1
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Didier A, Bourner M, Kleks G, Zolty A, Kumar B, Nichols T, Durynski K, Bender S, Gibison M, Murphy L, Ellis JC, Dong DW, Kashina A. Prospective fecal microbiomic biomarkers for chronic wasting disease. Microbiol Spectr 2024; 12:e0375022. [PMID: 38299851 PMCID: PMC10913453 DOI: 10.1128/spectrum.03750-22] [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: 09/16/2022] [Accepted: 12/19/2023] [Indexed: 02/02/2024] Open
Abstract
Chronic wasting disease (CWD) is a naturally occurring prion disease in cervids that has been rapidly proliferating in the United States. Here, we investigated a potential link between CWD infection and gut microbiome by analyzing 50 fecal samples obtained from CWD-positive animals of different sexes from various regions in the USA compared to 50 CWD-negative controls using high throughput sequencing of the 16S ribosomal RNA and targeted metabolomics. Our analysis reveals promising trends in the gut microbiota that could potentially be CWD-dependent, including several bacterial taxa at each rank level, as well as taxa pairs, that can differentiate between CWD-negative and CWD-positive deer. Through machine-learning, these taxa and taxa pairs at each rank level could facilitate identification of around 70% of both the CWD-negative and the CWD-positive samples. Our results provide a potential tool for diagnostics and surveillance of CWD in the wild, as well as conceptual advances in our understanding of the disease.IMPORTANCEThis is a comprehensive study that tests the connection between the composition of the gut microbiome in deer in response to chronic wasting disease (CWD). We analyzed 50 fecal samples obtained from CWD-positive animals compared to 50 CWD-negative controls to identify CWD-dependent changes in the gut microbiome, matched with the analysis of fecal metabolites. Our results show promising trends suggesting that fecal microbial composition can directly correspond to CWD disease status. These results point to the microbial composition of the feces as a potential tool for diagnostics and surveillance of CWD in the wild, including non-invasive CWD detection in asymptomatic deer and deer habitats, and enable conceptual advances in our understanding of the disease.
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Affiliation(s)
- Adam Didier
- MilliporeSigma, Merck KGaA, Darmstadt, Germany
| | | | - Guy Kleks
- Sigma Aldrich Israel Ltd., Merck KGaA, Darmstadt, Germany
| | - Avihai Zolty
- Sigma Aldrich Israel Ltd., Merck KGaA, Darmstadt, Germany
| | - Brajendra Kumar
- Sigma Aldrich Chemical Pvt. Ltd., Merck KGaA, Darmstadt, Germany
| | - Tracy Nichols
- United States Department of Agriculture, Washington, DC, USA
| | - Karie Durynski
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Susan Bender
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michelle Gibison
- Wildlife Futures Program, Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Lisa Murphy
- Wildlife Futures Program, Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Julie C. Ellis
- Wildlife Futures Program, Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Dawei W. Dong
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anna Kashina
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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2
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MacTaggart B, Shimogawa M, Lougee M, Tang HY, Petersson EJ, Kashina A. Global Analysis of Post-Translational Side-Chain Arginylation Using Pan-Arginylation Antibodies. Mol Cell Proteomics 2023; 22:100664. [PMID: 37832787 PMCID: PMC10656225 DOI: 10.1016/j.mcpro.2023.100664] [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: 03/03/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 10/15/2023] Open
Abstract
Arginylation is a post-translational modification mediated by the arginyltransferase 1 (ATE1), which transfers the amino acid arginine to a protein or peptide substrate from a tRNA molecule. Initially, arginylation was thought to occur only on N-terminally exposed acidic residues, and its function was thought to be limited to targeting proteins for degradation. However, more recent data have shown that ATE1 can arginylate side chains of internal acidic residues in a protein without necessarily affecting metabolic stability. This greatly expands the potential targets and functions of arginylation, but tools for studying this process have remained limited. Here, we report the first global screen specifically for side-chain arginylation. We generate and validate "pan-arginylation" antibodies, which are designed to detect side-chain arginylation in any amino acid sequence context. We use these antibodies for immunoaffinity enrichment of side-chain arginylated proteins from wildtype and Ate1 knockout cell lysates. In this way, we identify a limited set of proteins that likely undergo ATE1-dependent side-chain arginylation and that are enriched in specific cellular roles, including translation, splicing, and the cytoskeleton.
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Affiliation(s)
- Brittany MacTaggart
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marie Shimogawa
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marshall Lougee
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hsin-Yao Tang
- Proteomics and Metabolomics Facility, Wistar Institute, Philadelphia, Pennsylvania, USA
| | - E J Petersson
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anna Kashina
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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3
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Jung EJ, Sung KW, Bae TH, Kim HY, Choi HR, Kim SH, Jung CH, Mun SR, Son YS, Kim S, Suh YH, Kashina A, Park JW, Kwon YT. The N-degron pathway mediates lipophagy: The chemical modulation of lipophagy in obesity and NAFLD. Metabolism 2023; 146:155644. [PMID: 37385404 PMCID: PMC10529862 DOI: 10.1016/j.metabol.2023.155644] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/23/2023] [Accepted: 06/24/2023] [Indexed: 07/01/2023]
Abstract
BACKGROUND AND AIMS Central to the pathogenesis of nonalcoholic fatty liver disease (NAFLD) is the accumulation of lipids in the liver and various fat tissues. We aimed to elucidate the mechanisms by which lipid droplets (LDs) in the liver and adipocytes are degraded by the autophagy-lysosome system and develop therapeutic means to modulate lipophagy, i.e., autophagic degradation of LDs. METHODS We monitored the process in which LDs are pinched off by autophagic membranes and degraded by lysosomal hydrolases in cultured cells and mice. The autophagic receptor p62/SQSTM-1/Sequestosome-1 was identified as a key regulator and used as a target to develop drugs to induce lipophagy. The efficacy of p62 agonists was validated in mice to treat hepatosteatosis and obesity. RESULTS We found that the N-degron pathway modulates lipophagy. This autophagic degradation initiates when the molecular chaperones including BiP/GRP78, retro-translocated from the endoplasmic reticulum, is N-terminally (Nt-) arginylated by ATE1 R-transferase. The resulting Nt-arginine (Nt-Arg) binds the ZZ domain of p62 associated with LDs. Upon binding to Nt-Arg, p62 undergoes self-polymerization and recruits LC3+ phagophores to the site of lipophagy, leading to lysosomal degradation. Liver-specific Ate1 conditional knockout mice under high fat diet developed severe NAFLD. The Nt-Arg was modified into small molecule agonists to p62 that facilitate lipophagy in mice and exerted therapeutic efficacy in obesity and hepatosteatosis of wild-type but not p62 knockout mice. CONCLUSIONS Our results show that the N-degron pathway modulates lipophagy and provide p62 as a drug target to treat NAFLD and other diseases related with metabolic syndrome.
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Affiliation(s)
- Eui Jung Jung
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea; Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Ki Woon Sung
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea; Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea; AUTOTAC Bio Inc., Changgyeonggung-Ro 254, Jongno-Gu, Seoul, 03077, Republic of Korea
| | - Tae Hyun Bae
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea; Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Hee-Yeon Kim
- Department of Biochemistry, College of Medicine, Ewha Womans University, Seoul, 07804, Republic of Korea
| | - Ha Rim Choi
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Sung Hyun Kim
- AUTOTAC Bio Inc., Changgyeonggung-Ro 254, Jongno-Gu, Seoul, 03077, Republic of Korea
| | - Chan Hoon Jung
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea; Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Su Ran Mun
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Yeon Sung Son
- Neuroscience Research Institute, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Shin Kim
- Department of Immunology, School of Medicine, Keimyung University, Daegu, 42601, Republic of Korea
| | - Young Ho Suh
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea; Neuroscience Research Institute, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Anna Kashina
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Joo-Won Park
- Department of Biochemistry, College of Medicine, Ewha Womans University, Seoul, 07804, Republic of Korea.
| | - Yong Tae Kwon
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea; Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea; AUTOTAC Bio Inc., Changgyeonggung-Ro 254, Jongno-Gu, Seoul, 03077, Republic of Korea; Convergence Research Center for Dementia, Seoul National University Medical Research Center, Seoul, 03080, Republic of Korea; Ischemic/Hypoxic Disease Institute, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea.
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Vedula P, Fina ME, Bell BA, Nikonov SS, Kashina A, Dong DW. β -actin is essential for structural integrity and physiological function of the retina. bioRxiv 2023:2023.03.27.534392. [PMID: 37034790 PMCID: PMC10081178 DOI: 10.1101/2023.03.27.534392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Lack of non-muscle β -actin gene (Actb) leads to early embryonic lethality in mice, however mice with β - to γ -actin replacement develop normally and show no detectable phenotypes at young age. Here we investigated the effect of this replacement in the retina. During aging, these mice have accelerated de-generation of retinal structure and function, including elongated microvilli and defective mitochondria of retinal pigment epithelium (RPE), abnormally bulging photoreceptor outer segments (OS) accompanied by reduced transducin concentration and light sensitivity, and accumulation of autofluorescent microglia cells in the subretinal space between RPE and OS. These defects are accompanied by changes in the F-actin binding of several key actin interacting partners, including ezrin, myosin, talin, and vinculin known to play central roles in modulating actin cytoskeleton and cell adhesion and mediating the phagocytosis of OS. Our data show that β -actin protein is essential for maintaining normal retinal structure and function.
