1
|
Samovich SN, Mikulska-Ruminska K, Dar HH, Tyurina YY, Tyurin VA, Souryavong AB, Kapralov AA, Amoscato AA, Beharier O, Karumanchi SA, St Croix CM, Yang X, Holman TR, VanDemark AP, Sadovsky Y, Mallampalli RK, Wenzel SE, Gu W, Bunimovich YL, Bahar I, Kagan VE, Bayir H. Strikingly High Activity of 15-Lipoxygenase Towards Di-Polyunsaturated Arachidonoyl/Adrenoyl-Phosphatidylethanolamines Generates Peroxidation Signals of Ferroptotic Cell Death. Angew Chem Int Ed Engl 2024; 63:e202314710. [PMID: 38230815 PMCID: PMC11068323 DOI: 10.1002/anie.202314710] [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: 10/02/2023] [Indexed: 01/18/2024]
Abstract
The vast majority of membrane phospholipids (PLs) include two asymmetrically positioned fatty acyls: oxidizable polyunsaturated fatty acids (PUFA) attached predominantly at the sn2 position, and non-oxidizable saturated/monounsaturated acids (SFA/MUFA) localized at the sn1 position. The peroxidation of PUFA-PLs, particularly sn2-arachidonoyl(AA)- and sn2-adrenoyl(AdA)-containing phosphatidylethanolamines (PE), has been associated with the execution of ferroptosis, a program of regulated cell death. There is a minor subpopulation (≈1-2 mol %) of doubly PUFA-acylated phospholipids (di-PUFA-PLs) whose role in ferroptosis remains enigmatic. Here we report that 15-lipoxygenase (15LOX) exhibits unexpectedly high pro-ferroptotic peroxidation activity towards di-PUFA-PEs. We revealed that peroxidation of several molecular species of di-PUFA-PEs occurred early in ferroptosis. Ferrostatin-1, a typical ferroptosis inhibitor, effectively prevented peroxidation of di-PUFA-PEs. Furthermore, co-incubation of cells with di-AA-PE and 15LOX produced PUFA-PE peroxidation and induced ferroptotic death. The decreased contents of di-PUFA-PEs in ACSL4 KO A375 cells was associated with lower levels of di-PUFA-PE peroxidation and enhanced resistance to ferroptosis. Thus, di-PUFA-PE species are newly identified phospholipid peroxidation substrates and regulators of ferroptosis, representing a promising therapeutic target for many diseases related to ferroptotic death.
Collapse
Affiliation(s)
- Svetlana N Samovich
- Department of Pediatrics, Division of Critical Care and Hospital Medicine, Redox Health Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Karolina Mikulska-Ruminska
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Torun, PL87100, Poland
| | - Haider H Dar
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yulia Y Tyurina
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Vladimir A Tyurin
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Austin B Souryavong
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Alexander A Kapralov
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Andrew A Amoscato
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Ofer Beharier
- Obstetrics and Gynecology Division, Hadassah Medical Center, Faculty of Medicine of the Hebrew University of Jerusalem, 97654, Jerusalem, Israel
| | - S Ananth Karumanchi
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | | | - Xin Yang
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Theodore R Holman
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Andrew P VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Yoel Sadovsky
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Rama K Mallampalli
- Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Sally E Wenzel
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Wei Gu
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Yuri L Bunimovich
- Department of Dermatology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Ivet Bahar
- Laufer Center for Physical and Quantitative Biology, Laufer Center, Z-5252, Stony Brook University, Stony Brook, NY 11794, USA
| | - Valerian E Kagan
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Radiation Oncology, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Hülya Bayir
- Department of Pediatrics, Division of Critical Care and Hospital Medicine, Redox Health Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Critical Care Medicine, Safar Center for Resuscitation Research, Children's Neuroscience Institute, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15213, USA
| |
Collapse
|
2
|
Manivarma T, Kapralov AA, Samovich SN, Tyurina YY, Tyurin VA, VanDemark AP, Nowak W, Bayır H, Bahar I, Kagan VE, Mikulska-Ruminska K. Membrane regulation of 15LOX-1/PEBP1 complex prompts the generation of ferroptotic signals, oxygenated PEs. Free Radic Biol Med 2023; 208:458-467. [PMID: 37678654 PMCID: PMC10952060 DOI: 10.1016/j.freeradbiomed.2023.09.001] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 08/24/2023] [Accepted: 09/01/2023] [Indexed: 09/09/2023]
Abstract
Ferroptosis is a regulated form of cell death, the mechanism of which is still to be understood. 15-lipoxygenase (15LOX) complex with phosphatidylethanolamine (PE)-binding protein 1 (PEBP1) catalyzes the generation of pro-ferroptotic cell death signals, hydroperoxy-polyunsaturated PE. We focused on gaining new insights into the molecular basis of these pro-ferroptotic interactions using computational modeling and liquid chromatography-mass spectrometry experiments. Simulations of 15LOX-1/PEBP1 complex dynamics and interactions with lipids revealed that association with the membrane triggers a conformational change in the complex. This conformational change facilitates the access of stearoyl/arachidonoyl-PE (SAPE) substrates to the catalytic site. Furthermore, the binding of SAPE promotes tight interactions within the complex and induces further conformational changes that facilitate the oxidation reaction. The reaction yields two hydroperoxides as products, 15-HpETE-PE and 12-HpETE-PE, at a ratio of 5:1. A significant effect of PEBP1 is observed only on the predominant product. Moreover, combined experiments and simulations consistently demonstrate the significance of PEBP1 P112E mutation in generating ferroptotic cell death signals.
Collapse
Affiliation(s)
- Thiliban Manivarma
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Torun, Poland
| | - Aleksandr A Kapralov
- Department of Environmental and Occupational Health and Center for Free Radical and Antioxidant Health University of Pittsburgh, Pittsburgh, PA, USA
| | - Svetlana N Samovich
- Department of Environmental and Occupational Health and Center for Free Radical and Antioxidant Health University of Pittsburgh, Pittsburgh, PA, USA; Department of Pediatrics, Division of Critical Care and Hospital Medicine, Redox Health Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Yulia Y Tyurina
- Department of Environmental and Occupational Health and Center for Free Radical and Antioxidant Health University of Pittsburgh, Pittsburgh, PA, USA
| | - Vladimir A Tyurin
- Department of Environmental and Occupational Health and Center for Free Radical and Antioxidant Health University of Pittsburgh, Pittsburgh, PA, USA
| | - Andrew P VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wieslaw Nowak
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Torun, Poland
| | - Hülya Bayır
- Department of Environmental and Occupational Health and Center for Free Radical and Antioxidant Health University of Pittsburgh, Pittsburgh, PA, USA; Department of Pediatrics, Division of Critical Care and Hospital Medicine, Redox Health Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Ivet Bahar
- Laufer Center for Physical and Quantitative Biology and Department of Biochemistry and Cell Biology, Stony Brook University, New York, USA.
| | - Valerian E Kagan
- Department of Environmental and Occupational Health and Center for Free Radical and Antioxidant Health University of Pittsburgh, Pittsburgh, PA, USA; Department of Radiation Oncology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Karolina Mikulska-Ruminska
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Torun, Poland.
| |
Collapse
|
3
|
Binsabaan SA, Freeman KG, Hatfull GF, VanDemark AP. The Cytotoxic Mycobacteriophage Protein Phaedrus gp82 Interacts with and Modulates the Activity of the Host ATPase, MoxR. J Mol Biol 2023; 435:168261. [PMID: 37678706 PMCID: PMC10593117 DOI: 10.1016/j.jmb.2023.168261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/09/2023]
Abstract
Approximately 70% of bacteriophage-encoded proteins are of unknown function. Elucidating these protein functions represents opportunities to discover new phage-host interactions and mechanisms by which the phages modulate host activities. Here, we describe a pipeline for prioritizing phage-encoded proteins for structural analysis and characterize the gp82 protein encoded by mycobacteriophage Phaedrus. Structural and solution studies of gp82 show it is a trimeric protein containing two domains. Co-precipitation studies with the host Mycobacterium smegmatis identified the ATPase MoxR as an interacting partner protein. Phaedrus gp82-MoxR interaction requires the presence of a loop sequence within gp82 that is highly exposed and disordered in the crystallographic structure. We show that Phaedrus gp82 overexpression in M. smegmatis retards the growth of M. smegmatis on solid medium, resulting in a small colony phenotype. Overexpression of gp82 containing a mutant disordered loop or the overexpression of MoxR both rescue this phenotype. Lastly, we show that recombinant gp82 reduces levels of MoxR-mediated ATPase activity in vitro that is required for its chaperone function, and that the disordered loop plays an important role in this phenotype. We conclude that Phaedrus gp82 binds to and reduces mycobacterial MoxR activity, leading to reduced function of host proteins that require MoxR chaperone activity for their normal activity.
Collapse
Affiliation(s)
- Saeed A Binsabaan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260, USA
| | - Krista G Freeman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260, USA
| | - Andrew P VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260, USA; Department of Chemistry, University of Pittsburgh, Pittsburgh PA 15260, USA.
| |
Collapse
|
4
|
Hicks KG, Cluntun AA, Schubert HL, Hackett SR, Berg JA, Leonard PG, Ajalla Aleixo MA, Zhou Y, Bott AJ, Salvatore SR, Chang F, Blevins A, Barta P, Tilley S, Leifer A, Guzman A, Arok A, Fogarty S, Winter JM, Ahn HC, Allen KN, Block S, Cardoso IA, Ding J, Dreveny I, Gasper WC, Ho Q, Matsuura A, Palladino MJ, Prajapati S, Sun P, Tittmann K, Tolan DR, Unterlass J, VanDemark AP, Vander Heiden MG, Webb BA, Yun CH, Zhao P, Wang B, Schopfer FJ, Hill CP, Nonato MC, Muller FL, Cox JE, Rutter J. Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase. Science 2023; 379:996-1003. [PMID: 36893255 PMCID: PMC10262665 DOI: 10.1126/science.abm3452] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/07/2023] [Indexed: 03/11/2023]
Abstract
Metabolic networks are interconnected and influence diverse cellular processes. The protein-metabolite interactions that mediate these networks are frequently low affinity and challenging to systematically discover. We developed mass spectrometry integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS) to identify such interactions. Analysis of 33 enzymes from human carbohydrate metabolism identified 830 protein-metabolite interactions, including known regulators, substrates, and products as well as previously unreported interactions. We functionally validated a subset of interactions, including the isoform-specific inhibition of lactate dehydrogenase by long-chain acyl-coenzyme A. Cell treatment with fatty acids caused a loss of pyruvate-lactate interconversion dependent on lactate dehydrogenase isoform expression. These protein-metabolite interactions may contribute to the dynamic, tissue-specific metabolic flexibility that enables growth and survival in an ever-changing nutrient environment.
