome and the second proteomic investigation of global mitochondrial methylation to date in any organism.
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Affiliation(s)
- Katelyn E Caslavka Zempel
- Department of Chemistry and Biochemistry and the Molecular Biology Institute and ‡Department of Biological Chemistry and the David Geffen School of Medicine, UCLA , Los Angeles, California 90095, United States
| | - Ajay A Vashisht
- Department of Chemistry and Biochemistry and the Molecular Biology Institute and ‡Department of Biological Chemistry and the David Geffen School of Medicine, UCLA , Los Angeles, California 90095, United States
| | - William D Barshop
- Department of Chemistry and Biochemistry and the Molecular Biology Institute and ‡Department of Biological Chemistry and the David Geffen School of Medicine, UCLA , Los Angeles, California 90095, United States
| | - James A Wohlschlegel
- Department of Chemistry and Biochemistry and the Molecular Biology Institute and ‡Department of Biological Chemistry and the David Geffen School of Medicine, UCLA , Los Angeles, California 90095, United States
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute and ‡Department of Biological Chemistry and the David Geffen School of Medicine, UCLA , Los Angeles, California 90095, United States
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26
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Jain K, Warmack RA, Debler EW, Hadjikyriacou A, Stavropoulos P, Clarke SG. Protein Arginine Methyltransferase Product Specificity Is Mediated by Distinct Active-site Architectures. J Biol Chem 2016; 291:18299-308. [PMID: 27387499 DOI: 10.1074/jbc.m116.740399] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Indexed: 11/06/2022] Open
Abstract
In the family of protein arginine methyltransferases (PRMTs) that predominantly generate either asymmetric or symmetric dimethylarginine (SDMA), PRMT7 is unique in producing solely monomethylarginine (MMA) products. The type of methylation on histones and other proteins dictates changes in gene expression, and numerous studies have linked altered profiles of methyl marks with disease phenotypes. Given the importance of specific inhibitor development, it is crucial to understand the mechanisms by which PRMT product specificity is conferred. We have focused our attention on active-site residues of PRMT7 from the protozoan Trypanosoma brucei We have designed 26 single and double mutations in the active site, including residues in the Glu-Xaa8-Glu (double E) loop and the Met-Gln-Trp sequence of the canonical Thr-His-Trp (THW) loop known to interact with the methyl-accepting substrate arginine. Analysis of the reaction products by high resolution cation exchange chromatography combined with the knowledge of PRMT crystal structures suggests a model where the size of two distinct subregions in the active site determines PRMT7 product specificity. A dual mutation of Glu-181 to Asp in the double E loop and Gln-329 to Ala in the canonical THW loop enables the enzyme to produce SDMA. Consistent with our model, the mutation of Cys-431 to His in the THW loop of human PRMT9 shifts its product specificity from SDMA toward MMA. Together with previous results, these findings provide a structural basis and a general model for product specificity in PRMTs, which will be useful for the rational design of specific PRMT inhibitors.
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Affiliation(s)
- Kanishk Jain
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California 90095 and
| | - Rebeccah A Warmack
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California 90095 and
| | | | - Andrea Hadjikyriacou
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California 90095 and
| | - Peter Stavropoulos
- the Laboratory of Cell Biology and Laboratory of Lymphocyte Biology, The Rockefeller University, New York, New York 10065
| | - Steven G Clarke
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California 90095 and
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27
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Al-Hadid Q, Roy K, Chanfreau G, Clarke SG. Methylation of yeast ribosomal protein Rpl3 promotes translational elongation fidelity. RNA 2016; 22:489-98. [PMID: 26826131 PMCID: PMC4793205 DOI: 10.1261/rna.054569.115] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 12/14/2015] [Indexed: 05/05/2023]
Abstract
Rpl3, a highly conserved ribosomal protein, is methylated at histidine 243 by the Hpm1 methyltransferase in Saccharomyces cerevisiae. Histidine 243 lies close to the peptidyl transferase center in a functionally important region of Rpl3 designated as the basic thumb that coordinates the decoding, peptidyl transfer, and translocation steps of translation elongation. Hpm1 was recently implicated in ribosome biogenesis and translation. However, the biological role of methylation of its Rpl3 substrate has not been identified. Here we interrogate the role of Rpl3 methylation at H243 by investigating the functional impact of mutating this histidine residue to alanine (rpl3-H243A). Akin to Hpm1-deficient cells, rpl3-H243A cells accumulate 35S and 23S pre-rRNA precursors to a similar extent, confirming an important role for histidine methylation in pre-rRNA processing. In contrast, Hpm1-deficient cells but not rpl3-H243A mutants show perturbed levels of ribosomal subunits. We show that Hpm1 has multiple substrates in different subcellular fractions, suggesting that methylation of proteins other than Rpl3 may be important for controlling ribosomal subunit levels. Finally, translational fidelity assays demonstrate that like Hpm1-deficient cells, rpl3-H243A mutants have defects in translation elongation resulting in decreased translational accuracy. These data suggest that Rpl3 methylation at H243 is playing a significant role in translation elongation, likely via the basic thumb, but has little impact on ribosomal subunit levels. Hpm1 is therefore a multifunctional methyltransferase with independent roles in ribosome biogenesis and translation.
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Affiliation(s)
- Qais Al-Hadid
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Kevin Roy
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Guillaume Chanfreau
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
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28
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Abstract
The quantification of aspartic acid racemization in the proteins of nonmetabolically active tissues can be used as a measure of chronological aging in humans and other long-lived organisms. However, very few studies have been conducted in shorter-lived animals such as rodents, which are increasingly used as genetic and metabolic models of aging. An initial study had reported significant changes in the ratio of d- to l-aspartate in rat molars with age. Using a sensitive HPLC method for the determination of d- and l-aspartate from protein hydrolysates, we found no accumulation of d-aspartate in the molars of 17 rats that ranged in age from 2 to 44 months, and the amount of d-aspartate per molar did not correspond with molar eruption date as had been previously reported. However, developing an alternate approach, we found significant accumulation of isomerized aspartyl residues in eye lens proteins that are also formed by spontaneous degradation processes. In this study, we used the human protein l-isoaspartate/d-aspartate O-methyltransferase (PCMT1) as an analytical reagent in a sensitive and convenient procedure that could be used to rapidly examine multiple samples simultaneously. We found levels of isomerized aspartyl residues to be about 35 times higher in the lens extracts of 18-month-old rats versus 2-month-old rats, suggesting that isomerization may be an effective marker for biological aging in this range of ages. Importantly, we found that the accumulation appeared to plateau in rats of 18 months and older, indicating that potentially novel mechanisms for removing altered proteins may develop with age.
