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Kitazawa Y, Iwabuchi N, Maejima K, Matsumoto O, Suzuki M, Matsuyama J, Koinuma H, Oshima K, Namba S, Yamaji Y. Random mutagenesis-based screening of the interface of phyllogen, a bacterial phyllody-inducing effector, for interaction with plant MADS-box proteins. FRONTIERS IN PLANT SCIENCE 2023; 14:1058059. [PMID: 37056494 PMCID: PMC10086140 DOI: 10.3389/fpls.2023.1058059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
To understand protein function deeply, it is important to identify how it interacts physically with its target. Phyllogen is a phyllody-inducing effector that interacts with the K domain of plant MADS-box transcription factors (MTFs), which is followed by proteasome-mediated degradation of the MTF. Although several amino acid residues of phyllogen have been identified as being responsible for the interaction, the exact interface of the interaction has not been elucidated. In this study, we comprehensively explored interface residues based on random mutagenesis using error-prone PCR. Two novel residues, at which mutations enhanced the affinity of phyllogen to MTF, were identified. These residues, and all other known interaction-involved residues, are clustered together at the surface of the protein structure of phyllogen, indicating that they constitute the interface of the interaction. Moreover, in silico structural prediction of the protein complex using ColabFold suggested that phyllogen interacts with the K domain of MTF via the putative interface. Our study facilitates an understanding of the interaction mechanisms between phyllogen and MTF.
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Affiliation(s)
- Yugo Kitazawa
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Nozomu Iwabuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kensaku Maejima
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Oki Matsumoto
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masato Suzuki
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Juri Matsuyama
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Koinuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kenro Oshima
- Faculty of Bioscience and Applied Chemistry, Hosei University, Tokyo, Japan
| | - Shigetou Namba
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yasuyuki Yamaji
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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2
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Van Wyngene L, Vanderhaeghen T, Petta I, Timmermans S, Corbeels K, Van der Schueren B, Vandewalle J, Van Looveren K, Wallaeys C, Eggermont M, Dewaele S, Catrysse L, van Loo G, Beyaert R, Vangoitsenhoven R, Nakayama T, Tavernier J, De Bosscher K, Libert C. ZBTB32 performs crosstalk with the glucocorticoid receptor and is crucial in glucocorticoid responses to starvation. iScience 2021; 24:102790. [PMID: 34337361 PMCID: PMC8324811 DOI: 10.1016/j.isci.2021.102790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 03/25/2021] [Accepted: 06/24/2021] [Indexed: 12/15/2022] Open
Abstract
The hypothalamic-pituitary-adrenal (HPA) axis forms a complex neuroendocrine system that regulates the body’s response to stress such as starvation. In contrast with the glucocorticoid receptor (GR), Zinc finger and BTB domain containing 32 (ZBTB32) is a transcription factor with poorly described functional relevance in physiology. This study shows that ZBTB32 is essential for the production of glucocorticoids (GCs) in response to starvation, since ZBTB32−/− mice fail to increase their GC production in the absence of nutrients. In terms of mechanism, GR-mediated upregulation of adrenal Scarb1 gene expression was absent in ZBTB32−/− mice, implicating defective cholesterol import as the cause of the poor GC synthesis. These lower GC levels are further associated with aberrations in the metabolic adaptation to starvation, which could explain the progressive weight gain of ZBTB32−/− mice. In conclusion, ZBTB32 performs a crosstalk with the GR in the metabolic adaptation to starvation via regulation of adrenal GC production. ZBTB32 is involved in the glucocorticoid production in response to starvation GR-mediated upregulation of adrenal Scarb1 regulates cholesterol import The weight gain of ZBTB32−/− mice is associated with aberrant metabolic adaptations
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Affiliation(s)
- Lise Van Wyngene
- Center for Inflammation Research, VIB Center for Inflammation Research, 9000 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Tineke Vanderhaeghen
- Center for Inflammation Research, VIB Center for Inflammation Research, 9000 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Ioanna Petta
- Center for Inflammation Research, VIB Center for Inflammation Research, 9000 Ghent, Belgium.,Ghent Gut Inflammation Group (GGIG), Ghent University, 9000 Ghent, Belgium.,Department of Rheumatology, Ghent University, 9000 Ghent, Belgium
| | - Steven Timmermans
- Center for Inflammation Research, VIB Center for Inflammation Research, 9000 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Katrien Corbeels
- Department of Chronic Diseases and Metabolism - Endocrinology, KU Leuven, Leuven, Belgium
| | - Bart Van der Schueren
- Department of Chronic Diseases and Metabolism - Endocrinology, KU Leuven, Leuven, Belgium
| | - Jolien Vandewalle
