1
|
Adrees S, Imtiaz A, Yaseen A, Irfan Fareed M, Anwar W, Ashraf A, Shabbir RMK, Andlib S, Hussain M, Tariq A, Mateen RM, Saqib MAN, Parveen R. In-silico analysis of potential anticancer drug for NEK7 and PPP1CA proteins overexpressed in pancreatic ductal adenocarcinoma. J Biomol Struct Dyn 2024:1-17. [PMID: 38469816 DOI: 10.1080/07391102.2024.2318484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 02/07/2024] [Indexed: 03/13/2024]
Abstract
NIMA-related kinase 7 (NEK7) and phosphoprotein phosphatase-1 catalytic subunit alpha (PPP1CA) are the most common proteins overexpressed in pancreatic ductal adenocarcinoma, which is the most common type of pancreatic cancer. The goal of the current study was to identify a possible NEK7 and PPP1CA therapeutic inhibitor. For this investigation, 5000 compounds were retrieved from the IMPPAT library of phytochemicals, which were docked with our respective target proteins. Also, a reference compound, gemcitabine, which is a Food and Drug Administration (FDA) approved drug, was docked with the target proteins. The binding energy of the reference compound for both the targeted proteins was -6.5 kcal/mol. The common ligand with the lowest binding energy for both targets is boeravinone B (PubChem ID: 14018348) with -9.2 kcal/mol of NEK7 and -7.6 kcal/mol for PPP1CA. The compound was further investigated through density function theory (DFT) and molecular dynamic simulation analysis. The root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), and hydrogen bonding analysis indicated the stability of the boeravinone B with the target proteins (NEK7 and PPP1CA).Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Safa Adrees
- Department of Life sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Anam Imtiaz
- Department of Life sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Aiman Yaseen
- Department of Life sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Muhammad Irfan Fareed
- Department of Life sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Waqar Anwar
- Department of Life sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Asma Ashraf
- Department of Zoology, Division of science and Technology, University of Education, Lahore, Pakistan
| | | | - Shaista Andlib
- Department of Microbiology, Faculty of Biological Sciences, Quaid-e-Azam University, Islamabad, Pakistan
| | - Mureed Hussain
- Department of Life sciences, School of Science, University of Management and Technology, Lahore, Pakistan
- Center for Regenerative Medicine and Stem Cell Research, Agha Khan University, Karachi, Pakistan
| | - Asma Tariq
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Rana Muhammad Mateen
- Department of Life sciences, School of Science, University of Management and Technology, Lahore, Pakistan
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | | | - Rukhsana Parveen
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| |
Collapse
|
2
|
Zhang Y, Sabatini R. Leishmania PNUTS discriminates between PP1 catalytic subunits through an RVxF-ΦΦ-F motif and polymorphisms in the PP1 C-tail and catalytic domain. J Biol Chem 2023; 299:105432. [PMID: 37926279 PMCID: PMC10731240 DOI: 10.1016/j.jbc.2023.105432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/10/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023] Open
Abstract
Phosphoprotein phosphatase 1 (PP1) associates with specific regulatory subunits to achieve, among other functions, substrate selectivity. Among the eight PP1 isotypes in Leishmania, PP1-8e associates with the regulatory protein PNUTS along with the structural factors JBP3 and Wdr82 in the PJW/PP1 complex that modulates RNA polymerase II (pol II) phosphorylation and transcription termination. Little is known regarding interactions involved in PJW/PP1 complex formation, including how PP1-8e is the selective isotype associated with PNUTS. Here, we show that PNUTS uses an established RVxF-ΦΦ-F motif to bind the PP1 catalytic domain with similar interfacial interactions as mammalian PP1-PNUTS and noncanonical motifs. These atypical interactions involve residues within the PP1-8e catalytic domain and N and C terminus for isoform-specific regulator binding. This work advances our understanding of PP1 isoform selectivity and reveals key roles of PP1 residues in regulator binding. We also explore the role of PNUTS as a scaffold protein for the complex by identifying the C-terminal region involved in binding JBP3 and Wdr82 and impact of PNUTS on the stability of complex components and function in pol II transcription in vivo. Taken together, these studies provide a potential mechanism where multiple motifs within PNUTS are used combinatorially to tune binding affinity to PP1, and the C terminus for JBP3 and Wdr82 association, in the Leishmania PJW/PP1 complex. Overall, our data provide insights in the formation of the PJW/PP1 complex involved in regulating pol II transcription in divergent protozoans where little is understood.
Collapse
Affiliation(s)
- Yang Zhang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Robert Sabatini
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA.
| |
Collapse
|
3
|
Liu Z, Xin B, Smith IN, Sency V, Szekely J, Alkelai A, Shuldiner A, Efthymiou S, Rajabi F, Coury S, Brownstein CA, Rudnik-Schöneborn S, Bruel AL, Thevenon J, Zeidler S, Jayakar P, Schmidt A, Cremer K, Engels H, Peters SO, Zaki MS, Duan R, Zhu C, Xu Y, Gao C, Sepulveda-Morales T, Maroofian R, Alkhawaja IA, Khawaja M, Alhalasah H, Houlden H, Madden JA, Turchetti V, Marafi D, Agrawal PB, Schatz U, Rotenberg A, Rotenberg J, Mancini GMS, Bakhtiari S, Kruer M, Thiffault I, Hirsch S, Hempel M, Stühn LG, Haack TB, Posey JE, Lupski JR, Lee H, Sarn NB, Eng C, Gonzaga-Jauregui C, Zhang B, Wang H. Hemizygous variants in protein phosphatase 1 regulatory subunit 3F (PPP1R3F) are associated with a neurodevelopmental disorder characterized by developmental delay, intellectual disability and autistic features. Hum Mol Genet 2023; 32:2981-2995. [PMID: 37531237 PMCID: PMC10549786 DOI: 10.1093/hmg/ddad124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/20/2023] [Accepted: 07/26/2023] [Indexed: 08/04/2023] Open
Abstract
Protein phosphatase 1 regulatory subunit 3F (PPP1R3F) is a member of the glycogen targeting subunits (GTSs), which belong to the large group of regulatory subunits of protein phosphatase 1 (PP1), a major eukaryotic serine/threonine protein phosphatase that regulates diverse cellular processes. Here, we describe the identification of hemizygous variants in PPP1R3F associated with a novel X-linked recessive neurodevelopmental disorder in 13 unrelated individuals. This disorder is characterized by developmental delay, mild intellectual disability, neurobehavioral issues such as autism spectrum disorder, seizures and other neurological findings including tone, gait and cerebellar abnormalities. PPP1R3F variants segregated with disease in affected hemizygous males that inherited the variants from their heterozygous carrier mothers. We show that PPP1R3F is predominantly expressed in brain astrocytes and localizes to the endoplasmic reticulum in cells. Glycogen content in PPP1R3F knockout astrocytoma cells appears to be more sensitive to fluxes in extracellular glucose levels than in wild-type cells, suggesting that PPP1R3F functions in maintaining steady brain glycogen levels under changing glucose conditions. We performed functional studies on nine of the identified variants and observed defects in PP1 binding, protein stability, subcellular localization and regulation of glycogen metabolism in most of them. Collectively, the genetic and molecular data indicate that deleterious variants in PPP1R3F are associated with a new X-linked disorder of glycogen metabolism, highlighting the critical role of GTSs in neurological development. This research expands our understanding of neurodevelopmental disorders and the role of PP1 in brain development and proper function.