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Tomer D, Arriagada C, Munshi S, Alexander BE, French B, Vedula P, Caorsi V, House A, Guvendiren M, Kashina A, Schwarzbauer JE, Astrof S. A new mechanism of fibronectin fibril assembly revealed by live imaging and super-resolution microscopy. J Cell Sci 2022; 135:jcs260120. [PMID: 35851804 PMCID: PMC9481930 DOI: 10.1242/jcs.260120] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/11/2022] [Indexed: 08/27/2023] Open
Abstract
Fibronectin (Fn1) fibrils have long been viewed as continuous fibers composed of extended, periodically aligned Fn1 molecules. However, our live-imaging and single-molecule localization microscopy data are inconsistent with this traditional view and show that Fn1 fibrils are composed of roughly spherical nanodomains containing six to eleven Fn1 dimers. As they move toward the cell center, Fn1 nanodomains become organized into linear arrays, in which nanodomains are spaced with an average periodicity of 105±17 nm. Periodical Fn1 nanodomain arrays can be visualized between cells in culture and within tissues; they are resistant to deoxycholate treatment and retain nanodomain periodicity in the absence of cells. The nanodomain periodicity in fibrils remained constant when probed with antibodies recognizing distinct Fn1 epitopes or combinations of antibodies recognizing epitopes spanning the length of Fn1. Treatment with FUD, a peptide that binds the Fn1 N-terminus and disrupts Fn1 fibrillogenesis, blocked the organization of Fn1 nanodomains into periodical arrays. These studies establish a new paradigm of Fn1 fibrillogenesis. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Darshika Tomer
- Department of Cell Biology and Molecular Medicine, Cardiovascular Research Institute, Rutgers Biomedical, and Health Sciences, 185 South Orange Ave, Newark, NJ 07103, USA
| | - Cecilia Arriagada
- Department of Cell Biology and Molecular Medicine, Cardiovascular Research Institute, Rutgers Biomedical, and Health Sciences, 185 South Orange Ave, Newark, NJ 07103, USA
| | - Sudipto Munshi
- Center for Translational Medicine, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Brianna E. Alexander
- Department of Cell Biology and Molecular Medicine, Cardiovascular Research Institute, Rutgers Biomedical, and Health Sciences, 185 South Orange Ave, Newark, NJ 07103, USA
- Multidisciplinary Ph.D. Program in Biomedical Sciences. Cell Biology, Neuroscience and Physiology track, Rutgers Biomedical and Health Sciences, Newark, NJ 07103, USA
| | - Brenda French
- Center for Translational Medicine, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Pavan Vedula
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Andrew House
- Otto H. York Chemical and Materials Engineering, Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Murat Guvendiren
- Otto H. York Chemical and Materials Engineering, Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Anna Kashina
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jean E. Schwarzbauer
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014, USA
| | - Sophie Astrof
- Department of Cell Biology and Molecular Medicine, Cardiovascular Research Institute, Rutgers Biomedical, and Health Sciences, 185 South Orange Ave, Newark, NJ 07103, USA
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6
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Lazar I, Fabre B, Feng Y, Khateb A, Frit P, Kashina A, Zhang T, Avitan-Hersh E, Kim H, Brown K, Topisirovic I, Ronai ZA. Arginyl-tRNA-protein transferase 1 (ATE1) promotes melanoma cell growth and migration. FEBS Lett 2022; 596:1468-1480. [PMID: 35561126 PMCID: PMC10118390 DOI: 10.1002/1873-3468.14376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 11/10/2022]
Abstract
Arginyl-tRNA-protein transferase 1 (ATE1) catalyses N-terminal protein arginylation, a post-translational modification implicated in cell migration, invasion and the cellular stress response. Herein, we report that ATE1 is overexpressed in NRAS-mutant melanomas, while it is downregulated in BRAF-mutant melanomas. ATE1 expression was higher in metastatic tumours, compared with primary tumours. Consistent with these findings, ATE1 depletion reduced melanoma cell viability, migration and colony formation. Reduced ATE1 expression also affected cell responses to mTOR and MEK inhibitors and to serum deprivation. Among putative ATE1 substrates is the tumour suppressor AXIN1, pointing to the possibility that ATE1 may fine-tune AXIN1 function in melanoma. Our findings highlight an unexpected role for ATE1 in melanoma cell aggressiveness and suggest that ATE1 constitutes a potential new therapeutic target.
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Affiliation(s)
- Ikrame Lazar
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.,Technion Integrated Cancer Center, Faculty of Medicine, Technion Institute of Technology, Haifa, Israel.,MCD, Centre de Biologie Intégrative (CBI), CNRS, UT3, Université de Toulouse, France
| | - Bertrand Fabre
- Technion Integrated Cancer Center, Faculty of Medicine, Technion Institute of Technology, Haifa, Israel.,Laboratoire de Recherche en Sciences Végétales, UMR5546, UT3, INP, CNRS, Université de Toulouse, Auzeville-Tolosane, France
| | - Yongmei Feng
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Ali Khateb
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.,Technion Integrated Cancer Center, Faculty of Medicine, Technion Institute of Technology, Haifa, Israel
| | - Philippe Frit
- Institut de Pharmacologie et de Biologie Structurale (IPBS), UMR 5089, CNRS, UT3, Université de Toulouse, France
| | - Anna Kashina
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Emily Avitan-Hersh
- Technion Integrated Cancer Center, Faculty of Medicine, Technion Institute of Technology, Haifa, Israel
| | - Hyungsoo Kim
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Kevin Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Ivan Topisirovic
- Gerald Bronfman Department of Oncology, Departments of Experimental Medicine and Biochemistry, Lady Davis Institute, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Ze'ev A Ronai
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
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Pan B, Shimogawa M, Zhao J, Rhoades E, Kashina A, Petersson EJ. Cysteine-Based Mimic of Arginylation Reproduces Neuroprotective Effects of the Authentic Post-Translational Modification on α-Synuclein. J Am Chem Soc 2022; 144:7911-7918. [PMID: 35451816 PMCID: PMC9922158 DOI: 10.1021/jacs.2c02499] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Arginylation is an understudied post-translational modification (PTM) involving the transfer of arginine to aspartate or glutamate sidechains in a protein. Among the targets of this PTM is α-synuclein (αS), a neuronal protein involved in regulating synaptic vesicles. The aggregation of αS is implicated in neurodegenerative diseases, particularly in Parkinson's disease, and arginylation has been found to protect against this pathological process. Arginylated αS has been studied through semisynthesis involving multipart native chemical ligation (NCL), but this can be very labor-intensive with low yields. Here, we present a facile way to introduce a mimic of the arginylation modification into a protein of interest, compatible with orthogonal installation of labels such as fluorophores. We synthesize bromoacetyl arginine and react it with recombinant, site-specific cysteine mutants of αS. We validate the mimic by testing the vesicle binding affinity of mimic-arginylated αS, as well as its aggregation kinetics and monomer incorporation into fibrils, and comparing these results to those of authentically arginylated αS produced through NCL. In cultured neurons, we compare the fibril seeding capabilities of preformed fibrils carrying a small percentage of arginylated αS. We find that, consistent with authentically arginylated αS, mimic-arginylated αS does not perturb the protein's native function but alters aggregation kinetics and monomer incorporation. Both mimic and authentically modified αS suppress aggregation in neuronal cells. Our results provide further insight into the neuroprotective effects of αS arginylation, and our alternative strategy to generate arginylated αS enables the study of this PTM in proteins not accessible through NCL.
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Affiliation(s)
- Buyan Pan
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, Pennsylvania 19104, USA
| | - Marie Shimogawa
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, Pennsylvania 19104, USA
| | - Jun Zhao
- Department of Biomedical Sciences; University of Pennsylvania School of Veterinary Medicine; 3800 Spruce Street; Philadelphia, Pennsylvania, 19104, USA
| | - Elizabeth Rhoades
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, Pennsylvania 19104, USA
| | - Anna Kashina
- Department of Biomedical Sciences; University of Pennsylvania School of Veterinary Medicine; 3800 Spruce Street; Philadelphia, Pennsylvania, 19104, USA
| | - E. James Petersson
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, Pennsylvania 19104, USA
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8
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Zhao J, Pan B, Fina M, Huang Y, Shimogawa M, Luk KC, Rhoades E, Petersson EJ, Dong DW, Kashina A. α-Synuclein arginylation in the human brain. Transl Neurodegener 2022; 11:20. [PMID: 35395956 PMCID: PMC8991655 DOI: 10.1186/s40035-022-00295-0] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/23/2022] [Indexed: 12/11/2022] Open
Abstract
Background Alpha-synuclein (α-syn) exhibits pathological misfolding in many human neurodegenerative disorders. We previously showed that α-syn is arginylated in the mouse brain and that lack of arginylation leads to neurodegeneration in mice.
Methods Here, we tested α-syn arginylation in human brain pathology using newly derived antibodies in combination with Western blotting, biochemical assays, and experiments in live neurons. Results We found that α-syn was arginylated in the human brain on E46 and E83, two sites previously implicated in α-syn pathology and familial cases of Parkinson’s disease. The levels of arginylation in different brain samples ranged between ~ 3% and ~ 50% of the total α-syn pool, and this arginylation nearly exclusively concentrated in the subcellular α-syn fraction that sedimented at low centrifugation speeds and appeared to be simultaneously targeted by multiple posttranslational modifications. Arginylated α-syn was less susceptible to S129 phosphorylation and pathological aggregation in neurons. The arginylation level inversely correlated with the overall α-syn levels and with patient age, suggesting a possible causal relationship between arginylation decline and α-syn-dependent neuropathology. Conclusion We propose that α-syn arginylation constitutes a potential neuroprotective mechanism that prevents its abnormal accumulation during neurodegeneration and aging in the human brain. Supplementary Information The online version contains supplementary material available at 10.1186/s40035-022-00295-0.
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Affiliation(s)
- Jun Zhao
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, 19104, USA
| | - Buyan Pan
- Department of Chemistry, University of Pennsylvania School of Arts and Sciences, Philadelphia, Pennsylvania, 19104, USA
| | - Marie Fina
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, 19104, USA
| | - Yun Huang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, 19104, USA
| | - Marie Shimogawa
- Department of Chemistry, University of Pennsylvania School of Arts and Sciences, Philadelphia, Pennsylvania, 19104, USA
| | - Kelvin C Luk
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, 19104, USA
| | - Elizabeth Rhoades
- Department of Chemistry, University of Pennsylvania School of Arts and Sciences, Philadelphia, Pennsylvania, 19104, USA
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania School of Arts and Sciences, Philadelphia, Pennsylvania, 19104, USA
| | - Dawei W Dong
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, 19104, USA
| | - Anna Kashina
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, 19104, USA.