- Center for Inflammation Research, VIB Center for Inflammation Research, 9000 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Kelly Van Looveren
- Center for Inflammation Research, VIB Center for Inflammation Research, 9000 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Charlotte Wallaeys
- Center for Inflammation Research, VIB Center for Inflammation Research, 9000 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Melanie Eggermont
- Center for Inflammation Research, VIB Center for Inflammation Research, 9000 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Sylviane Dewaele
- Center for Inflammation Research, VIB Center for Inflammation Research, 9000 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Leen Catrysse
- Center for Inflammation Research, VIB Center for Inflammation Research, 9000 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Geert van Loo
- Center for Inflammation Research, VIB Center for Inflammation Research, 9000 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium.,Ghent Gut Inflammation Group (GGIG), Ghent University, 9000 Ghent, Belgium
| | - Rudi Beyaert
- Center for Inflammation Research, VIB Center for Inflammation Research, 9000 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium.,Ghent Gut Inflammation Group (GGIG), Ghent University, 9000 Ghent, Belgium
| | - Roman Vangoitsenhoven
- Department of Chronic Diseases and Metabolism - Endocrinology, KU Leuven, Leuven, Belgium
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Jan Tavernier
- Center for Medical Biotechnology, VIB Center for Medical Biotechnology, 9000 Ghent, Belgium.,Cytokine Receptor Laboratory (CRL), Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 3 Albert Baertsoenkaai, 9000 Ghent, Belgium
| | - Karolien De Bosscher
- Center for Medical Biotechnology, VIB Center for Medical Biotechnology, 9000 Ghent, Belgium.,Translational Nuclear Receptor Research Lab, Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 3 Albert Baertsoenkaai,9000 Ghent, Belgium
| | - Claude Libert
- Center for Inflammation Research, VIB Center for Inflammation Research, 9000 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium.,Ghent Gut Inflammation Group (GGIG), Ghent University, 9000 Ghent, Belgium
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3
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Chong ZX, Yeap SK, Ho WY. Transfection types, methods and strategies: a technical review. PeerJ 2021; 9:e11165. [PMID: 33976969 PMCID: PMC8067914 DOI: 10.7717/peerj.11165] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/05/2021] [Indexed: 12/17/2022] Open
Abstract
Transfection is a modern and powerful method used to insert foreign nucleic acids into eukaryotic cells. The ability to modify host cells' genetic content enables the broad application of this process in studying normal cellular processes, disease molecular mechanism and gene therapeutic effect. In this review, we summarized and compared the findings from various reported literature on the characteristics, strengths, and limitations of various transfection methods, type of transfected nucleic acids, transfection controls and approaches to assess transfection efficiency. With the vast choices of approaches available, we hope that this review will help researchers, especially those new to the field, in their decision making over the transfection protocol or strategy appropriate for their experimental aims.
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Affiliation(s)
- Zhi Xiong Chong
- School of Pharmacy, University of Nottingham Malaysia, Semenyih, Selangor, Malaysia
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, Selangor, Malaysia
| | - Wan Yong Ho
- School of Pharmacy, University of Nottingham Malaysia, Semenyih, Selangor, Malaysia
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4
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Sarrou I, Feiler CG, Falke S, Peard N, Yefanov O, Chapman H. C-phycocyanin as a highly attractive model system in protein crystallography: unique crystallization properties and packing-diversity screening. Acta Crystallogr D Struct Biol 2021; 77:224-236. [PMID: 33559611 PMCID: PMC7869899 DOI: 10.1107/s2059798320016071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/09/2020] [Indexed: 01/08/2023] Open
Abstract
The unique crystallization properties of the antenna protein C-phycocyanin (C-PC) from the thermophilic cyanobacterium Thermosynechococcus elongatus are reported and discussed. C-PC crystallizes in hundreds of significantly different conditions within a broad pH range and in the presence of a wide variety of precipitants and additives. Remarkably, the crystal dimensions vary from a few micrometres, as used in serial crystallography, to several hundred micrometres, with a very diverse crystal morphology. More than 100 unique single-crystal X-ray diffraction data sets were collected from randomly selected crystals and analysed. The addition of small-molecule additives revealed three new crystal packings of C-PC, which are discussed in detail. The high propensity of this protein to crystallize, combined with its natural blue colour and its fluorescence characteristics, make it an excellent candidate as a superior and highly adaptable model system in crystallography. C-PC can be used in technical and methods development approaches for X-ray and neutron diffraction techniques, and as a system for comprehending the fundamental principles of protein crystallography.
