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Kaulich PT, Jeong K, Kohlbacher O, Tholey A. Influence of different sample preparation approaches on proteoform identification by top-down proteomics. Nat Methods 2024:10.1038/s41592-024-02481-6. [PMID: 39438734 DOI: 10.1038/s41592-024-02481-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 09/23/2024] [Indexed: 10/25/2024]
Abstract
Top-down proteomics using mass spectrometry facilitates the identification of intact proteoforms, that is, all molecular forms of proteins. Multiple past advances have lead to the development of numerous sample preparation workflows. Here we systematically investigated the influence of different sample preparation steps on proteoform and protein identifications, including cell lysis, reduction and alkylation, proteoform enrichment, purification and fractionation. We found that all steps in sample preparation influence the subset of proteoforms identified (for example, their number, confidence, physicochemical properties and artificially generated modifications). The various sample preparation strategies resulted in complementary identifications, substantially increasing the proteome coverage. Overall, we identified 13,975 proteoforms from 2,720 proteins of human Caco-2 cells. The results presented can serve as suggestions for designing and adapting top-down proteomics sample preparation strategies to particular research questions. Moreover, we expect that the sampling bias and modifications identified at the intact protein level will also be useful in improving bottom-up proteomics approaches.
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Affiliation(s)
- Philipp T Kaulich
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Kyowon Jeong
- Applied Bioinformatics, Computer Science Department, University of Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Computer Science Department, University of Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | - Andreas Tholey
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
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52
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Leddy O, Cui Y, Ahn R, Stopfer L, Choe E, Kim DH, Roerden M, Spranger S, Bryson BD, White FM. Validation and quantification of peptide antigens presented on MHCs using SureQuant. Nat Protoc 2024:10.1038/s41596-024-01076-x. [PMID: 39438697 DOI: 10.1038/s41596-024-01076-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 09/19/2024] [Indexed: 10/25/2024]
Abstract
Vaccines and immunotherapies that target peptide-major histocompatibility complexes (peptide-MHCs) have the potential to address multiple unmet medical needs in cancer and infectious disease. Designing vaccines and immunotherapies to target peptide-MHCs requires accurate identification of target peptides in infected or cancerous cells or tissue, and may require absolute or relative quantification to identify abundant targets and measure changes in presentation under different treatment conditions. Internal standard parallel reaction monitoring (also known as 'SureQuant') can be used to validate and/or quantify MHC peptides previously identified by using untargeted methods such as data-dependent acquisition. SureQuant MHC has three main use cases: (i) conclusive confirmation of the identities of putative MHC peptides via comparison with an internal synthetic stable isotope labeled (SIL) peptide standard; (ii) accurate relative quantification by using pre-formed heavy isotope-labeled peptide-MHC complexes (hipMHCs) containing SIL peptides as internal controls for technical variation; and (iii) absolute quantification of each target peptide by using different amounts of hipMHCs loaded with synthetic peptides containing one, two or three SIL amino acids to provide an internal standard curve. Absolute quantification can help determine whether the abundance of a peptide-MHC is sufficient for certain therapeutic modalities. SureQuant MHC therefore provides unique advantages for immunologists seeking to confidently validate antigenic targets and understand the dynamics of the MHC repertoire. After synthetic standards are ordered (3-4 weeks), this protocol can be carried out in 3-4 days and is suitable for individuals with mass spectrometry experience who are comfortable with customizing instrument methods.
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Affiliation(s)
- Owen Leddy
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Medicine, Cambridge, MA, USA
| | - Yufei Cui
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Medicine, Cambridge, MA, USA
| | - Ryuhjin Ahn
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Medicine, Cambridge, MA, USA
| | - Lauren Stopfer
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Medicine, Cambridge, MA, USA
- Aethon Therapeutics, New York, NY, USA
| | - Elizabeth Choe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Medicine, Cambridge, MA, USA
| | - Do Hun Kim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Medicine, Cambridge, MA, USA
| | - Malte Roerden
- Koch Institute for Integrative Cancer Medicine, Cambridge, MA, USA
| | - Stefani Spranger
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Medicine, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bryan D Bryson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA, USA
| | - Forest M White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Medicine, Cambridge, MA, USA.
- Center for Precision Cancer Medicine, Cambridge, MA, USA.