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9
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Vedula P, Tang HY, Speicher DW, Kashina A. Protein Posttranslational Signatures Identified in COVID-19 Patient Plasma. Front Cell Dev Biol 2022; 10:807149. [PMID: 35223838 PMCID: PMC8873527 DOI: 10.3389/fcell.2022.807149] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 11/01/2021] [Accepted: 01/06/2022] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a highly contagious virus of the coronavirus family that causes coronavirus disease-19 (COVID-19) in humans and a number of animal species. COVID-19 has rapidly propagated in the world in the past 2 years, causing a global pandemic. Here, we performed proteomic analysis of plasma samples from COVID-19 patients compared to healthy control donors in an exploratory study to gain insights into protein-level changes in the patients caused by SARS-CoV-2 infection and to identify potential proteomic and posttranslational signatures of this disease. Our results suggest a global change in protein processing and regulation that occurs in response to SARS-CoV-2, and the existence of a posttranslational COVID-19 signature that includes an elevation in threonine phosphorylation, a change in glycosylation, and a decrease in arginylation, an emerging posttranslational modification not previously implicated in infectious disease. This study provides a resource for COVID-19 researchers and, longer term, and will inform our understanding of this disease and its treatment.
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Affiliation(s)
- Pavan Vedula
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, United States
| | - Hsin-Yao Tang
- The Wistar Institute, Philadelphia, PA, United States
| | | | - Anna Kashina
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, United States,*Correspondence: Anna Kashina,
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10
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Fina ME, Wang J, Vedula P, Tang HY, Kashina A, Dong DW. Arginylation Regulates G-protein Signaling in the Retina. Front Cell Dev Biol 2022; 9:807345. [PMID: 35127722 PMCID: PMC8815403 DOI: 10.3389/fcell.2021.807345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/17/2021] [Indexed: 12/03/2022] Open
Abstract
Arginylation is a post-translational modification mediated by the arginyltransferase (Ate1). We recently showed that conditional deletion of Ate1 in the nervous system leads to increased light-evoked response sensitivities of ON-bipolar cells in the retina, indicating that arginylation regulates the G-protein signaling complexes of those neurons and/or photoreceptors. However, none of the key players in the signaling pathway were previously shown to be arginylated. Here we show that Gαt1, Gβ1, RGS6, and RGS7 are arginylated in the retina and RGS6 and RGS7 protein levels are elevated in Ate1 knockout, suggesting that arginylation plays a direct role in regulating their protein level and the G-protein-mediated responses in the retina.
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Affiliation(s)
- Marie E. Fina
- Department of Biomedical Sciences, School of Veterinary Medicines, University of Pennsylvania, Philadelphia, PA, United States
| | - Junling Wang
- Department of Biomedical Sciences, School of Veterinary Medicines, University of Pennsylvania, Philadelphia, PA, United States
| | - Pavan Vedula
- Department of Biomedical Sciences, School of Veterinary Medicines, University of Pennsylvania, Philadelphia, PA, United States
| | - Hsin-Yao Tang
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, PA, United States
| | - Anna Kashina
- Department of Biomedical Sciences, School of Veterinary Medicines, University of Pennsylvania, Philadelphia, PA, United States
- *Correspondence: Anna Kashina, ; Dawei W. Dong,
| | - Dawei W. Dong
- Department of Biomedical Sciences, School of Veterinary Medicines, University of Pennsylvania, Philadelphia, PA, United States
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- *Correspondence: Anna Kashina, ; Dawei W. Dong,
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11
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Avcilar-Kucukgoze I, MacTaggart B, Kashina A. Availability of Arg, but Not tRNA, Is a Rate-Limiting Factor for Intracellular Arginylation. Int J Mol Sci 2021; 23:314. [PMID: 35008737 PMCID: PMC8745564 DOI: 10.3390/ijms23010314] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 11/24/2022] Open
Abstract
Protein arginylation, mediated by arginyltransferase ATE1, is a posttranslational modification of emerging biological importance that consists of transfer of the amino acid Arg from tRNA to protein and peptide targets. ATE1 can bind tRNA and exhibits specificity toward particular tRNA types, but its dependence on the availability of the major components of the arginylation reaction has never been explored. Here we investigated key intracellular factors that can potentially regulate arginylation in vivo, including several tRNA types that show strong binding to ATE1, as well as availability of free Arg, in an attempt to identify intracellular rate limiting steps for this enzyme. Our results demonstrate that, while modulation of tRNA levels in cells does not lead to any changes in intracellular arginylation efficiency, availability of free Arg is a potentially rate-limiting factor that facilitates arginylation if added to the cultured cells. Our results broadly outline global pathways that may be involved in the regulation of arginylation in vivo.
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Affiliation(s)
| | | | - Anna Kashina
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (I.A.-K.); (B.M.)
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12
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Abstract
Post-translational modifications (PTM) involve enzyme-mediated covalent addition of functional groups to proteins during or after synthesis. These modifications greatly increase biological complexity and are responsible for orders of magnitude change between the variety of proteins encoded in the genome and the variety of their biological functions. Many of these modifications occur at the protein termini, which contain reactive amino- and carboxy-groups of the polypeptide chain and often are pre-primed through the actions of cellular machinery to expose highly reactive residues. Such modifications have been known for decades, but only a few of them have been functionally characterized. The vast majority of eukaryotic proteins are N- and C-terminally modified by acetylation, arginylation, tyrosination, lipidation, and many others. Post-translational modifications of the protein termini have been linked to different normal and disease-related processes and constitute a rapidly emerging area of biological regulation. Here we highlight recent progress in our understanding of post-translational modifications of the protein termini and outline the role that these modifications play in vivo.
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Affiliation(s)
| | - Anna Kashina
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
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13
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MacTaggart B, Kashina A. Posttranslational modifications of the cytoskeleton. Cytoskeleton (Hoboken) 2021; 78:142-173. [PMID: 34152688 DOI: 10.1002/cm.21679] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/13/2021] [Accepted: 06/16/2021] [Indexed: 12/12/2022]
Abstract
The cytoskeleton plays important roles in many essential processes at the cellular and organismal levels, including cell migration and motility, cell division, and the establishment and maintenance of cell and tissue architecture. In order to facilitate these varied functions, the main cytoskeletal components-microtubules, actin filaments, and intermediate filaments-must form highly diverse intracellular arrays in different subcellular areas and cell types. The question of how this diversity is conferred has been the focus of research for decades. One key mechanism is the addition of posttranslational modifications (PTMs) to the major cytoskeletal proteins. This posttranslational addition of various chemical groups dramatically increases the complexity of the cytoskeletal proteome and helps facilitate major global and local cytoskeletal functions. Cytoskeletal proteins undergo many PTMs, most of which are not well understood. Recent technological advances in proteomics and cell biology have allowed for the in-depth study of individual PTMs and their functions in the cytoskeleton. Here, we provide an overview of the major PTMs that occur on the main structural components of the three cytoskeletal systems-tubulin, actin, and intermediate filament proteins-and highlight the cellular function of these modifications.
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Affiliation(s)
- Brittany MacTaggart
- School of Veterinary Medicine, Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anna Kashina
- School of Veterinary Medicine, Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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14
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Vedula P, Kurosaka S, MacTaggart B, Ni Q, Papoian G, Jiang Y, Dong DW, Kashina A. Different translation dynamics of β- and γ-actin regulates cell migration. eLife 2021; 10:68712. [PMID: 34165080 PMCID: PMC8328520 DOI: 10.7554/elife.68712] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/19/2021] [Indexed: 12/13/2022] Open
Abstract
β- and γ-cytoplasmic actins are ubiquitously expressed in every cell type and are nearly identical at the amino acid level but play vastly different roles in vivo. Their essential roles in embryogenesis and mesenchymal cell migration critically depend on the nucleotide sequences of their genes, rather than their amino acid sequences; however, it is unclear which gene elements underlie this effect. Here we address the specific role of the coding sequence in β- and γ-cytoplasmic actins’ intracellular functions, using stable polyclonal populations of immortalized mouse embryonic fibroblasts with exogenously expressed actin isoforms and their ‘codon-switched’ variants. When targeted to the cell periphery using β-actin 3′UTR; β-actin and γ-actin have differential effects on cell migration. These effects directly depend on the coding sequence. Single-molecule measurements of actin isoform translation, combined with fluorescence recovery after photobleaching, demonstrate a pronounced difference in β- and γ-actins’ translation elongation rates in cells, leading to changes in their dynamics at focal adhesions, impairments in actin bundle formation, and reduced cell anchoring to the substrate during migration. Our results demonstrate that coding sequence-mediated differences in actin translation play a key role in cell migration. Most mammalian cells make both β- and γ-actin, two proteins which shape the cell’s internal skeleton and its ability to migrate. The molecules share over 99% of their sequence, yet they play distinct roles. In fact, deleting the β-actin gene in mice causes death in the womb, while the animals can survive with comparatively milder issues without their γ-actin gene. How two similar proteins can have such different biological roles is a long-standing mystery. A closer look could hold some clues: β- and γ-actin may contain the same blocks (or amino acids), but the genetic sequences that encode these proteins differ by about 13%. This is because different units of genetic information – known as synonymous codons – can encode the same amino acid. These ‘silent substitutions’ have no effect on the sequence of the proteins, yet a cell reads synonymous codons (and therefore produces proteins) at different speeds. To find out the impact of silent substitutions, Vedula et al. swapped the codons for the two proteins, forcing mouse cells to produce β-actin using γ-actin codons, and vice versa. Cells with non-manipulated γ-actin and those with β-actin made using γ-actin codons could move much faster than cells with β-actin. This suggested that silent substitutions were indeed affecting the role of the protein. Vedula et al. found that cells read γ-codons – and therefore made γ-actin – much more slowly than β-codons: this also affected how quickly the protein could be dispatched where it was needed in the cell. Slower production meant that bundles of γ-actin were shorter, which allowed cells to move faster by providing a weaker anchoring system. Overall, this work provides new links between silent substitutions and protein behavior, a relatively new research area which is likely to shed light on other protein families.
