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Qin Q, Liu R, Li Z, Liu M, Wu X, Wang H, Yang S, Sun X, Yi X. Resolving candidate genes of duck ovarian tissue transplantation via RNA-Seq and expression network analyses. Poult Sci 2024; 103:103788. [PMID: 38692177 PMCID: PMC11070914 DOI: 10.1016/j.psj.2024.103788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 05/03/2024] Open
Abstract
This study aims to identify candidate genes related to ovarian development after ovarian tissue transplantation through transcriptome sequencing (RNA-seq) and expression network analyses, as well as to provide a reference for determining the molecular mechanism of improving ovarian development following ovarian tissue transplantation. We collected ovarian tissues from 15 thirty-day-old ducks and split each ovary into 4 equal portions of comparable sizes before orthotopically transplanting them into 2-day-old ducks. Samples were collected on days 0 (untransplanted), 3, 6, and 9. The samples were paraffin sectioned and then subjected to Hematoxylin-Eosin (HE) staining and follicular counting. We extracted RNA from ovarian samples via the Trizol method to construct a transcriptome library, which was then sequenced by the Illumina Novaseq 6000 sequencing platform. The sequencing results were examined for differentially expressed genes (DEG) through gene ontology (GO) function and the Kyoto encyclopedia of genes and genomes (KEGG) pathway analyses, gene set enrichment analysis (GSEA), weighted correlation network analysis (WGCNA), and protein-protein interaction (PPI) networks. Some of the candidate genes were selected for verification using real-time fluorescence quantitative PCR (qRT-PCR). Histological analysis revealed a significant reduction in the number of morphologically normal follicles at 3, 6, and 9 d after ovarian transplantation, along with significantly higher abnormality rates (P < 0.05). The transcriptome analysis results revealed 2,114, 2,224, and 2,257 upregulated DEGs and 2,647, 2,883, and 2,665 downregulated DEGs at 3, 6, and 9 d after ovarian transplantation, respectively. Enrichment analysis revealed the involvement multiple pathways in inflammatory signaling, signal transduction, and cellular processes. Furthermore, WGCNA yielded 13 modules, with 10, 4, and 6 candidate genes mined at 3, 6 and 9 d after ovarian transplantation, respectively. Transcription factor (TF) prediction showed that STAT1 was the most important TF. Finally, the qRT-PCR verification results revealed that 12 candidate genes exhibited an expression trend consistent with sequencing data. In summary, significant differences were observed in the number of follicles in duck ovaries following ovarian transplantation. Candidate genes involved in ovarian vascular remodeling and proliferation were screened using RNA-Seq and WGCNA.
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Affiliation(s)
- Qingming Qin
- College of Animal Science and Technology, Xinyang Agriculture and Forestry University, Xinyang, Henan Province, 464000, P. R. China
| | - Rongxu Liu
- College of Animal Science and Technology, Xinyang Agriculture and Forestry University, Xinyang, Henan Province, 464000, P. R. China
| | - Zhili Li
- College of Animal Science and Technology, Xinyang Agriculture and Forestry University, Xinyang, Henan Province, 464000, P. R. China
| | - Midi Liu
- College of Animal Science and Technology, Xinyang Agriculture and Forestry University, Xinyang, Henan Province, 464000, P. R. China
| | - Xian Wu
- College of Animal Science and Technology, Xinyang Agriculture and Forestry University, Xinyang, Henan Province, 464000, P. R. China
| | - Huimin Wang
- College of Animal Science and Technology, Xinyang Agriculture and Forestry University, Xinyang, Henan Province, 464000, P. R. China
| | - Shuailiang Yang
- College of Animal Science and Technology, Xinyang Agriculture and Forestry University, Xinyang, Henan Province, 464000, P. R. China
| | - Xuyang Sun
- College of Animal Science and Technology, Xinyang Agriculture and Forestry University, Xinyang, Henan Province, 464000, P. R. China
| | - Xianguo Yi
- College of Animal Science and Technology, Xinyang Agriculture and Forestry University, Xinyang, Henan Province, 464000, P. R. China.