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53
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Fu S, Chen Z, Luo Z, Nie M, Fu T, Zhou Y, Yang Q, Zhu F, Ni F. Chem(Pro)2: the atlas of chemoproteomic probes labelling human proteins. Nucleic Acids Res 2024:gkae943. [PMID: 39436046 DOI: 10.1093/nar/gkae943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Revised: 09/25/2024] [Accepted: 10/11/2024] [Indexed: 10/23/2024] Open
Abstract
Chemoproteomic probes (CPPs) have been widely considered as powerful molecular biological tools that enable the highly efficient discovery of both binding proteins and modes of action for the studied compounds. They have been successfully used to validate targets and identify binders. The design of CPP has been considered extremely challenging, which asks for the generalization using a large number of probe data. However, none of the existing databases gives such valuable data of CPPs. Herein, a database entitled 'Chem(Pro)2' was therefore developed to systematically describe the atlas of diverse types of CPPs labelling human protein in living cell/lysate. With the booming application of chemoproteomic technique and artificial intelligence in current chemical biology study, Chem(Pro)2 was expected to facilitate the AI-based learning of interacting pattern among molecules for discovering innovative targets and new drugs. Till now, Chem(Pro)2 has been open to all users without any login requirement at: https://idrblab.org/chemprosquare/.
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Affiliation(s)
- Songsen Fu
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
- LeadArt Biotechnologies Ltd., Ningbo 315201, China
| | - Zhen Chen
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, State Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Zhiming Luo
- LeadArt Biotechnologies Ltd., Ningbo 315201, China
| | - Meiyun Nie
- LeadArt Biotechnologies Ltd., Ningbo 315201, China
| | - Tingting Fu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, State Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Ying Zhou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, State Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Qingxia Yang
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, State Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Feng Ni
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
- LeadArt Biotechnologies Ltd., Ningbo 315201, China
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54
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Griesel L, Kaleja P, Tholey A, Lettau M, Janssen O. Comparative Analysis of Extracellular Vesicles from Cytotoxic CD8 + αβ T Cells and γδ T Cells. Cells 2024; 13:1745. [PMID: 39451262 PMCID: PMC11506423 DOI: 10.3390/cells13201745] [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: 09/16/2024] [Revised: 10/16/2024] [Accepted: 10/18/2024] [Indexed: 10/26/2024] Open
Abstract
BACKGROUND Although belonging to different branches of the immune system, cytotoxic CD8+ αβ T cells and γδ T cells utilize common cytolytic effectors including FasL, granzymes, perforin and granulysin. The effector proteins are stored in different subsets of lysosome-related effector vesicles (LREVs) and released to the immunological synapse upon target cell encounter. Notably, in activated cells, LREVs and potentially other vesicles are continuously produced and released as extracellular vesicles (EVs). Presumably, EVs serve as mediators of intercellular communication in the local microenvironment or at distant sites. METHODS EVs of activated and expanded cytotoxic CD8+ αβ T cells or γδ T cells were enriched from culture supernatants by differential and ultracentrifugation and characterized by nanoparticle tracking analyses and Western blotting. For a comparative proteomic profiling, EV preparations from both cell types were isobaric labeled with tandem mass tags (TMT10plex) and subjected to mass spectrometry analysis. RESULTS 686 proteins were quantified in EV preparations of cytotoxic CD8+ αβ T cells and γδ T cells. Both populations shared a major set of similarly abundant proteins, while much fewer proteins presented higher abundance levels in either CD8+ αβ T cells or γδ T cells. To our knowledge, we provide the first comparative analysis of EVs from cytotoxic CD8+ αβ T cells and γδ T cells.
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MESH Headings
- Extracellular Vesicles/metabolism
- Extracellular Vesicles/immunology
- Humans
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
- Receptors, Antigen, T-Cell, gamma-delta/immunology
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
- Proteomics/methods
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Affiliation(s)
- Lisa Griesel
- Molecular Immunology—Institute for Immunology, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Patrick Kaleja
- Systematic Proteomics & Bioanalytics—Institute for Experimental Medicine, University of Kiel, 24105 Kiel, Germany; (P.K.); (A.T.)
| | - Andreas Tholey
- Systematic Proteomics & Bioanalytics—Institute for Experimental Medicine, University of Kiel, 24105 Kiel, Germany; (P.K.); (A.T.)