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Affiliation(s)
- Rebeccah A Warmack
- 1 Department of Chemistry and Biochemistry, The Molecular Biology Institute, University of California , Los Angeles, Los Angeles, California
| | - Eduardo Mansilla
- 2 Tissue Engineering, Regenerative Medicine and Cell Therapies Laboratory, CUCAIBA, Buenos Aires Province Ministry of Public Health , Buenos Aires, Argentina
| | - Rodolfo G Goya
- 3 Institute for Biochemical Research (INIBIOLP)-Cathedra of Histology B, Cathedra of Pathology B, School of Medicine, National University of La Plata , La Plata, Argentina
| | - Steven G Clarke
- 1 Department of Chemistry and Biochemistry, The Molecular Biology Institute, University of California , Los Angeles, Los Angeles, California
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29
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Fu X, Chin RM, Vergnes L, Hwang H, Deng G, Xing Y, Pai MY, Li S, Ta L, Fazlollahi F, Chen C, Prins RM, Teitell MA, Nathanson DA, Lai A, Faull KF, Jiang M, Clarke SG, Cloughesy TF, Graeber TG, Braas D, Christofk HR, Jung ME, Reue K, Huang J. 2-Hydroxyglutarate Inhibits ATP Synthase and mTOR Signaling. Cell Metab 2015; 22:508-15. [PMID: 26190651 PMCID: PMC4663076 DOI: 10.1016/j.cmet.2015.06.009] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 02/27/2015] [Accepted: 06/10/2015] [Indexed: 10/23/2022]
Abstract
We discovered recently that the central metabolite α-ketoglutarate (α-KG) extends the lifespan of C. elegans through inhibition of ATP synthase and TOR signaling. Here we find, unexpectedly, that (R)-2-hydroxyglutarate ((R)-2HG), an oncometabolite that interferes with various α-KG-mediated processes, similarly extends worm lifespan. (R)-2HG accumulates in human cancers carrying neomorphic mutations in the isocitrate dehydrogenase (IDH) 1 and 2 genes. We show that, like α-KG, both (R)-2HG and (S)-2HG bind and inhibit ATP synthase and inhibit mTOR signaling. These effects are mirrored in IDH1 mutant cells, suggesting a growth-suppressive function of (R)-2HG. Consistently, inhibition of ATP synthase by 2-HG or α-KG in glioblastoma cells is sufficient for growth arrest and tumor cell killing under conditions of glucose limitation, e.g., when ketone bodies (instead of glucose) are supplied for energy. These findings inform therapeutic strategies and open avenues for investigating the roles of 2-HG and metabolites in biology and disease.
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Affiliation(s)
- Xudong Fu
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Randall M Chin
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Laurent Vergnes
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Heejun Hwang
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Gang Deng
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Yanpeng Xing
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Melody Y Pai
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Sichen Li
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Lisa Ta
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Farbod Fazlollahi
- Pasarow Mass Spectrometry Laboratory, Department of Psychiatry and Biobehavioral Sciences, and Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Chuo Chen
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Robert M Prins
- Department of Neurosurgery, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Michael A Teitell
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - David A Nathanson
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Albert Lai
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kym F Faull
- Pasarow Mass Spectrometry Laboratory, Department of Psychiatry and Biobehavioral Sciences, and Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Meisheng Jiang
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Steven G Clarke
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Timothy F Cloughesy
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Thomas G Graeber
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; UCLA Metabolomics Center, University of California Los Angeles, Los Angeles, CA 90095, USA; Crump Institute for Molecular Imaging, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel Braas
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; UCLA Metabolomics Center, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Heather R Christofk
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; UCLA Metabolomics Center, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Michael E Jung
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Karen Reue
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jing Huang
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.
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30
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Hadjikyriacou A, Yang Y, Espejo A, Bedford MT, Clarke SG. Unique Features of Human Protein Arginine Methyltransferase 9 (PRMT9) and Its Substrate RNA Splicing Factor SF3B2. J Biol Chem 2015; 290:16723-43. [PMID: 25979344 DOI: 10.1074/jbc.m115.659433] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Indexed: 12/29/2022] Open
Abstract
Human protein arginine methyltransferase (PRMT) 9 symmetrically dimethylates arginine residues on splicing factor SF3B2 (SAP145) and has been functionally linked to the regulation of alternative splicing of pre-mRNA. Site-directed mutagenesis studies on this enzyme and its substrate had revealed essential unique residues in the double E loop and the importance of the C-terminal duplicated methyltransferase domain. In contrast to what had been observed with other PRMTs and their physiological substrates, a peptide containing the methylatable Arg-508 of SF3B2 was not recognized by PRMT9 in vitro. Although amino acid substitutions of residues surrounding Arg-508 had no great effect on PRMT9 recognition of SF3B2, moving the arginine residue within this sequence abolished methylation. PRMT9 and PRMT5 are the only known mammalian enzymes capable of forming symmetric dimethylarginine (SDMA) residues as type II PRMTs. We demonstrate here that the specificity of these enzymes for their substrates is distinct and not redundant. The loss of PRMT5 activity in mouse embryo fibroblasts results in almost complete loss of SDMA, suggesting that PRMT5 is the primary SDMA-forming enzyme in these cells. PRMT9, with its duplicated methyltransferase domain and conserved sequence in the double E loop, appears to have a unique structure and specificity among PRMTs for methylating SF3B2 and potentially other polypeptides.
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Affiliation(s)
- Andrea Hadjikyriacou
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los, Angeles, California 90095 and
| | - Yanzhong Yang
- the Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, Texas 78957
| | - Alexsandra Espejo
- the Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, Texas 78957
| | - Mark T Bedford
- the Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, Texas 78957
| | - Steven G Clarke
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los, Angeles, California 90095 and
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31
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Yang Y, Hadjikyriacou A, Xia Z, Gayatri S, Kim D, Zurita-Lopez C, Kelly R, Guo A, Li W, Clarke SG, Bedford MT. PRMT9 is a type II methyltransferase that methylates the splicing factor SAP145. Nat Commun 2015; 6:6428. [PMID: 25737013 PMCID: PMC4351962 DOI: 10.1038/ncomms7428] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 01/28/2015] [Indexed: 12/18/2022] Open
Abstract
The human genome encodes a family of nine protein arginine methyltransferases (PRMT1-9), whose members can catalyse three distinct types of methylation on arginine residues. Here we identify two spliceosome-associated proteins-SAP145 and SAP49-as PRMT9-binding partners, linking PRMT9 to U2 snRNP maturation. We show that SAP145 is methylated by PRMT9 at arginine 508, which takes the form of monomethylated arginine (MMA) and symmetrically dimethylated arginine (SDMA). PRMT9 thus joins PRMT5 as the only mammalian enzymes capable of depositing the SDMA mark. Methylation of SAP145 on Arg 508 generates a binding site for the Tudor domain of the Survival of Motor Neuron (SMN) protein, and RNA-seq analysis reveals gross splicing changes when PRMT9 levels are attenuated. These results identify PRMT9 as a nonhistone methyltransferase that primes the U2 snRNP for interaction with SMN.
