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Orlova SY, Ruzina MN, Emelianova OR, Sergeev AA, Chikurova EA, Orlov AM, Mugue NS. In Search of a Target Gene for a Desirable Phenotype in Aquaculture: Genome Editing of Cyprinidae and Salmonidae Species. Genes (Basel) 2024; 15:726. [PMID: 38927661 PMCID: PMC11202958 DOI: 10.3390/genes15060726] [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: 04/24/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Aquaculture supplies the world food market with a significant amount of valuable protein. Highly productive aquaculture fishes can be derived by utilizing genome-editing methods, and the main problem is to choose a target gene to obtain the desirable phenotype. This paper presents a review of the studies of genome editing for genes controlling body development, growth, pigmentation and sex determination in five key aquaculture Salmonidae and Cyprinidae species, such as rainbow trout (Onchorhynchus mykiss), Atlantic salmon (Salmo salar), common carp (Cyprinus carpio), goldfish (Carassius auratus), Gibel carp (Carassius gibelio) and the model fish zebrafish (Danio rerio). Among the genes studied, the most applicable for aquaculture are mstnba, pomc, and acvr2, the knockout of which leads to enhanced muscle growth; runx2b, mutants of which do not form bones in myoseptae; lepr, whose lack of function makes fish fast-growing; fads2, Δ6abc/5Mt, and Δ6bcMt, affecting the composition of fatty acids in fish meat; dnd mettl3, and wnt4a, mutants of which are sterile; and disease-susceptibility genes prmt7, gab3, gcJAM-A, and cxcr3.2. Schemes for obtaining common carp populations consisting of only large females are promising for use in aquaculture. The immobilized and uncolored zebrafish line is of interest for laboratory use.
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Affiliation(s)
- Svetlana Yu. Orlova
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
| | - Maria N. Ruzina
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
| | - Olga R. Emelianova
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
- Department of Biological Evolution, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Alexey A. Sergeev
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
| | - Evgeniya A. Chikurova
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
| | - Alexei M. Orlov
- Laboratory of Oceanic Ichthyofauna, Shirshov Institute of Oceanology, Russian Academy of Sciences, 117218 Moscow, Russia
- Laboratory of Behavior of Lower Vertebrates, Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Ichthyology, Dagestan State University, 367000 Makhachkala, Russia
| | - Nikolai S. Mugue
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
- Laboratory of Genome Evolution and Speciation, Institute of Developmental Biology Russian Academy of Sciences, 117808 Moscow, Russia
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Silva GD, Milan TM, Chagas PS, Trevisan GL, Ferraz CL, Leopoldino AM. SET protein as an epigenetics target. Epigenomics 2024; 16:249-257. [PMID: 38131159 DOI: 10.2217/epi-2023-0297] [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] [Indexed: 12/23/2023] Open
Abstract
The SET gene has four transcripts reported in NCBI, coding two isoforms of SET proteins. The most known function of SET protein is inhibiting protein phosphatase 2A, a tumor suppressor, which has been associated with different biological processes. In this review, our focus was on exploring the other SET functions related to epigenetic mechanisms, which impact cellular migration, cell cycle and apoptosis.
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Affiliation(s)
- Gabriel da Silva
- Department of Clinical Analyses, Toxicology & Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Brazil
| | - Thaís Moré Milan
- Department of Clinical Analyses, Toxicology & Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Brazil
| | - Pablo Shimaoka Chagas
- Department of Clinical Analyses, Toxicology & Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Brazil
| | - Glauce Lunardelli Trevisan
- Department of Clinical Analyses, Toxicology & Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Brazil
| | - Camila Lopes Ferraz
- Department of Clinical Analyses, Toxicology & Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Brazil
| | - Andréia Machado Leopoldino
- Department of Clinical Analyses, Toxicology & Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Brazil
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Casado-Combreras MÁ, Rivero-Rodríguez F, Elena-Real CA, Molodenskiy D, Díaz-Quintana A, Martinho M, Gerbaud G, González-Arzola K, Velázquez-Campoy A, Svergun D, Belle V, De la Rosa MA, Díaz-Moreno I. PP2A is activated by cytochrome c upon formation of a diffuse encounter complex with SET/TAF-Iβ. Comput Struct Biotechnol J 2022; 20:3695-3707. [PMID: 35891793 PMCID: PMC9293736 DOI: 10.1016/j.csbj.2022.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 11/25/2022] Open
Abstract
Intrinsic protein flexibility is of overwhelming relevance for intermolecular recognition and adaptability of highly dynamic ensemble of complexes, and the phenomenon is essential for the understanding of numerous biological processes. These conformational ensembles-encounter complexes-lack a unique organization, which prevents the determination of well-defined high resolution structures. This is the case for complexes involving the oncoprotein SET/template-activating factor-Iβ (SET/TAF-Iβ), a histone chaperone whose functions and interactions are significantly affected by its intrinsic structural plasticity. Besides its role in chromatin remodeling, SET/TAF-Iβ is an inhibitor of protein phosphatase 2A (PP2A), which is a key phosphatase counteracting transcription and signaling events controlling the activity of DNA damage response (DDR) mediators. During DDR, SET/TAF-Iβ is sequestered by cytochrome c (Cc) upon migration of the hemeprotein from mitochondria to the cell nucleus. Here, we report that the nuclear SET/TAF-Iβ:Cc polyconformational ensemble is able to activate PP2A. In particular, the N-end folded, globular region of SET/TAF-Iβ (a.k.a. SET/TAF-Iβ ΔC)-which exhibits an unexpected, intrinsically highly dynamic behavior-is sufficient to be recognized by Cc in a diffuse encounter manner. Cc-mediated blocking of PP2A inhibition is deciphered using an integrated structural and computational approach, combining small-angle X-ray scattering, electron paramagnetic resonance, nuclear magnetic resonance, calorimetry and molecular dynamics simulations.