| | - Marcus Lettau
- Stem Cell Transplantation and Immunotherapy—Internal Medicine II, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Ottmar Janssen
- Molecular Immunology—Institute for Immunology, University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
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55
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Narang K, Nath A, Hemstrom W, Chu SKS. HaloClass: Salt-Tolerant Protein Classification with Protein Language Models. Protein J 2024:10.1007/s10930-024-10236-7. [PMID: 39432175 DOI: 10.1007/s10930-024-10236-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2024] [Indexed: 10/22/2024]
Abstract
Salt-tolerant proteins, also known as halophilic proteins, have unique adaptations to function in high-salinity environments. These proteins have naturally evolved in extremophilic organisms, and more recently, are being increasingly applied as enzymes in industrial processes. Due to an abundance of salt-tolerant sequences and a simultaneous lack of experimental structures, most computational methods to predict stability are sequence-based only. These approaches, however, are hindered by a lack of structural understanding of these proteins. Here, we present HaloClass, an SVM classifier that leverages ESM-2 protein language model embeddings to accurately identify salt-tolerant proteins. On a newer and larger test dataset, HaloClass outperforms existing approaches when predicting the stability of never-before-seen proteins that are distal to its training set. Finally, on a mutation study that evaluated changes in salt tolerance based on single- and multiple-point mutants, HaloClass outperforms existing approaches, suggesting applications in the guided design of salt-tolerant enzymes.
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Affiliation(s)
- Kush Narang
- College of Biological Sciences, University of California, Davis, USA.
| | - Abhigyan Nath
- Department of Biochemistry, Pt. Jawahar Lal Nehru Memorial Medical College, Raipur, India
| | - William Hemstrom
- Department of Biological Sciences, Purdue University, West Lafayette, USA
| | - Simon K S Chu
- Biophysics Graduate Program, University of California, Davis, USA
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56
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Gheeraert A, Bailly T, Ren Y, Hamraoui A, Te J, Vander Meersche Y, Cretin G, Leon Foun Lin R, Gelly JC, Pérez S, Guyon F, Galochkina T. DIONYSUS: a database of protein-carbohydrate interfaces. Nucleic Acids Res 2024:gkae890. [PMID: 39436020 DOI: 10.1093/nar/gkae890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 09/03/2024] [Accepted: 09/26/2024] [Indexed: 10/23/2024] Open
Abstract
Protein-carbohydrate interactions govern a wide variety of biological processes and play an essential role in the development of different diseases. Here, we present DIONYSUS, the first database of protein-carbohydrate interfaces annotated according to structural, chemical and functional properties of both proteins and carbohydrates. We provide exhaustive information on the nature of interactions, binding site composition, biological function and specific additional information retrieved from existing databases. The user can easily search the database using protein sequence and structure information or by carbohydrate binding site properties. Moreover, for a given interaction site, the user can perform its comparison with a representative subset of non-covalent protein-carbohydrate interactions to retrieve information on its potential function or specificity. Therefore, DIONYSUS is a source of valuable information both for a deeper understanding of general protein-carbohydrate interaction patterns, for annotation of the previously unannotated proteins and for such applications as carbohydrate-based drug design. DIONYSUS is freely available at www.dsimb.inserm.fr/DIONYSUS/.
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Affiliation(s)
- Aria Gheeraert
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, DSIMB, F-75015 Paris, France
| | - Thomas Bailly
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, DSIMB, F-75015 Paris, France
| | - Yani Ren
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, DSIMB, F-75015 Paris, France
- Université Paris-Saclay, INRAE, MetaGenoPolis, 78350 Jouy-en-Josas, France
| | - Ali Hamraoui
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, DSIMB, F-75015 Paris, France
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Universite Paris, 75005 Paris, France
| | - Julie Te
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, DSIMB, F-75015 Paris, France
| | - Yann Vander Meersche
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, DSIMB, F-75015 Paris, France
| | - Gabriel Cretin
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, DSIMB, F-75015 Paris, France
| | - Ravy Leon Foun Lin
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, DSIMB, F-75015 Paris, France
| | - Jean-Christophe Gelly
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, DSIMB, F-75015 Paris, France
| | - Serge Pérez
- Centre de Recherches sur les Macromolécules Végétales, University Grenoble Alpes, CNRS, UPR, 5301 Grenoble, France
| | - Frédéric Guyon
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, DSIMB, F-75015 Paris, France
| | - Tatiana Galochkina
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, DSIMB, F-75015 Paris, France
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Pant J, Singh L, Mittal P, Kumar N. Valencene as a novel potential downregulator of THRB in NSCLC: network pharmacology, molecular docking, molecular dynamics simulation, ADMET analysis, and in vitro analysis. Mol Divers 2024:10.1007/s11030-024-11008-2. [PMID: 39425858 DOI: 10.1007/s11030-024-11008-2] [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: 08/23/2024] [Accepted: 09/30/2024] [Indexed: 10/21/2024]
Abstract
This study investigates the molecular targets and pathways affected by valencene in non-small cell lung cancer (NSCLC) through network pharmacology and in vitro assays. Valencene's chemical structure was sourced from PubChem, and target identification utilized the PharmMapper database, cross-referenced with UniProtKB for official gene symbols. NSCLC-associated targets were identified via GeneCards, followed by protein-protein interaction analysis using STRING. Molecular docking studies employed AutoDock Vina to assess binding interactions with key nuclear receptors (RXRA, RXRB, RARA, RARB, THRB). Molecular dynamics simulations were conducted in GROMACS over 200 ns, while ADME/T properties were evaluated using Protox. In vitro assays measured cell viability in A549 and HEL 299 cells via MTT assays, assessed apoptosis through Hoechst staining, and evaluated mitochondrial potential with JC-1. Molecular docking revealed strong binding affinities of valencene (below - 5 kcal/mol) to nuclear receptors, outperforming 5-fluorouracil (5-FU). Molecular dynamics simulations indicated robust structural stability of the THRB-valencene complex, with favorable interaction energies. Notably, valencene exhibited a selectivity index of 2.293, higher than 5-FU's 2.231, suggesting enhanced safety for normal cells (HEL 299). Fluorescence microscopy confirmed dose-dependent DNA fragmentation and decreased mitochondrial membrane potential. These findings underscore valencene's potential as an effective therapeutic agent for lung cancer, demonstrating an IC50 of 16.71 μg/ml in A549 cells compared to 5-FU's 12.7 μg/ml, warranting further investigation in preclinical models and eventual clinical trials.