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Affiliation(s)
- Yanzhong Yang
- 1] Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas 78957, USA [2] Department of Radiation Biology, Beckman Research Institute, City of Hope Cancer Center, Duarte, California 91010, USA
| | - Andrea Hadjikyriacou
- Department of Chemistry and Biochemistry, Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Zheng Xia
- Division of Biostatistics, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sitaram Gayatri
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Daehoon Kim
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Cecilia Zurita-Lopez
- Department of Chemistry and Biochemistry, Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Ryan Kelly
- Department of Chemistry and Biochemistry, Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Ailan Guo
- Cell Signaling Technology Inc., Danvers, Massachusetts 01923, USA
| | - Wei Li
- Division of Biostatistics, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Steven G Clarke
- Department of Chemistry and Biochemistry, Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Mark T Bedford
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas 78957, USA
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32
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Patananan AN, Budenholzer LM, Pedraza ME, Torres ER, Adler LN, Clarke SG. The invertebrate Caenorhabditis elegans biosynthesizes ascorbate. Arch Biochem Biophys 2015; 569:32-44. [PMID: 25668719 PMCID: PMC4357563 DOI: 10.1016/j.abb.2015.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [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: 12/07/2014] [Revised: 01/28/2015] [Accepted: 02/01/2015] [Indexed: 01/01/2023]
Abstract
L-ascorbate, commonly known as vitamin C, serves as an antioxidant and cofactor essential for many biological processes. Distinct ascorbate biosynthetic pathways have been established for animals and plants, but little is known about the presence or synthesis of this molecule in invertebrate species. We have investigated ascorbate metabolism in the nematode Caenorhabditis elegans, where this molecule would be expected to play roles in oxidative stress resistance and as cofactor in collagen and neurotransmitter synthesis. Using high-performance liquid chromatography and gas-chromatography mass spectrometry, we determined that ascorbate is present at low amounts in the egg stage, L1 larvae, and mixed animal populations, with the egg stage containing the highest concentrations. Incubating C. elegans with precursor molecules necessary for ascorbate synthesis in plants and animals did not significantly alter ascorbate levels. Furthermore, bioinformatic analyses did not support the presence in C. elegans of either the plant or the animal biosynthetic pathway. However, we observed the complete 13C-labeling of ascorbate when C. elegans was grown with 13C-labeled Escherichia coli as a food source. These results support the hypothesis that ascorbate biosynthesis in invertebrates may proceed by a novel pathway and lay the foundation for a broader understanding of its biological role.
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Affiliation(s)
- Alexander N Patananan
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Lauren M Budenholzer
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Maria E Pedraza
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Eric R Torres
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Lital N Adler
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA.
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33
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Dzialo MC, Travaglini KJ, Shen S, Loo JA, Clarke SG. A new type of protein lysine methyltransferase trimethylates Lys-79 of elongation factor 1A. Biochem Biophys Res Commun 2014; 455:382-9. [PMID: 25446118 DOI: 10.1016/j.bbrc.2014.11.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [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: 10/29/2014] [Accepted: 11/10/2014] [Indexed: 11/19/2022]
Abstract
The elongation factors of Saccharomyces cerevisiae are extensively methylated, containing a total of ten methyllysine residues. Elongation factor methyltransferases (Efm1, Efm2, Efm3, and Efm4) catalyze at least four of these modifications. Here we report the identification of a new type of protein lysine methyltransferase, Efm5 (Ygr001c), which was initially classified as N6-adenine DNA methyltransferase-like. Efm5 is required for trimethylation of Lys-79 on EF1A. We directly show the loss of this modification in efm5Δ strains by both mass spectrometry and amino acid analysis. Close homologs of Efm5 are found in vertebrates, invertebrates, and plants, although some fungal species apparently lack this enzyme. This suggests possible unique functions of this modification in S. cerevisiae and higher eukaryotes. The misannotation of Efm5 was due to the presence of a DPPF sequence in post-Motif II, typically associated with DNA methylation. Further analysis of this motif and others like it demonstrates a potential consensus sequence for N-methyltransferases.
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Affiliation(s)
- Maria C Dzialo
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Kyle J Travaglini
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Sean Shen
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA; Department of Biological Chemistry and UCLA/DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA 90095, USA
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA.
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34
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Abstract
Biological responses due to nutrient deprivation in the nematode Caenorhabditis elegans, including L1 diapause and autophagy during dauer formation, can be mediated through the linked DAF-2/insulin/IGF receptor and target-of-rapamycin (TOR) kinase pathways. Here we discuss how altered insulin/TOR signaling may underlie the previously reported phenotypes of worms with a null mutation in the pcm-1 gene that results in reduced autophagy during dauer formation and decreased L1 arrest survival. PCM-1 encodes a protein repair methyltransferase and mutants of the encoding pcm-1 gene are incapable of converting spontaneously damaged l-isoaspartyl residues in cellular proteins to normal forms by this pathway. We speculate that PCM-1 may function either directly or indirectly as an inhibitor of insulin/TOR signaling, perhaps in a role to balance autophagy with alternative protein degradation pathways that may be more specific for recognizing age-damaged proteins.
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Affiliation(s)
- Tara A Gomez
- Department of Chemistry and Biochemistry, Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
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35
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Feng Y, Hadjikyriacou A, Clarke SG. Substrate specificity of human protein arginine methyltransferase 7 (PRMT7): the importance of acidic residues in the double E loop. J Biol Chem 2014; 289:32604-16. [PMID: 25294873 DOI: 10.1074/jbc.m114.609271] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein arginine methyltransferase 7 (PRMT7) methylates arginine residues on various protein substrates and is involved in DNA transcription, RNA splicing, DNA repair, cell differentiation, and metastasis. The substrate sequences it recognizes in vivo and the enzymatic mechanism behind it, however, remain to be explored. Here we characterize methylation catalyzed by a bacterially expressed GST-tagged human PRMT7 fusion protein with a broad range of peptide and protein substrates. After confirming its type III activity generating only ω-N(G)-monomethylarginine and its distinct substrate specificity for RXR motifs surrounded by basic residues, we performed site-directed mutagenesis studies on this enzyme, revealing that two acidic residues within the double E loop, Asp-147 and Glu-149, modulate the substrate preference. Furthermore, altering a single acidic residue, Glu-478, on the C-terminal domain to glutamine nearly abolished the activity of the enzyme. Additionally, we demonstrate that PRMT7 has unusual temperature dependence and salt tolerance. These results provide a biochemical foundation to understanding the broad biological functions of PRMT7 in health and disease.