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Affiliation(s)
- Pavan Vedula
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States
| | - Satoshi Kurosaka
- Institute of Advanced Technology, Kindai University, Kainan, Wakayama, Japan
| | - Brittany MacTaggart
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States
| | - Qin Ni
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, United States
| | - Garegin Papoian
- Department of Chemistry, University of Maryland, College Park, United States
| | - Yi Jiang
- Department of Mathematics and Statistics, Georgia State University, Atlanta, United States
| | - Dawei W Dong
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States.,Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Anna Kashina
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States
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15
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Fina ME, Wang J, Nikonov SS, Sterling S, Vardi N, Kashina A, Dong DW. Arginyltransferase (Ate1) regulates the RGS7 protein level and the sensitivity of light-evoked ON-bipolar responses. Sci Rep 2021; 11:9376. [PMID: 33931669 PMCID: PMC8087773 DOI: 10.1038/s41598-021-88628-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022] Open
Abstract
Regulator of G-protein signaling 7 (RGS7) is predominately present in the nervous system and is essential for neuronal signaling involving G-proteins. Prior studies in cultured cells showed that RGS7 is regulated via proteasomal degradation, however no protein is known to facilitate proteasomal degradation of RGS7 and it has not been shown whether this regulation affects G-protein signaling in neurons. Here we used a knockout mouse model with conditional deletion of arginyltransferase (Ate1) in the nervous system and found that in retinal ON bipolar cells, where RGS7 modulates a G-protein to signal light increments, deletion of Ate1 raised the level of RGS7. Electroretinographs revealed that lack of Ate1 leads to increased light-evoked response sensitivities of ON-bipolar cells, as well as their downstream neurons. In cultured mouse embryonic fibroblasts (MEF), RGS7 was rapidly degraded via proteasome pathway and this degradation was abolished in Ate1 knockout MEF. Our results indicate that Ate1 regulates RGS7 protein level by facilitating proteasomal degradation of RGS7 and thus affects G-protein signaling in neurons.
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Affiliation(s)
- Marie E Fina
- Department of Biomedical Sciences, School of Veterinary Medicines, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Junling Wang
- Department of Biomedical Sciences, School of Veterinary Medicines, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sergei S Nikonov
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stephanie Sterling
- Department of Biomedical Sciences, School of Veterinary Medicines, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Noga Vardi
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Anna Kashina
- Department of Biomedical Sciences, School of Veterinary Medicines, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Dawei W Dong
- Department of Biomedical Sciences, School of Veterinary Medicines, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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16
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Vedula P, Kurosaka S, Dong D, MacTaggart B, Ni Q, Jiang Y, Kashina A. Functional Differences between β- and γ-Actin: From Translation Dynamics to Amino Acid Changes. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.2155] [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: 10/22/2022] Open
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17
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Pan B, Kamo N, Shimogawa M, Huang Y, Kashina A, Rhoades E, Petersson EJ. Effects of Glutamate Arginylation on α-Synuclein: Studying an Unusual Post-Translational Modification through Semisynthesis. J Am Chem Soc 2020; 142:21786-21798. [PMID: 33337869 DOI: 10.1021/jacs.0c10054] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A variety of post-translational modifications (PTMs) are believed to regulate the behavior and function of α-synuclein (αS), an intrinsically disordered protein that mediates synaptic vesicle trafficking. Fibrils of αS are implicated in neurodegenerative disorders such as Parkinson's disease. In this study, we used chemical synthesis and biophysical techniques to characterize the neuroprotective effects of glutamate arginylation, a hitherto little characterized PTM in αS. We developed semisynthetic routes combining peptide synthesis, unnatural amino acid mutagenesis, and native chemical ligation (NCL) to site-specifically introduce the PTM of interest along with fluorescent probes into αS. We synthesized the arginylated glutamate as a protected amino acid, as well as a novel ligation handle for NCL, in order to generate full-length αS modified at various individual sites or a combination of sites. We assayed the lipid-vesicle binding affinities of arginylated αS using fluorescence correlation spectroscopy (FCS) and found that arginylated αS has the same vesicle affinity compared to control protein, suggesting that this PTM does not alter the native function of αS. On the other hand, we studied the aggregation kinetics of modified αS and found that arginylation at E83, but not E46, slows aggregation and decreases the percentage incorporation of monomer into fibrils in a dose-dependent manner. Arginylation at both sites also resulted in deceleration of fibril formation. Our study represents the first synthetic strategy for incorporating glutamate arginylation into proteins and provides insight into the neuroprotective effect of this unusual PTM.
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Affiliation(s)
- Buyan Pan
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Naoki Kamo
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States.,Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Marie Shimogawa
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Yun Huang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Anna Kashina
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, Pennsylvania 19104, United States
| | - Elizabeth Rhoades
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
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18
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Avcilar-Kucukgoze I, Kashina A. Hijacking tRNAs From Translation: Regulatory Functions of tRNAs in Mammalian Cell Physiology. Front Mol Biosci 2020; 7:610617. [PMID: 33392265 PMCID: PMC7773854 DOI: 10.3389/fmolb.2020.610617] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 09/26/2020] [Accepted: 11/10/2020] [Indexed: 12/12/2022] Open
Abstract
Transfer tRNAs (tRNAs) are small non-coding RNAs that are highly conserved in all kingdoms of life. Originally discovered as the molecules that deliver amino acids to the growing polypeptide chain during protein synthesis, tRNAs have been believed for a long time to play exclusive role in translation. However, recent studies have identified key roles for tRNAs and tRNA-derived small RNAs in multiple other processes, including regulation of transcription and translation, posttranslational modifications, stress response, and disease. These emerging roles suggest that tRNAs may be central players in the complex machinery of biological regulatory pathways. Here we overview these non-canonical roles of tRNA in normal physiology and disease, focusing largely on eukaryotic and mammalian systems.
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Affiliation(s)
- Irem Avcilar-Kucukgoze
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Anna Kashina
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
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19
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Abstract
Post-translational addition of amino acids to proteins by enzymes using aminoacyl-tRNA is an emerging regulatory mechanism. Examples include Arg transfer in eukaryotes, Leu/Phe transfer in bacteria, and tRNA-synthetase-mediated addition of amino acids to Lys side chains. Here, we present a method of purification and use of tRNA for such reactions, focusing on tRNAArg and its use for arginylation. This method can also be used for other tRNA-mediated reactions. For complete details on the use and execution of this protocol, please refer to Avcilar-Kucukgoze et al. (2020) Preparing specific tRNAs by in vitro transcription and enriched bacterial expression tRNA aminoacylation and preparation of charged aa-tRNA for enzymatic reactions Preparation of aa-tRNA-derived fragments (aa-tRF) using in vitro cleavage with RNase T2 Using Arg-tRNA and Arg-tRF for in vitro arginylation
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Affiliation(s)
- Irem Avcilar-Kucukgoze
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Anna Kashina
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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20
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Avcilar-Kucukgoze I, Gamper H, Polte C, Ignatova Z, Kraetzner R, Shtutman M, Hou YM, Dong DW, Kashina A. tRNA Arg-Derived Fragments Can Serve as Arginine Donors for Protein Arginylation. Cell Chem Biol 2020; 27:839-849.e4. [PMID: 32553119 DOI: 10.1016/j.chembiol.2020.05.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/12/2020] [Accepted: 05/27/2020] [Indexed: 12/23/2022]
Abstract
Arginyltransferase ATE1 mediates posttranslational arginylation and plays key roles in multiple physiological processes. ATE1 utilizes arginyl (Arg)-tRNAArg as the donor of Arg, putting this reaction into a direct competition with the protein synthesis machinery. Here, we address the question of ATE1- Arg-tRNAArg specificity as a potential mechanism enabling this competition in vivo. Using in vitro arginylation assays and Ate1 knockout models, we find that, in addition to full-length tRNA, ATE1 is also able to utilize short tRNAArg fragments that bear structural resemblance to tRNA-derived fragments (tRF), a recently discovered class of small regulatory non-coding RNAs with global emerging biological role. Ate1 knockout cells show a decrease in tRFArg generation and a significant increase in the ratio of tRNAArg:tRFArg compared with wild type, suggesting a functional link between tRFArg and arginylation. We propose that generation of physiologically important tRFs can serve as a switch between translation and protein arginylation.
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Affiliation(s)
- Irem Avcilar-Kucukgoze
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Christine Polte
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20148 Hamburg, Germany
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20148 Hamburg, Germany
| | - Ralph Kraetzner
- Department of Pediatrics and Adolescent Medicine, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Michael Shtutman
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Dawei W Dong
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anna Kashina
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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21
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Levit M, Zashikhina N, Vdovchenko A, Dobrodumov A, Zakharova N, Kashina A, Rühl E, Lavrentieva A, Scheper T, Tennikova T, Korzhikova-Vlakh E. Bio-Inspired Amphiphilic Block-Copolymers Based on Synthetic Glycopolymer and Poly(Amino Acid) as Potential Drug Delivery Systems. Polymers (Basel) 2020; 12:polym12010183. [PMID: 32284516 PMCID: PMC7023050 DOI: 10.3390/polym12010183] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 12/04/2019] [Revised: 01/03/2020] [Accepted: 01/05/2020] [Indexed: 12/27/2022] Open
Abstract
In this work, a method to prepare hybrid amphiphilic block copolymers consisting of biocompatible synthetic glycopolymer with non-degradable backbone and biodegradable poly(amino acid) (PAA) was developed. The glycopolymer, poly(2-deoxy-2-methacrylamido-D-glucose) (PMAG), was synthesized via reversible addition-fragmentation chain transfer (RAFT) polymerization. Two methods for modifying the terminal dithiobenzoate-group of PMAG was investigated to obtain the macroinitiator bearing a primary aliphatic amino group, which is required for ring-opening polymerization of N-carboxyanhydrides of hydrophobic α-amino acids. The synthesized amphiphilic block copolymers were carefully analyzed using a set of different physico-chemical methods to establish their composition and molecular weight. The developed amphiphilic copolymers tended to self-assemble in nanoparticles of different morphology that depended on the nature of the hydrophobic amino acid present in the copolymer. The hydrodynamic diameter, morphology, and cytotoxicity of polymer particles based on PMAG-b-PAA were evaluated using dynamic light scattering (DLS) and transmission electron microscopy (TEM), as well as CellTiter-Blue (CTB) assay, respectively. The redox-responsive properties of nanoparticles were evaluated in the presence of glutathione taken at different concentrations. Moreover, the encapsulation of paclitaxel into PMAG-b-PAA particles and their cytotoxicity on human lung carcinoma cells (A549) and human breast adenocarcinoma cells (MCF-7) were studied.