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Affiliation(s)
- Janmejay Pant
- University Institute of Pharma Sciences, Chandigarh University, Mohali, Punjab, India
| | - Lovedeep Singh
- University Institute of Pharma Sciences, Chandigarh University, Mohali, Punjab, India.
| | - Payal Mittal
- University Institute of Pharma Sciences, Chandigarh University, Mohali, Punjab, India
| | - Nitish Kumar
- Sri Sai College of Pharmacy, Pathankot, Punjab, 145001, India.
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58
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Zhou K, Xie M, Liu Y, Zheng L, Pu J, Wang C. Virtual screening and network pharmacology-based synergistic coagulation mechanism identification of multiple components contained in compound Kushen Injection against hepatocellular carcinoma. J Ayurveda Integr Med 2024; 15:101055. [PMID: 39427483 DOI: 10.1016/j.jaim.2024.101055] [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: 03/25/2024] [Revised: 07/14/2024] [Accepted: 08/20/2024] [Indexed: 10/22/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a primary liver malignancy commonly encountered in the setting of chronic liver disease and cirrhosis. Compound Kushen Injection (CKI) has been widely used in HCC, however, the underlying mechanisms are scarce. OBJECTIVE To explore the molecular mechanisms of CKI for HCC.To explore the molecular mechanisms of CKI for HCC. MATERIALS AND METHODS The chemical ingredients of CKI were reviewed from published articles and the potential targets were got from Herbal Ingredients' Targets Platform. Coagulation-related targets were from Kyoto Encyclopedia of Genes and Genomes and HCC-related targets were from Therapeutic Target Database, Gene Expression Omnibus, and The Cancer Genome Atlas. Then the CKI-Herb-Target and CKI-Herb-Target-HCC networks were built. The shared targets between CKI and HCC were used for functional enrichment through Metascape and the shared coagulation-related target was used for molecular docking and survival analysis. RESULTS A total of 23 chemical ingredients and 41 potential targets shared between CKI and HCC were obtained. The results of functional enrichment indicated that several canonical pathways of CKI mostly participated in the treatment of HCC. Furthermore, a chemical ingredient of CKI formed a stable hydrogen bond link with the ASN-189 on PLG, with a best binding energy of -4.7 kcal/mol. Finally, PLG was confirmed as the shared coagulation-related target and interrelated with the prognosis of HCC. CONCLUSION CKI probably improves HCC prognosis through PLG. Our research undoubtedly deepened the understanding of the molecular mechanism of CKI anti-HCC.
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Affiliation(s)
- Kejun Zhou
- Department of Pediatric Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Mengyi Xie
- Hepatobiliary Research Institute, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Yu Liu
- Department of Pediatric Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Lei Zheng
- Department of Pediatric Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Juan Pu
- Department of Pediatric Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Cheng Wang
- Department of Pediatric Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.