Collapse
Affiliation(s)
- Zhigang Liu
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Baozhong Xin
- DDC Clinic for Special Needs Children, Middlefield, OH 44062, USA
| | - Iris N Smith
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Valerie Sency
- DDC Clinic for Special Needs Children, Middlefield, OH 44062, USA
| | - Julia Szekely
- DDC Clinic for Special Needs Children, Middlefield, OH 44062, USA
| | - Anna Alkelai
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Alan Shuldiner
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, London WC1N 3BG, UK
| | - Farrah Rajabi
- Division of Genetics & Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Stephanie Coury
- Division of Genetics & Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Catherine A Brownstein
- Division of Genetics & Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | | | - Ange-Line Bruel
- Inserm UMR1231 GAD, Génétique des Anomalies du Développement, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), CHU Dijon Bourgogne, Dijon 21000, France
- UF Innovation en diagnostic génomique des maladies rares, CHU Dijon Bourgogne, Dijon 21000, France
| | - Julien Thevenon
- Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Shimriet Zeidler
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam 3015 GD, The Netherlands
| | - Parul Jayakar
- Division of Genetics and Metabolism, Nicklaus Children's Hospital, Miami, FL 33155, USA
| | - Axel Schmidt
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, 53105 Bonn, Germany
| | - Kirsten Cremer
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, 53105 Bonn, Germany
| | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, 53105 Bonn, Germany
| | - Sophia O Peters
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, 53105 Bonn, Germany
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute National Research Centre, Cairo 12622, Egypt
| | - Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Changlian Zhu
- Center for Brain Repair and Rehabilitation, Institute of Neuroscience and Physiology, University of Gothenburg, Göteborg 417 56, Sweden
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yiran Xu
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Chao Gao
- Department of Pediatric Rehabilitation Medicine, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450012, China
| | - Tania Sepulveda-Morales
- International Laboratory for Human Genome Research, Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro 76226, México
| | - Reza Maroofian
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, London WC1N 3BG, UK
| | - Issam A Alkhawaja
- Al-Bashir Hospital, Pediatric Department, Pediatric Neurology Unit, Amman, Jordan
| | - Mariam Khawaja
- Prince Hamzah Hospital, Amman, Jordan
- Hospital Clínic and Fundació Hospital Sant Joan de Déu de Martorell/Barcelona, Barcelona, Spain
| | | | - Henry Houlden
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, London WC1N 3BG, UK
| | - Jill A Madden
- Division of Genetics & Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Valentina Turchetti
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, London WC1N 3BG, UK
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City 13060, Kuwait
| | - Pankaj B Agrawal
- Division of Genetics & Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
- Division of Neonatology, Department of Pediatrics, University of Miami School of Medicine and Jackson Health System, Miami, FL 33136, USA
| | - Ulrich Schatz
- Institute for Human Genetics, Medical University Innsbruck, Innsbruck 6020, Austria
| | | | | | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam 3015 GD, The Netherlands
| | - Somayeh Bakhtiari
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Departments of Child Health, Neurology, and Cellular & Molecular Medicine, and Program in Genetics, University of Arizona College of Medicine–Phoenix, Phoenix, AZ 85004, USA
| | - Michael Kruer
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Departments of Child Health, Neurology, and Cellular & Molecular Medicine, and Program in Genetics, University of Arizona College of Medicine–Phoenix, Phoenix, AZ 85004, USA
| | - Isabelle Thiffault
- Genomic Medicine Center, Children’s Mercy Kansas City, Children's Mercy Research Institute, Kansas City, MO 64108, USA
| | - Steffen Hirsch
- Institute if Human Genetics, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Maja Hempel
- Institute if Human Genetics, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Lara G Stühn
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hyunpil Lee
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Nicholas B Sarn
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Charis Eng
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Claudia Gonzaga-Jauregui
- International Laboratory for Human Genome Research, Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro 76226, México
| | - Bin Zhang
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Heng Wang
- DDC Clinic for Special Needs Children, Middlefield, OH 44062, USA
| |
Collapse
|
4
|
Bonsor DA, Simanshu DK. Structural insights into the role of SHOC2-MRAS-PP1C complex in RAF activation. FEBS J 2023; 290:4852-4863. [PMID: 37074066 PMCID: PMC10584989 DOI: 10.1111/febs.16800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/07/2023] [Accepted: 04/18/2023] [Indexed: 04/20/2023]
Abstract
RAF activation is a key step for signalling through the mitogen-activated protein kinase (MAPK) pathway. The SHOC2 protein, along with MRAS and PP1C, forms a high affinity, heterotrimeric holoenzyme that activates RAF kinases by dephosphorylating a specific phosphoserine. Recently, our research, along with that of three other teams, has uncovered valuable structural and functional insights into the SHOC2-MRAS-PP1C (SMP) holoenzyme complex. In this structural snapshot, we review SMP complex assembly, the dependency on the bound-nucleotide state of MRAS, the substitution of MRAS by the canonical RAS proteins and the roles of SHOC2 and MRAS on PP1C activity and specificity. Furthermore, we discuss the effect of several RASopathy mutations identified within the SMP complex and explore potential therapeutic approaches for targeting the SMP complex in RAS/RAF-driven cancers and RASopathies.
Collapse
Affiliation(s)
- Daniel A. Bonsor
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dhirendra K. Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| |
Collapse
|
5
|
Yao Z, Gong Y, Chen W, Shao S, Song Y, Guo H, Li Q, Liu S, Wang X, Zhang Z, Wang Q, Xu Y, Wu Y, Wan Q, Zhao X, Xuan Q, Wang D, Lin X, Xu J, Liu J, Proud CG, Wang X, Yang R, Fu L, Niu S, Kong J, Gao L, Bo T, Zhao J. Upregulation of WDR6 drives hepatic de novo lipogenesis in insulin resistance in mice. Nat Metab 2023; 5:1706-1725. [PMID: 37735236 PMCID: PMC10590755 DOI: 10.1038/s42255-023-00896-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 08/23/2023] [Indexed: 09/23/2023]
Abstract
Under normal conditions, insulin promotes hepatic de novo lipogenesis (DNL). However, during insulin resistance (IR), when insulin signalling is blunted and accompanied by hyperinsulinaemia, the promotion of hepatic DNL continues unabated and hepatic steatosis increases. Here, we show that WD40 repeat-containing protein 6 (WDR6) promotes hepatic DNL during IR. Mechanistically, WDR6 interacts with the beta-type catalytic subunit of serine/threonine-protein phosphatase 1 (PPP1CB) to facilitate PPP1CB dephosphorylation at Thr316, which subsequently enhances fatty acid synthases transcription through DNA-dependent protein kinase and upstream stimulatory factor 1. Using molecular dynamics simulation analysis, we find a small natural compound, XLIX, that inhibits the interaction of WDR6 with PPP1CB, thus reducing DNL in IR states. Together, these results reveal WDR6 as a promising target for the treatment of hepatic steatosis.