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Affiliation(s)
- Mariia Levit
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia; (M.L.); (N.Z.); (A.D.); or (N.Z.); (A.K.)
| | - Natalia Zashikhina
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia; (M.L.); (N.Z.); (A.D.); or (N.Z.); (A.K.)
| | - Alena Vdovchenko
- Institute of Chemistry, Saint-Petersburg State University, Universitetsky pr. 26, 198504 St. Petersburg, Russia; (A.V.); (T.T.)
| | - Anatoliy Dobrodumov
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia; (M.L.); (N.Z.); (A.D.); or (N.Z.); (A.K.)
| | - Natalya Zakharova
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia; (M.L.); (N.Z.); (A.D.); or (N.Z.); (A.K.)
| | - Anna Kashina
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia; (M.L.); (N.Z.); (A.D.); or (N.Z.); (A.K.)
| | - Eckart Rühl
- Physical Chemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany;
| | - Antonina Lavrentieva
- Institute of Technical Chemistry, Gottfried-Wilhelm-Leibniz University of Hannover, 30167 Hannover, Germany; (A.L.); (T.S.)
| | - Thomas Scheper
- Institute of Technical Chemistry, Gottfried-Wilhelm-Leibniz University of Hannover, 30167 Hannover, Germany; (A.L.); (T.S.)
| | - Tatiana Tennikova
- Institute of Chemistry, Saint-Petersburg State University, Universitetsky pr. 26, 198504 St. Petersburg, Russia; (A.V.); (T.T.)
| | - Evgenia Korzhikova-Vlakh
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia; (M.L.); (N.Z.); (A.D.); or (N.Z.); (A.K.)
- Institute of Chemistry, Saint-Petersburg State University, Universitetsky pr. 26, 198504 St. Petersburg, Russia; (A.V.); (T.T.)
- Correspondence: ; Tel.: +7-(812)323-04-61
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22
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Abstract
Actin is a ubiquitous, essential, and highly abundant protein in all eukaryotic cells that performs key roles in contractility, adhesion, migration, and leading edge dynamics. The two non-muscle actins, β- and γ-, are ubiquitously present in every cell type and are nearly identical to each other at the amino acid level, but play distinct intracellular roles. The mechanisms regulating this distinction have been the focus of recent interest in the field. Work from our lab has previously shown that β-, but not γ-, actin undergoes N-terminal arginylation on Asp3. While functional evidence suggest that this arginylation may be important to actin's function, progress in these studies so far has been hindered by difficulties in arginylated actin detection, precluding estimations of the abundance of arginylated actin in cells, and its occurrence in different tissues and cell types. The present study represents the first antibody-based quantification of the percentage of arginylated actin in migratory non-muscle cells under different physiological conditions, as well as in different cells and tissues. We find that while the steady-state level of arginylated actin is relatively low, it is consistently present in vivo, and is somewhat more prominent in migratory cells. Inhibition of N-terminal actin acetylation dramatically increases the intracellular actin arginylation level, suggesting that these two modifications may directly compete in vivo. These findings constitute an essential step in our understanding of actin regulation by arginylation, and in uncovering the dynamic interplay of actin's N-terminal modifications in vivo.
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Affiliation(s)
- Li Chen
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Anna Kashina
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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23
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Abstract
Protein arginylation-enzymatic addition of the amino acid arginine (Arg) to proteins, mediated by arginyltransferase ATE1, has been discovered in 1963, but is still relatively poorly understood. Studies of arginylation present many technical challenges, which arise from the fact that Arg is a regular amino acid that also incorporates into proteins during translation. Thus, in vitro arginylation needs to be conducted in a strictly ribosome-free system, in highly controlled conditions. Identification of arginylated proteins is currently only possible by high precision mass spectrometry, which relies on very high mass accuracy of the instruments, specific ionization patterns during mass fragmentation, as well as multiple stringent steps of automated and manual validation. Below we describe the methods of in vitro arginylation and mass spectrometry analysis of arginylated proteins, developed by our groups during the last 15 years.
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Affiliation(s)
- Junling Wang
- University of Pennsylvania, Philadelphia, PA, United States
| | - John R Yates
- The Scripps Research Institute, LaJolla, CA, United States
| | - Anna Kashina
- University of Pennsylvania, Philadelphia, PA, United States.
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24
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Abstract
The cytoskeleton drives many essential processes in normal physiology, and its impairments underlie many diseases, including skeletal myopathies, cancer, and heart failure, that broadly affect developed countries worldwide. Cytoskeleton regulation is a field of investigation of rapidly emerging global importance and a new venue for the development of potential therapies. This review overviews our present understanding of the posttranslational regulation of the muscle cytoskeleton through arginylation, a tRNA-dependent addition of arginine to proteins mediated by arginyltransferase 1. We focus largely on arginylation-dependent regulation of striated muscles, shown to play critical roles in facilitating muscle integrity, contractility, regulation, and strength.
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Affiliation(s)
- Dilson E Rassier
- Department of Kinesiology and Physical Education, McGill University , Montreal, Quebec , Canada
| | - Anna Kashina
- Department of Biomedical Sciences, University of Pennsylvania , Philadelphia, Pennsylvania
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25
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Rodriguez A, Kashina A. Posttranscriptional and Posttranslational Regulation of Actin. Anat Rec (Hoboken) 2018; 301:1991-1998. [PMID: 30312009 DOI: 10.1002/ar.23958] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/12/2018] [Accepted: 04/14/2018] [Indexed: 12/14/2022]
Abstract
Actin is one of the most abundant intracellular proteins, essential in every eukaryotic cell type. Actin plays key roles in tissue morphogenesis, cell adhesion, muscle contraction, and developmental reprogramming. Most actin studies have focused on its regulation at the protein level, either directly or through differential interactions with over a hundred intracellular binding partners. However, numerous studies emerging in recent years demonstrate specific types of nucleotide-level regulation that strongly affect non-muscle actins during cell migration and adhesion and are potentially applicable to other members of the actin family. This regulation involves zipcode-mediated actin mRNA targeting to the cell periphery, proposed to mediate local synthesis of actin at the cell leading edge, as well as the recently discovered N-terminal arginylation that specifically targets non-muscle β-actin via a nucleotide-dependent mechanism. Moreover, a study published this year suggests that actin's essential roles at the organismal level may be entirely nucleotide-dependent. This review summarizes the emerging data on actin's nucleotide-level regulation. Anat Rec, 301:1991-1998, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Alexis Rodriguez
- Department of Biological Sciences, Rutgers University, Newark, New Jersey
| | - Anna Kashina
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, Pennsylvania
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26
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Wang J, Pejaver VR, Dann GP, Wolf MY, Kellis M, Huang Y, Garcia BA, Radivojac P, Kashina A. Target site specificity and in vivo complexity of the mammalian arginylome. Sci Rep 2018; 8:16177. [PMID: 30385798 PMCID: PMC6212499 DOI: 10.1038/s41598-018-34639-6] [Citation(s) in RCA: 18] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 10/22/2018] [Indexed: 01/16/2023] Open
Abstract
Protein arginylation mediated by arginyltransferase ATE1 is a key regulatory process essential for mammalian embryogenesis, cell migration, and protein regulation. Despite decades of studies, very little is known about the specificity of ATE1-mediated target site recognition. Here, we used in vitro assays and computational analysis to dissect target site specificity of mouse arginyltransferases and gain insights into the complexity of the mammalian arginylome. We found that the four ATE1 isoforms have different, only partially overlapping target site specificity that includes more variability in the target residues than previously believed. Based on all the available data, we generated an algorithm for identifying potential arginylation consensus motif and used this algorithm for global prediction of proteins arginylated in vivo on the N-terminal D and E. Our analysis reveals multiple proteins with potential ATE1 target sites and expand our understanding of the biological complexity of the intracellular arginylome.
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Affiliation(s)
- Junling Wang
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Vikas Rao Pejaver
- Department of Computer Science, Indiana University, Bloomington, IN, 47405, USA
- Department of Biomedical Informatics and Medical Education and the eScience Institute, University of Washington, Washington, USA
| | - Geoffrey P Dann
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Max Y Wolf
- Broad Institute of MIT and Harvard, and MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, and MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - Yun Huang
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Predrag Radivojac
- Department of Computer Science, Indiana University, Bloomington, IN, 47405, USA.
| | - Anna Kashina
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Affiliation(s)
- Felipe de Souza Leite
- 1Department of Kinesiology and Physical Education, Physics and Physiology, McGill University, Montreal, Quebec, Canada; and 2Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA
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Levit M, Zashikhina N, Dobrodumov A, Kashina A, Tarasenko I, Panarin E, Fiorucci S, Korzhikova-Vlakh E, Tennikova T. Synthesis and characterization of well-defined poly(2-deoxy-2-methacrylamido-d-glucose) and its biopotential block copolymers via RAFT and ROP polymerization. Eur Polym J 2018. [DOI: 10.1016/j.eurpolymj.2018.05.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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29
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Vedula P, Kashina A. The makings of the 'actin code': regulation of actin's biological function at the amino acid and nucleotide level. J Cell Sci 2018; 131:131/9/jcs215509. [PMID: 29739859 DOI: 10.1242/jcs.215509] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The actin cytoskeleton plays key roles in every eukaryotic cell and is essential for cell adhesion, migration, mechanosensing, and contractility in muscle and non-muscle tissues. In higher vertebrates, from birds through to mammals, actin is represented by a family of six conserved genes. Although these genes have evolved independently for more than 100 million years, they encode proteins with ≥94% sequence identity, which are differentially expressed in different tissues, and tightly regulated throughout embryogenesis and adulthood. It has been previously suggested that the existence of such similar actin genes is a fail-safe mechanism to preserve the essential function of actin through redundancy. However, knockout studies in mice and other organisms demonstrate that the different actins have distinct biological roles. The mechanisms maintaining this distinction have been debated in the literature for decades. This Review summarizes data on the functional regulation of different actin isoforms, and the mechanisms that lead to their different biological roles in vivo We focus here on recent studies demonstrating that at least some actin functions are regulated beyond the amino acid level at the level of the actin nucleotide sequence.