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Key Words
- ANP32B, Acidic leucine-rich nuclear phosphoprotein family member B
- BTFA, 3-bromo-1,1,1-trifluoroacetone
- CD, Circular dichroism
- CDK9, Cyclin-dependent kinase 9
- CW, Continuous wave
- Cc, Cytochrome c
- Cytochrome c
- DDR, DNA damage response
- DEER, Double electron–electron resonance
- DLS, Dynamic light scattering
- DMEM, Dulbecco’s modified Eagle’s medium
- DNA, Deoxyribonucleic acid
- DTT, Dithiotreitol
- Dmax, Maximum dimension
- EDTA, Ethylenediamine tetraacetic acid
- EGTA, Ethyleneglycol tetraacetic acid
- EPR, Electron paramagnetic resonance
- Encounter complex
- FBS, Fetal bovine serum
- GUI, Graphical user interface
- HEK, Human embryonic kidney cells
- HRP, Horseradish peroxidase
- I2PP2A, Inhibitor 2 of the protein phosphatase 2A
- I3PP2A, Inhibitor 3 of the protein phosphatase 2A
- INTAC, Integrator-PP2A complex
- IPTG, Isopropyl-β-D-1-thiogalactopyranoside
- ITC, Isothermal titration calorimetry
- Ip/Id, Intensity ratio of NMR resonances between paramagnetic and diamagnetic samples
- LB, Luria-Bertani
- MD, Molecular dynamics
- MTS, (1-acetoxy-2,2,5,5-tetramethyl-δ-3-pyrroline-3-methyl) methanethiosulfonate
- MTSL, (1-oxyl-2,2,5,5-tetramethyl- δ −3-pyrroline-3-methyl) methanethiosulfonate
- MW, Molecular weight
- Molecular dynamics
- NAP1, Nucleosome assembly protein 1
- NAPL, Nucleosome assembly protein L
- NMA, Normal mode analysis
- NMR, Nuclear magnetic resonance
- NPT, Constant number, pressure and temperature
- NVT, Constant number, volume and temperature
- Nuclear magnetic resonance
- OD600, Optical density measured at 600 nm
- OPC, Optimal 3-charge, 4-point rigid water model
- PCR, Polymerase chain reaction
- PME, Particle mesh Ewald
- PMSF, Phenylmethylsulfonyl fluoride
- PP2A, Protein phosphatase 2A
- PRE, Paramagnetic relaxation enhancement
- PVDF, Polyvinylidene fluoride
- Protein phosphatase 2A
- RNA, Ribonucleic acid
- RNApol II, RNA polymerase II
- Rg, Radius of gyration
- SAXS, Small-angle X-ray scattering
- SC, Sample changer
- SDS-PAGE, Sodium dodecylsulfate-polyacrylamide gel electrophoresis
- SDSL, Site-directed spin labeling
- SEC, Size-exclusion chromatography
- SET/TAF-Iβ
- SET/TAF-Iβ ΔC, SET/template-activating factor-Iβ construct lacking its C-terminal domain
- SET/TAF-Iβ, SET/template-activating factor-Iβ
- SPRi, Surface plasmon resonance imaging
- TAF-Iα, Template-activating factor-Iα
- TPBS, Tween 20-phosphate buffered saline
- VPS75, Vacuolar protein sorting-associated protein 75
- WT, Wild type
- XRD, X-ray diffraction
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Affiliation(s)
- Miguel Á. Casado-Combreras
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Francisco Rivero-Rodríguez
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Carlos A. Elena-Real
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
- Centre de Biologie Structurale (CBS), INSERM, Centre National de la Recherche Scientifique (CNRS) and Université de Montpellier. 29 rue de Navacelles, 34090 Montpellier, France
| | - Dmitry Molodenskiy
- European Molecular Biology Laboratory, Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestr. 85, 22607 Hamburg, Germany
| | - Antonio Díaz-Quintana
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Marlène Martinho
- Aix Marseille Univ. Centre National de la Recherche Scientifique (CNRS), BIP UMR7281, Bioénergétique et Ingénierie des protéines, 13402 Marseille, France
| | - Guillaume Gerbaud
- Aix Marseille Univ. Centre National de la Recherche Scientifique (CNRS), BIP UMR7281, Bioénergétique et Ingénierie des protéines, 13402 Marseille, France
| | - Katiuska González-Arzola
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Adrián Velázquez-Campoy
- Institute of Biocomputation and Physic of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza. C. de Mariano Esquillor Gómez, Edificio I+D, 50018 Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, C. Pedro Cerbuna, 12, 50009 Zaragoza, Spain
- Instituto de Investigación Sanitaria de Aragón (IIS Aragon), Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), C. de Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestr. 85, 22607 Hamburg, Germany
| | - Valérie Belle
- Aix Marseille Univ. Centre National de la Recherche Scientifique (CNRS), BIP UMR7281, Bioénergétique et Ingénierie des protéines, 13402 Marseille, France
| | - Miguel A. De la Rosa
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Irene Díaz-Moreno
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
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