Collapse
Affiliation(s)
- Zhenyu Yao
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Clinical Research Center of Diabetes and Metabolic Diseases, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China
- Shandong Prevention and Control Engineering Laboratory of Endocrine and Metabolic Diseases, Jinan, China
| | - Ying Gong
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Clinical Research Center of Diabetes and Metabolic Diseases, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China
- Shandong Prevention and Control Engineering Laboratory of Endocrine and Metabolic Diseases, Jinan, China
| | - Wenbin Chen
- Central Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Shanshan Shao
- Shandong Prevention and Control Engineering Laboratory of Endocrine and Metabolic Diseases, Jinan, China
| | - Yongfeng Song
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Clinical Research Center of Diabetes and Metabolic Diseases, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China
- Shandong Prevention and Control Engineering Laboratory of Endocrine and Metabolic Diseases, Jinan, China
| | - Honglin Guo
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Qihang Li
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Clinical Research Center of Diabetes and Metabolic Diseases, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China
- Shandong Prevention and Control Engineering Laboratory of Endocrine and Metabolic Diseases, Jinan, China
| | - Sijin Liu
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Ximing Wang
- Department of Radiology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Zhenhai Zhang
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Shandong University, Jinan, China
| | - Qian Wang
- Department of Ultrasound, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yunyun Xu
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Clinical Research Center of Diabetes and Metabolic Diseases, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China
- Shandong Prevention and Control Engineering Laboratory of Endocrine and Metabolic Diseases, Jinan, China
| | - Yingjie Wu
- Shandong Provincial Hospital, School of Laboratory Animal & Shandong Laboratory Animal Center, Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- Institute of Genome Engineered Animal Models, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Qiang Wan
- Center of Cell Metabolism and Disease, Jinan Central Hospital, Shandong First Medical University, Jinan, China
| | - Xinya Zhao
- Department of Radiology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Qiuhui Xuan
- Shandong Clinical Research Center of Diabetes and Metabolic Diseases, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China
- Shandong Prevention and Control Engineering Laboratory of Endocrine and Metabolic Diseases, Jinan, China
| | - Dawei Wang
- Shandong Clinical Research Center of Diabetes and Metabolic Diseases, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China
- Shandong Prevention and Control Engineering Laboratory of Endocrine and Metabolic Diseases, Jinan, China
| | - Xiaoyan Lin
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Jiawen Xu
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Jun Liu
- Department of Liver Transplantation and Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Christopher G Proud
- Lifelong Health, South Australian Health & Medical Research Institute, North Terrace, Adelaide, South Australia, Australia
| | - Xuemin Wang
- Lifelong Health, South Australian Health & Medical Research Institute, North Terrace, Adelaide, South Australia, Australia
| | - Rui Yang
- Institute of Genome Engineered Animal Models, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Lili Fu
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Clinical Research Center of Diabetes and Metabolic Diseases, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China
- Shandong Prevention and Control Engineering Laboratory of Endocrine and Metabolic Diseases, Jinan, China
| | - Shaona Niu
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Clinical Research Center of Diabetes and Metabolic Diseases, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China
- Shandong Prevention and Control Engineering Laboratory of Endocrine and Metabolic Diseases, Jinan, China
| | - Junjie Kong
- Department of Liver Transplantation and Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Ling Gao
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China.
| | - Tao Bo
- Central Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.
| | - Jiajun Zhao
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.
- Shandong Clinical Research Center of Diabetes and Metabolic Diseases, Jinan, China.
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China.
- Shandong Prevention and Control Engineering Laboratory of Endocrine and Metabolic Diseases, Jinan, China.
| |
Collapse
|
6
|
Zhang Y, Sabatini R. Leishmania PNUTS discriminates between PP1 catalytic subunits through a RVxF-ΦΦ-F motif and polymorphisms in the PP1 C-tail and catalytic domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.558696. [PMID: 37790576 PMCID: PMC10542515 DOI: 10.1101/2023.09.20.558696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
PP1 phosphatases lack substrate specificity and associate with specific regulatory subunits to achieve selectivity. Among the eight PP1 isotypes in Leishmania, PP1-8e associates with the regulatory protein PNUTS along with the structural factors JBP3 and Wdr82 in the PJW/PP1 complex that modulates RNA polymerase II (Pol II) phosphorylation and transcription termination. Little is known regarding interactions involved in PJW/PP1 complex formation, including how PP1-8e is the selective isotype associated with PNUTS. Here, we show that PNUTS uses an established RVxF-ΦΦ-F motif to bind the PP1 catalytic domain with similar interfacial interactions as mammalian PP1- PNUTS and non-canonical motifs. These atypical interactions involve residues within the PP1-8e catalytic domain and N- and C-terminus for isoform specific regulator binding. This work advances our understanding of PP1 isoform selectivity and reveals key roles of PP1 residues in regulator binding. We also explore the role of PNUTS as a scaffold protein for the complex by identifying the C-terminal region involved in binding JBP3 and Wdr82, and impact of PNUTS on the stability of complex components and function in Pol II transcription in vivo . Taken together, these studies provide a potential mechanism where multiple motifs within PNUTS are used combinatorially to tune binding affinity to PP1, and the C-termini for independent binding of JBP3 and Wdr82, in the Leishmania PJW/PP1 complex. Overall, our data provide insights in the formation of the PJW/PP1 complex involved in regulating Pol II transcription in divergent protozoans where little is understood.