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Affiliation(s)
- You Feng
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California 90095-1569
| | - Andrea Hadjikyriacou
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California 90095-1569
| | - Steven G Clarke
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California 90095-1569
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36
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Dzialo MC, Travaglini KJ, Shen S, Roy K, Chanfreau GF, Loo JA, Clarke SG. Translational roles of elongation factor 2 protein lysine methylation. J Biol Chem 2014; 289:30511-30524. [PMID: 25231983 DOI: 10.1074/jbc.m114.605527] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Methylation of various components of the translational machinery has been shown to globally affect protein synthesis. Little is currently known about the role of lysine methylation on elongation factors. Here we show that in Saccharomyces cerevisiae, the product of the EFM3/YJR129C gene is responsible for the trimethylation of lysine 509 on elongation factor 2. Deletion of EFM3 or of the previously described EFM2 increases sensitivity to antibiotics that target translation and decreases translational fidelity. Furthermore, the amino acid sequences of Efm3 and Efm2, as well as their respective methylation sites on EF2, are conserved in other eukaryotes. These results suggest the importance of lysine methylation modification of EF2 in fine tuning the translational apparatus.
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Affiliation(s)
- Maria C Dzialo
- Department of Chemistry and Biochemistry and the Molecular Biology Institute and UCLA, Los Angeles, California 90095
| | - Kyle J Travaglini
- Department of Chemistry and Biochemistry and the Molecular Biology Institute and UCLA, Los Angeles, California 90095
| | - Sean Shen
- Department of Chemistry and Biochemistry and the Molecular Biology Institute and UCLA, Los Angeles, California 90095
| | - Kevin Roy
- Department of Chemistry and Biochemistry and the Molecular Biology Institute and UCLA, Los Angeles, California 90095
| | - Guillaume F Chanfreau
- Department of Chemistry and Biochemistry and the Molecular Biology Institute and UCLA, Los Angeles, California 90095
| | - Joseph A Loo
- Department of Chemistry and Biochemistry and the Molecular Biology Institute and UCLA, Los Angeles, California 90095; Department of Biological Chemistry and UCLA/Department of Energy Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute and UCLA, Los Angeles, California 90095.
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37
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Patananan AN, Capri J, Whitelegge JP, Clarke SG. Non-repair pathways for minimizing protein isoaspartyl damage in the yeast Saccharomyces cerevisiae. J Biol Chem 2014; 289:16936-53. [PMID: 24764295 DOI: 10.1074/jbc.m114.564385] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The spontaneous degradation of asparaginyl and aspartyl residues to isoaspartyl residues is a common type of protein damage in aging organisms. Although the protein-l-isoaspartyl (d-aspartyl) O-methyltransferase (EC 2.1.1.77) can initiate the repair of l-isoaspartyl residues to l-aspartyl residues in most organisms, no gene homolog or enzymatic activity is present in the budding yeast Saccharomyces cerevisiae. Therefore, we used biochemical approaches to elucidate how proteins containing isoaspartyl residues are metabolized in this organism. Surprisingly, the level of isoaspartyl residues in yeast proteins (50-300 pmol of isoaspartyl residues/mg of protein extract) is comparable with organisms with protein-l-isoaspartyl (d-aspartyl) O-methyltransferase, suggesting a novel regulatory pathway. Interfering with common protein quality control mechanisms by mutating and inhibiting the proteasomal and autophagic pathways in vivo did not increase isoaspartyl residue levels compared with wild type or uninhibited cells. However, the inhibition of metalloproteases in in vitro aging experiments by EDTA resulted in an ∼3-fold increase in the level of isoaspartyl-containing peptides. Characterization by mass spectrometry of these peptides identified several proteins involved in metabolism as targets of isoaspartyl damage. Further analysis of these peptides revealed that many have an N-terminal isoaspartyl site and originate from proteins with short half-lives. These results suggest that one or more metalloproteases participate in limiting isoaspartyl formation by robust proteolysis.
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Affiliation(s)
- Alexander N Patananan
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute and
| | - Joseph Capri
- the Pasarow Mass Spectrometry Laboratory, Neuropsychiatric Institute-Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles, California 90095
| | - Julian P Whitelegge
- the Pasarow Mass Spectrometry Laboratory, Neuropsychiatric Institute-Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles, California 90095
| | - Steven G Clarke
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute and
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38
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Lissina E, Weiss D, Young B, Rella A, Cheung-Ong K, Del Poeta M, Clarke SG, Giaever G, Nislow C. A novel small molecule methyltransferase is important for virulence in Candida albicans. ACS Chem Biol 2013; 8:2785-93. [PMID: 24083538 DOI: 10.1021/cb400607h] [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] [Indexed: 12/30/2022]
Abstract
Candida albicans is an opportunistic pathogen capable of causing life-threatening infections in immunocompromised individuals. Despite its significant health impact, our understanding of C. albicans pathogenicity is limited, particularly at the molecular level. One of the largely understudied enzyme families in C. albicans are small molecule AdoMet-dependent methyltransferases (smMTases), which are important for maintenance of cellular homeostasis by clearing toxic chemicals, generating novel cellular intermediates, and regulating intra- and interspecies interactions. In this study, we demonstrated that C. albicans Crg1 (CaCrg1) is a bona fide smMTase that interacts with the toxin in vitro and in vivo. We report that CaCrg1 is important for virulence-related processes such as adhesion, hyphal elongation, and membrane trafficking. Biochemical and genetic analyses showed that CaCrg1 plays a role in the complex sphingolipid pathway: it binds to exogenous short-chain ceramides in vitro and interacts genetically with genes of glucosylceramide pathway, and the deletion of CaCRG1 leads to significant changes in the abundance of phytoceramides. Finally we found that this novel lipid-related smMTase is required for virulence in the waxmoth Galleria mellonella, a model of infection.