Collapse
Affiliation(s)
- Kevin G Hicks
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Ahmad A Cluntun
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Heidi L Schubert
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Jordan A Berg
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Paul G Leonard
- Core for Biomolecular Structure and Function, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Institute for Applied Cancer Sciences, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mariana A Ajalla Aleixo
- Laboratório de Cristalografia de Proteinas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Youjia Zhou
- School of Computing, University of Utah, Salt Lake City, UT, USA
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA
| | - Alex J Bott
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Sonia R Salvatore
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Fei Chang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Aubrie Blevins
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Paige Barta
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Samantha Tilley
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Aaron Leifer
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Andrea Guzman
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Ajak Arok
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Sarah Fogarty
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jacob M Winter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Hee-Chul Ahn
- Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, The Republic of Korea
| | - Karen N Allen
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Samuel Block
- The Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Iara A Cardoso
- Laboratório de Cristalografia de Proteinas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Jianping Ding
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Shanghai, China
| | - Ingrid Dreveny
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, UK
| | | | - Quinn Ho
- Department of Biology, Boston University, Boston, MA, USA
| | - Atsushi Matsuura
- Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, The Republic of Korea
| | - Michael J Palladino
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sabin Prajapati
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, University of Göttingen, Göttingen, Germany
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Pengkai Sun
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Shanghai, China
| | - Kai Tittmann
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, University of Göttingen, Göttingen, Germany
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Dean R Tolan
- Department of Biology, Boston University, Boston, MA, USA
| | - Judith Unterlass
- Department of Oncology and Pathology, Karolinska Institute, Stockholm, Sweden
| | - Andrew P VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew G Vander Heiden
- The Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bradley A Webb
- Department of Biochemistry, West Virginia University, Morgantown, WV, USA
| | - Cai-Hong Yun
- Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Pengkai Zhao
- Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Bei Wang
- School of Computing, University of Utah, Salt Lake City, UT, USA
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA
| | - Francisco J Schopfer
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Pittsburgh Heart, Lung, and Blood Vascular Medicine Institute, Pittsburgh, PA, USA
- Pittsburgh Liver Research Center, Pittsburgh, PA, USA
- Center for Metabolism and Mitochondrial Medicine, Pittsburgh, PA, USA
| | - Christopher P Hill
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Maria Cristina Nonato
- Laboratório de Cristalografia de Proteinas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Florian L Muller
- Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James E Cox
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| |
Collapse
|
5
|
Van Oss SB, Parikh SB, Castilho Coelho N, Wacholder A, Belashov I, Zdancewicz S, Michaca M, Xu J, Kang YP, Ward NP, Yoon SJ, McCourt KM, McKee J, Ideker T, VanDemark AP, DeNicola GM, Carvunis AR. On the illusion of auxotrophy: met15Δ yeast cells can grow on inorganic sulfur, thanks to the previously uncharacterized homocysteine synthase Yll058w. J Biol Chem 2022; 298:102697. [PMID: 36379252 PMCID: PMC9763685 DOI: 10.1016/j.jbc.2022.102697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 11/01/2022] [Accepted: 11/05/2022] [Indexed: 11/15/2022] Open
Abstract
Organisms must either synthesize or assimilate essential organic compounds to survive. The homocysteine synthase Met15 has been considered essential for inorganic sulfur assimilation in yeast since its discovery in the 1970s. As a result, MET15 has served as a genetic marker for hundreds of experiments that play a foundational role in eukaryote genetics and systems biology. Nevertheless, we demonstrate here through structural and evolutionary modeling, in vitro kinetic assays, and genetic complementation, that an alternative homocysteine synthase encoded by the previously uncharacterized gene YLL058W enables cells lacking Met15 to assimilate enough inorganic sulfur for survival and proliferation. These cells however fail to grow in patches or liquid cultures unless provided with exogenous methionine or other organosulfurs. We show that this growth failure, which has historically justified the status of MET15 as a classic auxotrophic marker, is largely explained by toxic accumulation of the gas hydrogen sulfide because of a metabolic bottleneck. When patched or cultured with a hydrogen sulfide chelator, and when propagated as colony grids, cells without Met15 assimilate inorganic sulfur and grow, and cells with Met15 achieve even higher yields. Thus, Met15 is not essential for inorganic sulfur assimilation in yeast. Instead, MET15 is the first example of a yeast gene whose loss conditionally prevents growth in a manner that depends on local gas exchange. Our results have broad implications for investigations of sulfur metabolism, including studies of stress response, methionine restriction, and aging. More generally, our findings illustrate how unappreciated experimental variables can obfuscate biological discovery.
Collapse
Affiliation(s)
- S. Branden Van Oss
- Department of Computational and System Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Saurin Bipin Parikh
- Department of Computational and System Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Nelson Castilho Coelho
- Department of Computational and System Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Aaron Wacholder
- Department of Computational and System Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ivan Belashov
- Department of Biological Sciences, University of Pittsburgh, Dietrich School of Arts & Sciences, Pittsburgh, Pennsylvania, USA
| | - Sara Zdancewicz
- Department of Biological Sciences, University of Pittsburgh, Dietrich School of Arts & Sciences, Pittsburgh, Pennsylvania, USA
| | - Manuel Michaca
- Department of Computational and System Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jiazhen Xu
- Department of Computational and System Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yun Pyo Kang
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center, Tampa, Florida, USA
| | - Nathan P. Ward
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center, Tampa, Florida, USA
| | - Sang Jun Yoon
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center, Tampa, Florida, USA
| | - Katherine M. McCourt
- Department of Computational and System Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jake McKee
- Department of Computational and System Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Trey Ideker
- Departments of Medicine, Bioengineering, Computer Science and Engineering, Institute for Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - Andrew P. VanDemark
- Department of Biological Sciences, University of Pittsburgh, Dietrich School of Arts & Sciences, Pittsburgh, Pennsylvania, USA
| | - Gina M. DeNicola
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center, Tampa, Florida, USA
| | - Anne-Ruxandra Carvunis
- Department of Computational and System Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,For correspondence: Anne-Ruxandra Carvunis
| |
Collapse
|
6
|
VanDemark AP, Hrizo SL, Eicher SL, Kowalski J, Myers TD, Pfeifer MR, Riley KN, Koeberl DD, Palladino MJ. Itavastatin and resveratrol increase triosephosphate isomerase protein in a newly identified variant of TPI deficiency. Dis Model Mech 2022; 15:274792. [PMID: 35315486 PMCID: PMC9150114 DOI: 10.1242/dmm.049261] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 03/14/2022] [Indexed: 11/20/2022] Open
Abstract
Triosephosphate isomerase (TPI) deficiency (TPI Df) is an untreatable glycolytic enzymopathy that results in hemolytic anemia, progressive muscular impairment and irreversible brain damage. Although there is a ‘common’ mutation (TPIE105D), other pathogenic mutations have been described. We identified patients who were compound heterozygous for a newly described mutation, TPIQ181P, and the common TPIE105D mutation. Intriguingly, these patients lacked neuropathy or cognitive impairment. We then initiated biochemical and structural studies of TPIQ181P. Surprisingly, we found that purified TPIQ181P protein had markedly impaired catalytic properties whereas crystallographic studies demonstrated that the TPIQ181P mutation resulted in a highly disordered catalytic lid. We propose that genetic complementation occurs between the two alleles, one with little activity (TPIQ181P) and one with low stability (TPIE105D). Consistent with this, TPIQ181P/E105D fibroblasts exhibit a significant reduction in the TPI protein. These data suggest that impaired stability, and not catalytic activity, is a better predictor of TPI Df severity. Lastly, we tested two recently discovered chemical modulators of mutant TPI stability, itavastatin and resveratrol, and observed a significant increase in TPI in TPIQ181P/E105D patient cells. Summary: A newly identified triosephosphate isomerase (TPI) variant (TPIQ181P) confers TPI deficiency, suggests a molecular and genetic model for its pathogenesis, and the potential for therapeutic intervention.
Collapse
Affiliation(s)
- Andrew P VanDemark
- Biological Sciences and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Stacy L Hrizo
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.,Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.,Department of Biology, Slippery Rock University of Pennsylvania, Slippery Rock, PA 16057, USA
| | - Samantha L Eicher
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.,Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Jules Kowalski
- Biological Sciences and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Tracey D Myers
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.,Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Megan R Pfeifer
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.,Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Kacie N Riley
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC 27710, USA
| | - Dwight D Koeberl
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC 27710, USA
| | - Michael J Palladino
- Biological Sciences and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| |
Collapse
|
7
|
Lamade AM, Wu L, Dar HH, Mentrup HL, Shrivastava IH, Epperly MW, St Croix CM, Tyurina YY, Anthonymuthu TS, Yang Q, Kapralov AA, Huang Z, Mao G, Amoscato AA, Hier ZE, Artyukhova MA, Shurin G, Rosenbaum JC, Gough PJ, Bertin J, VanDemark AP, Watkins SC, Mollen KP, Bahar I, Greenberger JS, Kagan VE, Whalen MJ, Bayır H. Inactivation of RIP3 kinase sensitizes to 15LOX/PEBP1-mediated ferroptotic death. Redox Biol 2022; 50:102232. [PMID: 35101798 PMCID: PMC8804265 DOI: 10.1016/j.redox.2022.102232] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 12/23/2021] [Accepted: 01/06/2022] [Indexed: 01/02/2023] Open
Abstract
Ferroptosis and necroptosis are two pro-inflammatory cell death programs contributing to major pathologies and their inhibition has gained attention to treat a wide range of disease states. Necroptosis relies on activation of RIP1 and RIP3 kinases. Ferroptosis is triggered by oxidation of polyunsaturated phosphatidylethanolamines (PUFA-PE) by complexes of 15-Lipoxygenase (15LOX) with phosphatidylethanolamine-binding protein 1 (PEBP1). The latter, also known as RAF kinase inhibitory protein, displays promiscuity towards multiple proteins. In this study we show that RIP3 K51A kinase inactive mice have increased ferroptotic burden and worse outcome after irradiation and brain trauma rescued by anti-ferroptotic compounds Liproxstatin-1 and Ferrostatin 16-86. Given structural homology between RAF and RIP3, we hypothesized that PEBP1 acts as a necroptosis-to-ferroptosis switch interacting with either RIP3 or 15LOX. Using genetic, biochemical, redox lipidomics and computational approaches, we uncovered that PEBP1 complexes with RIP3 and inhibits necroptosis. Elevated expression combined with higher affinity enables 15LOX to pilfer PEBP1 from RIP3, thereby promoting PUFA-PE oxidation and ferroptosis which sensitizes Rip3K51A/K51A kinase-deficient mice to total body irradiation and brain trauma. This newly unearthed PEBP1/15LOX-driven mechanism, along with previously established switch between necroptosis and apoptosis, can serve multiple and diverse cell death regulatory functions across various human disease states.