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59
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Toporowska J, Kapoor P, Musgaard M, Gherbi K, Sengmany K, Qu F, Soave M, Yen HY, Hansen K, Jazayeri A, Hopper JTS, Politis A. Ligand-induced conformational changes in the β1-adrenergic receptor revealed by hydrogen-deuterium exchange mass spectrometry. Nat Commun 2024; 15:8993. [PMID: 39424782 PMCID: PMC11489754 DOI: 10.1038/s41467-024-53161-0] [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: 03/29/2024] [Accepted: 10/02/2024] [Indexed: 10/21/2024] Open
Abstract
G Protein Coupled Receptors (GPCRs) constitute the largest family of signalling proteins responsible for translating extracellular stimuli into intracellular functions. They play crucial roles in numerous physiological processes and are major targets for drug discovery. Dysregulation of GPCRs is implicated in various diseases, making understanding their structural dynamics critical for therapeutic development. Here, we use Hydrogen Deuterium Exchange Mass Spectrometry (HDX-MS) to explore the structural dynamics of the turkey β1-adrenergic receptor (tβ1AR) bound with nine different ligands, including agonists, partial agonists, and antagonists. We find that these ligands induce distinct dynamic patterns across the receptor, which can be grouped by compound modality. Notably, full agonist binding destabilises the intracellular loop 1 (ICL1), while antagonist binding stabilises it, highlighting ICL1's role in G protein recruitment. Our findings indicate that the conserved L72 residue in ICL1 is crucial for maintaining receptor structural integrity and stabilising the GDP-bound state. Overall, our results provide a platform for determining drug modality and highlight how HDX-MS can be used to dissect receptor ligand interaction properties and GPCR mechanism.
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Affiliation(s)
| | | | | | | | | | - Feng Qu
- OMass Therapeutics, Oxford, UK
| | | | | | | | | | | | - Argyris Politis
- King's College London, London, UK.
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, UK.
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK.
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60
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Demeester W, De Paepe B, De Mey M. Fundamentals and Exceptions of the LysR-type Transcriptional Regulators. ACS Synth Biol 2024; 13:3069-3092. [PMID: 39306765 PMCID: PMC11495319 DOI: 10.1021/acssynbio.4c00219] [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: 04/02/2024] [Revised: 07/17/2024] [Accepted: 08/13/2024] [Indexed: 10/19/2024]
Abstract
LysR-type transcriptional regulators (LTTRs) are emerging as a promising group of macromolecules for the field of biosensors. As the largest family of bacterial transcription factors, the LTTRs represent a vast and mostly untapped repertoire of sensor proteins. To fully harness these regulators for transcription factor-based biosensor development, it is crucial to understand their underlying mechanisms and functionalities. In the first part, this Review discusses the established model and features of LTTRs. As dual-function regulators, these inducible transcription factors exude precise control over their regulatory targets. In the second part of this Review, an overview is given of the exceptions to the "classic" LTTR model. While a general regulatory mechanism has helped elucidate the intricate regulation performed by LTTRs, it is essential to recognize the variations within the family. By combining this knowledge, characterization of new regulators can be done more efficiently and accurately, accelerating the expansion of transcriptional sensors for biosensor development. Unlocking the pool of LTTRs would significantly expand the currently limited range of detectable molecules and regulatory functions available for the implementation of novel synthetic genetic circuitry.
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Affiliation(s)
- Wouter Demeester
- Department of Biotechnology,
Center for Synthetic Biology, Ghent University, Ghent 9000, Belgium
| | - Brecht De Paepe
- Department of Biotechnology,
Center for Synthetic Biology, Ghent University, Ghent 9000, Belgium
| | - Marjan De Mey
- Department of Biotechnology,
Center for Synthetic Biology, Ghent University, Ghent 9000, Belgium
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61
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Reeves AE, Vilen Z, Fuentecilla TR, Parker CG, Huang ML. Charting the Dynamic Trophoblast Plasma Membrane Identifies LYN As a Functional Regulator of Syncytialization. ACS Chem Biol 2024; 19:2220-2231. [PMID: 39289808 DOI: 10.1021/acschembio.4c00443] [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: 09/19/2024]
Abstract
The differentiation of placental cytotrophoblasts (CTBs) into the syncytiotrophoblast (STB) layer results in a significant remodeling of the plasma membrane proteome. Here, we use a peroxidase-catalyzed proximity labeling strategy to map the dynamic plasma membrane proteomes of CTBs and STBs. Coupled with mass-spectrometry-based proteomics, we identify hundreds of plasma membrane proteins and observe relative changes in protein abundance throughout differentiation, including the upregulation of the plasma-membrane-localized nonreceptor tyrosine kinase LYN. We show that both siRNA-mediated knockdown and small molecule inhibition of LYN kinase function impairs CTB fusion and reduces the expression of syncytialization markers, presenting a function for LYN outside of its canonical role in immunological signaling. Our results demonstrate the use of the proximity labeling platform to discover functional regulators within the plasma membrane and provide new avenues to regulate trophoblast differentiation.