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Affiliation(s)
- Elena Lissina
- Department
of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, 160 College St., Toronto, M5S 3E1, Canada
| | - David Weiss
- Department
of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Brian Young
- Department
of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Antonella Rella
- Department
of Molecular Genetics and Microbiology, Stony Brook University, 150 Life Sciences Building, Stony Brook, New York 11794-5222, United States
| | - Kahlin Cheung-Ong
- Department
of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, 160 College St., Toronto, M5S 3E1, Canada
| | - Maurizio Del Poeta
- Department
of Molecular Genetics and Microbiology, Stony Brook University, 150 Life Sciences Building, Stony Brook, New York 11794-5222, United States
| | - Steven G. Clarke
- Department
of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Guri Giaever
- Department
of Pharmaceutical Sciences, University of British Columbia, 2405
Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Corey Nislow
- Department
of Pharmaceutical Sciences, University of British Columbia, 2405
Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
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39
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Feng Y, Maity R, Whitelegge JP, Hadjikyriacou A, Li Z, Zurita-Lopez C, Al-Hadid Q, Clark AT, Bedford MT, Masson JY, Clarke SG. Mammalian protein arginine methyltransferase 7 (PRMT7) specifically targets RXR sites in lysine- and arginine-rich regions. J Biol Chem 2013; 288:37010-25. [PMID: 24247247 DOI: 10.1074/jbc.m113.525345] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mammalian protein arginine methyltransferase 7 (PRMT7) has been implicated in roles of transcriptional regulation, DNA damage repair, RNA splicing, cell differentiation, and metastasis. However, the type of reaction that it catalyzes and its substrate specificity remain controversial. In this study, we purified a recombinant mouse PRMT7 expressed in insect cells that demonstrates a robust methyltransferase activity. Using a variety of substrates, we demonstrate that the enzyme only catalyzes the formation of ω-monomethylarginine residues, and we confirm its activity as the prototype type III protein arginine methyltransferase. This enzyme is active on all recombinant human core histones, but histone H2B is a highly preferred substrate. Analysis of the specific methylation sites within intact histone H2B and within H2B and H4 peptides revealed novel post-translational modification sites and a unique specificity of PRMT7 for methylating arginine residues in lysine- and arginine-rich regions. We demonstrate that a prominent substrate recognition motif consists of a pair of arginine residues separated by one residue (RXR motif). These findings will significantly accelerate substrate profile analysis, biological function study, and inhibitor discovery for PRMT7.
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Affiliation(s)
- You Feng
- From the Departments of Chemistry and Biochemistry and
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40
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Shen-Miller J, Lindner P, Xie Y, Villa S, Wooding K, Clarke SG, Loo RRO, Loo JA. Thermal-stable proteins of fruit of long-living Sacred Lotus Nelumbo nucifera Gaertn var. China Antique. Trop Plant Biol 2013; 6:10.1007/s12042-013-9124-2. [PMID: 24363819 PMCID: PMC3869599 DOI: 10.1007/s12042-013-9124-2] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Single-seeded fruit of the sacred lotus Nelumbo nucifera Gaertn var. China Antique from NE China have viability as long as ~1300 years determined by direct radiocarbon-dating, having a germination rate of 84%. The pericarp, a fruit tissue that encloses the single seeds of Nelumbo, is considered one of the major factors that contribute to fruit longevity. Proteins that are heat stable and have protective function may be equally important to seed viability. We show proteins of Nelumbo fruit that are able to withstand heating, 31% of which remained soluble in the 110°C-treated embryo-axis of a 549-yr-old fruit and 76% retained fluidity in its cotyledons. Genome of Nelumbo is published. The amino-acid sequences of 11 "thermal proteins" (soluble at 100°C) of modern Nelumbo embryo-axes and cotyledons, identified by mass spectrometry, Western blot and bioassay, are assembled and aligned with those of an archaeal-hyperthermophile Methancaldococcus jannaschii (Mj; an anaerobic methanogen having a growth optimum of 85°C) and with five mesophile angiosperms. These thermal proteins have roles in protection and repair under stress. More than half of the Nelumbo thermal proteins (55%) are present in the archaean Mj, indicating their long-term durability and history. One Nelumbo protein-repair enzyme exhibits activity at 100°C, having a higher heat-tolerance than that of Arabidopsis. A list of 30 sequenced but unassembled thermal proteins of Nelumbo is supplemented.
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Affiliation(s)
- J Shen-Miller
- IGPP Center for the Study of Evolution and Origin of Life, Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Geology Building, Room 5676, 595 Charles E. Young Drive East, Los Angeles, CA 90095-1567, USA, Telephone: (310) 825-2891, ,
| | - Petra Lindner
- Lehrstuhl Mikrobiologie Regensburg University Universitat Str. 31 93053 Regensburg, Germany
| | - Yongming Xie
- Department of Chemistry and Biochemistry University of California, Los Angeles 402 Boyer Hall, Hilgard Avenue Los Angeles, CA 90095-1569, USA
| | - Sarah Villa
- Department of Chemistry and Biochemistry University of California, Los Angeles 640 Boyer Hall, Hilgard Avenue Los Angeles, CA 90095-1570, USA
| | - Kerry Wooding
- Department of Chemistry and Biochemistry University of California, Los Angeles 402 Boyer Hall, Hilgard Avenue Los Angeles, CA 90095-1569, USA
| | - Steven G Clarke
- Department of Chemistry and Biochemistry University of California, Los Angeles 640 Boyer Hall, Hilgard Avenue Los Angeles, CA 90095-1570, USA
| | - Rachel R O Loo
- Department of Chemistry and Biochemistry University of California, Los Angeles 402 Boyer Hall, Hilgard Avenue Los Angeles, CA 90095-1569, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry University of California, Los Angeles 402 Boyer Hall, Hilgard Avenue Los Angeles, CA 90095-1569, USA
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41
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Nayak NR, Putnam AA, Addepalli B, Lowenson JD, Chen T, Jankowsky E, Perry SE, Dinkins RD, Limbach PA, Clarke SG, Downie AB. An Arabidopsis ATP-dependent, DEAD-box RNA helicase loses activity upon IsoAsp formation but is restored by PROTEIN ISOASPARTYL METHYLTRANSFERASE. Plant Cell 2013; 25:2573-86. [PMID: 23903319 PMCID: PMC3753384 DOI: 10.1105/tpc.113.113456] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Orthodox seeds are capable of withstanding severe dehydration. However, in the dehydrated state, Asn and Asp residues in proteins can convert to succinimide residues that can further react to predominantly form isomerized isoAsp residues upon rehydration (imbibition). IsoAsp residues can impair protein function and can render seeds nonviable, but PROTEIN ISOASPARTYL METHYLTRANSFERASE (PIMT) can initiate isoAsp conversion to Asp residues. The proteins necessary for translation upon imbibition in orthodox seeds may be particularly important to maintain in an active state. One such protein is the large, multidomain protein, Arabidopsis thaliana PLANT RNA HELICASE75 (PRH75), a DEAD-box helicase known to be susceptible to isoAsp residue accumulation. However, the consequences of such isomerization on PRH75 catalysis and for the plant are unknown. Here, it is demonstrated that PRH75 is necessary for successful seed development. It acquires isoAsp rapidly during heat stress, which eliminates RNA unwinding (but not rewinding) competence. The repair by PIMT is able to restore PRH75's complex biochemical activity provided isoAsp formation has not led to subsequent, destabilizing conformational alterations. For PRH75, an important enzymatic activity associated with translation would be eliminated unless rapidly repaired by PIMT prior to additional, deleterious conformational changes that would compromise seed vitality and germination.
