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Lepeta K, Roubinet C, Bauer M, Vigano MA, Aguilar G, Kanca O, Ochoa-Espinosa A, Bieli D, Cabernard C, Caussinus E, Affolter M. Engineered kinases as a tool for phosphorylation of selected targets in vivo. J Cell Biol 2022; 221:213463. [PMID: 36102907 PMCID: PMC9477969 DOI: 10.1083/jcb.202106179] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 05/19/2022] [Accepted: 07/27/2022] [Indexed: 11/22/2022] Open
Abstract
Reversible protein phosphorylation by kinases controls a plethora of processes essential for the proper development and homeostasis of multicellular organisms. One main obstacle in studying the role of a defined kinase–substrate interaction is that kinases form complex signaling networks and most often phosphorylate multiple substrates involved in various cellular processes. In recent years, several new approaches have been developed to control the activity of a given kinase. However, most of them fail to regulate a single protein target, likely hiding the effect of a unique kinase–substrate interaction by pleiotropic effects. To overcome this limitation, we have created protein binder-based engineered kinases that permit a direct, robust, and tissue-specific phosphorylation of fluorescent fusion proteins in vivo. We show the detailed characterization of two engineered kinases based on Rho-associated protein kinase (ROCK) and Src. Expression of synthetic kinases in the developing fly embryo resulted in phosphorylation of their respective GFP-fusion targets, providing for the first time a means to direct the phosphorylation to a chosen and tagged target in vivo. We presume that after careful optimization, the novel approach we describe here can be adapted to other kinases and targets in various eukaryotic genetic systems to regulate specific downstream effectors.
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Affiliation(s)
| | - Chantal Roubinet
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK 2
| | - Milena Bauer
- Biozentrum, University of Basel, Basel, Switzerland 1
| | | | | | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 3
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2
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Lepeta K, Bauer M, Aguilar G, Vigano MA, Matsuda S, Affolter M. Studying Protein Function Using Nanobodies and Other Protein Binders in Drosophila. Methods Mol Biol 2022; 2540:219-237. [PMID: 35980580 DOI: 10.1007/978-1-0716-2541-5_10] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The direct manipulation of proteins by nanobodies and other protein binders has become an additional and valuable approach to investigate development and homeostasis in Drosophila. In contrast to other techniques, that indirectly interfere with proteins via their nucleic acids (CRISPR, RNAi, etc.), protein binders permit direct and acute protein manipulation. Since the first use of a nanobody in Drosophila a decade ago, many different applications exploiting protein binders have been introduced. Most of these applications use nanobodies against GFP to regulate GFP fusion proteins. In order to exert specific protein manipulations, protein binders are linked to domains that confer them precise biochemical functions. Here, we reflect on the use of tools based on protein binders in Drosophila. We describe their key features and provide an overview of the available reagents. Finally, we briefly explore the future avenues that protein binders might open up and thus further contribute to better understand development and homeostasis of multicellular organisms.
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Affiliation(s)
| | - Milena Bauer
- Biozentrum der Universität Basel, Basel, Switzerland
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3
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Lepeta K, Purzycka KJ, Pachulska-Wieczorek K, Mitjans M, Begemann M, Vafadari B, Bijata K, Adamiak RW, Ehrenreich H, Dziembowska M, Kaczmarek L. A normal genetic variation modulates synaptic MMP-9 protein levels and the severity of schizophrenia symptoms. EMBO Mol Med 2018. [PMID: 28623238 PMCID: PMC5538295 DOI: 10.15252/emmm.201707723] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Matrix metalloproteinase 9 (MMP‐9) has recently emerged as a molecule that contributes to pathological synaptic plasticity in schizophrenia, but explanation of the underlying mechanisms has been missing. In the present study, we performed a phenotype‐based genetic association study (PGAS) in > 1,000 schizophrenia patients from the Göttingen Research Association for Schizophrenia (GRAS) data collection and found an association between the MMP‐9 rs20544 C/T single‐nucleotide polymorphism (SNP) located in the 3′untranslated region (UTR) and the severity of a chronic delusional syndrome. In cultured neurons, the rs20544 SNP influenced synaptic MMP‐9 activity and the morphology of dendritic spines. We demonstrated that Fragile X mental retardation protein (FMRP) bound the MMP‐9 3′UTR. We also found dramatic changes in RNA structure folding and alterations in the affinity of FMRP for MMP‐9 RNA, depending on the SNP variant. Finally, we observed greater sensitivity to psychosis‐related locomotor hyperactivity in Mmp‐9 heterozygous mice. We propose a novel mechanism that involves MMP‐9‐dependent changes in dendritic spine morphology and the pathophysiology of schizophrenia, providing the first mechanistic insights into the way in which the single base change in the MMP‐9 gene (rs20544) influences gene function and results in phenotypic changes observed in schizophrenia patients.