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Affiliation(s)
- Abigail E Reeves
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - Zak Vilen
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - Trinity R Fuentecilla
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - Christopher G Parker
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - Mia L Huang
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States
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Skrypnyk C, AlHarmi R, Mathur A, AlHafnawi HH, Chandan Appikonda SH, Matsa LS. Expanding families: a pilot study on preconception expanded carrier screening in Bahrain. BMC Pregnancy Childbirth 2024; 24:684. [PMID: 39425040 PMCID: PMC11490169 DOI: 10.1186/s12884-024-06878-1] [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: 07/18/2024] [Accepted: 10/03/2024] [Indexed: 10/21/2024] Open
Abstract
BACKGROUND Preconception expanded carrier screening (ECS) is a genetic test that enables the identification of at-risk carriers of recessive disorders by screening for up to hundreds of genes. Next-generation sequencing (NGS) development has paved the way for its integration into ECS. This study aims to identify the carrier genetic status of couples experiencing or anticipating conception challenges through NGS-based ECS and to gain an overview of the rare genetic disorders in a population with increased consanguinity. METHODS Thirty couples who presented to the Genetic Disease Clinic between 2015 and 2024 with failed reproductive outcomes or with a positive personal or family history of genetic disorders and underwent ECS were included and retrospectively analyzed. RESULTS Fifty-four individuals (90.00%) were found to carry at least one variant of 95 identified genes, totaling 174 variants. Six individuals (10.00%) tested negative for any variant. Seven individuals had one variant (11.67%), 13 had two variants (21.67%), and 34 had 3 or more variants (56.67%). The most common variants identified were of HBA, HBB, CYP21A2, and G6PD genes. Most of the detected variants were unknown or unexpected (n = 143, 82.18%). Eight couples carried two or more variants in common. Consanguinity was reported in 14 couples (46.67%). CONCLUSIONS Preconception ECS is crucial for reproductive planning, permitting couples to evaluate their combined genetic risks and make informed decisions, reducing the chance of having children with genetic disorders.
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Affiliation(s)
- Cristina Skrypnyk
- Department of Molecular Medicine, AlJawhara Center, College of Medicine and Health Sciences, Arabian Gulf University, Manama, Bahrain.
- Genetic Disease Clinic, University Medical Center, King Abdullah Medical City, Manama, Bahrain.
| | - Rawan AlHarmi
- Regenerative Medicine Unit, AlJawhara Center, Arabian Gulf University, Manama, Bahrain
| | - Aanchal Mathur
- Regenerative Medicine Unit, AlJawhara Center, Arabian Gulf University, Manama, Bahrain
| | - Hussein Hifnawi AlHafnawi
- Clinical Research Center, College of Medicine and Health Sciences, Arabian Gulf University, Manama, Bahrain
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Hayden AN, Brandel KL, Pietryk EW, Merlau PR, Vijayakumar P, Leptich EJ, Gaytan ES, Williams MI, Ni CW, Chao HT, Rosenfeld JA, Arey RN. Behavioral screening reveals a conserved residue in Y-Box RNA-binding protein required for associative learning and memory in C. elegans. PLoS Genet 2024; 20:e1011443. [PMID: 39423228 DOI: 10.1371/journal.pgen.1011443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 09/30/2024] [Indexed: 10/21/2024] Open
Abstract
RNA-binding proteins (RBPs) regulate translation and plasticity which are required for memory. RBP dysfunction has been linked to a range of neurological disorders where cognitive impairments are a key symptom. However, of the 2,000 RBPs in the human genome, many are uncharacterized with regards to neurological phenotypes. To address this, we used the model organism C. elegans to assess the role of 20 conserved RBPs in memory. We identified eight previously uncharacterized memory regulators, three of which are in the C. elegans Y-Box (CEY) RBP family. Of these, we determined that cey-1 is the closest ortholog to the mammalian Y-Box (YBX) RBPs. We found that CEY-1 is both necessary in the nervous system for memory ability and sufficient to promote memory. Leveraging human datasets, we found both copy number variation losses and single nucleotide variants in YBX1 and YBX3 in individuals with neurological symptoms. We identified one predicted deleterious YBX3 variant of unknown significance, p.Asn127Tyr, in two individuals with neurological symptoms. Introducing this variant into endogenous cey-1 locus caused memory deficits in the worm. We further generated two humanized worm lines expressing human YBX3 or YBX1 at the cey-1 locus to test evolutionary conservation of YBXs in memory and the potential functional significance of the p.Asn127Tyr variant. Both YBX1/3 can functionally replace cey-1, and introduction of p.Asn127Tyr into the humanized YBX3 locus caused memory deficits. Our study highlights the worm as a model to reveal memory regulators and identifies YBX dysfunction as a potential new source of rare neurological disease.