Collapse
|
7
|
Yang J, Guo X, Li T, Xie Y, Wang D, Yi L, Mi M. Sulforaphane Inhibits Exhaustive Exercise-Induced Liver Injury and Transcriptome-Based Mechanism Analysis. Nutrients 2023; 15:3220. [PMID: 37513640 PMCID: PMC10386178 DOI: 10.3390/nu15143220] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/18/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Exhaustive exercise (EE) induces liver injury and has recently gained much attention. Sulforaphane (SFN) can protect the liver from inflammation and oxidative stress. However, the effects of SFN on EE-induced liver injury and its underlying mechanisms are still unclear. C57BL/6J mice swimming to exhaustion for seven days were used to simulate the liver injury caused by EE. Different doses of SFN (10, 30, 90 mg/kg body weight) were gavage-fed one week before and during the exercise. SFN intervention significantly reduced the EE-induced lactate dehydrogenase (LDH), creatine kinase (CK), alanine aminotransferase (ALT), and aspartate aminotransferase (AST) in the serum, as well as attenuating liver tissue morphological abnormality, oxidative stress injury, and inflammation. Liver transcriptomic analysis showed that the differentially expressed genes altered by SFN intervention in the exercise model were mainly enriched in glucose and lipid metabolism pathways. The most altered gene by SFN intervention screened by RNA-seq and validated by qRT-PCR is Ppp1r3g, a gene involved in regulating hepatic glycogenesis, which may play a vital role in the protective effects of SFN in EE-induced liver damage. SFN can protect the liver from EE-induced damage, and glucose and lipid metabolism may be involved in the mechanism of the protective effects.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Mantian Mi
- Research Center for Nutrition and Food Safety, Chongqing Key Laboratory of Nutrition and Food Safety, Institute of Military Preventive Medicine, Third Military Medical University, Chongqing 400038, China
| |
Collapse
|
8
|
Vertyshev AY, Akberdin IR, Kolpakov FA. Numerous Trigger-like Interactions of Kinases/Protein Phosphatases in Human Skeletal Muscles Can Underlie Transient Processes in Activation of Signaling Pathways during Exercise. Int J Mol Sci 2023; 24:11223. [PMID: 37446402 DOI: 10.3390/ijms241311223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
Optimizing physical training regimens to increase muscle aerobic capacity requires an understanding of the internal processes that occur during exercise that initiate subsequent adaptation. During exercise, muscle cells undergo a series of metabolic events that trigger downstream signaling pathways and induce the expression of many genes in working muscle fibers. There are a number of studies that show the dependence of changes in the activity of AMP-activated protein kinase (AMPK), one of the mediators of cellular signaling pathways, on the duration and intensity of single exercises. The activity of various AMPK isoforms can change in different directions, increasing for some isoforms and decreasing for others, depending on the intensity and duration of the load. This review summarizes research data on changes in the activity of AMPK, Ca2+/calmodulin-dependent protein kinase II (CaMKII), and other components of the signaling pathways in skeletal muscles during exercise. Based on these data, we hypothesize that the observed changes in AMPK activity may be largely related to metabolic and signaling transients rather than exercise intensity per se. Probably, the main events associated with these transients occur at the beginning of the exercise in a time window of about 1-10 min. We hypothesize that these transients may be partly due to putative trigger-like kinase/protein phosphatase interactions regulated by feedback loops. In addition, numerous dynamically changing factors, such as [Ca2+], metabolite concentration, and reactive oxygen and nitrogen species (RONS), can shift the switching thresholds and change the states of these triggers, thereby affecting the activity of kinases (in particular, AMPK and CaMKII) and phosphatases. The review considers the putative molecular mechanisms underlying trigger-like interactions. The proposed hypothesis allows for a reinterpretation of the experimental data available in the literature as well as the generation of ideas to optimize future training regimens.
Collapse
Affiliation(s)
| | - Ilya R Akberdin
- Department of Computational Biology, Scientific Center for Information Technologies and Artificial Intelligence, Sirius University of Science and Technology, 354340 Sochi, Russia
- Biosoft.Ru, Ltd., 630058 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Fedor A Kolpakov
- Department of Computational Biology, Scientific Center for Information Technologies and Artificial Intelligence, Sirius University of Science and Technology, 354340 Sochi, Russia
- Biosoft.Ru, Ltd., 630058 Novosibirsk, Russia
- Federal Research Center for Information and Computational Technologies, 630090 Novosibirsk, Russia
| |
Collapse
|
9
|
Wang Y, Fan M, Qian H, Ying H, Li Y, Wang L. Whole grains-derived functional ingredients against hyperglycemia: targeting hepatic glucose metabolism. Crit Rev Food Sci Nutr 2023; 64:7268-7289. [PMID: 36847153 DOI: 10.1080/10408398.2023.2183382] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Type 2 diabetes mellitus (T2DM) is characterized by the dysregulation of glucose homeostasis, resulting in hyperglycemia. However, concerns have been raised about the safety and efficacy of current hypoglycemic drugs due to undesirable side effects. Increasing studies have shown that whole grains (WG) consumption is inversely associated with the risk of T2DM and its subsequent complications. Thus, dietary strategies involving functional components from the WG provide an intriguing approach to restoring and maintaining glucose homeostasis. This review provides a comprehensive understanding of the major functional components derived from WG and their positive effects on glucose homeostasis, demonstrates the underlying molecular mechanisms targeting hepatic glucose metabolism, and discusses the unclear aspects according to the latest viewpoints and current research. Improved glycemic response and insulin resistance were observed after consumption of WG-derived bioactive ingredients, which are involved in the integrated, multi-factorial, multi-targeted regulation of hepatic glucose metabolism. Promotion of glucose uptake, glycolysis, and glycogen synthesis pathways, while inhibition of gluconeogenesis, contributes to amelioration of abnormal hepatic glucose metabolism and insulin resistance by bioactive components. Hence, the development of WG-based functional food ingredients with potent hypoglycemic properties is necessary to manage insulin resistance and T2DM.
Collapse
Affiliation(s)
- Yu Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Mingcong Fan
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Haifeng Qian
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hao Ying
- CAS Key laboratory of nutrition, metabolism and food safety, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yan Li
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Li Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| |
Collapse
|
10
|
The ribosomal RNA processing 1B:protein phosphatase 1 holoenzyme reveals non-canonical PP1 interaction motifs. Cell Rep 2022; 41:111726. [PMID: 36450254 PMCID: PMC9813921 DOI: 10.1016/j.celrep.2022.111726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 09/20/2022] [Accepted: 11/03/2022] [Indexed: 12/03/2022] Open
Abstract
The serine/threonine protein phosphatase 1 (PP1) dephosphorylates hundreds of substrates by associating with >200 regulatory proteins to form specific holoenzymes. The major PP1 targeting protein in the nucleolus is RRP1B (ribosomal RNA processing 1B). In addition to selectively recruiting PP1β/PP1γ to the nucleolus, RRP1B also has a key role in ribosome biogenesis, among other functions. How RRP1B binds PP1 and regulates nucleolar phosphorylation signaling is not yet known. Here, we show that RRP1B recruits PP1 via established (RVxF/SILK/ΦΦ) and non-canonical motifs. These atypical interaction sites, the PP1β/γ specificity, and N-terminal AF-binding pockets rely on hydrophobic interactions that contribute to binding and, via phosphorylation, regulate complex formation. This work advances our understanding of PP1 isoform selectivity, reveals key roles of N-terminal PP1 residues in regulator binding, and suggests that additional PP1 interaction sites have yet to be identified, all of which are necessary for a systems biology understanding of PP1 function.