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2
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Morano NC, Lopez DH, Meltzer H, Sergeeva AP, Katsamba PS, Rostam KD, Gupta HP, Becker JE, Bornstein B, Cosmanescu F, Schuldiner O, Honig B, Mann RS, Shapiro L. Cis inhibition of co-expressed DIPs and Dprs shapes neural development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583391. [PMID: 38895375 PMCID: PMC11185508 DOI: 10.1101/2024.03.04.583391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
In Drosophila , two interacting adhesion protein families, Dprs and DIPs, coordinate the assembly of neural networks. While intercellular DIP/Dpr interactions have been well characterized, DIPs and Dprs are often co-expressed within the same cells, raising the question as to whether they also interact in cis . We show, in cultured cells and in vivo, that DIP-α and DIP-δ can interact in cis with their ligands, Dpr6/10 and Dpr12, respectively. When co-expressed in cis with their cognate partners, these Dprs regulate the extent of trans binding, presumably through competitive cis interactions. We demonstrate the neurodevelopmental effects of cis inhibition in fly motor neurons and in the mushroom body. We further show that a long disordered region of DIP-α at the C-terminus is required for cis but not trans interactions, likely because it alleviates geometric constraints on cis binding. Thus, the balance between cis and trans interactions plays a role in controlling neural development.
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Wang Y, Salazar RJ, Simonetta LT, Sorrentino V, Gatton TJ, Wu B, Vecsey CG, Carrillo RA. hkb is required for DIP-α expression and target recognition in the Drosophila neuromuscular circuit. Commun Biol 2024; 7:507. [PMID: 38678127 PMCID: PMC11055905 DOI: 10.1038/s42003-024-06184-8] [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: 07/19/2023] [Accepted: 04/11/2024] [Indexed: 04/29/2024] Open
Abstract
Our nervous system contains billions of neurons that form precise connections with each other through interactions between cell surface proteins. In Drosophila, the Dpr and DIP immunoglobulin protein subfamilies form homophilic or heterophilic interactions to instruct synaptic connectivity, synaptic growth, and cell survival. However, the upstream regulatory mechanisms of Dprs and DIPs are not clear. On the other hand, while transcription factors have been implicated in target recognition, their downstream cell surface proteins remain mostly unknown. We conduct an F1 dominant modifier genetic screen to identify regulators of Dprs and DIPs. We identify huckebein (hkb), a transcription factor previously implicated in target recognition of the dorsal Is motor neuron. We show that hkb genetically interacts with DIP-α and loss of hkb leads to complete removal of DIP-α expression specifically in dorsal Is motor neurons. We then confirm that this specificity is through the dorsal Is motor neuron specific transcription factor, even-skipped (eve), which acts downstream of hkb. Analysis of the genetic interaction between hkb and eve reveals that they act in the same pathway to regulate dorsal Is motor neuron connectivity. Our study provides insight into the transcriptional regulation of DIP-α and suggests that distinct regulatory mechanisms exist for the same CSP in different neurons.
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Affiliation(s)
- Yupu Wang
- Department of Molecular Genetics and Cellular Biology, University of Chicago, Chicago, IL, 60637, USA.
- Neuroscience Institute, University of Chicago, Chicago, IL, 60637, USA.
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, 20147, USA.
| | - Rio J Salazar
- Department of Molecular Genetics and Cellular Biology, University of Chicago, Chicago, IL, 60637, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, 60637, USA
- Program in Cell and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Luciano T Simonetta
- Department of Molecular Genetics and Cellular Biology, University of Chicago, Chicago, IL, 60637, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, 60637, USA
| | - Violet Sorrentino
- Department of Molecular Genetics and Cellular Biology, University of Chicago, Chicago, IL, 60637, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, 60637, USA
| | - Terrence J Gatton
- Neuroscience Program, Skidmore College, 815 N. Broadway, Saratoga Springs, NY, 12866, USA
| | - Bill Wu
- Neuroscience Program, Skidmore College, 815 N. Broadway, Saratoga Springs, NY, 12866, USA
| | - Christopher G Vecsey
- Neuroscience Program, Skidmore College, 815 N. Broadway, Saratoga Springs, NY, 12866, USA
| | - Robert A Carrillo
- Department of Molecular Genetics and Cellular Biology, University of Chicago, Chicago, IL, 60637, USA.
- Neuroscience Institute, University of Chicago, Chicago, IL, 60637, USA.
- Program in Cell and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA.