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Affiliation(s)
- Nihar R. Nayak
- Department of Horticulture, University of Kentucky, Lexington, Kentucky 40546-0312
- Seed Biology Group, University of Kentucky, Lexington, Kentucky 40546-0312
| | - Andrea A. Putnam
- Center for RNA Molecular Biology and Department of Biochemistry, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106
| | | | - Jonathan D. Lowenson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569
| | - Tingsu Chen
- Department of Horticulture, University of Kentucky, Lexington, Kentucky 40546-0312
- Seed Biology Group, University of Kentucky, Lexington, Kentucky 40546-0312
| | - Eckhard Jankowsky
- Center for RNA Molecular Biology and Department of Biochemistry, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106
| | - Sharyn E. Perry
- Seed Biology Group, University of Kentucky, Lexington, Kentucky 40546-0312
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546-0312
| | - Randy D. Dinkins
- U.S. Department of Agriculture–Agricultural Research Service Forage Animal Production Research Unit, N220C Agriculture Science Center North, University of Kentucky, Lexington, Kentucky 40546-0312
| | - Patrick A. Limbach
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221
| | - Steven G. Clarke
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569
| | - A. Bruce Downie
- Department of Horticulture, University of Kentucky, Lexington, Kentucky 40546-0312
- Seed Biology Group, University of Kentucky, Lexington, Kentucky 40546-0312
- Address correspondence to
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MacKay KB, Tu Y, Young SG, Clarke SG. Circumventing embryonic lethality with Lcmt1 deficiency: generation of hypomorphic Lcmt1 mice with reduced protein phosphatase 2A methyltransferase expression and defects in insulin signaling. PLoS One 2013; 8:e65967. [PMID: 23840384 PMCID: PMC3688711 DOI: 10.1371/journal.pone.0065967] [Citation(s) in RCA: 11] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 05/03/2013] [Indexed: 11/18/2022] Open
Abstract
Protein phosphatase 2A (PP2A), the major serine/threonine phosphatase in eukaryotic cells, is a heterotrimeric protein composed of structural, catalytic, and targeting subunits. PP2A assembly is governed by a variety of mechanisms, one of which is carboxyl-terminal methylation of the catalytic subunit by the leucine carboxyl methyltransferase LCMT1. PP2A is nearly stoichiometrically methylated in the cytosol, and although some PP2A targeting subunits bind independently of methylation, this modification is required for the binding of others. To examine the role of this methylation reaction in mammalian tissues, we generated a mouse harboring a gene-trap cassette within intron 1 of Lcmt1. Due to splicing around the insertion, Lcmt1 transcript and LCMT1 protein levels were reduced but not eliminated. LCMT1 activity and methylation of PP2A were reduced in a coordinate fashion, suggesting that LCMT1 is the only PP2A methyltransferase. These mice exhibited an insulin-resistance phenotype, indicating a role for this methyltransferase in signaling in insulin-sensitive tissues. Tissues from these animals will be vital for the in vivo identification of methylation-sensitive substrates of PP2A and how they respond to differing physiological conditions.
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Affiliation(s)
- Kennen B. MacKay
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Yiping Tu
- Department of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Stephen G. Young
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Steven G. Clarke
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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Patananan AN, Palmer JM, Garvey GS, Keller NP, Clarke SG. A novel automethylation reaction in the Aspergillus nidulans LaeA protein generates S-methylmethionine. J Biol Chem 2013; 288:14032-14045. [PMID: 23532849 PMCID: PMC3656261 DOI: 10.1074/jbc.m113.465765] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The filamentous fungi in the genus Aspergillus are opportunistic plant and animal pathogens that can adapt to their environment by producing various secondary metabolites, including lovastatin, penicillin, and aflatoxin. The synthesis of these small molecules is dependent on gene clusters that are globally regulated by the LaeA protein. Null mutants of LaeA in all pathogenic fungi examined to date show decreased virulence coupled with reduced secondary metabolism. Although the amino acid sequence of LaeA contains the motifs characteristic of seven-β-strand methyltransferases, a methyl-accepting substrate of LaeA has not been identified. In this work we did not find a methyl-accepting substrate in Aspergillus nidulans with various assays, including in vivo S-adenosyl-[methyl-(3)H]methionine labeling, targeted in vitro methylation experiments using putative protein substrates, or in vitro methylation assays using whole cell extracts grown under different conditions. However, in each experiment LaeA was shown to self-methylate. Amino acid hydrolysis of radioactively labeled LaeA followed by cation exchange and reverse phase chromatography identified methionine as the modified residue. Point mutations show that the major site of modification of LaeA is on methionine 207. However, in vivo complementation showed that methionine 207 is not required for the biological function of LaeA. LaeA is the first protein to exhibit automethylation at a methionine residue. These findings not only indicate LaeA may perform novel chemistry with S-adenosylmethionine but also provide new insights into the physiological function of LaeA.