Collapse
|
11
|
Molecular architecture of the glycogen- committed PP1/PTG holoenzyme. Nat Commun 2022; 13:6199. [PMID: 36261419 PMCID: PMC9582199 DOI: 10.1038/s41467-022-33693-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 09/27/2022] [Indexed: 12/24/2022] Open
Abstract
The delicate alternation between glycogen synthesis and degradation is governed by the interplay between key regulatory enzymes altering the activity of glycogen synthase and phosphorylase. Among these, the PP1 phosphatase promotes glycogenesis while inhibiting glycogenolysis. PP1 is, however, a master regulator of a variety of cellular processes, being conveniently directed to each of them by scaffolding subunits. PTG, Protein Targeting to Glycogen, addresses PP1 action to glycogen granules. In Lafora disease, the most aggressive pediatric epilepsy, genetic alterations leading to PTG accumulation cause the deposition of insoluble polyglucosans in neurons. Here, we report the crystallographic structure of the ternary complex PP1/PTG/carbohydrate. We further refine the mechanism of the PTG-mediated PP1 recruitment to glycogen by identifying i) an unusual combination of recruitment sites, ii) their contributions to the overall binding affinity, and iii) the conformational heterogeneity of this complex by in solution SAXS analyses.
Collapse
|
12
|
Bonsor DA, Alexander P, Snead K, Hartig N, Drew M, Messing S, Finci LI, Nissley DV, McCormick F, Esposito D, Rodriguez-Viciana P, Stephen AG, Simanshu DK. Structure of the SHOC2-MRAS-PP1C complex provides insights into RAF activation and Noonan syndrome. Nat Struct Mol Biol 2022; 29:966-977. [PMID: 36175670 PMCID: PMC10365013 DOI: 10.1038/s41594-022-00841-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 08/12/2022] [Indexed: 11/08/2022]
Abstract
SHOC2 acts as a strong synthetic lethal interactor with MEK inhibitors in multiple KRAS cancer cell lines. SHOC2 forms a heterotrimeric complex with MRAS and PP1C that is essential for regulating RAF and MAPK-pathway activation by dephosphorylating a specific phosphoserine on RAF kinases. Here we present the high-resolution crystal structure of the SHOC2-MRAS-PP1C (SMP) complex and apo-SHOC2. Our structures reveal that SHOC2, MRAS, and PP1C form a stable ternary complex in which all three proteins synergistically interact with each other. Our results show that dephosphorylation of RAF substrates by PP1C is enhanced upon interacting with SHOC2 and MRAS. The SMP complex forms only when MRAS is in an active state and is dependent on SHOC2 functioning as a scaffolding protein in the complex by bringing PP1C and MRAS together. Our results provide structural insights into the role of the SMP complex in RAF activation and how mutations found in Noonan syndrome enhance complex formation, and reveal new avenues for therapeutic interventions.
Collapse
Affiliation(s)
- Daniel A Bonsor
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Patrick Alexander
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kelly Snead
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Nicole Hartig
- UCL Cancer Institute, University College London, London, UK
| | - Matthew Drew
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lorenzo I Finci
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- University of California, San Francisco Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| |
Collapse
|
13
|
McCorvie TJ, Loria PM, Tu M, Han S, Shrestha L, Froese DS, Ferreira IM, Berg AP, Yue WW. Molecular basis for the regulation of human glycogen synthase by phosphorylation and glucose-6-phosphate. Nat Struct Mol Biol 2022; 29:628-638. [PMID: 35835870 PMCID: PMC9287172 DOI: 10.1038/s41594-022-00799-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 05/02/2022] [Indexed: 11/17/2022]
Abstract
Glycogen synthase (GYS1) is the central enzyme in muscle glycogen biosynthesis. GYS1 activity is inhibited by phosphorylation of its amino (N) and carboxyl (C) termini, which is relieved by allosteric activation of glucose-6-phosphate (Glc6P). We present cryo-EM structures at 3.0-4.0 Å resolution of phosphorylated human GYS1, in complex with a minimal interacting region of glycogenin, in the inhibited, activated and catalytically competent states. Phosphorylations of specific terminal residues are sensed by different arginine clusters, locking the GYS1 tetramer in an inhibited state via intersubunit interactions. The Glc6P activator promotes conformational change by disrupting these interactions and increases the flexibility of GYS1, such that it is poised to adopt a catalytically competent state when the sugar donor UDP-glucose (UDP-glc) binds. We also identify an inhibited-like conformation that has not transitioned into the activated state, in which the locking interaction of phosphorylation with the arginine cluster impedes subsequent conformational changes due to Glc6P binding. Our results address longstanding questions regarding the mechanism of human GYS1 regulation.
Collapse
Affiliation(s)
- Thomas J McCorvie
- Centre for Medicines Discovery, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Paula M Loria
- Discovery Sciences, Worldwide Research and Development, Pfizer Inc., Groton, CT, USA
| | - Meihua Tu
- Medicine Design, Worldwide Research and Development, Pfizer Inc., Cambridge, MA, USA
| | - Seungil Han
- Discovery Sciences, Worldwide Research and Development, Pfizer Inc., Groton, CT, USA
| | - Leela Shrestha
- Centre for Medicines Discovery, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - D Sean Froese
- Centre for Medicines Discovery, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Zürich, Switzerland
| | - Igor M Ferreira
- Centre for Medicines Discovery, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Allison P Berg
- Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., Cambridge, MA, USA.
| | - Wyatt W Yue
- Centre for Medicines Discovery, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK.
| |
Collapse
|
14
|
Khan NH, Chen HJ, Fan Y, Surfaraz M, Ahammad MD, Qin YZ, Shahid M, Virk R, Jiang E, Wu DD, Ji XY. Biology of PEST‐Containing Nuclear Protein: A Potential Molecular Target for Cancer Research. Front Oncol 2022; 12:784597. [PMID: 35186732 PMCID: PMC8855108 DOI: 10.3389/fonc.2022.784597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/06/2022] [Indexed: 11/24/2022] Open
Abstract
PEST-containing nuclear protein (PCNP), a novel nuclear protein, is involved in vital cellular processes like cell proliferation and mediates tumorigenesis. PCNP is a short-living, small nuclear protein of only 178 amino acids with two remarkable PEST sequences that are rich in proline (P), glutamic acid (E), serine (S), and threonine (T). The current understanding of PCNP reveals that PCNP has the ability to interact with cell cycle regulatory proteins; tumor suppressors (p53 and pRB), and promoters (cyclin E and cyclin D) to determine the fate of tissues to facilitate the process of either apoptosis or cell proliferation. In many preclinical studies, it has been evaluated that PCNP expression has associations with the development and progression of various cancers like neuroblastoma, lung adenocarcinoma, and ovarian cancer. Based on these depicted novel roles of PCNP in cell cycleregulation and of PCNP in tumorigenesis, it is logical to consider PCNP as a potential molecular target for cancer research. The aim of the current communication is to present an update on PCNP research and discussion on the potential role of PCNP in cancer development with challenges and opportunities perspectives. Considering the available evidence as a baseline for our statement, we anticipate that in the future, new research insights will strengthen the aim to develop PCNP-based diagnostic and therapeutic approaches that will move the PCNP from the laboratory to the cancer clinic.