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Affiliation(s)
- Katarzyna Lepeta
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Katarzyna J Purzycka
- Department of RNA Structure and Function, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland‡
| | - Katarzyna Pachulska-Wieczorek
- Department of RNA Structure and Function, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland‡
| | - Marina Mitjans
- Clinical Neuroscience, Max Planck Institute of Experimental Medicine, DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
| | - Martin Begemann
- Clinical Neuroscience, Max Planck Institute of Experimental Medicine, DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
| | - Behnam Vafadari
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Krystian Bijata
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Laboratory of RNA Biology and Functional Genomics, Warsaw, Poland
| | - Ryszard W Adamiak
- Department of RNA Structure and Function, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland‡
| | - Hannelore Ehrenreich
- Clinical Neuroscience, Max Planck Institute of Experimental Medicine, DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
| | - Magdalena Dziembowska
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland .,Laboratory of Molecular Basis of Synaptic Plasticity, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Leszek Kaczmarek
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
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4
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Schaefer N, Rotermund C, Blumrich EM, Lourenco MV, Joshi P, Hegemann RU, Jamwal S, Ali N, García Romero EM, Sharma S, Ghosh S, Sinha JK, Loke H, Jain V, Lepeta K, Salamian A, Sharma M, Golpich M, Nawrotek K, Paidi RK, Shahidzadeh SM, Piermartiri T, Amini E, Pastor V, Wilson Y, Adeniyi PA, Datusalia AK, Vafadari B, Saini V, Suárez-Pozos E, Kushwah N, Fontanet P, Turner AJ. The malleable brain: plasticity of neural circuits and behavior - a review from students to students. J Neurochem 2017. [PMID: 28632905 DOI: 10.1111/jnc.14107] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
One of the most intriguing features of the brain is its ability to be malleable, allowing it to adapt continually to changes in the environment. Specific neuronal activity patterns drive long-lasting increases or decreases in the strength of synaptic connections, referred to as long-term potentiation and long-term depression, respectively. Such phenomena have been described in a variety of model organisms, which are used to study molecular, structural, and functional aspects of synaptic plasticity. This review originated from the first International Society for Neurochemistry (ISN) and Journal of Neurochemistry (JNC) Flagship School held in Alpbach, Austria (Sep 2016), and will use its curriculum and discussions as a framework to review some of the current knowledge in the field of synaptic plasticity. First, we describe the role of plasticity during development and the persistent changes of neural circuitry occurring when sensory input is altered during critical developmental stages. We then outline the signaling cascades resulting in the synthesis of new plasticity-related proteins, which ultimately enable sustained changes in synaptic strength. Going beyond the traditional understanding of synaptic plasticity conceptualized by long-term potentiation and long-term depression, we discuss system-wide modifications and recently unveiled homeostatic mechanisms, such as synaptic scaling. Finally, we describe the neural circuits and synaptic plasticity mechanisms driving associative memory and motor learning. Evidence summarized in this review provides a current view of synaptic plasticity in its various forms, offers new insights into the underlying mechanisms and behavioral relevance, and provides directions for future research in the field of synaptic plasticity. Read the Editorial Highlight for this article on page 788. Cover Image for this issue: doi: 10.1111/jnc.13815.