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Affiliation(s)
- Ashley N Hayden
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, United States of America
| | - Katie L Brandel
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, United States of America
| | - Edward W Pietryk
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Paul R Merlau
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, United States of America
| | - Priyadharshini Vijayakumar
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, United States of America
| | - Emily J Leptich
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, United States of America
| | - Elizabeth S Gaytan
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, United States of America
- Postbaccalaureate Research Education Program, Baylor College of Medicine, Houston, Texas, United States of America
| | - Meredith I Williams
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, United States of America
| | - Connie W Ni
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Neuroscience, Rice University, Houston, Texas, United States of America
| | - Hsiao-Tuan Chao
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
- Cain Pediatric Neurology Research Foundation Laboratories, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, United States of America
- McNair Medical Institute, The Robert and Janice McNair Foundation, Houston, Texas, United States of America
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Baylor Genetics Laboratories, Houston, Texas, United States of America
| | - Rachel N Arey
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
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Elizalde-Bielsa A, Lázaro-Antón L, de Miguel MJ, Muñoz PM, Conde-Álvarez R, Zúñiga-Ripa A. Disruption of Erythritol Catabolism via the Deletion of Fructose-Bisphosphate Aldolase (Fba) and Transaldolase (Tal) as a Strategy to Improve the Brucella Rev1 Vaccine. Int J Mol Sci 2024; 25:11230. [PMID: 39457012 DOI: 10.3390/ijms252011230] [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: 08/30/2024] [Revised: 09/27/2024] [Accepted: 10/01/2024] [Indexed: 10/28/2024] Open
Abstract
Brucellosis is a bacterial zoonosis caused by the genus Brucella, which mainly affects domestic animals. In these natural hosts, brucellae display a tropism towards the reproductive organs, such as the placenta, replicating in high numbers and leading to placentitis and abortion, an ability also exerted by the B. melitensis live-attenuated Rev1 strain, the only vaccine available for ovine brucellosis. It is broadly accepted that this tropism is mediated, at least in part, by the presence of certain preferred nutrients in the placenta, particularly erythritol, a polyol that is ultimately incorporated into the Brucella central carbon metabolism via two reactions dependent on transaldolase (Tal) or fructose-bisphosphate aldolase (Fba). In the light of these remarks, we propose that blocking the incorporation of erythritol into the central carbon metabolism of Rev1 by deleting the genes encoding Tal and Fba may impair the ability of the vaccine to proliferate massively in the placenta. Therefore, a Rev1ΔfbaΔtal double mutant was generated and confirmed to be unable to use erythritol. This mutant exhibited a reduced intracellular fitness both in BeWo trophoblasts and THP-1 macrophages. In the murine model, Rev1ΔfbaΔtal provided comparable protection to the Rev1 reference vaccine while inducing fewer adverse reproductive events in pregnant animals. Altogether, these results postulate the Rev1ΔfbaΔtal mutant as a reproductively safer Rev1-derived vaccine candidate to be studied in the natural host.
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Affiliation(s)
- Aitor Elizalde-Bielsa
- Department of Microbiology and Parasitology, Instituto de Investigación Sanitaria de Navarra (IdiSNA), University of Navarra, 31008 Pamplona, Spain
| | - Leticia Lázaro-Antón
- Department of Microbiology and Parasitology, Instituto de Investigación Sanitaria de Navarra (IdiSNA), University of Navarra, 31008 Pamplona, Spain
- Department of Medical Microbiology and Immunology, University of California, Davis, CA 95616, USA
| | - María Jesús de Miguel
- Department of Animal Science, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), 50059 Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2, CITA-Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Pilar M Muñoz
- Department of Animal Science, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), 50059 Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2, CITA-Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Raquel Conde-Álvarez
- Department of Microbiology and Parasitology, Instituto de Investigación Sanitaria de Navarra (IdiSNA), University of Navarra, 31008 Pamplona, Spain
| | - Amaia Zúñiga-Ripa
- Department of Microbiology and Parasitology, Instituto de Investigación Sanitaria de Navarra (IdiSNA), University of Navarra, 31008 Pamplona, Spain
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Podlesainski D, Adeniyi ET, Gröner Y, Schulz F, Krisilia V, Rehberg N, Richter T, Sehr D, Xie H, Simons VE, Kiffe-Delf AL, Kaschani F, Ioerger TR, Kaiser M, Kalscheuer R. The anti-tubercular callyaerins target the Mycobacterium tuberculosis-specific non-essential membrane protein Rv2113. Cell Chem Biol 2024; 31:1755-1771.e73. [PMID: 38981479 DOI: 10.1016/j.chembiol.2024.06.002] [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: 09/01/2023] [Revised: 04/19/2024] [Accepted: 06/11/2024] [Indexed: 07/11/2024]
Abstract
Spread of antimicrobial resistances urges a need for new drugs against Mycobacterium tuberculosis (Mtb) with mechanisms differing from current antibiotics. Previously, callyaerins were identified as promising anti-tubercular agents, representing a class of hydrophobic cyclopeptides with an unusual (Z)-2,3-di-aminoacrylamide unit. Here, we investigated the molecular mechanisms underlying their antimycobacterial properties. Structure-activity relationship studies enabled the identification of structural determinants relevant for antibacterial activity. Callyaerins are bacteriostatics selectively active against Mtb, including extensively drug-resistant strains, with minimal cytotoxicity against human cells and promising intracellular activity. By combining mutant screens and various chemical proteomics approaches, we showed that callyaerins target the non-essential, Mtb-specific membrane protein Rv2113, triggering a complex dysregulation of the proteome, characterized by global downregulation of lipid biosynthesis, cell division, DNA repair, and replication. Our study thus identifies Rv2113 as a previously undescribed Mtb-specific drug target and demonstrates that also non-essential proteins may represent efficacious targets for antimycobacterial drugs.