Collapse
Affiliation(s)
- Nazeer Hussain Khan
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, China
- School of Life Sciences, Henan University, Kaifeng, China
| | - Hao-Jie Chen
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Yuanyuan Fan
- School of Life Sciences, Henan University, Kaifeng, China
| | | | - MD.Faysal Ahammad
- Key Laboratory of Natural Medicine and Immune Engineering, School of Medicine, Henan University, Kaifeng, China
| | - Yang-Zhe Qin
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Muhammad Shahid
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Razia Virk
- Department of Bio-Sciences, University Wah, Rawalpindi, Pakistan
| | - Enshe Jiang
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Institute of Nursing and Health, Henan University, Kaifeng, China
- *Correspondence: Enshe Jiang, ; Dong-Dong Wu, ; Xin-Ying Ji,
| | - Dong-Dong Wu
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, China
- School of Stomatology, Henan University, Kaifeng, China
- *Correspondence: Enshe Jiang, ; Dong-Dong Wu, ; Xin-Ying Ji,
| | - Xin-Ying Ji
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Kaifeng Key Laboratory of Infection and Biological Safety, Henan University College of Medicine, Kaifeng, China
- *Correspondence: Enshe Jiang, ; Dong-Dong Wu, ; Xin-Ying Ji,
| |
Collapse
|
15
|
Multi-Omics Approach Profiling Metabolic Remodeling in Early Systolic Dysfunction and in Overt Systolic Heart Failure. Int J Mol Sci 2021; 23:ijms23010235. [PMID: 35008662 PMCID: PMC8745344 DOI: 10.3390/ijms23010235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/06/2021] [Accepted: 12/22/2021] [Indexed: 01/19/2023] Open
Abstract
Metabolic remodeling plays an important role in the pathophysiology of heart failure (HF). We sought to characterize metabolic remodeling and implicated signaling pathways in two rat models of early systolic dysfunction (MOD), and overt systolic HF (SHF). Tandem mass tag-labeled shotgun proteomics, phospho-(p)-proteomics, and non-targeted metabolomics analyses were performed in left ventricular myocardium tissue from Sham, MOD, and SHF using liquid chromatography–mass spectrometry, n = 3 biological samples per group. Mitochondrial proteins were predominantly down-regulated in MOD (125) and SHF (328) vs. Sham. Of these, 82% (103/125) and 66% (218/328) were involved in metabolism and respiration. Oxidative phosphorylation, mitochondrial fatty acid β-oxidation, Krebs cycle, branched-chain amino acids, and amino acid (glutamine and tryptophan) degradation were highly enriched metabolic pathways that decreased in SHF > MOD. Glycogen and glucose degradation increased predominantly in MOD, whereas glycolysis and pyruvate metabolism decreased predominantly in SHF. PKA signaling at the endoplasmic reticulum–mt interface was attenuated in MOD, whereas overall PKA and AMPK cellular signaling were attenuated in SHF vs. Sham. In conclusion, metabolic remodeling plays an important role in myocardial remodeling. PKA and AMPK signaling crosstalk governs metabolic remodeling in progression to SHF.
Collapse
|
16
|
Fowle H, Zhao Z, Xu Q, Wasserman JS, Wang X, Adeyemi M, Feiser F, Kurimchak AN, Atar D, McEwan BC, Kettenbach AN, Page R, Peti W, Dunbrack RL, Graña X. PP2A/B55α substrate recruitment as defined by the retinoblastoma-related protein p107. eLife 2021; 10:63181. [PMID: 34661528 PMCID: PMC8575462 DOI: 10.7554/elife.63181] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 10/17/2021] [Indexed: 12/23/2022] Open
Abstract
Protein phosphorylation is a reversible post-translation modification essential in cell signaling. This study addresses a long-standing question as to how the most abundant serine/threonine protein phosphatase 2 (PP2A) holoenzyme, PP2A/B55α, specifically recognizes substrates and presents them to the enzyme active site. Here, we show how the PP2A regulatory subunit B55α recruits p107, a pRB-related tumor suppressor and B55α substrate. Using molecular and cellular approaches, we identified a conserved region 1 (R1, residues 615–626) encompassing the strongest p107 binding site. This enabled us to identify an ‘HxRVxxV619-625’ short linear motif (SLiM) in p107 as necessary for B55α binding and dephosphorylation of the proximal pSer-615 in vitro and in cells. Numerous B55α/PP2A substrates, including TAU, contain a related SLiM C-terminal from a proximal phosphosite, ‘p[ST]-P-x(4,10)-[RK]-V-x-x-[VI]-R.’ Mutation of conserved SLiM residues in TAU dramatically inhibits dephosphorylation by PP2A/B55α, validating its generality. A data-guided computational model details the interaction of residues from the conserved p107 SLiM, the B55α groove, and phosphosite presentation. Altogether, these data provide key insights into PP2A/B55α’s mechanisms of substrate recruitment and active site engagement, and also facilitate identification and validation of new substrates, a key step towards understanding PP2A/B55α’s role in multiple cellular processes.
Collapse
Affiliation(s)
- Holly Fowle
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, United States
| | - Ziran Zhao
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, United States
| | - Qifang Xu
- Fels Institute for Cancer Research and Molecular Biology, Temple University Lewis Katz School of Medicine, Philadelphia, United States
| | - Jason S Wasserman
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, United States
| | - Xinru Wang
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, United States
| | - Mary Adeyemi
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, United States
| | - Felicity Feiser
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, United States
| | - Alison N Kurimchak
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, United States
| | - Diba Atar
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, United States
| | - Brennan C McEwan
- Department of Biochemistry and Cell Biology, Hitchcock Medical Center at Dartmouth, Lebanon, United States
| | - Arminja N Kettenbach
- Department of Biochemistry and Cell Biology, Hitchcock Medical Center at Dartmouth, Lebanon, United States
| | - Rebecca Page
- Department Cell Biology, UConn Health, Farmington, United States
| | - Wolfgang Peti
- Department Molecular Biology and Biophysics, UConn Health, Farmington, United States
| | - Roland L Dunbrack
- Fels Institute for Cancer Research and Molecular Biology, Temple University Lewis Katz School of Medicine, Philadelphia, United States
| | - Xavier Graña
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, United States
| |
Collapse
|
17
|
Fujimitsu K, Yamano H. Dynamic regulation of mitotic ubiquitin ligase APC/C by coordinated Plx1 kinase and PP2A phosphatase action on a flexible Apc1 loop. EMBO J 2021; 40:e107516. [PMID: 34291488 PMCID: PMC8441438 DOI: 10.15252/embj.2020107516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 07/02/2021] [Accepted: 07/06/2021] [Indexed: 11/29/2022] Open
Abstract
The anaphase-promoting complex/cyclosome (APC/C), a multi-subunit ubiquitin ligase essential for cell cycle control, is regulated by reversible phosphorylation. APC/C phosphorylation by cyclin-dependent kinase 1 (Cdk1) promotes Cdc20 co-activator loading in mitosis to form active APC/C-Cdc20. However, detailed phospho-regulation of APC/C dynamics through other kinases and phosphatases is still poorly understood. Here, we show that an interplay between polo-like kinase (Plx1) and PP2A-B56 phosphatase on a flexible loop domain of the subunit Apc1 (Apc1-loop500 ) controls APC/C activity and mitotic progression. Plx1 directly binds to the Apc1-loop500 in a phosphorylation-dependent manner and promotes the formation of APC/C-Cdc20 via Apc3 phosphorylation. Upon phosphorylation of loop residue T532, PP2A-B56 is recruited to the Apc1-loop500 and differentially promotes dissociation of Plx1 and PP2A-B56 through dephosphorylation of Plx1-binding sites. Stable Plx1 binding, which prevents PP2A-B56 recruitment, prematurely activates the APC/C and delays APC/C dephosphorylation during mitotic exit. Furthermore, the phosphorylation status of the Apc1-loop500 is controlled by distant Apc3-loop phosphorylation. Our study suggests that phosphorylation-dependent feedback regulation through flexible loop domains within a macromolecular complex coordinates the activity and dynamics of the APC/C during the cell cycle.