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Affiliation(s)
- Iosifina Sarrou
- Centre for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Christian G. Feiler
- Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Sven Falke
- Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
| | - Nolan Peard
- Centre for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Oleksandr Yefanov
- Centre for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Henry Chapman
- Centre for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
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5
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Lee LY, Pandey AK, Maron BA, Loscalzo J. Network medicine in Cardiovascular Research. Cardiovasc Res 2020; 117:2186-2202. [PMID: 33165538 DOI: 10.1093/cvr/cvaa321] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/08/2020] [Accepted: 10/30/2020] [Indexed: 12/21/2022] Open
Abstract
The ability to generate multi-omics data coupled with deeply characterizing the clinical phenotype of individual patients promises to improve understanding of complex cardiovascular pathobiology. There remains an important disconnection between the magnitude and granularity of these data and our ability to improve phenotype-genotype correlations for complex cardiovascular diseases. This shortcoming may be due to limitations associated with traditional reductionist analytical methods, which tend to emphasize a single molecular event in the pathogenesis of diseases more aptly characterized by crosstalk between overlapping molecular pathways. Network medicine is a rapidly growing discipline that considers diseases as the consequences of perturbed interactions between multiple interconnected biological components. This powerful integrative approach has enabled a number of important discoveries in complex disease mechanisms. In this review, we introduce the basic concepts of network medicine and highlight specific examples by which this approach has accelerated cardiovascular research. We also review how network medicine is well-positioned to promote rational drug design for patients with cardiovascular diseases, with particular emphasis on advancing precision medicine.
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Affiliation(s)
- Laurel Y Lee
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - Arvind K Pandey
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - Bradley A Maron
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA.,Department of Cardiology, Boston VA Healthcare System, Boston, MA, USA
| | - Joseph Loscalzo
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
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6
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Rose J, Visser F, Müller B, Senft M, Groscurth S, Sicking KF, Twyman RM, Prüfer D, Noll GA. Identification and molecular analysis of interaction sites in the MtSEO-F1 protein involved in forisome assembly. Int J Biol Macromol 2019; 144:603-614. [PMID: 31843608 DOI: 10.1016/j.ijbiomac.2019.12.092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/11/2019] [Accepted: 12/11/2019] [Indexed: 11/26/2022]
Abstract
Forisomes are large mechanoprotein complexes found solely in legumes such as Medicago truncatula. They comprise several "sieve element occlusion by forisome" (SEO-F) subunits, with MtSEO-F1 as the major structure-forming component. SEO-F proteins possess three conserved domains -an N-terminal domain (SEO-NTD), a potential thioredoxin fold, and a C-terminal domain (SEO-CTD)- but structural and biochemical data are scarce and little is known about the contribution of these domains to forisome assembly. To identify key amino acids involved in MtSEO-F1 dimerization and complex formation, we investigated protein-protein interactions by bimolecular fluorescence complementation and the analysis of yeast two-hybrid and random mutagenesis libraries. We identified a SEO-NTD core region as the major dimerization site, with abundant hydrophobic residues and rare charged residues suggesting dimerization is driven by the hydrophobic effect. We also found that ~45% of the full-length MtSEO-F1 sequence must be conserved for higher-order protein assembly, indicating that large interaction surfaces facilitate stable interactions, contributing to the high resilience of forisome bodies. Interestingly, the removal of 62 amino acids from the C-terminus did not disrupt forisome assembly. This is the first study unraveling interaction sites and mechanisms within the MtSEO-F1 protein at the level of dimerization and complex formation.
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Affiliation(s)
- Judith Rose
- Institute for Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany
| | - Franziska Visser
- Institute for Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany
| | - Boje Müller
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143 Münster, Germany
| | - Matthias Senft
- Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Sira Groscurth
- Stem Cell Network North Rhine-Westphalia, Merowingerplatz 1, 40225 Düsseldorf, Germany
| | - Kevin F Sicking
- Institute for Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany
| | | | - Dirk Prüfer
- Institute for Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143 Münster, Germany
| | - Gundula A Noll
- Institute for Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143 Münster, Germany.
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