Collapse
Affiliation(s)
- Andrew M. Lamade
- Safar Center for Resuscitation Research, Department of Critical Care Medicine, University of Pittsburgh Medical Center, 4401 Penn Ave, Pittsburgh, PA, 15224, USA,Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, 130 Desoto St, Pittsburgh, PA, 15261, USA
| | - Limin Wu
- Neuroscience Center and Department of Pediatrics, Massachusetts General Hospital and Harvard Medical School, 55 Fruit St. Boston, MA, 02114, USA
| | - Haider H. Dar
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, 130 Desoto St, Pittsburgh, PA, 15261, USA
| | - Heather L. Mentrup
- Division of Pediatric General and Thoracic Surgery, UPMC Children's Hospital of Pittsburgh, 4401 Penn Ave, Pittsburgh, PA, 15224, USA
| | - Indira H. Shrivastava
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, 130 Desoto St, Pittsburgh, PA, 15261, USA,Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch I Bldg, 3420 Forbes Avenue, Pittsburgh, PA, 15213, USA
| | - Michael W. Epperly
- Department of Radiation Oncology, University of Pittsburgh Medical Center, 200 Lothrop St, Pittsburgh, PA, 15213, USA
| | - Claudette M. St Croix
- Department of Cell Biology, University of Pittsburgh School of Medicine, 3550 Terrace St, Pittsburgh, PA, 15261, USA
| | - Yulia Y. Tyurina
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, 130 Desoto St, Pittsburgh, PA, 15261, USA
| | - Tamil S. Anthonymuthu
- Safar Center for Resuscitation Research, Department of Critical Care Medicine, University of Pittsburgh Medical Center, 4401 Penn Ave, Pittsburgh, PA, 15224, USA,Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, 130 Desoto St, Pittsburgh, PA, 15261, USA
| | - Qin Yang
- Safar Center for Resuscitation Research, Department of Critical Care Medicine, University of Pittsburgh Medical Center, 4401 Penn Ave, Pittsburgh, PA, 15224, USA,Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, 130 Desoto St, Pittsburgh, PA, 15261, USA
| | - Aleksandr A. Kapralov
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, 130 Desoto St, Pittsburgh, PA, 15261, USA
| | - Zhentai Huang
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, 130 Desoto St, Pittsburgh, PA, 15261, USA
| | - Gaowei Mao
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, 130 Desoto St, Pittsburgh, PA, 15261, USA
| | - Andrew A. Amoscato
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, 130 Desoto St, Pittsburgh, PA, 15261, USA
| | - Zachary E. Hier
- Safar Center for Resuscitation Research, Department of Critical Care Medicine, University of Pittsburgh Medical Center, 4401 Penn Ave, Pittsburgh, PA, 15224, USA,Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, 130 Desoto St, Pittsburgh, PA, 15261, USA
| | - Margarita A. Artyukhova
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, 130 Desoto St, Pittsburgh, PA, 15261, USA
| | - Galina Shurin
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, 130 Desoto St, Pittsburgh, PA, 15261, USA
| | - Joel C. Rosenbaum
- Department of Biological Sciences, University of Pittsburgh, 4249 5th Ave, Pittsburgh, PA, 15213, USA
| | - Peter J. Gough
- Inzen Therapeutics, 790 Memorial Dr Ste 2C, Cambridge, MA, 02139, USA
| | - John Bertin
- Pattern Recognition Receptor Discovery Performance Unit, Immuno-inflammation Therapeutic Area, GlaxoSmithKline, 1250 S Collegeville Rd, Collegeville, PA, 19426, USA
| | - Andrew P. VanDemark
- Department of Biological Sciences, University of Pittsburgh, 4249 5th Ave, Pittsburgh, PA, 15213, USA
| | - Simon C. Watkins
- Department of Cell Biology, University of Pittsburgh School of Medicine, 3550 Terrace St, Pittsburgh, PA, 15261, USA
| | - Kevin P. Mollen
- Division of Pediatric General and Thoracic Surgery, UPMC Children's Hospital of Pittsburgh, 4401 Penn Ave, Pittsburgh, PA, 15224, USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch I Bldg, 3420 Forbes Avenue, Pittsburgh, PA, 15213, USA
| | - Joel S. Greenberger
- Department of Radiation Oncology, University of Pittsburgh Medical Center, 200 Lothrop St, Pittsburgh, PA, 15213, USA
| | - Valerian E. Kagan
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, 130 Desoto St, Pittsburgh, PA, 15261, USA,Children’s Neuroscience Institute, Children’s Hospital of Pittsburgh, 4401 Penn Ave, Pittsburgh, PA, 15224, USA,Corresponding author. Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, 130 Desoto St, Pittsburgh, PA, 15261, USA.
| | - Michael J. Whalen
- Neuroscience Center and Department of Pediatrics, Massachusetts General Hospital and Harvard Medical School, 55 Fruit St. Boston, MA, 02114, USA,Corresponding author. Neuroscience Center and Department of Pediatrics, Massachusetts General Hospital and Harvard Medical School, 55 Fruit St. Boston, MA, 02114, USA
| | - Hülya Bayır
- Safar Center for Resuscitation Research, Department of Critical Care Medicine, University of Pittsburgh Medical Center, 4401 Penn Ave, Pittsburgh, PA, 15224, USA,Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, 130 Desoto St, Pittsburgh, PA, 15261, USA,Children’s Neuroscience Institute, Children’s Hospital of Pittsburgh, 4401 Penn Ave, Pittsburgh, PA, 15224, USA,Corresponding author. Safar Center for Resuscitation Research, Department of Critical Care Medicine, University of Pittsburgh Medical Center, 4401 Penn Ave, Pittsburgh, PA, 15224, USA.
| |
Collapse
|
8
|
Anthonymuthu TS, Tyurina YY, Sun WY, Mikulska-Ruminska K, Shrivastava IH, Tyurin VA, Cinemre FB, Dar HH, VanDemark AP, Holman TR, Sadovsky Y, Stockwell BR, He RR, Bahar I, Bayır H, Kagan VE. Resolving the paradox of ferroptotic cell death: Ferrostatin-1 binds to 15LOX/PEBP1 complex, suppresses generation of peroxidized ETE-PE, and protects against ferroptosis. Redox Biol 2021; 38:101744. [PMID: 33126055 PMCID: PMC7596334 DOI: 10.1016/j.redox.2020.101744] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [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: 08/19/2020] [Revised: 10/04/2020] [Accepted: 10/04/2020] [Indexed: 12/20/2022] Open
Abstract
Hydroperoxy-eicosatetraenoyl-phosphatidylethanolamine (HpETE-PE) is a ferroptotic cell death signal. HpETE-PE is produced by the 15-Lipoxygenase (15LOX)/Phosphatidylethanolamine Binding Protein-1 (PEBP1) complex or via an Fe-catalyzed non-enzymatic radical reaction. Ferrostatin-1 (Fer-1), a common ferroptosis inhibitor, is a lipophilic radical scavenger but a poor 15LOX inhibitor arguing against 15LOX having a role in ferroptosis. In the current work, we demonstrate that Fer-1 does not affect 15LOX alone, however, it effectively inhibits HpETE-PE production by the 15LOX/PEBP1 complex. Computational molecular modeling shows that Fer-1 binds to the 15LOX/PEBP1 complex at three sites and could disrupt the catalytically required allosteric motions of the 15LOX/PEBP1 complex. Using nine ferroptosis cell/tissue models, we show that HpETE-PE is produced by the 15LOX/PEBP1 complex and resolve the long-existing Fer-1 anti-ferroptotic paradox.
Collapse
Affiliation(s)
- Tamil S Anthonymuthu
- Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, USA; Children's Neuroscience Institute, University of Pittsburgh, Pittsburgh, PA, USA; Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yulia Y Tyurina
- Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA, USA; Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wan-Yang Sun
- Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA, USA; Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA; Guangdong Engineering Research Center of Chinese Medicine & Disease Susceptibility, Jinan University, College of Pharmacy, Guangzhou, China
| | - Karolina Mikulska-Ruminska
- Department of Computational and System Biology, University of Pittsburgh, Pittsburgh, PA, USA; Institute of Physics, Faculty of Physics Astronomy and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Torun, Poland
| | - Indira H Shrivastava
- Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA, USA; Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA; Department of Computational and System Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Vladimir A Tyurin
- Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA, USA; Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Fatma B Cinemre
- Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA, USA; Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA; Sakarya University School of Medicine, Sakarya, Turkey
| | - Haider H Dar
- Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA, USA; Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Andrew P VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Theodore R Holman
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Yoel Sadovsky
- Magee-Womens Research Institute and Departments of OBGYN and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Brent R Stockwell
- Department of Biological Sciences and Department of Chemistry, Columbia University, New York, NY, USA
| | - Rong-Rong He
- Guangdong Engineering Research Center of Chinese Medicine & Disease Susceptibility, Jinan University, College of Pharmacy, Guangzhou, China
| | - Ivet Bahar
- Department of Computational and System Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hülya Bayır
- Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, USA; Children's Neuroscience Institute, University of Pittsburgh, Pittsburgh, PA, USA; Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA, USA; Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Valerian E Kagan
- Children's Neuroscience Institute, University of Pittsburgh, Pittsburgh, PA, USA; Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA, USA; Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA; Navigational Redox Lipidomics Group, Institute for Regenerative Medicine, IM Sechenov First Moscow State Medical University, Russian Federation.
| |
Collapse
|
9
|
Googins MR, Woghiren-Afegbua AO, Calderon M, St Croix CM, Kiselyov KI, VanDemark AP. Structural and functional divergence of GDAP1 from the glutathione S-transferase superfamily. FASEB J 2020; 34:7192-7207. [PMID: 32274853 DOI: 10.1096/fj.202000110r] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/12/2020] [Accepted: 03/24/2020] [Indexed: 11/11/2022]
Abstract
Mutations in ganglioside-induced differentiation-associated protein 1 (GDAP1) alter mitochondrial morphology and result in several subtypes of the inherited peripheral neuropathy Charcot-Marie-Tooth disease; however, the mechanism by which GDAP1 functions has remained elusive. GDAP1 contains primary sequence homology to the GST superfamily; however, the question of whether GDAP1 is an active GST has not been clearly resolved. Here, we present biochemical evidence, suggesting that GDAP1 has lost the ability to bind glutathione without a loss of substrate binding activity. We have revealed that the α-loop, located within the H-site motif is the primary determinant for substrate binding. Using structural data of GDAP1, we have found that critical residues and configurations in the G-site which canonically interact with glutathione are altered in GDAP1, rendering it incapable of binding glutathione. Last, we have found that the overexpression of GDAP1 in HeLa cells results in a mitochondrial phenotype which is distinct from oxidative stress-induced mitochondrial fragmentation. This phenotype is dependent on the presence of the transmembrane domain, as well as a unique hydrophobic domain that is not found in canonical GSTs. Together, we data point toward a non-enzymatic role for GDAP1, such as a sensor or receptor.