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Affiliation(s)
- Pavan Vedula
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anna Kashina
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
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30
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Pavlyk I, Leu NA, Vedula P, Kurosaka S, Kashina A. Rapid and dynamic arginylation of the leading edge β-actin is required for cell migration. Traffic 2018; 19:263-272. [PMID: 29384244 DOI: 10.1111/tra.12551] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 01/26/2018] [Accepted: 01/26/2018] [Indexed: 12/24/2022]
Abstract
β-actin plays key roles in cell migration. Our previous work demonstrated that β-actin in migratory non-muscle cells is N-terminally arginylated and that this arginylation is required for normal lamellipodia extension. Here, we examined the function of β-actin arginylation in cell migration. We found that arginylated β-actin is concentrated at the leading edge of lamellipodia and that this enrichment is abolished after serum starvation as well as in contact-inhibited cells in confluent cultures, suggesting that arginylated β-actin at the cell leading edge is coupled to active migration. Arginylated actin levels exhibit dynamic changes in response to cell stimuli, lowered after serum starvation and dramatically elevating within minutes after cell stimulation by readdition of serum or lysophosphatidic acid. These dynamic changes require active translation and are not seen in confluent contact-inhibited cell cultures. Microinjection of arginylated actin antibodies into cells severely and specifically inhibits their migration rates. Together, these data strongly suggest that arginylation of β-actin is a tightly regulated dynamic process that occurs at the leading edge of locomoting cells in response to stimuli and is integral to the signaling network that regulates cell migration.
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Affiliation(s)
- Iuliia Pavlyk
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Nicolae A Leu
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Pavan Vedula
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Satoshi Kurosaka
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anna Kashina
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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31
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Vedula P, Kurosaka S, Leu NA, Wolf YI, Shabalina SA, Wang J, Sterling S, Dong DW, Kashina A. Diverse functions of homologous actin isoforms are defined by their nucleotide, rather than their amino acid sequence. eLife 2017; 6:31661. [PMID: 29244021 PMCID: PMC5794254 DOI: 10.7554/elife.31661] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [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: 08/31/2017] [Accepted: 12/13/2017] [Indexed: 12/28/2022] Open
Abstract
β‐ and γ‐cytoplasmic actin are nearly indistinguishable in their amino acid sequence, but are encoded by different genes that play non‐redundant biological roles. The key determinants that drive their functional distinction are unknown. Here, we tested the hypothesis that β- and γ-actin functions are defined by their nucleotide, rather than their amino acid sequence, using targeted editing of the mouse genome. Although previous studies have shown that disruption of β-actin gene critically impacts cell migration and mouse embryogenesis, we demonstrate here that generation of a mouse lacking β-actin protein by editing β-actin gene to encode γ-actin protein, and vice versa, does not affect cell migration and/or organism survival. Our data suggest that the essential in vivo function of β-actin is provided by the gene sequence independent of the encoded protein isoform. We propose that this regulation constitutes a global ‘silent code’ mechanism that controls the functional diversity of protein isoforms. Mammalian cells, including human cells, contain high levels of a protein called actin. This protein is essential for many of the processes that organisms use to develop and survive. For example, filaments of actin maintain the shape of cells, and help generate the forces needed for cells to move and divide. As in many other animals, every cell in the human body contains two related actin proteins – known as β-actin and γ-actin. These proteins are made from almost identical amino acid building blocks. Yet the genes that encode these two proteins vary much more. The two actin proteins also play different roles: disrupting the gene for β-actin causes mouse embryos to die, but mice without the gene for γ-actin develop almost like normal. It was not fully understood how these almost identical proteins could perform such different roles. Earlier studies exploring the mechanisms that underlie the unique roles of β- and γ-actin focused on the differences in their amino acid sequences. Now, Vedula, Kurosaka et al. test the hypothesis that the differing roles of these two actin proteins are due to the pronounced differences in the DNA sequences of their genes. A gene-editing technique called CRISPR/Cas9 was used to make small changes to the mouse gene for β-actin so that it coded for the γ-actin protein. As a consequence, these mice did not make any β-actin protein and instead made the γ-actin protein from a mostly intact gene for β-actin. These mice lacking the β-actin protein survived as normal and were fertile. The shape of their organs and the movement of their cells – two other major processes that need β-actin – were also unaffected. Hence, the γ-actin protein can substitute for β-actin when the β-actin gene is intact. These observations imply that it is the DNA sequence of the gene rather than the amino acid sequence of the protein that determines the essential role of β-actin in cell migration and the organism’s survival. The next step will be to see if other proteins work in a similar way. If so, this mechanism might allow scientists to discover new ways to fine-tune how proteins behave in healthy and diseased human cells.
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Affiliation(s)
- Pavan Vedula
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, United States
| | - Satoshi Kurosaka
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, United States
| | - Nicolae Adrian Leu
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, United States
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, United States
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, United States
| | - Junling Wang
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, United States
| | - Stephanie Sterling
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, United States
| | - Dawei W Dong
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, United States.,Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Anna Kashina
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, United States
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32
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Wang J, Han X, Leu NA, Sterling S, Kurosaka S, Fina M, Lee VM, Dong DW, Yates JR, Kashina A. Protein arginylation targets alpha synuclein, facilitates normal brain health, and prevents neurodegeneration. Sci Rep 2017; 7:11323. [PMID: 28900170 PMCID: PMC5595787 DOI: 10.1038/s41598-017-11713-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 06/06/2017] [Accepted: 08/29/2017] [Indexed: 12/15/2022] Open
Abstract
Alpha synuclein (α-syn) is a central player in neurodegeneration, but the mechanisms triggering its pathology are not fully understood. Here we found that α-syn is a highly efficient substrate for arginyltransferase ATE1 and is arginylated in vivo by a novel mid-chain mechanism that targets the acidic side chains of E46 and E83. Lack of arginylation leads to increased α-syn aggregation and causes the formation of larger pathological aggregates in neurons, accompanied by impairments in its ability to be cleared via normal degradation pathways. In the mouse brain, lack of arginylation leads to an increase in α-syn’s insoluble fraction, accompanied by behavioral changes characteristic for neurodegenerative pathology. Our data show that lack of arginylation in the brain leads to neurodegeneration, and suggests that α-syn arginylation can be a previously unknown factor that facilitates normal α-syn folding and function in vivo.
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Affiliation(s)
- Junling Wang
- University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, 19104, USA
| | - Xuemei Han
- The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Nicolae Adrian Leu
- University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, 19104, USA
| | - Stephanie Sterling
- University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, 19104, USA
| | - Satoshi Kurosaka
- University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, 19104, USA
| | - Marie Fina
- University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, 19104, USA
| | - Virginia M Lee
- University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Dawei W Dong
- University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, 19104, USA.,Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, USA
| | - John R Yates
- The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Anna Kashina
- University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, 19104, USA.
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33
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Wang J, Pavlyk I, Vedula P, Sterling S, Leu NA, Dong DW, Kashina A. Arginyltransferase ATE1 is targeted to the neuronal growth cones and regulates neurite outgrowth during brain development. Dev Biol 2017; 430:41-51. [PMID: 28844905 PMCID: PMC5628761 DOI: 10.1016/j.ydbio.2017.08.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 06/07/2017] [Revised: 08/01/2017] [Accepted: 08/23/2017] [Indexed: 01/17/2023]
Abstract
Arginylation is an emerging protein modification mediated by arginyltransferase ATE1, shown to regulate embryogenesis and actin cytoskeleton, however its functions in different physiological systems are not well understood. Here we analyzed the role of ATE1 in brain development and neuronal growth by producing a conditional mouse knockout with Ate1 deletion in the nervous system driven by Nestin promoter (Nes-Ate1 mice). These mice were weaker than wild type, resulting in low postnatal survival rates, and had abnormalities in the brain that suggested defects in neuronal migration. Cultured Ate1 knockout neurons showed a reduction in the neurite outgrowth and the levels of doublecortin and F-actin in the growth cones. In wild type, ATE1 prominently localized to the growth cones, in addition to the cell bodies. Examination of the Ate1 mRNA sequence reveals the existence of putative zipcode-binding sequences involved in mRNA targeting to the cell periphery and local translation at the growth cones. Fluorescence in situ hybridization showed that Ate1 mRNA localized to the tips of the growth cones, likely due to zipcode-mediated targeting, and this localization coincided with spots of localization of arginylated β-actin, which disappeared in the presence of protein synthesis inhibitors. We propose that zipcode-mediated co-targeting of Ate1 and β-actin mRNA leads to localized co-translational arginylation of β-actin that drives the growth cone migration and neurite outgrowth.
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Affiliation(s)
- Junling Wang
- University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, United States
| | - Iuliia Pavlyk
- University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, United States
| | - Pavan Vedula
- University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, United States
| | - Stephanie Sterling
- University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, United States
| | - N Adrian Leu
- University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, United States
| | - Dawei W Dong
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Anna Kashina
- University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, United States.
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34
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Srinivasan S, Guha M, Kashina A, Avadhani NG. Mitochondrial dysfunction and mitochondrial dynamics-The cancer connection. Biochim Biophys Acta Bioenerg 2017; 1858:602-614. [PMID: 28104365 DOI: 10.1016/j.bbabio.2017.01.004] [Citation(s) in RCA: 248] [Impact Index Per Article: 35.4] [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: 10/15/2016] [Revised: 01/03/2017] [Accepted: 01/05/2017] [Indexed: 02/07/2023]
Abstract
Mitochondrial dysfunction is a hallmark of many diseases. The retrograde signaling initiated by dysfunctional mitochondria can bring about global changes in gene expression that alters cell morphology and function. Typically, this is attributed to disruption of important mitochondrial functions, such as ATP production, integration of metabolism, calcium homeostasis and regulation of apoptosis. Recent studies showed that in addition to these factors, mitochondrial dynamics might play an important role in stress signaling. Normal mitochondria are highly dynamic organelles whose size, shape and network are controlled by cell physiology. Defective mitochondrial dynamics play important roles in human diseases. Mitochondrial DNA defects and defective mitochondrial function have been reported in many cancers. Recent studies show that increased mitochondrial fission is a pro-tumorigenic phenotype. In this paper, we have explored the current understanding of the role of mitochondrial dynamics in pathologies. We present new data on mitochondrial dynamics and dysfunction to illustrate a causal link between mitochondrial DNA defects, excessive fission, mitochondrial retrograde signaling and cancer progression. This article is part of a Special Issue entitled Mitochondria in Cancer, edited by Giuseppe Gasparre, Rodrigue Rossignol and Pierre Sonveaux.