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4
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Osaka J, Ishii A, Wang X, Iwanaga R, Kawamura H, Akino S, Sugie A, Hakeda-Suzuki S, Suzuki T. Complex formation of immunoglobulin superfamily molecules Side-IV and Beat-IIb regulates synaptic specificity. Cell Rep 2024; 43:113798. [PMID: 38381608 DOI: 10.1016/j.celrep.2024.113798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/03/2023] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
Neurons establish specific synapses based on the adhesive properties of cell-surface proteins while also retaining the ability to form synapses in a relatively non-selective manner. However, comprehensive understanding of the underlying mechanism reconciling these opposing characteristics remains incomplete. Here, we have identified Side-IV/Beat-IIb, members of the Drosophila immunoglobulin superfamily, as a combination of cell-surface recognition molecules inducing synapse formation. The Side-IV/Beat-IIb combination transduces bifurcated signaling with Side-IV's co-receptor, Kirre, and a synaptic scaffold protein, Dsyd-1. Genetic experiments and subcellular protein localization analyses showed the Side-IV/Beat-IIb/Kirre/Dsyd-1 complex to have two essential functions. First, it narrows neuronal binding specificity through Side-IV/Beat-IIb extracellular interactions. Second, it recruits synapse formation factors, Kirre and Dsyd-1, to restrict synaptic loci and inhibit miswiring. This dual function explains how the combinations of cell-surface molecules enable the ranking of preferred interactions among neuronal pairs to achieve synaptic specificity in complex circuits in vivo.
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Affiliation(s)
- Jiro Osaka
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan; Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Arisa Ishii
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Xu Wang
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Riku Iwanaga
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Hinata Kawamura
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Shogo Akino
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Atsushi Sugie
- Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Satoko Hakeda-Suzuki
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan; Research Initiatives and Promotion Organization, Yokohama National University, Yokohama 240-8501, Japan
| | - Takashi Suzuki
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan.
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Goulard Coderc de Lacam E, Roux B, Chipot C. Classifying Protein-Protein Binding Affinity with Free-Energy Calculations and Machine Learning Approaches. J Chem Inf Model 2024; 64:1081-1091. [PMID: 38272021 DOI: 10.1021/acs.jcim.3c01586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Understanding the intricate phenomenon of neuronal wiring in the brain is of great interest in neuroscience. In the fruit fly, Drosophila melanogaster, the Dpr-DIP interactome has been identified to play an important role in this process. However, experimental data suggest that a merely limited subset of complexes, essentially 57 out of a total of 231, exhibit strong binding affinity. In this work, we sought to identify the residue-level molecular basis underlying the difference in binding affinity using a state-of-the-art methodology consisting of standard binding free-energy calculations with a geometrical route and machine learning (ML) techniques. We determined the binding affinity for two complexes using statistical mechanics simulations, achieving an excellent reproduction of the experimental data. Moreover, we predicted the binding free energy for two additional low-affinity complexes, devoid of experimental estimation, while simultaneously identifying key residues for the binding. Furthermore, through the use of ML algorithms, linear discriminant analysis, and random forest, we achieved remarkable accuracy, as high as 0.99, in discerning between strong (cognate) and weak (noncognate) binders. The presented ML approach encompasses easily transferable input features, enabling its broad application to any interactome while facilitating the identification of pivotal residues critical for binding interactions. The predictive power of the generated model was probed on similar protein families from 13 diverse species. Our ML model exhibited commendable performance on these additional data sets, showcasing its reliability and robustness across the species barrier.
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Affiliation(s)
- Emma Goulard Coderc de Lacam
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche no. 7019, Université de Lorraine, B.P. 70239, 54506 Vandœuvre-lès-Nancy Cedex, France
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E. 57th Street W225, Chicago, Illinois 60637, United States
- Department of Chemistry, The University of Chicago, 5735 S Ellis Avenue, Chicago, Illinois 60637, United States
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche no. 7019, Université de Lorraine, B.P. 70239, 54506 Vandœuvre-lès-Nancy Cedex, France
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E. 57th Street W225, Chicago, Illinois 60637, United States
- Theoretical and Computational Biophysics Group, Beckman Institute, and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, United States
- Department of Chemistry, The University of Hawai'i at Ma̅noa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
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6
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Lobb-Rabe M, Nawrocka WI, Zhang R, Ashley J, Carrillo RA, Özkan E. Neuronal Wiring Receptors Dprs and DIPs Are GPI Anchored and This Modification Contributes to Their Cell Surface Organization. eNeuro 2024; 11:ENEURO.0184-23.2023. [PMID: 38233143 PMCID: PMC10863630 DOI: 10.1523/eneuro.0184-23.2023] [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: 05/26/2023] [Revised: 11/20/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024] Open
Abstract
The Drosophila Dpr and DIP proteins belong to the immunoglobulin superfamily of cell surface proteins (CSPs). Their hetero- and homophilic interactions have been implicated in a variety of neuronal functions, including synaptic connectivity, cell survival, and axon fasciculation. However, the signaling pathways underlying these diverse functions are unknown. To gain insight into Dpr-DIP signaling, we sought to examine how these CSPs are associated with the membrane. Specifically, we asked whether Dprs and DIPs are integral membrane proteins or membrane anchored through the addition of glycosylphosphatidylinositol (GPI) linkage. We demonstrate that most Dprs and DIPs are GPI anchored to the membrane of insect cells and validate these findings for some family members in vivo using Drosophila larvae, where GPI anchor cleavage results in loss of surface labeling. Additionally, we show that GPI cleavage abrogates aggregation of insect cells expressing cognate Dpr-DIP partners. To test if the GPI anchor affects Dpr and DIP localization, we replaced it with a transmembrane domain and observed perturbation of subcellular localization on motor neurons and muscles. These data suggest that membrane anchoring of Dprs and DIPs through GPI linkage is required for localization and that Dpr-DIP intracellular signaling likely requires transmembrane coreceptors.