Collapse
Affiliation(s)
- Matthew R Googins
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Michael Calderon
- Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Kirill I Kiselyov
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Andrew P VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| |
Collapse
|
10
|
Rosenbaum JC, Bonilla B, Hengel SR, Mertz TM, Herken BW, Kazemier HG, Pressimone CA, Ratterman TC, MacNary E, De Magis A, Kwon Y, Godin SK, Van Houten B, Normolle DP, Sung P, Das SR, Paeschke K, Roberts SA, VanDemark AP, Bernstein KA. The Rad51 paralogs facilitate a novel DNA strand specific damage tolerance pathway. Nat Commun 2019; 10:3515. [PMID: 31383866 PMCID: PMC6683157 DOI: 10.1038/s41467-019-11374-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 05/15/2018] [Accepted: 07/10/2019] [Indexed: 12/12/2022] Open
Abstract
Accurate DNA replication is essential for genomic stability and cancer prevention. Homologous recombination is important for high-fidelity DNA damage tolerance during replication. How the homologous recombination machinery is recruited to replication intermediates is unknown. Here, we provide evidence that a Rad51 paralog-containing complex, the budding yeast Shu complex, directly recognizes and enables tolerance of predominantly lagging strand abasic sites. We show that the Shu complex becomes chromatin associated when cells accumulate abasic sites during S phase. We also demonstrate that purified recombinant Shu complex recognizes an abasic analog on a double-flap substrate, which prevents AP endonuclease activity and endonuclease-induced double-strand break formation. Shu complex DNA binding mutants are sensitive to methyl methanesulfonate, are not chromatin enriched, and exhibit increased mutation rates. We propose a role for the Shu complex in recognizing abasic sites at replication intermediates, where it recruits the homologous recombination machinery to mediate strand specific damage tolerance. The homologous recombination machinery needs to be recruited at replication intermediates for accurate functioning. Here, the authors reveal that a Rad51 paralog-containing complex, called the Shu complex, recognizes and enables tolerance of predominantly lagging strand abasic sites.
Collapse
Affiliation(s)
- Joel C Rosenbaum
- University of Pittsburgh, Department of Biological Sciences Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Braulio Bonilla
- University of Pittsburgh, School of Medicine, Department of Microbiology and Molecular Genetics, Pittsburgh, PA, 15213, USA
| | - Sarah R Hengel
- University of Pittsburgh, School of Medicine, Department of Microbiology and Molecular Genetics, Pittsburgh, PA, 15213, USA
| | - Tony M Mertz
- Washington State University, School of Molecular Biosciences and Center for Reproductive Biology, College of Veterinary Medicine, Pullman, WA, 99164, USA
| | - Benjamin W Herken
- University of Pittsburgh, School of Medicine, Department of Microbiology and Molecular Genetics, Pittsburgh, PA, 15213, USA
| | - Hinke G Kazemier
- University of Groningen, University Medical Center Groningen, European Research Institute for the Biology of Ageing, 9713 AV, Groningen, Netherlands
| | - Catherine A Pressimone
- University of Pittsburgh, School of Medicine, Department of Microbiology and Molecular Genetics, Pittsburgh, PA, 15213, USA
| | - Timothy C Ratterman
- Carnegie Mellon University, Department of Chemistry and Center for Nucleic Acids Science & Technology, Pittsburgh, PA, 15213, USA
| | - Ellen MacNary
- Washington State University, School of Molecular Biosciences and Center for Reproductive Biology, College of Veterinary Medicine, Pullman, WA, 99164, USA
| | - Alessio De Magis
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Youngho Kwon
- Yale University, School of Medicine, Department of Molecular Biophysics and Biochemistry, New Haven, CT, 06511, USA.,University of Texas Health Science Center at San Antonio, Department of Biochemistry and Structural Biology, San Antonio, TX, 78229, USA
| | - Stephen K Godin
- University of Pittsburgh, School of Medicine, Department of Microbiology and Molecular Genetics, Pittsburgh, PA, 15213, USA
| | - Bennett Van Houten
- University of Pittsburgh, School of Medicine, Department of Pharmacology and Chemical Biology, Pittsburgh, PA, 15213, USA
| | - Daniel P Normolle
- University of Pittsburgh, School of Public Health, Department of Biostatistics, Pittsburgh, PA, 15261, USA
| | - Patrick Sung
- Yale University, School of Medicine, Department of Molecular Biophysics and Biochemistry, New Haven, CT, 06511, USA.,University of Texas Health Science Center at San Antonio, Department of Biochemistry and Structural Biology, San Antonio, TX, 78229, USA
| | - Subha R Das
- Carnegie Mellon University, Department of Chemistry and Center for Nucleic Acids Science & Technology, Pittsburgh, PA, 15213, USA
| | - Katrin Paeschke
- University of Groningen, University Medical Center Groningen, European Research Institute for the Biology of Ageing, 9713 AV, Groningen, Netherlands.,Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Steven A Roberts
- Washington State University, School of Molecular Biosciences and Center for Reproductive Biology, College of Veterinary Medicine, Pullman, WA, 99164, USA
| | - Andrew P VanDemark
- University of Pittsburgh, Department of Biological Sciences Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Kara A Bernstein
- University of Pittsburgh, School of Medicine, Department of Microbiology and Molecular Genetics, Pittsburgh, PA, 15213, USA.
| |
Collapse
|
11
|
Roland BP, Richards KR, Hrizo SL, Eicher S, Barile ZJ, Chang TC, Savon G, Bianchi P, Fermo E, Ricerca BM, Tortorolo L, Vockley J, VanDemark AP, Palladino MJ. Missense variant in TPI1 (Arg189Gln) causes neurologic deficits through structural changes in the triosephosphate isomerase catalytic site and reduced enzyme levels in vivo. Biochim Biophys Acta Mol Basis Dis 2019; 1865:2257-2266. [PMID: 31075491 DOI: 10.1016/j.bbadis.2019.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 12/20/2018] [Accepted: 01/06/2019] [Indexed: 12/27/2022]
Abstract
Mutations in the gene triosephosphate isomerase (TPI) lead to a severe multisystem condition that is characterized by hemolytic anemia, a weakened immune system, and significant neurologic symptoms such as seizures, distal neuropathy, and intellectual disability. No effective therapy is available. Here we report a compound heterozygous patient with a novel TPI pathogenic variant (NM_000365.5:c.569G>A:p.(Arg189Gln)) in combination with the common (NM_000365.5:c.315G>C:p.(Glu104Asp)) allele. We characterized the novel variant by mutating the homologous Arg in Drosophila using a genomic engineering system, demonstrating that missense mutations at this position cause a strong loss of function. Compound heterozygote animals were generated and exhibit motor behavioural deficits and markedly reduced protein levels. Furthermore, examinations of the TPIArg189Gln/TPIGlu104Asp patient fibroblasts confirmed the reduction of TPI levels, suggesting that Arg189Gln may also affect the stability of the protein. The Arg189 residue participates in two salt bridges on the backside of the TPI enzyme dimer, and we reveal that a mutation at this position alters the coordination of the substrate-binding site and important catalytic residues. Collectively, these data reveal a new human pathogenic variant associated with TPI deficiency, identify the Arg189 salt bridge as critical for organizing the catalytic site of the TPI enzyme, and demonstrates that reduced TPI levels are associated with human TPI deficiency. These findings advance our understanding of the molecular pathogenesis of the disease, and suggest new therapeutic avenues for pre-clinical trials.
Collapse
Affiliation(s)
- Bartholomew P Roland
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
| | - Kristen R Richards
- Biological Sciences and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Stacy L Hrizo
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Department of Biology, Slippery Rock University, Slippery Rock, PA 16057, USA
| | - Samantha Eicher
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Zackery J Barile
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Tien-Chien Chang
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Grace Savon
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Paola Bianchi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, UOC Ematologia, UOS Fisiopatologia delle Anemie, Via F Sforza, 35, 20122 Milan, Italy
| | - Elisa Fermo
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, UOC Ematologia, UOS Fisiopatologia delle Anemie, Via F Sforza, 35, 20122 Milan, Italy
| | - Bianca Maria Ricerca
- Hematology Institute, Universitary Hospital A. Gemelli, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Luca Tortorolo
- Pediatric Intensive Care Unit, Universitary Hospital A. Gemelli, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Jerry Vockley
- Department of Pediatrics and Human Genetics, University of Pittsburgh Schools of Medicine and Public health, Pittsburgh, PA 15261, USA
| | - Andrew P VanDemark
- Biological Sciences and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Michael J Palladino
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.
| |
Collapse
|
12
|
Mikulska-Ruminska K, Shrivastava I, Krieger J, Zhang S, Li H, Bayır H, Wenzel SE, VanDemark AP, Kagan VE, Bahar I. Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members. J Chem Inf Model 2019; 59:2496-2508. [PMID: 30762363 PMCID: PMC6541894 DOI: 10.1021/acs.jcim.9b00006] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Accurate modeling of structural dynamics of proteins and their differentiation across different species can help us understand generic mechanisms of function shared by family members and the molecular basis of the specificity of individual members. We focused here on the family of lipoxygenases, enzymes that catalyze lipid oxidation, the mammalian and bacterial structures of which have been elucidated. We present a systematic method of approach for characterizing the sequence, structure, dynamics, and allosteric signaling properties of these enzymes using a combination of structure-based models and methods and bioinformatics tools applied to a data set of 88 structures. The analysis elucidates the signature dynamics of the lipoxygenase family and its differentiation among members, as well as key sites that enable its adaptation to specific substrate binding and allosteric activity.