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Affiliation(s)
- Natascha Schaefer
- Institute for Clinical Neurobiology, Julius-Maximilians-University of Wuerzburg, Würzburg, Germany
| | - Carola Rotermund
- German Center of Neurodegenerative Diseases, University of Tuebingen, Tuebingen, Germany
| | - Eva-Maria Blumrich
- Centre for Biomolecular Interactions Bremen, Faculty 2 (Biology/Chemistry), University of Bremen, Bremen, Germany.,Centre for Environmental Research and Sustainable Technology, University of Bremen, Bremen, Germany
| | - Mychael V Lourenco
- Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Pooja Joshi
- Inserm UMR 1141, Robert Debre Hospital, Paris, France
| | - Regina U Hegemann
- Department of Psychology, Brain Health Research Centre, University of Otago, Dunedin, New Zealand
| | - Sumit Jamwal
- Department of Pharmacology, ISF College of Pharmacy, Moga, Punjab, India
| | - Nilufar Ali
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | | | - Sorabh Sharma
- Neuropharmacology Division, Department of Pharmacy, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Shampa Ghosh
- National Institute of Nutrition (NIN), Indian Council of Medical Research (ICMR), Tarnaka, Hyderabad, India
| | - Jitendra K Sinha
- National Institute of Nutrition (NIN), Indian Council of Medical Research (ICMR), Tarnaka, Hyderabad, India
| | - Hannah Loke
- Hudson Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Molecular and Translational Science, Monash University, Melbourne, Victoria, Australia
| | - Vishal Jain
- Defence Institute of Physiology and Allied Sciences, Delhi, India
| | - Katarzyna Lepeta
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Ahmad Salamian
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Mahima Sharma
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Mojtaba Golpich
- Department of Medicine, University Kebangsaan Malaysia Medical Centre (HUKM), Cheras, Kuala Lumpur, Malaysia
| | - Katarzyna Nawrotek
- Department of Process Thermodynamics, Faculty of Process and Environmental Engineering, Lodz University of Technology, Lodz, Poland
| | - Ramesh K Paidi
- CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Sheila M Shahidzadeh
- Department of Biology, Program in Neuroscience, Syracuse University, Syracuse, New York, USA
| | - Tetsade Piermartiri
- Programa de Pós-Graduação em Neurociências, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Brazil
| | - Elham Amini
- Department of Medicine, University Kebangsaan Malaysia Medical Centre (HUKM), Cheras, Kuala Lumpur, Malaysia
| | - Veronica Pastor
- Instituto de Biología Celular y Neurociencia Prof. Eduardo De Robertis, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Yvette Wilson
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, Australia
| | - Philip A Adeniyi
- Cell Biology and Neurotoxicity Unit, Department of Anatomy, College of Medicine and Health Sciences, Afe Babalola University, Ado - Ekiti, Ekiti State, Nigeria
| | | | - Benham Vafadari
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Vedangana Saini
- Department of Developmental Neuroscience, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Edna Suárez-Pozos
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Toxicología, México
| | - Neetu Kushwah
- Defence Institute of Physiology and Allied Sciences, Delhi, India
| | - Paula Fontanet
- Division of Molecular and Cellular Neuroscience, Institute of Cellular Biology and Neuroscience (IBCN), CONICET-UBA, School of Medicine, Buenos Aires, Argentina
| | - Anthony J Turner
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
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5
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Lepeta K, Lourenco MV, Schweitzer BC, Martino Adami PV, Banerjee P, Catuara-Solarz S, de La Fuente Revenga M, Guillem AM, Haidar M, Ijomone OM, Nadorp B, Qi L, Perera ND, Refsgaard LK, Reid KM, Sabbar M, Sahoo A, Schaefer N, Sheean RK, Suska A, Verma R, Vicidomini C, Wright D, Zhang XD, Seidenbecher C. Synaptopathies: synaptic dysfunction in neurological disorders - A review from students to students. J Neurochem 2016; 138:785-805. [PMID: 27333343 PMCID: PMC5095804 DOI: 10.1111/jnc.13713] [Citation(s) in RCA: 203] [Impact Index Per Article: 25.4] [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: 04/29/2016] [Revised: 06/03/2016] [Accepted: 06/06/2016] [Indexed: 12/12/2022]
Abstract
Synapses are essential components of neurons and allow information to travel coordinately throughout the nervous system to adjust behavior to environmental stimuli and to control body functions, memories, and emotions. Thus, optimal synaptic communication is required for proper brain physiology, and slight perturbations of synapse function can lead to brain disorders. In fact, increasing evidence has demonstrated the relevance of synapse dysfunction as a major determinant of many neurological diseases. This notion has led to the concept of synaptopathies as brain diseases with synapse defects as shared pathogenic features. In this review, which was initiated at the 13th International Society for Neurochemistry Advanced School, we discuss basic concepts of synapse structure and function, and provide a critical view of how aberrant synapse physiology may contribute to neurodevelopmental disorders (autism, Down syndrome, startle disease, and epilepsy) as well as neurodegenerative disorders (Alzheimer and Parkinson disease). We finally discuss the appropriateness and potential implications of gathering synapse diseases under a single term. Understanding common causes and intrinsic differences in disease-associated synaptic dysfunction could offer novel clues toward synapse-based therapeutic intervention for neurological and neuropsychiatric disorders. In this Review, which was initiated at the 13th International Society for Neurochemistry (ISN) Advanced School, we discuss basic concepts of synapse structure and function, and provide a critical view of how aberrant synapse physiology may contribute to neurodevelopmental (autism, Down syndrome, startle disease, and epilepsy) as well as neurodegenerative disorders (Alzheimer's and Parkinson's diseases), gathered together under the term of synaptopathies. Read the Editorial Highlight for this article on page 783.