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Affiliation(s)
- Meike Lobb-Rabe
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois 60637
- Program in Cell and Molecular Biology, The University of Chicago, Chicago, Illinois 60637
- Neuroscience Institute, The University of Chicago, Chicago, Illinois 60637
| | - Wioletta I Nawrocka
- Neuroscience Institute, The University of Chicago, Chicago, Illinois 60637
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637
| | - Ruiling Zhang
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois 60637
- Neuroscience Institute, The University of Chicago, Chicago, Illinois 60637
- Committee on Development, Regeneration, and Stem Cell Biology, The University of Chicago, Chicago, Illinois 60637
| | - James Ashley
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois 60637
- Neuroscience Institute, The University of Chicago, Chicago, Illinois 60637
| | - Robert A Carrillo
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois 60637
- Program in Cell and Molecular Biology, The University of Chicago, Chicago, Illinois 60637
- Neuroscience Institute, The University of Chicago, Chicago, Illinois 60637
| | - Engin Özkan
- Neuroscience Institute, The University of Chicago, Chicago, Illinois 60637
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637
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7
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Carrier Y, Rio LQ, Formicola N, de Sousa-Xavier V, Tabet M, Chen YCD, Wislez M, Orts L, Pinto-Teixeira F. Biased cell adhesion organizes a circuit for visual motion integration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.11.571076. [PMID: 38168373 PMCID: PMC10760042 DOI: 10.1101/2023.12.11.571076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Layer specific computations in the brain rely on neuronal processes establishing synaptic connections with specific partners in distinct laminae. In the Drosophila lobula plate neuropile, the axons of the four subtypes of T4 and T5 visual motion direction-selective neurons segregate into four layers, based on their directional preference, and form synapses with distinct subsets of postsynaptic neurons. Four bi-stratified inhibitory lobula plate intrinsic cells exhibit a consistent synaptic pattern, receiving excitatory T4/T5 inputs in one layer, and conveying inhibitory signals to an adjacent layer. This layered arrangement establishes motion opponency. Here, we identify layer-specific expression of different receptor-ligand pairs belonging to the Beat and Side families of Cell Adhesion Molecules (CAMs) between T4/T5 neurons and their postsynaptic partners. Genetic analysis reveals that Beat/Side mediated interactions are required to restrict T4/T5 axonal innervation to a single layer. We propose that Beat/Side contribute to synaptic specificity by biasing adhesion between synaptic partners before synaptogenesis.
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Affiliation(s)
- Yannick Carrier
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Laura Quintana Rio
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Nadia Formicola
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Vicente de Sousa-Xavier
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Maha Tabet
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | | | - Maëva Wislez
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Lisa Orts
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Filipe Pinto-Teixeira
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
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8
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Wang Y, Salazar R, Simonetta L, Sorrentino V, Gatton TJ, Wu B, Vecsey CG, Carrillo RA. hkb is required for DIP-α expression and target recognition in the Drosophila neuromuscular circuit. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.15.562341. [PMID: 37905128 PMCID: PMC10614772 DOI: 10.1101/2023.10.15.562341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Our nervous system contains billions of neurons that form precise connections with each other through interactions between cell surface proteins (CSPs). In Drosophila, the Dpr and DIP immunoglobulin protein subfamilies form homophilic or heterophilic interactions to instruct synaptic connectivity, synaptic growth and cell survival. However, the upstream regulation and downstream signaling mechanisms of Dprs and DIPs are not clear. In the Drosophila larval neuromuscular system, DIP-α is expressed in the dorsal and ventral type-Is motor neurons (MNs). We conducted an F1 dominant modifier genetic screen to identify regulators of Dprs and DIPs. We found that the transcription factor, huckebein (hkb), genetically interacts with DIP-α and is important for target recognition specifically in the dorsal Is MN, but not the ventral Is MN. Loss of hkb led to complete removal of DIP-α expression. We then confirmed that this specificity is through the dorsal Is MN specific transcription factor, even-skipped (eve), which acts downstream of hkb. Genetic interaction between hkb and eve revealed that they act in the same pathway to regulate dorsal Is MN connectivity. Our study provides insight into the transcriptional regulation of DIP-α and suggests that distinct regulatory mechanisms exist for the same CSP in different neurons.