Collapse
Affiliation(s)
- Karolina Mikulska-Ruminska
- Institute of Physics, Department of Biophysics and Medical Physics , Nicolaus Copernicus University , 87-100 Torun , Poland
| | | | | | | | | | | | | | | | - Valerian E Kagan
- Laboratory of Navigational Redox Lipidomics , I M Sechenov Moscow State Medical University , Moskva 119146 , Russia
| | - Ivet Bahar
- Mol & Cell Cancer Biology , UPMC Hillman Cancer Center , Pittsburgh , Pennsylvania 15232 , United States
| |
Collapse
|
13
|
Anthonymuthu TS, Kenny EM, Shrivastava I, Tyurina YY, Hier ZE, Ting HC, Dar HH, Tyurin VA, Nesterova A, Amoscato AA, Mikulska-Ruminska K, Rosenbaum JC, Mao G, Zhao J, Conrad M, Kellum JA, Wenzel SE, VanDemark AP, Bahar I, Kagan VE, Bayır H. Empowerment of 15-Lipoxygenase Catalytic Competence in Selective Oxidation of Membrane ETE-PE to Ferroptotic Death Signals, HpETE-PE. J Am Chem Soc 2018; 140:17835-17839. [PMID: 30525572 DOI: 10.1021/jacs.8b09913] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
sn2-15-Hydroperoxy-eicasotetraenoyl-phosphatidylethanolamines ( sn2-15-HpETE-PE) generated by mammalian 15-lipoxygenase/phosphatidylethanolamine binding protein-1 (15-LO/PEBP1) complex is a death signal in a recently identified type of programmed cell demise, ferroptosis. How the enzymatic complex selects sn2-ETE-PE as the substrate among 1 of ∼100 total oxidizable membrane PUFA phospholipids is a central, yet unresolved question. To unearth the highly selective and specific mechanisms of catalytic competence, we used a combination of redox lipidomics, mutational and computational structural analysis to show they stem from (i) reactivity toward readily accessible hexagonally organized membrane sn2-ETE-PEs, (ii) relative preponderance of sn2-ETE-PE species vs other sn2-ETE-PLs, and (iii) allosteric modification of the enzyme in the complex with PEBP1. This emphasizes the role of enzymatic vs random stochastic free radical reactions in ferroptotic death signaling.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Anastasia Nesterova
- Laboratory of Navigational Redox Lipidomics, IM Sechenov Moscow State Medical University , Moscow 119146 , Russian Federation
| | | | | | - Joel C Rosenbaum
- Department of Biological Sciences , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | | | | | - Marcus Conrad
- Institute of Developmental Genetics, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) , Neuherberg 85764 , Germany
| | | | | | - Andrew P VanDemark
- Department of Biological Sciences , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | | | - Valerian E Kagan
- Laboratory of Navigational Redox Lipidomics, IM Sechenov Moscow State Medical University , Moscow 119146 , Russian Federation
| | | |
Collapse
|
14
|
Wenzel SE, Tyurina YY, Zhao J, St Croix CM, Dar HH, Mao G, Tyurin VA, Anthonymuthu TS, Kapralov AA, Amoscato AA, Mikulska-Ruminska K, Shrivastava IH, Kenny EM, Yang Q, Rosenbaum JC, Sparvero LJ, Emlet DR, Wen X, Minami Y, Qu F, Watkins SC, Holman TR, VanDemark AP, Kellum JA, Bahar I, Bayır H, Kagan VE. PEBP1 Wardens Ferroptosis by Enabling Lipoxygenase Generation of Lipid Death Signals. Cell 2017; 171:628-641.e26. [PMID: 29053969 DOI: 10.1016/j.cell.2017.09.044] [Citation(s) in RCA: 537] [Impact Index Per Article: 76.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 07/05/2017] [Accepted: 09/25/2017] [Indexed: 02/07/2023]
Abstract
Ferroptosis is a form of programmed cell death that is pathogenic to several acute and chronic diseases and executed via oxygenation of polyunsaturated phosphatidylethanolamines (PE) by 15-lipoxygenases (15-LO) that normally use free polyunsaturated fatty acids as substrates. Mechanisms of the altered 15-LO substrate specificity are enigmatic. We sought a common ferroptosis regulator for 15LO. We discovered that PEBP1, a scaffold protein inhibitor of protein kinase cascades, complexes with two 15LO isoforms, 15LO1 and 15LO2, and changes their substrate competence to generate hydroperoxy-PE. Inadequate reduction of hydroperoxy-PE due to insufficiency or dysfunction of a selenoperoxidase, GPX4, leads to ferroptosis. We demonstrated the importance of PEBP1-dependent regulatory mechanisms of ferroptotic death in airway epithelial cells in asthma, kidney epithelial cells in renal failure, and cortical and hippocampal neurons in brain trauma. As master regulators of ferroptotic cell death with profound implications for human disease, PEBP1/15LO complexes represent a new target for drug discovery.
Collapse
Affiliation(s)
- Sally E Wenzel
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Yulia Y Tyurina
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jinming Zhao
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Haider H Dar
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Gaowei Mao
- Department of Critical Care Medicine, Center for Critical Care Nephrology, Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Vladimir A Tyurin
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tamil S Anthonymuthu
- Department of Critical Care Medicine, Center for Critical Care Nephrology, Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alexandr A Kapralov
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Andrew A Amoscato
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Karolina Mikulska-Ruminska
- Department of Computational and System Biology, University of Pittsburgh, Pittsburgh, PA, USA; Institute of Physics, Nicolaus Copernicus University, Torun, Poland
| | - Indira H Shrivastava
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA, USA; Department of Computational and System Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Elizabeth M Kenny
- Department of Critical Care Medicine, Center for Critical Care Nephrology, Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Qin Yang
- Department of Critical Care Medicine, Center for Critical Care Nephrology, Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joel C Rosenbaum
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Louis J Sparvero
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - David R Emlet
- Department of Critical Care Medicine, Center for Critical Care Nephrology, Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xiaoyan Wen
- Department of Critical Care Medicine, Center for Critical Care Nephrology, Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yoshinori Minami
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Feng Qu
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Simon C Watkins
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Theodore R Holman
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Andrew P VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - John A Kellum
- Department of Critical Care Medicine, Center for Critical Care Nephrology, Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ivet Bahar
- Department of Computational and System Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hülya Bayır
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA, USA; Department of Critical Care Medicine, Center for Critical Care Nephrology, Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, USA; Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA.
| | - Valerian E Kagan
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA, USA; Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Radiation Oncology, University of Pittsburgh, Pittsburgh, PA, USA.
| |
Collapse
|
15
|
Ravi S, VanDemark AP, Kiselyov K. Regulation of Lysosomal Exocytosis by Oxidative Stress and Calcium Ions. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.537] [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: 11/16/2022] Open
|
16
|
Ravi S, VanDemark AP, Kiselyov K. GDAP1 Regulation by Oxidative Stress. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.2338] [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: 10/20/2022] Open
|
17
|
Zalewski JK, Heber S, Mo JH, O'Conor K, Hildebrand JD, VanDemark AP. Combining Wet and Dry Lab Techniques to Guide the Crystallization of Large Coiled-coil Containing Proteins. J Vis Exp 2017. [PMID: 28117766 DOI: 10.3791/54886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Obtaining crystals for structure determination can be a difficult and time consuming proposition for any protein. Coiled-coil proteins and domains are found throughout nature, however, because of their physical properties and tendency to aggregate, they are traditionally viewed as being especially difficult to crystallize. Here, we utilize a variety of quick and simple techniques designed to identify a series of possible domain boundaries for a given coiled-coil protein, and then quickly characterize the behavior of these proteins in solution. With the addition of a strongly fluorescent tag (mRuby2), protein characterization is simple and straightforward. The target protein can be readily visualized under normal lighting and can be quantified with the use of an appropriate imager. The goal is to quickly identify candidates that can be removed from the crystallization pipeline because they are unlikely to succeed, affording more time for the best candidates and fewer funds expended on proteins that do not produce crystals. This process can be iterated to incorporate information gained from initial screening efforts, can be adapted for high-throughput expression and purification procedures, and is augmented by robotic screening for crystallization.
Collapse
Affiliation(s)
| | - Simone Heber
- Department of Biological Sciences, University of Pittsburgh; Institute of Structural Biology, German Research Center for Environmental Health
| | - Joshua H Mo
- Department of Biological Sciences, University of Pittsburgh
| | - Keith O'Conor
- Department of Biological Sciences, University of Pittsburgh
| | | | | |
Collapse
|
18
|
Van Oss SB, Shirra MK, Bataille AR, Wier AD, Yen K, Vinayachandran V, Byeon IJL, Cucinotta CE, Héroux A, Jeon J, Kim J, VanDemark AP, Pugh BF, Arndt KM. The Histone Modification Domain of Paf1 Complex Subunit Rtf1 Directly Stimulates H2B Ubiquitylation through an Interaction with Rad6. Mol Cell 2016; 64:815-825. [PMID: 27840029 DOI: 10.1016/j.molcel.2016.10.008] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [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: 06/23/2016] [Revised: 09/09/2016] [Accepted: 10/05/2016] [Indexed: 10/24/2022]
Abstract
The five-subunit yeast Paf1 complex (Paf1C) regulates all stages of transcription and is critical for the monoubiquitylation of histone H2B (H2Bub), a modification that broadly influences chromatin structure and eukaryotic transcription. Here, we show that the histone modification domain (HMD) of Paf1C subunit Rtf1 directly interacts with the ubiquitin conjugase Rad6 and stimulates H2Bub independently of transcription. We present the crystal structure of the Rtf1 HMD and use site-specific, in vivo crosslinking to identify a conserved Rad6 interaction surface. Utilizing ChIP-exo analysis, we define the localization patterns of the H2Bub machinery at high resolution and demonstrate the importance of Paf1C in targeting the Rtf1 HMD, and thereby H2Bub, to its appropriate genomic locations. Finally, we observe HMD-dependent stimulation of H2Bub in a transcription-free, reconstituted in vitro system. Taken together, our results argue for an active role for Paf1C in promoting H2Bub and ensuring its proper localization in vivo.
Collapse
Affiliation(s)
- S Branden Van Oss
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Margaret K Shirra
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Alain R Bataille
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA 16802, USA
| | - Adam D Wier
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Kuangyu Yen
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA 16802, USA; Department of Developmental Biology, Southern Medical University, Guangzhou 510515, China
| | - Vinesh Vinayachandran
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA 16802, USA
| | - In-Ja L Byeon
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Christine E Cucinotta
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Annie Héroux
- Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jongcheol Jeon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Andrew P VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - B Franklin Pugh
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA 16802, USA
| | - Karen M Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| |
Collapse
|
19
|
Zalewski JK, Mo JH, Heber S, Heroux A, Gardner RG, Hildebrand JD, VanDemark AP. Structure of the Shroom-Rho Kinase Complex Reveals a Binding Interface with Monomeric Shroom That Regulates Cell Morphology and Stimulates Kinase Activity. J Biol Chem 2016; 291:25364-25374. [PMID: 27758857 DOI: 10.1074/jbc.m116.738559] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 09/27/2016] [Indexed: 12/21/2022] Open
Abstract
Shroom-mediated remodeling of the actomyosin cytoskeleton is a critical driver of cellular shape and tissue morphology that underlies the development of many tissues including the neural tube, eye, intestines, and vasculature. Shroom uses a conserved SD2 domain to direct the subcellular localization of Rho-associated kinase (Rock), which in turn drives changes in the cytoskeleton and cellular morphology through its ability to phosphorylate and activate non-muscle myosin II. Here, we present the structure of the human Shroom-Rock binding module, revealing an unexpected stoichiometry for Shroom in which two Shroom SD2 domains bind independent surfaces on Rock. Mutation of interfacial residues impaired Shroom-Rock binding in vitro and resulted in altered remodeling of the cytoskeleton and loss of Shroom-mediated changes in cellular morphology. Additionally, we provide the first direct evidence that Shroom can function as a Rock activator. These data provide molecular insight into the Shroom-Rock interface and demonstrate that Shroom directly participates in regulating cytoskeletal dynamics, adding to its known role in Rock localization.