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Affiliation(s)
- Satish Srinivasan
- The Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, #189E, Philadelphia, PA 19104, United States
| | - Manti Guha
- The Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, #189E, Philadelphia, PA 19104, United States
| | - Anna Kashina
- The Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, #189E, Philadelphia, PA 19104, United States
| | - Narayan G Avadhani
- The Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, #189E, Philadelphia, PA 19104, United States.
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35
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Rai R, Zhang F, Colavita K, Leu NA, Kurosaka S, Kumar A, Birnbaum MD, Győrffy B, Dong DW, Shtutman M, Kashina A. Arginyltransferase suppresses cell tumorigenic potential and inversely correlates with metastases in human cancers. Oncogene 2015; 35:4058-68. [PMID: 26686093 PMCID: PMC4916053 DOI: 10.1038/onc.2015.473] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [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: 05/07/2015] [Revised: 11/09/2015] [Accepted: 11/14/2015] [Indexed: 02/07/2023]
Abstract
Arginylation is an emerging post-translational modification mediated by arginyltransferase (ATE1) that is essential for mammalian embryogenesis and regulation of the cytoskeleton. Here, we discovered that Ate1-knockout (KO) embryonic fibroblasts exhibit tumorigenic properties, including abnormally rapid contact-independent growth, reduced ability to form cell-cell contacts and chromosomal aberrations. Ate1-KO fibroblasts can form large colonies in Matrigel and exhibit invasive behavior, unlike wild-type fibroblasts. Furthermore, Ate1-KO cells form tumors in subcutaneous xenograft assays in immunocompromised mice. Abnormal growth in these cells can be partially rescued by reintroduction of stably expressed specific Ate1 isoforms, which also reduce the ability of these cells to form tumors. Tumor array studies and bioinformatics analysis show that Ate1 is downregulated in several types of human cancer samples at the protein level, and that its transcription level inversely correlates with metastatic progression and patient survival. We conclude that Ate1-KO results in carcinogenic transformation of cultured fibroblasts, suggesting that in addition to its previously known activities Ate1 gene is essential for tumor suppression and also likely participates in suppression of metastatic growth.
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Affiliation(s)
- R Rai
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - F Zhang
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Molecular & Cellular Pharmacology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - K Colavita
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - N A Leu
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - S Kurosaka
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - A Kumar
- Department of Molecular & Cellular Pharmacology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - M D Birnbaum
- Department of Molecular & Cellular Pharmacology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - B Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Budapest, Hungary.,Second Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - D W Dong
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - M Shtutman
- University of South Carolina, Columbia, SC, USA
| | - A Kashina
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
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36
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Kashina A. Protein arginylation, a global biological regulator that targets actin cytoskeleton and the muscle. Anat Rec (Hoboken) 2015; 297:1630-6. [PMID: 25125176 DOI: 10.1002/ar.22969] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [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: 02/12/2014] [Accepted: 03/14/2014] [Indexed: 12/20/2022]
Abstract
Posttranslational addition of Arg to proteins, mediated by arginyltransferase ATE1 has been first observed in 1963 and remained poorly understood for decades since its original discovery. Recent work demonstrated the global nature of arginylation and its essential role in multiple physiological pathways during embryogenesis and adulthood and identified over a hundred of proteins arginylated in vivo. Among these proteins, the prominent role belongs to the actin cytoskeleton and the muscle, and follow up studies strongly suggests that arginylation constitutes a novel biological regulator of contractility. This review presents an overview of the studies of protein arginylation that led to the discovery of its major role in the muscle.
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Affiliation(s)
- Anna Kashina
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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37
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de Souza Leite F, Minozzo FC, Trecarten N, Han X, Yates JR, Kashina A, Rassier DE. Passive Force Analysis of Single Sarcomeres from Muscles Lacking Arginyl-tRNA-Protein Transferase (Ate1). Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.3219] [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: 11/29/2022] Open
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38
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Anderson SE, Kashina A, Bau HH, Cooperman BS. Microinjection of fl-tRNA for the Study of tRNA Subcellular Dynamics. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.3123] [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: 11/30/2022] Open
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39
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Dong D, Fina M, Nikonov S, Vardi N, Wang J, Kashina A. Arginylation affects G-protein signaling and visual processing in the retina. J Vis 2014. [DOI: 10.1167/14.15.59] [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: 11/24/2022] Open
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40
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Cornachione AS, Leite FS, Wang J, Leu NA, Kalganov A, Volgin D, Han X, Xu T, Cheng YS, Yates JRR, Rassier DE, Kashina A. Arginylation of myosin heavy chain regulates skeletal muscle strength. Cell Rep 2014; 8:470-6. [PMID: 25017061 PMCID: PMC4126752 DOI: 10.1016/j.celrep.2014.06.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [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: 01/26/2014] [Revised: 04/02/2014] [Accepted: 06/13/2014] [Indexed: 11/16/2022] Open
Abstract
Protein arginylation is a posttranslational modification with an emerging global role in the regulation of actin cytoskeleton. To test the role of arginylation in the skeletal muscle, we generated a mouse model with Ate1 deletion driven by the skeletal muscle-specific creatine kinase (Ckmm) promoter. Ckmm-Ate1 mice were viable and outwardly normal; however, their skeletal muscle strength was significantly reduced in comparison to controls. Mass spectrometry of isolated skeletal myofibrils showed a limited set of proteins, including myosin heavy chain, arginylated on specific sites. Atomic force microscopy measurements of contractile strength in individual myofibrils and isolated myosin filaments from these mice showed a significant reduction of contractile forces, which, in the case of myosin filaments, could be fully rescued by rearginylation with purified Ate1. Our results demonstrate that arginylation regulates force production in muscle and exerts a direct effect on muscle strength through arginylation of myosin.
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Affiliation(s)
- Anabelle S Cornachione
- Department of Kinesiology and Physical Education, Physics and Physiology, McGill University, Montreal, QC H2W 1S4, Canada
| | - Felipe S Leite
- Department of Kinesiology and Physical Education, Physics and Physiology, McGill University, Montreal, QC H2W 1S4, Canada
| | - Junling Wang
- Department of Animal Biology, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Nicolae A Leu
- Department of Animal Biology, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Albert Kalganov
- Department of Kinesiology and Physical Education, Physics and Physiology, McGill University, Montreal, QC H2W 1S4, Canada
| | - Denys Volgin
- Department of Animal Biology, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Xuemei Han
- The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tao Xu
- The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yu-Shu Cheng
- Department of Kinesiology and Physical Education, Physics and Physiology, McGill University, Montreal, QC H2W 1S4, Canada
| | | | - Dilson E Rassier
- Department of Kinesiology and Physical Education, Physics and Physiology, McGill University, Montreal, QC H2W 1S4, Canada
| | - Anna Kashina
- Department of Animal Biology, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, USA.
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Wang J, Han X, Wong CCL, Cheng H, Aslanian A, Xu T, Leavis P, Roder H, Hedstrom L, Yates JR, Kashina A. Arginyltransferase ATE1 catalyzes midchain arginylation of proteins at side chain carboxylates in vivo. ACTA ACUST UNITED AC 2014; 21:331-7. [PMID: 24529990 DOI: 10.1016/j.chembiol.2013.12.017] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/20/2013] [Accepted: 12/30/2013] [Indexed: 10/25/2022]
Abstract
Arginylation is an emerging posttranslational modification mediated by Arg-tRNA-protein-transferase (ATE1). It is believed that ATE1 links Arg solely to the N terminus of proteins, requiring prior proteolysis or action by Met-aminopeptidases to expose the arginylated site. Here, we tested the possibility of Arg linkage to midchain sites within intact protein targets and found that many proteins in vivo are modified on the side chains of Asp and Glu by unconventional chemistry that targets the carboxy rather than the amino groups at the target sites. Such arginylation appears to be functionally regulated, and it can be directly mediated by ATE1, in addition to the more conventional ATE1-mediated linkage of Arg to the N-terminal alpha amino group. This midchain arginylation implies an unconventional mechanism of ATE1 action that likely facilitates its major biological role.
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Affiliation(s)
- Junling Wang
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, Philadelphia, PA 19104, USA
| | - Xuemei Han
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Catherine C L Wong
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Hong Cheng
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - Aaron Aslanian
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Tao Xu
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Paul Leavis
- Tufts University School of Medicine, 145 Harrison Avenue, Boston, MA 02111, USA
| | - Heinrich Roder
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - Lizbeth Hedstrom
- Department of Biology and Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | - John R Yates
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Anna Kashina
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, Philadelphia, PA 19104, USA.
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Lian L, Suzuki A, Hayes V, Saha S, Han X, Xu T, Yates JR, Poncz M, Kashina A, Abrams CS. Loss of ATE1-mediated arginylation leads to impaired platelet myosin phosphorylation, clot retraction, and in vivo thrombosis formation. Haematologica 2013; 99:554-60. [PMID: 24293517 DOI: 10.3324/haematol.2013.093047] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Protein arginylation by arginyl-transfer RNA protein transferase (ATE1) is emerging as a regulator protein function that is reminiscent of phosphorylation. For example, arginylation of β-actin has been found to regulate lamellipodial formation at the leading edge in fibroblasts. This finding suggests that similar functions of β-actin in other cell types may also require arginylation. Here, we have tested the hypothesis that ATE1 regulates the cytoskeletal dynamics essential for in vivo platelet adhesion and thrombus formation. To test this hypothesis, we generated conditional knockout mice specifically lacking ATE1 in their platelets and in their megakaryocytes and analyzed the role of arginylation during platelet activation. Surprisingly, rather than finding an impairment of the actin cytoskeleton structure and its rearrangement during platelet activation, we observed that the platelet-specific ATE1 knockout led to enhanced clot retraction and in vivo thrombus formation. This effect might be regulated by myosin II contractility since it was accompanied by enhanced phosphorylation of the myosin regulatory light chain on Ser19, which is an event that activates myosin in vivo. Furthermore, ATE1 and myosin co-immunoprecipitate from platelet lysates. This finding suggests that these proteins directly interact within platelets. These results provide the first evidence that arginylation is involved in phosphorylation-dependent protein regulation, and that arginylation affects myosin function in platelets during clot retraction.