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Affiliation(s)
- Yupu Wang
- Department of Molecular Genetics and Cellular Biology, University of Chicago, Chicago, IL 60637
- Neuroscience Institute, University of Chicago, Chicago, IL 60637
- Current address: Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147
- Co-first author
| | - Rio Salazar
- Department of Molecular Genetics and Cellular Biology, University of Chicago, Chicago, IL 60637
- Neuroscience Institute, University of Chicago, Chicago, IL 60637
- Program in Cell and Molecular Biology, University of Chicago, Chicago, IL 60637
- Co-first author
| | - Luciano Simonetta
- Department of Molecular Genetics and Cellular Biology, University of Chicago, Chicago, IL 60637
- Neuroscience Institute, University of Chicago, Chicago, IL 60637
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL 60637
| | - Violet Sorrentino
- Department of Molecular Genetics and Cellular Biology, University of Chicago, Chicago, IL 60637
- Neuroscience Institute, University of Chicago, Chicago, IL 60637
- Current address: Molecular and Cell Biology Graduate Program, University of Washington, Seattle, Washington 98195
| | - Terrence J. Gatton
- Neuroscience Program, Skidmore College, 815 N. Broadway, Saratoga Springs, NY 12866
| | - Bill Wu
- Neuroscience Program, Skidmore College, 815 N. Broadway, Saratoga Springs, NY 12866
| | | | - Robert A. Carrillo
- Department of Molecular Genetics and Cellular Biology, University of Chicago, Chicago, IL 60637
- Neuroscience Institute, University of Chicago, Chicago, IL 60637
- Program in Cell and Molecular Biology, University of Chicago, Chicago, IL 60637
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL 60637
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9
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Sergeeva AP, Katsamba PS, Liao J, Sampson JM, Bahna F, Mannepalli S, Morano NC, Shapiro L, Friesner RA, Honig B. Free Energy Perturbation Calculations of Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity. J Mol Biol 2023:168187. [PMID: 37355034 DOI: 10.1016/j.jmb.2023.168187] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/26/2023]
Abstract
The strength of binding between human angiotensin converting enzyme 2 (ACE2) and the receptor binding domain (RBD) of viral spike protein plays a role in the transmissibility of the SARS-CoV-2 virus. In this study we focus on a subset of RBD mutations that have been frequently observed in infected individuals and probe binding affinity changes to ACE2 using surface plasmon resonance (SPR) measurements and free energy perturbation (FEP) calculations. Our SPR results are largely in accord with previous studies but discrepancies do arise due to differences in experimental methods and to protocol differences even when a single method is used. Overall, we find that FEP performance is superior to that of other computational approaches examined as determined by agreement with experiment and, in particular, by its ability to identify stabilizing mutations. Moreover, the calculations successfully predict the observed cooperative stabilization of binding by the Q498R N501Y double mutant present in Omicron variants and offer a physical explanation for the underlying mechanism. Overall, our results suggest that despite the significant computational cost, FEP calculations may offer an effective strategy to understand the effects of interfacial mutations on protein-protein binding affinities and, hence, in a variety of practical applications such as the optimization of neutralizing antibodies.
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Affiliation(s)
- Alina P Sergeeva
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032
| | - Phinikoula S Katsamba
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Junzhuo Liao
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Jared M Sampson
- Department of Chemistry, Columbia University, New York, NY 10027, USA; Schrödinger, Inc., New York, NY 10036, USA
| | - Fabiana Bahna
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Seetha Mannepalli
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Nicholas C Morano
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Lawrence Shapiro
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| | | | - Barry Honig
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032; Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Medicine, Columbia University, New York, NY 10032.
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