Collapse
Affiliation(s)
- Jenna K Zalewski
- From the Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Joshua H Mo
- From the Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Simone Heber
- From the Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Annie Heroux
- the Department of Biology, Brookhaven National Laboratory, Upton, New York 11973, and
| | - Richard G Gardner
- the Department of Pharmacology, University of Washington, Seattle, Washington 98195
| | - Jeffrey D Hildebrand
- From the Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Andrew P VanDemark
- From the Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260,
| |
Collapse
|
20
|
Roland BP, Zeccola AM, Larsen SB, Amrich CG, Talsma AD, Stuchul KA, Heroux A, Levitan ES, VanDemark AP, Palladino MJ. Structural and Genetic Studies Demonstrate Neurologic Dysfunction in Triosephosphate Isomerase Deficiency Is Associated with Impaired Synaptic Vesicle Dynamics. PLoS Genet 2016; 12:e1005941. [PMID: 27031109 PMCID: PMC4816394 DOI: 10.1371/journal.pgen.1005941] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 02/24/2016] [Indexed: 01/05/2023] Open
Abstract
Triosephosphate isomerase (TPI) deficiency is a poorly understood disease characterized by hemolytic anemia, cardiomyopathy, neurologic dysfunction, and early death. TPI deficiency is one of a group of diseases known as glycolytic enzymopathies, but is unique for its severe patient neuropathology and early mortality. The disease is caused by missense mutations and dysfunction in the glycolytic enzyme, TPI. Previous studies have detailed structural and catalytic changes elicited by disease-associated TPI substitutions, and samples of patient erythrocytes have yielded insight into patient hemolytic anemia; however, the neuropathophysiology of this disease remains a mystery. This study combines structural, biochemical, and genetic approaches to demonstrate that perturbations of the TPI dimer interface are sufficient to elicit TPI deficiency neuropathogenesis. The present study demonstrates that neurologic dysfunction resulting from TPI deficiency is characterized by synaptic vesicle dysfunction, and can be attenuated with catalytically inactive TPI. Collectively, our findings are the first to identify, to our knowledge, a functional synaptic defect in TPI deficiency derived from molecular changes in the TPI dimer interface.
Collapse
Affiliation(s)
- Bartholomew P. Roland
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- The Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Alison M. Zeccola
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- The Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Samantha B. Larsen
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- The Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Christopher G. Amrich
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Aaron D. Talsma
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- The Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Kimberly A. Stuchul
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- The Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Annie Heroux
- Energy Sciences Directorate/Photon Science Division, Brookhaven National Laboratory, Upton, New York, United States of America
| | - Edwin S. Levitan
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Andrew P. VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michael J. Palladino
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- The Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
21
|
Gaines WA, Godin SK, Kabbinavar FF, Rao T, VanDemark AP, Sung P, Bernstein KA. Promotion of presynaptic filament assembly by the ensemble of S. cerevisiae Rad51 paralogues with Rad52. Nat Commun 2015. [PMID: 26215801 PMCID: PMC4525180 DOI: 10.1038/ncomms8834] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [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: 01/27/2023] Open
Abstract
The conserved budding yeast Rad51 paralogues, including Rad55, Rad57, Csm2 and Psy3 are indispensable for homologous recombination (HR)-mediated chromosome damage repair. Rad55 and Rad57 are associated in a heterodimer, while Csm2 and Psy3 form the Shu complex with Shu1 and Shu2. Here we show that Rad55 bridges an interaction between Csm2 with Rad51 and Rad52 and, using a fully reconstituted system, demonstrate that the Shu complex synergizes with Rad55-Rad57 and Rad52 to promote nucleation of Rad51 on single-stranded DNA pre-occupied by replication protein A (RPA). The csm2-F46A allele is unable to interact with Rad55, ablating the ability of the Shu complex to enhance Rad51 presynaptic filament assembly in vitro and impairing HR in vivo. Our results reveal that Rad55-Rad57, the Shu complex and Rad52 act as a functional ensemble to promote Rad51-filament assembly, which has important implications for understanding the role of the human RAD51 paralogues in Fanconi anaemia and cancer predisposition.
Collapse
Affiliation(s)
- William A Gaines
- Department of Molecular Biochemistry and Biophysics, Yale University School of Medicine, New Haven, Conneticut 06510, USA
| | - Stephen K Godin
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 5117 Centre Avenue, UPCI Research Pavilion, G5.c, Pittsburgh, Pennsylvania 15217, USA
| | - Faiz F Kabbinavar
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 5117 Centre Avenue, UPCI Research Pavilion, G5.c, Pittsburgh, Pennsylvania 15217, USA
| | - Timsi Rao
- Department of Molecular Biochemistry and Biophysics, Yale University School of Medicine, New Haven, Conneticut 06510, USA
| | - Andrew P VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Patrick Sung
- Department of Molecular Biochemistry and Biophysics, Yale University School of Medicine, New Haven, Conneticut 06510, USA
| | - Kara A Bernstein
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 5117 Centre Avenue, UPCI Research Pavilion, G5.c, Pittsburgh, Pennsylvania 15217, USA
| |
Collapse
|
22
|
Das D, Zalewski JK, Mohan S, Plageman TF, VanDemark AP, Hildebrand JD. The interaction between Shroom3 and Rho-kinase is required for neural tube morphogenesis in mice. Biol Open 2014; 3:850-60. [PMID: 25171888 PMCID: PMC4163662 DOI: 10.1242/bio.20147450] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [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] [Indexed: 12/17/2022] Open
Abstract
Shroom3 is an actin-associated regulator of cell morphology that is required for neural tube closure, formation of the lens placode, and gut morphogenesis in mice and has been linked to chronic kidney disease and directional heart looping in humans. Numerous studies have shown that Shroom3 likely regulates these developmental processes by directly binding to Rho-kinase and facilitating the assembly of apically positioned contractile actomyosin networks. We have characterized the molecular basis for the neural tube defects caused by an ENU-induced mutation that results in an arginine-to-cysteine amino acid substitution at position 1838 of mouse Shroom3. We show that this substitution has no effect on Shroom3 expression or localization but ablates Rock binding and renders Shroom3 non-functional for the ability to regulate cell morphology. Our results indicate that Rock is the major downstream effector of Shroom3 in the process of neural tube morphogenesis. Based on sequence conservation and biochemical analysis, we predict that the Shroom-Rock interaction is highly conserved across animal evolution and represents a signaling module that is utilized in a variety of biological processes.
Collapse
Affiliation(s)
- Debamitra Das
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Jenna K Zalewski
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Swarna Mohan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Timothy F Plageman
- College of Optometry, The Ohio State University, Columbus, OH 43210, USA
| | - Andrew P VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Jeffrey D Hildebrand
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| |
Collapse
|
23
|
Mohan S, Das D, Bauer RJ, Heroux A, Zalewski JK, Heber S, Dosunmu-Ogunbi AM, Trakselis MA, Hildebrand JD, VanDemark AP. Structure of a highly conserved domain of Rock1 required for Shroom-mediated regulation of cell morphology. PLoS One 2013; 8:e81075. [PMID: 24349032 PMCID: PMC3857177 DOI: 10.1371/journal.pone.0081075] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [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: 07/15/2013] [Accepted: 10/08/2013] [Indexed: 01/07/2023] Open
Abstract
Rho-associated coiled coil containing protein kinase (Rho-kinase or Rock) is a well-defined determinant of actin organization and dynamics in most animal cells characterized to date. One of the primary effectors of Rock is non-muscle myosin II. Activation of Rock results in increased contractility of myosin II and subsequent changes in actin architecture and cell morphology. The regulation of Rock is thought to occur via autoinhibition of the kinase domain via intramolecular interactions between the N-terminus and the C-terminus of the kinase. This autoinhibited state can be relieved via proteolytic cleavage, binding of lipids to a Pleckstrin Homology domain near the C-terminus, or binding of GTP-bound RhoA to the central coiled-coil region of Rock. Recent work has identified the Shroom family of proteins as an additional regulator of Rock either at the level of cellular distribution or catalytic activity or both. The Shroom-Rock complex is conserved in most animals and is essential for the formation of the neural tube, eye, and gut in vertebrates. To address the mechanism by which Shroom and Rock interact, we have solved the structure of the coiled-coil region of Rock that binds to Shroom proteins. Consistent with other observations, the Shroom binding domain is a parallel coiled-coil dimer. Using biochemical approaches, we have identified a large patch of residues that contribute to Shrm binding. Their orientation suggests that there may be two independent Shrm binding sites on opposing faces of the coiled-coil region of Rock. Finally, we show that the binding surface is essential for Rock colocalization with Shroom and for Shroom-mediated changes in cell morphology.
Collapse
Affiliation(s)
- Swarna Mohan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Debamitra Das
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Robert J. Bauer
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Annie Heroux
- Department of Biology, Brookhaven National Laboratory, Upton, New York, United States of America
| | - Jenna K. Zalewski
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Simone Heber
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Atinuke M. Dosunmu-Ogunbi
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michael A. Trakselis
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jeffrey D. Hildebrand
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (JDH); (AV)
| | - Andrew P. VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (JDH); (AV)
| |
Collapse
|
24
|
Singh S, Rockenbach K, Dedrick RM, VanDemark AP, Hatfull GF. Cross-talk between diverse serine integrases. J Mol Biol 2013; 426:318-31. [PMID: 24161951 DOI: 10.1016/j.jmb.2013.10.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 10/09/2013] [Accepted: 10/10/2013] [Indexed: 01/06/2023]
Abstract
Phage-encoded serine integrases are large serine recombinases that mediate integrative and excisive site-specific recombination of temperate phage genomes. They are well suited for use in heterologous systems and for synthetic genetic circuits as the attP and attB attachment sites are small (<50 bp), there are no host factor or DNA supercoiling requirements, and they are strongly directional, doing only excisive recombination in the presence of a recombination directionality factor. Combining different recombinases that function independently and without cross-talk to construct complex synthetic circuits is desirable, and several different serine integrases are available. However, we show here that these functions are not reliably predictable, and we describe a pair of serine integrases encoded by mycobacteriophages Bxz2 and Peaches with unusual and unpredictable specificities. The integrases share only 59% amino acid sequence identity and the attP sites have fewer than 50% shared bases, but they use the same attB site and there is non-reciprocal cross-talk between the two systems. The DNA binding specificities do not result from differences in specific DNA contacts but from the constraints imposed by the configuration of the component half-sites within each of the attachment site DNAs.