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Affiliation(s)
- Alexander N. Patananan
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California 90095 and
| | | | | | - Nancy P. Keller
- the Departments of Medical Microbiology and Immunology and ,Bacteriology, University of Wisconsin, Madison, Wisconsin 53706
| | - Steven G. Clarke
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California 90095 and , To whom correspondence should be addressed: Dept. of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, 607 Charles E. Young Dr. East, Los Angeles, CA. Tel.: 310-825-8754; Fax: 310-825-1968; E-mail:
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Dai S, Ni W, Patananan AN, Clarke SG, Karger BL, Zhou ZS. Integrated proteomic analysis of major isoaspartyl-containing proteins in the urine of wild type and protein L-isoaspartate O-methyltransferase-deficient mice. Anal Chem 2013; 85:2423-30. [PMID: 23327623 DOI: 10.1021/ac303428h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The formation of isoaspartyl residues (isoAsp or isoD) via either aspartyl isomerization or asparaginyl deamidation alters protein structure and potentially biological function. This is a spontaneous and nonenzymatic process, ubiquitous both in vivo and in nonbiological systems, such as in protein pharmaceuticals. In almost all organisms, protein L-isoaspartate O-methyltransferase (PIMT, EC2.1.1.77) recognizes and initiates the conversion of isoAsp back to aspartic acid. Additionally, alternative proteolytic and excretion pathways to metabolize isoaspartyl-containing proteins have been proposed but not fully explored, largely due to the analytical challenges for detecting isoAsp. We report here the relative quantitation and site profiling of isoAsp in urinary proteins from wild type and PIMT-deficient mice, representing products from excretion pathways. First, using a biochemical approach, we found that the total isoaspartyl level of proteins in urine of PIMT-deficient male mice was elevated. Subsequently, the major isoaspartyl protein species in urine from these mice were identified as major urinary proteins (MUPs) by shotgun proteomics. To enhance the sensitivity of isoAsp detection, a targeted proteomic approach using electron transfer dissociation-selected reaction monitoring (ETD-SRM) was developed to investigate isoAsp sites in MUPs. A total of 38 putative isoAsp modification sites in MUPs were investigated, with five derived from the deamidation of asparagine that were confirmed to contribute to the elevated isoAsp levels. Our findings lend experimental evidence for the hypothesized excretion pathway for isoAsp proteins. Additionally, the developed method opens up the possibility to explore processing mechanisms of isoaspartyl proteins at the molecular level, such as the fate of protein pharmaceuticals in circulation.
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Affiliation(s)
- Shujia Dai
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston Massachusetts 02115, United States
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Abstract
Modifications of both DNA and protein by methylation are key factors in normal T and B cell immune responses as well as in the development of autoimmune disease. For example, the failure to maintain the methylation status of CpG dinucleotides in DNA triggers T cell autoreactivity. Methylated proteins are known targets of autoimmunity, including the symmetrical dimethylarginine residues of SmD1 and SmD3 in SLE. Herein, we demonstrate that altering the metabolism of S-adenosylmethionine (SAM), the major methyl donor for transmethylation reactions, can suppress T cell immunity. A by-product of SAM metabolism, 5'-deoxy-5'-methylthioadenosine (MTA), and an indirect inhibitor of methyltransferases, inhibits T cell responses including T cell activation markers, Th1/Th2 cytokines and TCR-related signaling events. Moreover, treatment of the lupus-prone MRL/lpr mouse with MTA markedly ameliorates splenomegaly, lymphadenopathy, autoantibody titers as well as IgG deposition and cellular infiltration in the kidney. Incubation of cells with SAM, which increases intracellular MTA levels, inhibits both TCR-mediated T cell proliferation and BCR (anti-IgM)-triggered B cell proliferation in a dose-dependent manner. These studies define the central role of MTA and SAM in immune responses and provide a simple approach to altering lymphocyte transmethylation and T cell mediated autoimmune syndromes.
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Affiliation(s)
- Mei-Ling Yang
- Section of Rheumatology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06520-8031, USA
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46
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Abstract
L-isoaspartyl (D-aspartyl) O-methyltransferase deficient mice (Pcmt1−/−) accumulate isomerized aspartyl residues in intracellular proteins until their death due to seizures at approximately 45 days. Previous studies have shown that these mice have constitutively activated insulin signaling in their brains, and that these brains are 20–30% larger than those from age-matched wild-type animals. To determine whether insulin pathway activation and brain enlargement is responsible for the fatal seizures, we administered wortmannin, an inhibitor of the phosphoinositide 3-kinase that catalyzes an early step in the insulin pathway. Oral wortmannin reduced the average brain size in the Pcmt1−/− animals to within 6% of the wild-type DMSO administered controls, and nearly doubled the lifespan of Pcmt1−/− at 60% survival of the original population. Immunoblotting revealed significant decreases in phosphorylation of Akt, PDK1, and mTOR in Pcmt1−/− mice and Akt and PDK1 in wild-type animals upon treatment with wortmannin. These data suggest activation of the insulin pathway and its resulting brain enlargement contributes to the early death of Pcmt1−/− mice, but is not solely responsible for the early death observed in these animals.
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Affiliation(s)
- Kennen B. MacKay
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Jonathan D. Lowenson
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Steven G. Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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47
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Urzica EI, Casero D, Yamasaki H, Hsieh SI, Adler LN, Karpowicz SJ, Blaby-Haas CE, Clarke SG, Loo JA, Pellegrini M, Merchant SS. Systems and trans-system level analysis identifies conserved iron deficiency responses in the plant lineage. Plant Cell 2012; 24:3921-48. [PMID: 23043051 PMCID: PMC3517228 DOI: 10.1105/tpc.112.102491] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 08/31/2012] [Accepted: 09/12/2012] [Indexed: 05/03/2023]
Abstract
We surveyed the iron nutrition-responsive transcriptome of Chlamydomonas reinhardtii using RNA-Seq methodology. Presumed primary targets were identified in comparisons between visually asymptomatic iron-deficient versus iron-replete cells. This includes the known components of high-affinity iron uptake as well as candidates for distributive iron transport in C. reinhardtii. Comparison of growth-inhibited iron-limited versus iron-replete cells revealed changes in the expression of genes in chloroplastic oxidative stress response pathways, among hundreds of other genes. The output from the transcriptome was validated at multiple levels: by quantitative RT-PCR for assessing the data analysis pipeline, by quantitative proteomics for assessing the impact of changes in RNA abundance on the proteome, and by cross-species comparison for identifying conserved or universal response pathways. In addition, we assessed the functional importance of three target genes, Vitamin C 2 (VTC2), monodehydroascorbate reductase 1 (MDAR1), and conserved in the green lineage and diatoms 27 (CGLD27), by biochemistry or reverse genetics. VTC2 and MDAR1, which are key enzymes in de novo ascorbate synthesis and ascorbate recycling, respectively, are likely responsible for the 10-fold increase in ascorbate content of iron-limited cells. CGLD27/At5g67370 is a highly conserved, presumed chloroplast-localized pioneer protein and is important for growth of Arabidopsis thaliana in low iron.