Collapse
Affiliation(s)
- Kazuyuki Fujimitsu
- Cell Cycle Control GroupUCL Cancer InstituteUniversity College LondonLondonUK
| | - Hiroyuki Yamano
- Cell Cycle Control GroupUCL Cancer InstituteUniversity College LondonLondonUK
| |
Collapse
|
18
|
An T, Hu H, Li Z. The kinetoplastid-specific phosphatase KPP1 attenuates PLK activity to facilitate flagellum inheritance in Trypanosoma brucei. Sci Signal 2021; 14:14/669/eabc6435. [PMID: 33563698 DOI: 10.1126/scisignal.abc6435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Trypanosoma brucei, an important human parasite, has a flagellum that controls cell motility, morphogenesis, proliferation, and cell-cell communication. Inheritance of the newly assembled flagellum during the cell cycle requires the Polo-like kinase homolog TbPLK and the kinetoplastid-specific protein phosphatase KPP1, although whether TbPLK acts on KPP1 or vice versa has been unclear. Here, we showed that dephosphorylation of TbPLK on Thr125 by KPP1 maintained low TbPLK activity in the flagellum-associated hook complex structure, thereby ensuring proper flagellum positioning and attachment. This dephosphorylation event required the recognition of phosphorylated Thr198 in the activation loop of TbPLK by the N-terminal Plus3 domain of KPP1 and the dephosphorylation of phosphorylated Thr125 in TbPLK by the C-terminal catalytic domain of KPP1. Dephosphorylation of TbPLK by KPP1 prevented hyperphosphorylation of the hook complex protein TbCentrin2, thereby allowing timely dephosphorylation of phosphorylated TbCentrin2 for hook complex duplication and flagellum positioning and attachment. Thus, KPP1 attenuates TbPLK activity by dephosphorylating TbPLK to facilitate flagellum inheritance.
Collapse
Affiliation(s)
- Tai An
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Huiqing Hu
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ziyin Li
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| |
Collapse
|
19
|
The Protein Phosphatase 1 Complex Is a Direct Target of AKT that Links Insulin Signaling to Hepatic Glycogen Deposition. Cell Rep 2020; 28:3406-3422.e7. [PMID: 31553910 DOI: 10.1016/j.celrep.2019.08.066] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 06/02/2019] [Accepted: 08/21/2019] [Indexed: 11/24/2022] Open
Abstract
Insulin-stimulated hepatic glycogen synthesis is central to glucose homeostasis. Here, we show that PPP1R3G, a regulatory subunit of protein phosphatase 1 (PP1), is directly phosphorylated by AKT. PPP1R3G phosphorylation fluctuates with fasting-refeeding cycle and is required for insulin-stimulated dephosphorylation, i.e., activation of glycogen synthase (GS) in hepatocytes. In this study, we demonstrate that knockdown of PPP1R3G significantly inhibits insulin response. The introduction of wild-type PPP1R3G, and not phosphorylation-defective mutants, increases hepatic glycogen deposition, blood glucose clearance, and insulin sensitivity in vivo. Mechanistically, phosphorylated PPP1R3G displays increased binding for, and promotes dephosphorylation of, phospho-GS. Furthermore, PPP1R3B, another regulatory subunit of PP1, binds to the dephosphorylated GS, thereby relaying insulin stimulation to hepatic glycogen deposition. Importantly, this PP1-mediated signaling cascade is independent of GSK3. Therefore, we reveal a regulatory axis consisting of insulin/AKT/PPP1R3G/PPP1R3B that operates in parallel to the GSK3-dependent pathway, controlling glycogen synthesis and glucose homeostasis in insulin signaling.
Collapse
|
20
|
Köhn M. Turn and Face the Strange: A New View on Phosphatases. ACS CENTRAL SCIENCE 2020; 6:467-477. [PMID: 32341996 PMCID: PMC7181316 DOI: 10.1021/acscentsci.9b00909] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Indexed: 05/08/2023]
Abstract
Phosphorylation as a post-translational modification is critical for cellular homeostasis. Kinases and phosphatases regulate phosphorylation levels by adding or removing, respectively, a phosphate group from proteins or other biomolecules. Imbalances in phosphorylation levels are involved in a multitude of diseases. Phosphatases are often thought of as the black sheep, the strangers, of phosphorylation-mediated signal transduction, particularly when it comes to drug discovery and development. This is due to past difficulties to study them and unsuccessful attempts to target them; however, phosphatases have regained strong attention and are actively pursued now in clinical trials. By giving examples for current hot topics in phosphatase biology and for new approaches to target them, it is illustrated here how and why phosphatases made their comeback, and what is envisioned to come in the future.
Collapse
Affiliation(s)
- Maja Köhn
- Faculty
of Biology, Institute of Biology III, University
of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- Signalling
Research Centres BIOSS and CIBSS, University
of Freiburg, Freiburg, Germany
| |
Collapse
|
21
|
Brauer BL, Moon TM, Sheftic SR, Nasa I, Page R, Peti W, Kettenbach AN. Leveraging New Definitions of the LxVP SLiM To Discover Novel Calcineurin Regulators and Substrates. ACS Chem Biol 2019; 14:2672-2682. [PMID: 31633908 PMCID: PMC6925343 DOI: 10.1021/acschembio.9b00606] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The Phosphoprotein Phosphatase Calcineurin (CN, PP2B, PP3) recognizes and binds to two short linear motifs (SLiMs), PxIxIT and LxVP, in its regulators and substrates. These interactions enable CN function in many key biological processes. The identification of SLiMs is difficult because of their short, degenerate sequence and often low binding affinity. Here we combine Structure Based Shape Complementarity (SBSC) analysis and proteome-wide affinity purification-mass spectrometry to identify PxIxIT and LxVP containing CN interactors to expand and thereby redefine the LxVP motif. We find that the new πφ-LxVx primary sequence defines an ensemble of binding competent confirmations and thus the binding on-rate, making it difficult to predict the LxVP binding strength from its sequence. Our analysis confirms existing and, more importantly, identifies novel CN interactors, substrates, and thus biological functions of CN.