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Affiliation(s)
- Katarzyna Lepeta
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Mychael V Lourenco
- Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Barbara C Schweitzer
- Department for Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology Magdeburg, Magdeburg, Germany
| | - Pamela V Martino Adami
- Laboratory of Amyloidosis and Neurodegeneration, Fundación Instituto Leloir-IIBBA-CONICET, Buenos Aires, Argentina
| | - Priyanjalee Banerjee
- Department of Biochemistry, Institute of Post Graduate Medical Education & Research, Kolkata, West Bengal, India
| | - Silvina Catuara-Solarz
- Systems Biology Program, Cellular and Systems Neurobiology, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Mario de La Fuente Revenga
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Alain Marc Guillem
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México D.F. 07000, Mexico
| | - Mouna Haidar
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Victoria, Australia
| | - Omamuyovwi M Ijomone
- Department of Human Anatomy, Cross River University of Technology, Okuku Campus, Cross River, Nigeria
| | - Bettina Nadorp
- The Department of Biological Chemistry, The Edmond and Lily Safra Center for Brain Sciences, The Alexander Grass Center for Bioengineering, The Hebrew University of Jerusalem, Israel
| | - Lin Qi
- Laboratory of Molecular Neuro-Oncology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, United States of America
| | - Nirma D Perera
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Victoria, Australia
| | - Louise K Refsgaard
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Kimberley M Reid
- Department of Pharmacology, UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Mariam Sabbar
- Brain Function Research Group, School of Physiology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Arghyadip Sahoo
- Department of Biochemistry, Midnapore Medical College, West Bengal University of Health Sciences, West Bengal, India
| | - Natascha Schaefer
- Institute for Clinical Neurobiology, Julius-Maximilians-University of Wuerzburg, Wuerzburg, Germany
| | - Rebecca K Sheean
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Victoria, Australia
| | - Anna Suska
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Rajkumar Verma
- Department of Neurosciences Uconn Health Center, Farmington, CT, United States of America
| | | | - Dean Wright
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Victoria, Australia
| | - Xing-Ding Zhang
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
| | - Constanze Seidenbecher
- Department for Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology Magdeburg, Magdeburg, Germany. .,Center for Behavioral Brain Sciences (CBBS) Magdeburg, Magdeburg, Germany.
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6
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Abstract
Recent findings implicate alterations in glutamate signaling, leading to aberrant synaptic plasticity, in schizophrenia. Matrix metalloproteinase-9 (MMP-9) has been shown to regulate glutamate receptors, be regulated by glutamate at excitatory synapses, and modulate physiological and morphological synaptic plasticity. By means of functional gene polymorphism, gene responsiveness to antipsychotics and blood plasma levels MMP-9 has recently been implicated in schizophrenia. This commentary critically reviews these findings based on the hypothesis that MMP-9 contributes to pathological synaptic plasticity in schizophrenia.
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Affiliation(s)
- Katarzyna Lepeta
- Department of Molecular and Cellular Neurobiology, Nencki Institute, Warsaw, Poland
| | - Leszek Kaczmarek
- Department of Molecular and Cellular Neurobiology, Nencki Institute, Warsaw, Poland
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