Collapse
Affiliation(s)
- Shweta Singh
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15241, USA
| | - Kate Rockenbach
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15241, USA
| | - Rebekah M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15241, USA
| | - Andrew P VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15241, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15241, USA.
| |
Collapse
|
25
|
Singh S, Plaks JG, Homa NJ, Amrich CG, Héroux A, Hatfull GF, VanDemark AP. The structure of Xis reveals the basis for filament formation and insight into DNA bending within a mycobacteriophage intasome. J Mol Biol 2013; 426:412-22. [PMID: 24112940 DOI: 10.1016/j.jmb.2013.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 09/26/2013] [Accepted: 10/01/2013] [Indexed: 11/27/2022]
Abstract
The recombination directionality factor, Xis, is a DNA bending protein that determines the outcome of integrase-mediated site-specific recombination by redesign of higher-order protein-DNA architectures. Although the attachment site DNA of mycobacteriophage Pukovnik is likely to contain four sites for Xis binding, Xis crystals contain five subunits in the asymmetric unit, four of which align into a Xis filament and a fifth that is generated by an unusual domain swap. Extensive intersubunit contacts stabilize a bent filament-like arrangement with Xis monomers aligned head to tail. The structure implies a DNA bend of ~120°, which is in agreement with DNA bending measured in vitro. Formation of attR-containing intasomes requires only Int and Xis, distinguishing Pukovnik from lambda. Therefore, we conclude that, in Pukovnik, Xis-induced DNA bending is sufficient to promote intramolecular Int-mediated bridges during intasome formation.
Collapse
Affiliation(s)
- Shweta Singh
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Joseph G Plaks
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Nicholas J Homa
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA; Present address: N. J. Homa, 426 CARL Building, Duke University, Durham, NC 27710, USA.
| | - Christopher G Amrich
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Annie Héroux
- Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Andrew P VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| |
Collapse
|
26
|
Arndt KM, Piro AS, Mayekar MK, Tomson BN, Wier AD, VanDemark AP, Heisler LE, Gebbia M, Nislow C. The role of the Paf1 complex in controlling transcriptioncoupled histone modifications. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.324.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | - Adam D. Wier
- Biological SciencesUniversity of PittsburghPittsburghPA
| | | | - Lawrence E. Heisler
- Terrance Donnelly Centre and Banting & Best Department of Medical ResearchUniversity of TorontoTorontoONCanada
| | - Marinella Gebbia
- Terrance Donnelly Centre and Banting & Best Department of Medical ResearchUniversity of TorontoTorontoONCanada
| | - Corey Nislow
- Terrance Donnelly Centre and Banting & Best Department of Medical ResearchUniversity of TorontoTorontoONCanada
| |
Collapse
|
27
|
Godin S, Wier A, Kabbinavar F, Bratton-Palmer DS, Ghodke H, Van Houten B, VanDemark AP, Bernstein KA. The Shu complex interacts with Rad51 through the Rad51 paralogues Rad55-Rad57 to mediate error-free recombination. Nucleic Acids Res 2013; 41:4525-34. [PMID: 23460207 PMCID: PMC3632125 DOI: 10.1093/nar/gkt138] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The Saccharomyces cerevisiae Shu complex, consisting of Shu1, Shu2, Csm2 and Psy3, promotes error-free homologous recombination (HR) by an unknown mechanism. Recent structural analysis of two Shu proteins, Csm2 and Psy3, has revealed that these proteins are Rad51 paralogues and mediate DNA binding of this complex. We show in vitro that the Csm2–Psy3 heterodimer preferentially binds synthetic forked DNA or 3′-DNA overhang substrates resembling structures used during HR in vivo. We find that Csm2 interacts with Rad51 and the Rad51 paralogues, the Rad55–Rad57 heterodimer and that the Shu complex functions in the same epistasis group as Rad55–Rad57. Importantly, Csm2’s interaction with Rad51 is dependent on Rad55, whereas Csm2’s interaction with Rad55 occurs independently of Rad51. Consistent with the Shu complex containing Rad51 paralogues, the methyl methanesulphonate sensitivity of Csm2 is exacerbated at colder temperatures. Furthermore, Csm2 and Psy3 are needed for efficient recruitment of Rad55 to DNA repair foci after DNA damage. Finally, we observe that the Shu complex preferentially promotes Rad51-dependent homologous recombination over Rad51-independent repair. Our data suggest a model in which Csm2–Psy3 recruit the Shu complex to HR substrates, where it interacts with Rad51 through Rad55–Rad57 to stimulate Rad51 filament assembly and stability, promoting error-free repair.
Collapse
Affiliation(s)
- Stephen Godin
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Celotto AM, Liu Z, VanDemark AP, Palladino MJ. A novel Drosophila SOD2 mutant demonstrates a role for mitochondrial ROS in neurodevelopment and disease. Brain Behav 2012; 2:424-34. [PMID: 22950046 PMCID: PMC3432965 DOI: 10.1002/brb3.73] [Citation(s) in RCA: 39] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 05/17/2012] [Accepted: 05/19/2012] [Indexed: 12/13/2022] Open
Abstract
Reactive oxygen species (ROS) play essential roles in cell signaling, survival, and homeostasis. Aberrant ROS lead to disease and contribute to the aging process. Numerous enzymes and vigilant antioxidant pathways are required to regulate ROS for normal cellular health. Mitochondria are a major source of ROS, and mechanisms to prevent elevated ROS during oxidative phosphorylation require super oxide dismutase (SOD) activity. SOD2, also known as MnSOD, is targeted to mitochondria and is instrumental in regulating ROS by conversion of superoxides to hydrogen peroxide, which is further broken down into H(2)O and oxygen. Here, we describe the identification of a novel mutation within the mitochondrial SOD2 enzyme in Drosophila that results in adults with an extremely shortened life span, sensitivity to hyperoxia, and neuropathology. Additional studies demonstrate that this novel mutant, SOD2(bewildered), exhibits abnormal brain morphology, suggesting a critical role for this protein in neurodevelopment. We investigated the basis of this neurodevelopmental defect and discovered an increase in aberrant axonal that could underlie the aberrant neurodevelopment and brain morphology defects. This novel allele, SOD2(bewildered), provides a unique opportunity to study the effects of increased mitochondrial ROS on neural development, axonal targeting, and neural cell degeneration in vivo.
Collapse
Affiliation(s)
- Alicia M. Celotto
- Department of Pharmacology and Chemical Biology University of Pittsburgh School of Medicine Pittsburgh Pennsylvania 15261
- Pittsburgh Institute for Neurodegenerative Diseases University of Pittsburgh School of Medicine Pittsburgh Pennsylvania 15261
| | - Zhaohui Liu
- Department of Pharmacology and Chemical Biology University of Pittsburgh School of Medicine Pittsburgh Pennsylvania 15261
- Pittsburgh Institute for Neurodegenerative Diseases University of Pittsburgh School of Medicine Pittsburgh Pennsylvania 15261
| | - Andrew P. VanDemark
- Department of Biological Sciences University of Pittsburgh Pittsburgh Pennsylvania 15260
| | - Michael J. Palladino
- Department of Pharmacology and Chemical Biology University of Pittsburgh School of Medicine Pittsburgh Pennsylvania 15261
- Pittsburgh Institute for Neurodegenerative Diseases University of Pittsburgh School of Medicine Pittsburgh Pennsylvania 15261
| |
Collapse
|
29
|
Mohan S, Rizaldy R, Das D, Bauer RJ, Heroux A, Trakselis MA, Hildebrand JD, VanDemark AP. Structure of Shroom domain 2 reveals a three-segmented coiled-coil required for dimerization, Rock binding, and apical constriction. Mol Biol Cell 2012; 23:2131-42. [PMID: 22493320 PMCID: PMC3364177 DOI: 10.1091/mbc.e11-11-0937] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Shroom (Shrm) proteins are essential regulators of cell shape and tissue morpho-logy during animal development that function by interacting directly with the coiled-coil region of Rho kinase (Rock). The Shrm-Rock interaction is sufficient to direct Rock subcellular localization and the subsequent assembly of contractile actomyosin networks in defined subcellular locales. However, it is unclear how the Shrm-Rock interaction is regulated at the molecular level. To begin investigating this issue, we present the structure of Shrm domain 2 (SD2), which mediates the interaction with Rock and is required for Shrm function. SD2 is a unique three-segmented dimer with internal symmetry, and we identify conserved residues on the surface and within the dimerization interface that are required for the Rock-Shrm interaction and Shrm activity in vivo. We further show that these residues are critical in both vertebrate and invertebrate Shroom proteins, indicating that the Shrm-Rock signaling module has been functionally and molecularly conserved. The structure and biochemical analysis of Shrm SD2 indicate that it is distinct from other Rock activators such as RhoA and establishes a new paradigm for the Rock-mediated assembly of contractile actomyosin networks.
Collapse
Affiliation(s)
- Swarna Mohan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | | | | | | | | | | | | | | |
Collapse
|
30
|
Amrich CG, Davis CP, Rogal WP, Shirra MK, Heroux A, Gardner RG, Arndt KM, VanDemark AP. Cdc73 subunit of Paf1 complex contains C-terminal Ras-like domain that promotes association of Paf1 complex with chromatin. J Biol Chem 2012; 287:10863-75. [PMID: 22318720 DOI: 10.1074/jbc.m111.325647] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The conserved Paf1 complex localizes to the coding regions of genes and facilitates multiple processes during transcription elongation, including the regulation of histone modifications. However, the mechanisms that govern Paf1 complex recruitment to active genes are undefined. Here we describe a previously unrecognized domain within the Cdc73 subunit of the Paf1 complex, the Cdc73 C-domain, and demonstrate its importance for Paf1 complex occupancy on transcribed chromatin. Deletion of the C-domain causes phenotypes associated with elongation defects without an apparent loss of complex integrity. Simultaneous mutation of the C-domain and another subunit of the Paf1 complex, Rtf1, causes enhanced mutant phenotypes and loss of histone H3 lysine 36 trimethylation. The crystal structure of the C-domain reveals unexpected similarity to the Ras family of small GTPases. Instead of a deep nucleotide-binding pocket, the C-domain contains a large but comparatively flat surface of highly conserved residues, devoid of ligand. Deletion of the C-domain results in reduced chromatin association for multiple Paf1 complex subunits. We conclude that the Cdc73 C-domain probably constitutes a protein interaction surface that functions with Rtf1 in coupling the Paf1 complex to the RNA polymerase II elongation machinery.