Collapse
Affiliation(s)
- Brooke L. Brauer
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, United States
| | - Thomas M. Moon
- Department of Chemistry and Biochemistry, University of Arizona, 1041 E. Lowell Street, Tucson, Arizona 85721, United States
| | - Sarah R. Sheftic
- Department of Chemistry and Biochemistry, University of Arizona, 1041 E. Lowell Street, Tucson, Arizona 85721, United States
| | - Isha Nasa
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, United States
| | - Rebecca Page
- Department of Chemistry and Biochemistry, University of Arizona, 1041 E. Lowell Street, Tucson, Arizona 85721, United States
| | - Wolfgang Peti
- Department of Chemistry and Biochemistry, University of Arizona, 1041 E. Lowell Street, Tucson, Arizona 85721, United States
| | - Arminja N. Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, United States
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03756, United States
| |
Collapse
|
22
|
Bouaïcha N, Miles CO, Beach DG, Labidi Z, Djabri A, Benayache NY, Nguyen-Quang T. Structural Diversity, Characterization and Toxicology of Microcystins. Toxins (Basel) 2019; 11:E714. [PMID: 31817927 PMCID: PMC6950048 DOI: 10.3390/toxins11120714] [Citation(s) in RCA: 206] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/02/2019] [Accepted: 12/04/2019] [Indexed: 11/22/2022] Open
Abstract
Hepatotoxic microcystins (MCs) are the most widespread class of cyanotoxins and the one that has most often been implicated in cyanobacterial toxicosis. One of the main challenges in studying and monitoring MCs is the great structural diversity within the class. The full chemical structure of the first MC was elucidated in the early 1980s and since then, the number of reported structural analogues has grown steadily and continues to do so, thanks largely to advances in analytical methodology. The structures of some of these analogues have been definitively elucidated after chemical isolation using a combination of techniques including nuclear magnetic resonance, amino acid analysis, and tandem mass spectrometry (MS/MS). Others have only been tentatively identified using liquid chromatography-MS/MS without chemical isolation. An understanding of the structural diversity of MCs, the genetic and environmental controls for this diversity and the impact of structure on toxicity are all essential to the ongoing study of MCs across several scientific disciplines. However, because of the diversity of MCs and the range of approaches that have been taken for characterizing them, comprehensive information on the state of knowledge in each of these areas can be challenging to gather. We have conducted an in-depth review of the literature surrounding the identification and toxicity of known MCs and present here a concise review of these topics. At present, at least 279 MCs have been reported and are tabulated here. Among these, about 20% (55 of 279) appear to be the result of chemical or biochemical transformations of MCs that can occur in the environment or during sample handling and extraction of cyanobacteria, including oxidation products, methyl esters, or post-biosynthetic metabolites. The toxicity of many MCs has also been studied using a range of different approaches and a great deal of variability can be observed between reported toxicities, even for the same congener. This review will help clarify the current state of knowledge on the structural diversity of MCs as a class and the impacts of structure on toxicity, as well as to identify gaps in knowledge that should be addressed in future research.
Collapse
Affiliation(s)
- Noureddine Bouaïcha
- Écologie, Systématique et Évolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91405 Orsay, France; (A.D.); (N.Y.B.)
| | - Christopher O. Miles
- Biotoxin Metrology, National Research Council Canada, 1411 Oxford St, Halifax, NS B3H 3Z1, Canada; (C.O.M.); (D.G.B.)
| | - Daniel G. Beach
- Biotoxin Metrology, National Research Council Canada, 1411 Oxford St, Halifax, NS B3H 3Z1, Canada; (C.O.M.); (D.G.B.)
| | - Zineb Labidi
- Laboratoire Biodiversité et Pollution des Écosystèmes, Faculté des Sciences de la Nature et de la Vie, Université Chadli Bendjedid d’El Taref, 36000 El Taref, Algeria;
| | - Amina Djabri
- Écologie, Systématique et Évolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91405 Orsay, France; (A.D.); (N.Y.B.)
- Laboratoire Biodiversité et Pollution des Écosystèmes, Faculté des Sciences de la Nature et de la Vie, Université Chadli Bendjedid d’El Taref, 36000 El Taref, Algeria;
| | - Naila Yasmine Benayache
- Écologie, Systématique et Évolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91405 Orsay, France; (A.D.); (N.Y.B.)
| | - Tri Nguyen-Quang
- Biofluids and Biosystems Modeling (BBML), Faculty of Agriculture, Dalhousie University, 39 Cox Road, Truro, B2N 5E3 Nova Scotia, Canada;
| |
Collapse
|
23
|
Abstract
The metalloenzyme protein phosphatase 1 (PP1), which is responsible for ≥50% of all dephosphorylation reactions, is regulated by scores of regulatory proteins, including the highly conserved SDS22 protein. SDS22 has numerous diverse functions, surprisingly acting as both a PP1 inhibitor and as an activator. Here, we integrate cellular, biophysical, and crystallographic studies to address this conundrum. We discovered that SDS22 selectively binds a unique conformation of PP1 that contains a single metal (M2) at its active site, i.e., SDS22 traps metal-deficient inactive PP1. Furthermore, we showed that SDS22 dissociation is accompanied by a second metal (M1) being loaded into PP1, as free metal cannot dissociate the complex and M1-deficient mutants remain constitutively trapped by SDS22. Together, our findings reveal that M1 metal loading and loss are essential for PP1 regulation in cells, which has broad implications for PP1 maturation, activity, and holoenzyme subunit exchange.
Collapse
|
24
|
Molecular basis for the binding and selective dephosphorylation of Na +/H + exchanger 1 by calcineurin. Nat Commun 2019; 10:3489. [PMID: 31375679 PMCID: PMC6677818 DOI: 10.1038/s41467-019-11391-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/08/2019] [Indexed: 01/26/2023] Open
Abstract
Very little is known about how Ser/Thr protein phosphatases specifically recruit and dephosphorylate substrates. Here, we identify how the Na+/H+-exchanger 1 (NHE1), a key regulator of cellular pH homeostasis, is regulated by the Ser/Thr phosphatase calcineurin (CN). NHE1 activity is increased by phosphorylation of NHE1 residue T779, which is specifically dephosphorylated by CN. While it is known that Ser/Thr protein phosphatases prefer pThr over pSer, we show that this preference is not key to this exquisite CN selectivity. Rather a combination of molecular mechanisms, including recognition motifs, dynamic charge-charge interactions and a substrate interaction pocket lead to selective dephosphorylation of pT779. Our data identify T779 as a site regulating NHE1-mediated cellular acid extrusion and provides a molecular understanding of NHE1 substrate selection by CN, specifically, and how phosphatases recruit specific substrates, generally.
Collapse
|