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43
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Ribeiro PA, Ribeiro JP, Minozzo FC, Pavlov I, Leu NA, Kurosaka S, Kashina A, Rassier DE. Contractility of myofibrils from the heart and diaphragm muscles measured with atomic force cantilevers: Effects of heart-specific deletion of arginyl-tRNA–protein transferase. Int J Cardiol 2013; 168:3564-71. [DOI: 10.1016/j.ijcard.2013.05.069] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 04/12/2013] [Accepted: 05/04/2013] [Indexed: 10/26/2022]
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Abstract
Messenger RNA is a key component of an intricate regulatory network of its own. It accommodates numerous nucleotide signals that overlap protein coding sequences and are responsible for multiple levels of regulation and generation of biological complexity. A wealth of structural and regulatory information, which mRNA carries in addition to the encoded amino acid sequence, raises the question of how these signals and overlapping codes are delineated along non-synonymous and synonymous positions in protein coding regions, especially in eukaryotes. Silent or synonymous codon positions, which do not determine amino acid sequences of the encoded proteins, define mRNA secondary structure and stability and affect the rate of translation, folding and post-translational modifications of nascent polypeptides. The RNA level selection is acting on synonymous sites in both prokaryotes and eukaryotes and is more common than previously thought. Selection pressure on the coding gene regions follows three-nucleotide periodic pattern of nucleotide base-pairing in mRNA, which is imposed by the genetic code. Synonymous positions of the coding regions have a higher level of hybridization potential relative to non-synonymous positions, and are multifunctional in their regulatory and structural roles. Recent experimental evidence and analysis of mRNA structure and interspecies conservation suggest that there is an evolutionary tradeoff between selective pressure acting at the RNA and protein levels. Here we provide a comprehensive overview of the studies that define the role of silent positions in regulating RNA structure and processing that exert downstream effects on proteins and their functions.
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Affiliation(s)
- Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20984, USA.
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Abstract
Many of the best-studied actin regulatory proteins use non-covalent means to modulate the properties of actin. Yet, actin is also susceptible to covalent modifications of its amino acids. Recent work is increasingly revealing that actin processing and its covalent modifications regulate important cellular events. In addition, numerous pathogens express enzymes that specifically use actin as a substrate to regulate their hosts' cells. Actin post-translational alterations have been linked to different normal and disease processes and the effects associated with metabolic and environmental stressors. Herein, we highlight specific co-translational and post-translational modifications of actin and discuss the current understanding of the role that these modifications play in regulating actin.
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Affiliation(s)
- Jonathan R Terman
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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46
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Zhang F, Saha S, Kashina A. Arginylation-dependent regulation of a proteolytic product of talin is essential for cell-cell adhesion. J Cell Biol 2012; 197:819-36. [PMID: 22665520 PMCID: PMC3373405 DOI: 10.1083/jcb.201112129] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 05/01/2012] [Indexed: 12/26/2022] Open
Abstract
Talin is a large scaffolding molecule that plays a major role in integrin-dependent cell-matrix adhesion. A role for talin in cell-cell attachment through cadherin has never been demonstrated, however. Here, we identify a novel calpain-dependent proteolytic cleavage of talin that results in the release of a 70-kD C-terminal fragment, which serves as a substrate of posttranslational arginylation. The intracellular levels of this fragment closely correlated with the formation of cell-cell adhesions, and this fragment localized to cadherin-containing cell-cell contacts. Moreover, reintroduction of this fragment rescued the cell-cell adhesion defects in arginyltransferase (Ate1) knockout cells, which normally have a very low level of this fragment. Arginylation of this fragment further enhanced its ability to rescue cell-cell adhesion formation. In addition, arginylation facilitated its turnover, suggesting a dual role of arginylation in its intracellular regulation. Thus, our work identifies a novel proteolytic product of talin that is regulated by arginylation and a new role of talin in cadherin-dependent cell-cell adhesion.
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Affiliation(s)
- Fangliang Zhang
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Kurosaka S, Leu NA, Pavlov I, Han X, Ribeiro PAB, Xu T, Bunte R, Saha S, Wang J, Cornachione A, Mai W, Yates JR, Rassier DE, Kashina A. Arginylation regulates myofibrils to maintain heart function and prevent dilated cardiomyopathy. J Mol Cell Cardiol 2012; 53:333-41. [PMID: 22626847 DOI: 10.1016/j.yjmcc.2012.05.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [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: 01/18/2012] [Revised: 04/25/2012] [Accepted: 05/12/2012] [Indexed: 01/25/2023]
Abstract
Protein arginylation mediated by arginyltransferase (ATE1) is essential for heart formation during embryogenesis, however its cell-autonomous role in cardiomyocytes and the differentiated heart muscle has never been investigated. To address this question, we generated cardiac muscle-specific Ate1 knockout mice, in which Ate1 deletion was driven by α-myosin heavy chain promoter (αMHC-Ate1 mouse). These mice were initially viable, but developed severe cardiac contractility defects, dilated cardiomyopathy, and thrombosis over time, resulting in high rates of lethality after 6months of age. These symptoms were accompanied by severe ultrastructural defects in cardiac myofibrils, seen in the newborns and far preceding the onset of cardiomyopathy, suggesting that these defects were primary and likely underlay the development of the future heart defects. Several major sarcomeric proteins were arginylated in vivo. Moreover, Ate1 deletion in the hearts resulted in a significant reduction of active and passive myofibril forces, suggesting that arginylation is critical for both myofibril structural integrity and contractility. Thus, arginylation is essential for maintaining the heart function by regulation of the major myofibril proteins and myofibril forces, and its absence in the heart muscle leads to progressive heart failure through cardiomyocyte-specific defects.
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Affiliation(s)
- Satoshi Kurosaka
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia 19104, USA
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Abstract
The mammalian cytoskeletal proteins β- and γ-actin are highly homologous, but only β-actin is amino-terminally arginylated in vivo, which regulates its function. We examined the metabolic fate of exogenously expressed arginylated and nonarginylated actin isoforms. Arginylated γ-actin, unlike β-, was highly unstable and was selectively ubiquitinated and degraded in vivo. This instability was regulated by the differences in the nucleotide coding sequence between the two actin isoforms, which conferred different translation rates. γ-actin was translated more slowly than β-actin, and this slower processing resulted in the exposure of a normally hidden lysine residue for ubiquitination, leading to the preferential degradation of γ-actin upon arginylation. This degradation mechanism, coupled to nucleotide coding sequence, may regulate protein arginylation in vivo.
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Affiliation(s)
- Fangliang Zhang
- University of Pennsylvania, School of Veterinary Medicine, Department of Animal Biology, Philadelphia, PA 19104, USA
| | - Sougata Saha
- University of Pennsylvania, School of Veterinary Medicine, Department of Animal Biology, Philadelphia, PA 19104, USA
| | - Svetlana Shabalina
- National Center for Biotechnology Information, NLM, NIH, Bethesda, MD 20894, USA
| | - Anna Kashina
- University of Pennsylvania, School of Veterinary Medicine, Department of Animal Biology, Philadelphia, PA 19104, USA
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Saha S, Mundia MM, Zhang F, Demers RW, Korobova F, Svitkina T, Perieteanu AA, Dawson JF, Kashina A. Arginylation regulates intracellular actin polymer level by modulating actin properties and binding of capping and severing proteins. Mol Biol Cell 2010; 21:1350-61. [PMID: 20181827 PMCID: PMC2854093 DOI: 10.1091/mbc.e09-09-0829] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Actin arginylation regulates lamella formation in motile fibroblasts, but the underlying molecular mechanisms are unknown. To understand how arginylation affects the actin cytoskeleton, we investigated the biochemical properties and the structural organization of actin filaments in wild-type and arginyltransferase (Ate1) knockout cells. We found that Ate1 knockout results in a dramatic reduction of the actin polymer levels in vivo accompanied by a corresponding increase in the monomer level. Purified nonarginylated actin has altered polymerization properties, and actin filaments from Ate1 knockout cells show altered interactions with several associated proteins. Ate1 knockout cells have severe impairment of cytoskeletal organization throughout the cell. Thus, arginylation regulates the ability of actin to form filaments in the whole cell rather than preventing the collapse of preformed actin networks at the cell leading edge as proposed in our previous model. This regulation is achieved through interconnected mechanisms that involve actin polymerization per se and through binding of actin-associated proteins.
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Affiliation(s)
- Sougata Saha
- Department of Animal Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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50
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Leu NA, Kurosaka S, Kashina A. Conditional Tek promoter-driven deletion of arginyltransferase in the germ line causes defects in gametogenesis and early embryonic lethality in mice. PLoS One 2009; 4:e7734. [PMID: 19890395 PMCID: PMC2767504 DOI: 10.1371/journal.pone.0007734] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [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: 06/12/2009] [Accepted: 10/13/2009] [Indexed: 11/19/2022] Open
Abstract
Posttranslational protein arginylation mediated by Ate1 is essential for cardiovascular development, actin cytoskeleton functioning, and cell migration. Ate1 plays a role in the regulation of cytoskeleton and is essential for cardiovascular development and angiogenesis—capillary remodeling driven by in-tissue migration of endothelial cells. To address the role of Ate1 in cytoskeleton-dependent processes and endothelial cell function during development, we produced a conditional mouse knockout with Ate1 deletion driven by Tek endothelial receptor tyrosine kinase promoter expressed in the endothelium and in the germ line. Contrary to expectations, Tek-Ate1 mice were viable and had no visible angiogenesis-related phenotypes; however, these mice showed reproductive defects, with high rates of embryonic lethality in the second generation, at stages much earlier than the complete Ate1 knockout strain. While some of the early lethality originated from the subpopulation of embryos with homozygous Tek-Cre transgene—a problem that has not previously been reported for this commercial mouse strain—a distinct subpopulation of embryos had lethality at early post-implantation stages that could be explained only by a previously unknown defect in gametogenesis originating from Tek-driven Ate1 deletion in premeiotic germs cells. These results demonstrate a novel role of Ate1 in germ cell development.
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Affiliation(s)
- Nicolae Adrian Leu
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Satoshi Kurosaka
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Anna Kashina
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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