Collapse
Affiliation(s)
- Christopher G Amrich
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | | | | | | | | | | | | |
Collapse
|
31
|
VanDemark AP, Xin H, McCullough L, Rawlins R, Bentley S, Heroux A, Stillman DJ, Hill CP, Formosa T. Structural and functional analysis of the Spt16p N-terminal domain reveals overlapping roles of yFACT subunits. J Biol Chem 2007; 283:5058-68. [PMID: 18089575 DOI: 10.1074/jbc.m708682200] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
yFACT (heterodimers of Saccharomyces cerevisiae Spt16-Pob3 combined with Nhp6) binds to and alters the properties of nucleosomes. The essential function of yFACT is not disrupted by deletion of the N-terminal domain (NTD) of Spt16 or by mutation of the middle domain of Pob3, but either alteration makes yeast cells sensitive to DNA replication stress. We have determined the structure of the Spt16 NTD and find evidence for a conserved potential peptide-binding site. Pob3-M also contains a putative binding site, and we show that these two sites perform an overlapping essential function. We find that yFACT can bind the N-terminal tails of some histones and that this interaction is important for yFACT-nucleosome binding. However, neither the Spt16 NTD nor a key residue in the putative Pob3-M-binding site was required for interactions with histone N termini or for yFACT-mediated nucleosome reorganization in vitro. Instead, both potential binding sites interact functionally with the C-terminal docking domain of the histone H2A. yFACT therefore appears to make multiple contacts with different sites within nucleosomes, and these interactions are partially redundant with one another. The docking domain of H2A is identified as an important participant in maintaining stability during yFACT-mediated nucleosome reorganization, suggesting new models for the mechanism of this activity.
Collapse
Affiliation(s)
- Andrew P VanDemark
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
32
|
VanDemark AP, Kasten MM, Ferris E, Heroux A, Hill CP, Cairns BR. Autoregulation of the rsc4 tandem bromodomain by gcn5 acetylation. Mol Cell 2007; 27:817-28. [PMID: 17803945 PMCID: PMC2788556 DOI: 10.1016/j.molcel.2007.08.018] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2007] [Revised: 07/26/2007] [Accepted: 08/22/2007] [Indexed: 01/31/2023]
Abstract
An important issue for chromatin remodeling complexes is how their bromodomains recognize particular acetylated lysine residues in histones. The Rsc4 subunit of the yeast remodeler RSC contains an essential tandem bromodomain (TBD) that binds acetylated K14 of histone H3 (H3K14ac). We report a series of crystal structures that reveal a compact TBD that binds H3K14ac in the second bromodomain and, remarkably, binds acetylated K25 of Rsc4 itself in the first bromodomain. Endogenous Rsc4 is acetylated only at K25, and Gcn5 is identified as necessary and sufficient for Rsc4 K25 acetylation in vivo and in vitro. Rsc4 K25 acetylation inhibits binding to H3K14ac, and mutation of Rsc4 K25 results in altered growth rates. These data suggest an autoregulatory mechanism in which Gcn5 performs both the activating (H3K14ac) and inhibitory (Rsc4 K25ac) modifications, perhaps to provide temporal regulation. Additional regulatory mechanisms are indicated as H3S10 phosphorylation inhibits Rsc4 binding to H3K14ac peptides.
Collapse
Affiliation(s)
- Andrew P. VanDemark
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Margaret M. Kasten
- Howard Hughes Medical Institute, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Elliott Ferris
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Annie Heroux
- Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Christopher P. Hill
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Correspondence: (B.R.C.), (C.P.H.)
| | - Bradley R. Cairns
- Howard Hughes Medical Institute, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Correspondence: (B.R.C.), (C.P.H.)
| |
Collapse
|
33
|
VanDemark AP, Blanksma M, Ferris E, Heroux A, Hill CP, Formosa T. The structure of the yFACT Pob3-M domain, its interaction with the DNA replication factor RPA, and a potential role in nucleosome deposition. Mol Cell 2006; 22:363-74. [PMID: 16678108 DOI: 10.1016/j.molcel.2006.03.025] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2005] [Revised: 01/10/2006] [Accepted: 03/21/2006] [Indexed: 11/30/2022]
Abstract
We report the crystal structure of the middle domain of the Pob3 subunit (Pob3-M) of S. cerevisiae FACT (yFACT, facilitates chromatin transcription), which unexpectedly adopts an unusual double pleckstrin homology (PH) architecture. A mutation within a conserved surface cluster in this domain causes a defect in DNA replication that is suppressed by mutation of replication protein A (RPA). The nucleosome reorganizer yFACT therefore interacts in a physiologically important way with the central single-strand DNA (ssDNA) binding factor RPA to promote a step in DNA replication. Purified yFACT and RPA display a weak direct physical interaction, although the genetic suppression is not explained by simple changes in affinity between the purified proteins. Further genetic analysis suggests that coordinated function by yFACT and RPA is important during nucleosome deposition. These results support the model that the FACT family has an essential role in constructing nucleosomes during DNA replication, and suggest that RPA contributes to this process.
Collapse
Affiliation(s)
- Andrew P VanDemark
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, 84132, USA
| | | | | | | | | | | |
Collapse
|
34
|
Abstract
We report the crystal structure of the catalytic domain of human ADAR2, an RNA editing enzyme, at 1.7 angstrom resolution. The structure reveals a zinc ion in the active site and suggests how the substrate adenosine is recognized. Unexpectedly, inositol hexakisphosphate (IP6) is buried within the enzyme core, contributing to the protein fold. Although there are no reports that adenosine deaminases that act on RNA (ADARs) require a cofactor, we show that IP6 is required for activity. Amino acids that coordinate IP6 in the crystal structure are conserved in some adenosine deaminases that act on transfer RNA (tRNA) (ADATs), related enzymes that edit tRNA. Indeed, IP6 is also essential for in vivo and in vitro deamination of adenosine 37 of tRNAala by ADAT1.
Collapse
Affiliation(s)
- Mark R. Macbeth
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84132, USA
- Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT 84132, USA
| | - Heidi L. Schubert
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84132, USA
| | - Andrew P. VanDemark
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84132, USA
| | - Arunth T. Lingam
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84132, USA
- Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT 84132, USA
| | - Christopher P. Hill
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84132, USA
| | - Brenda L. Bass
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84132, USA
- Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT 84132, USA
| |
Collapse
|
35
|
Abstract
E1 enzymes activate ubiquitin or related proteins and pass them to E2 enzymes. A recent structure and associated biochemical studies (Huang et al., 2005) show how an E1 binds its cognate E2 and indicates that large, conformational changes will be an integral component of the E1 reaction cycle.
Collapse
Affiliation(s)
- Andrew P VanDemark
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | | |
Collapse
|
36
|
|
37
|
|
38
|
Abstract
The attachment of the small protein ubiquitin to other proteins, a process known as ubiquitylation, is a widespread form of post-translational modification that regulates numerous cellular functions in eukaryotes. Ubiquitylation is performed by complexes of E2 and E3 enzymes that are assembled and select substrates via a series of protein-protein interactions. Recent structure determinations of the ubiquitylation machinery have revealed some of the various protein-protein interfaces involved.
Collapse
Affiliation(s)
- Andrew P VanDemark
- Department of Biochemistry, 20N 1900E RM 211, University of Utah, Salt Lake City 84132, USA
| | | |
Collapse
|
39
|
Abstract
A new structure reveals how substrates are recognized for conjugation to the ubiquitin-like protein SUMO, a posttranslational modification that functions in activation of transcription factors, nuclear import, and cell division.
Collapse
Affiliation(s)
- Andrew P VanDemark
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City 84132, USA
| | | |
Collapse
|
40
|
Abstract
While the signaling properties of ubiquitin depend on the topology of polyubiquitin chains, little is known concerning the molecular basis of specificity in chain assembly and recognition. UEV/Ubc complexes have been implicated in the assembly of Lys63-linked polyubiquitin chains that act as a novel signal in postreplicative DNA repair and I kappa B alpha kinase activation. The crystal structure of the Mms2/Ubc13 heterodimer shows the active site of Ubc13 at the intersection of two channels that are potential binding sites for the two substrate ubiquitins. Mutations that destabilize the heterodimer interface confer a marked UV sensitivity, providing direct evidence that the intact heterodimer is necessary for DNA repair. Selective mutations in the channels suggest a molecular model for specificity in the assembly of Lys63-linked polyubiquitin signals.
Collapse
Affiliation(s)
- A P VanDemark
- Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | | | | | | | | |
Collapse
|
41
|
|
42
|
Jabet C, Sprague ER, VanDemark AP, Wolberger C. Characterization of the N-terminal domain of the yeast transcriptional repressor Tup1. Proposal for an association model of the repressor complex Tup1 x Ssn6. J Biol Chem 2000; 275:9011-8. [PMID: 10722750 DOI: 10.1074/jbc.275.12.9011] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The yeast Tup1 and Ssn6 proteins form a transcriptional repression complex that represses transcription of a broad array of genes. It has been shown that the N-terminal domain of the Tup1 protein interacts with a region of the Ssn6 protein that consists of 10 tandem copies of a tetratricopeptide motif. In this work, we use a surface plasmon resonance assay to measure the affinity of the N-terminal domain of Tup1 for a minimal 3-TPR domain of Saccharomyces cerevisiae Ssn6 that is sufficient for binding to Tup1. This domain of Ssn6 binds with comparable affinity to S. cerevisiae and Candida albicans Tup1, but with 100-fold lower affinity to Tup1 protein containing a point mutation that gives rise to a defect in repression in vivo. Results from studies using analytical ultracentrifugation, CD spectroscopy, limited proteolysis, and (1)H NMR show that this domain of Tup1 is primarily alpha-helical and forms a stable tetramer that is highly nonglobular in shape. X-ray diffraction recorded from poorly ordered crystals of the Tup1 tetramerization domain contains fiber diffraction typical of a coiled coil. Our results are used to propose a model for the structure of the N-terminal domain of Tup1 and its interaction with the Ssn6 protein.
Collapse
Affiliation(s)
- C Jabet
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | | | | | | |
Collapse
|