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Affiliation(s)
- Eugen I. Urzica
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - David Casero
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095
- Institute of Genomics and Proteomics, David Geffen School of Medicine at the University of California, Los Angeles, California 90095
| | - Hiroaki Yamasaki
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
- Institute of Genomics and Proteomics, David Geffen School of Medicine at the University of California, Los Angeles, California 90095
| | - Scott I. Hsieh
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Lital N. Adler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Steven J. Karpowicz
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Crysten E. Blaby-Haas
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Steven G. Clarke
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
- Institute of Genomics and Proteomics, David Geffen School of Medicine at the University of California, Los Angeles, California 90095
- Department of Biological Chemistry, David Geffen School of Medicine at the University of California, Los Angeles, California 90095
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095
- Institute of Genomics and Proteomics, David Geffen School of Medicine at the University of California, Los Angeles, California 90095
| | - Sabeeha S. Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
- Institute of Genomics and Proteomics, David Geffen School of Medicine at the University of California, Los Angeles, California 90095
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Young BD, Weiss DI, Zurita-Lopez CI, Webb KJ, Clarke SG, McBride AE. Identification of methylated proteins in the yeast small ribosomal subunit: a role for SPOUT methyltransferases in protein arginine methylation. Biochemistry 2012; 51:5091-104. [PMID: 22650761 DOI: 10.1021/bi300186g] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have characterized the posttranslational methylation of Rps2, Rps3, and Rps27a, three small ribosomal subunit proteins in the yeast Saccharomyces cerevisiae, using mass spectrometry and amino acid analysis. We found that Rps2 is substoichiometrically modified at arginine-10 by the Rmt1 methyltransferase. We demonstrated that Rps3 is stoichiometrically modified by ω-monomethylation at arginine-146 by mass spectrometric and site-directed mutagenic analyses. Substitution of alanine for arginine at position 146 is associated with slow cell growth, suggesting that the amino acid identity at this site may influence ribosomal function and/or biogenesis. Analysis of the three-dimensional structure of Rps3 in S. cerevisiae shows that arginine-146 makes contacts with the small subunit rRNA. Screening of deletion mutants encoding potential yeast methyltransferases revealed that the loss of the YOR021C gene results in the absence of methylation of Rps3. We demonstrated that recombinant Yor021c catalyzes ω-monomethylarginine formation when incubated with S-adenosylmethionine and hypomethylated ribosomes prepared from a YOR021C deletion strain. Interestingly, Yor021c belongs to the family of SPOUT methyltransferases that, to date, have only been shown to modify RNA substrates. Our findings suggest a wider role for SPOUT methyltransferases in nature. Finally, we have demonstrated the presence of a stoichiometrically methylated cysteine residue at position 39 of Rps27a in a zinc-cysteine cluster. The discovery of these three novel sites of protein modification within the small ribosomal subunit will now allow for an analysis of their functional roles in translation and possibly other cellular processes.
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Affiliation(s)
- Brian D Young
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California 90095, USA
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49
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Urzica EI, Adler LN, Page MD, Linster CL, Arbing MA, Casero D, Pellegrini M, Merchant SS, Clarke SG. Impact of oxidative stress on ascorbate biosynthesis in Chlamydomonas via regulation of the VTC2 gene encoding a GDP-L-galactose phosphorylase. J Biol Chem 2012; 287:14234-45. [PMID: 22393048 PMCID: PMC3340187 DOI: 10.1074/jbc.m112.341982] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 02/23/2012] [Indexed: 12/30/2022] Open
Abstract
The L-galactose (Smirnoff-Wheeler) pathway represents the major route to L-ascorbic acid (vitamin C) biosynthesis in higher plants. Arabidopsis thaliana VTC2 and its paralogue VTC5 function as GDP-L-galactose phosphorylases converting GDP-L-galactose to L-galactose-1-P, thus catalyzing the first committed step in the biosynthesis of L-ascorbate. Here we report that the L-galactose pathway of ascorbate biosynthesis described in higher plants is conserved in green algae. The Chlamydomonas reinhardtii genome encodes all the enzymes required for vitamin C biosynthesis via the L-galactose pathway. We have characterized recombinant C. reinhardtii VTC2 as an active GDP-L-galactose phosphorylase. C. reinhardtii cells exposed to oxidative stress show increased VTC2 mRNA and L-ascorbate levels. Genes encoding enzymatic components of the ascorbate-glutathione system (e.g. ascorbate peroxidase, manganese superoxide dismutase, and dehydroascorbate reductase) are also up-regulated in response to increased oxidative stress. These results indicate that C. reinhardtii VTC2, like its plant homologs, is a highly regulated enzyme in ascorbate biosynthesis in green algae and that, together with the ascorbate recycling system, the L-galactose pathway represents the major route for providing protective levels of ascorbate in oxidatively stressed algal cells.
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Affiliation(s)
| | | | | | - Carole L. Linster
- From the Departments of Chemistry and Biochemistry
- the de Duve Institute, Université Catholique de Louvain, BCHM 7539, Ave. Hippocrate 75, B-1200 Brussels, Belgium
| | | | | | - Matteo Pellegrini
- Molecular, Cell, and Developmental Biology, and
- Institute of Genomics and Proteomics
| | - Sabeeha S. Merchant
- From the Departments of Chemistry and Biochemistry
- Institute of Genomics and Proteomics
- Molecular Biology Institute, UCLA, Los Angeles, California 90095 and
| | - Steven G. Clarke
- From the Departments of Chemistry and Biochemistry
- Molecular Biology Institute, UCLA, Los Angeles, California 90095 and
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50
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Clarke SG, Phillips ATM, Bull AMJ, Cobb JP. A hierarchy of computationally derived surgical and patient influences on metal on metal press-fit acetabular cup failure. J Biomech 2012; 45:1698-704. [PMID: 22513086 DOI: 10.1016/j.jbiomech.2012.03.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 02/20/2012] [Accepted: 03/14/2012] [Indexed: 10/28/2022]
Abstract
The impact of anatomical variation and surgical error on excessive wear and loosening of the acetabular component of large diameter metal-on-metal hip arthroplasties was measured using a multi-factorial analysis through 112 different simulations. Each surgical scenario was subject to eight different daily loading activities using finite element analysis. Excessive wear appears to be predominantly dependent on cup orientation, with inclination error having a higher influence than version error, according to the study findings. Acetabular cup loosening, as inferred from initial implant stability, appears to depend predominantly on factors concerning the area of cup-bone contact, specifically the level of cup seating achieved and the individual patient's anatomy. The extent of press fit obtained at time of surgery did not appear to influence either mechanism of failure in this study.
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Affiliation(s)
- S G Clarke
- Structural Biomechanics, Department of Civil and Environmental Engineering, Imperial College London, Skempton Building, South Kensington Campus, London SW7 2AZ, UK.
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