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Affiliation(s)
- David Podlesainski
- Center of Medical Biotechnology (ZMB), Faculty of Biology, Chemical Biology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Emmanuel T Adeniyi
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, 40225 Düsseldorf, Germany
| | - Yvonne Gröner
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, 40225 Düsseldorf, Germany
| | - Florian Schulz
- Center of Medical Biotechnology (ZMB), Faculty of Biology, Chemical Biology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Violetta Krisilia
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, 40225 Düsseldorf, Germany
| | - Nidja Rehberg
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, 40225 Düsseldorf, Germany
| | - Tim Richter
- Center of Medical Biotechnology (ZMB), Faculty of Biology, Chemical Biology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Daria Sehr
- Center of Medical Biotechnology (ZMB), Faculty of Biology, Chemical Biology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Huzhuyue Xie
- Center of Medical Biotechnology (ZMB), Faculty of Biology, Chemical Biology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Viktor E Simons
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, 40225 Düsseldorf, Germany
| | - Anna-Lene Kiffe-Delf
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, 40225 Düsseldorf, Germany
| | - Farnusch Kaschani
- Center of Medical Biotechnology (ZMB), Faculty of Biology, Chemical Biology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Thomas R Ioerger
- Department of Computer Science, Texas A&M University, College Station, TX 77843, USA
| | - Markus Kaiser
- Center of Medical Biotechnology (ZMB), Faculty of Biology, Chemical Biology, University of Duisburg-Essen, 45141 Essen, Germany.
| | - Rainer Kalscheuer
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, 40225 Düsseldorf, Germany.
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Sastre DE, Bournazos S, Du J, Boder EJ, Edgar JE, Azzam T, Sultana N, Huliciak M, Flowers M, Yoza L, Xu T, Chernova TA, Ravetch JV, Sundberg EJ. Potent efficacy of an IgG-specific endoglycosidase against IgG-mediated pathologies. Cell 2024:S0092-8674(24)01135-8. [PMID: 39437779 DOI: 10.1016/j.cell.2024.09.038] [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: 04/09/2024] [Revised: 08/09/2024] [Accepted: 09/24/2024] [Indexed: 10/25/2024]
Abstract
Endo-β-N-acetylglucosaminidases (ENGases) that specifically hydrolyze the Asn297-linked glycan on immunoglobulin G (IgG) antibodies, the major molecular determinant of fragment crystallizable (Fc) γ receptor (FcγR) binding, are exceedingly rare. All previously characterized IgG-specific ENGases are multi-domain proteins secreted as an immune evasion strategy by Streptococcus pyogenes strains. Here, using in silico analysis and mass spectrometry techniques, we identified a family of single-domain ENGases secreted by pathogenic corynebacterial species that exhibit strict specificity for IgG antibodies. By X-ray crystallographic and surface plasmon resonance analyses, we found that the most catalytically efficient IgG-specific ENGase family member recognizes both protein and glycan components of IgG. Employing in vivo models, we demonstrated the remarkable efficacy of this IgG-specific ENGase in mitigating numerous pathologies that rely on FcγR-mediated effector functions, including T and B lymphocyte depletion, autoimmune hemolytic anemia, and antibody-dependent enhancement of dengue disease, revealing its potential for treating and/or preventing a wide range of IgG-mediated diseases in humans.
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Affiliation(s)
- Diego E Sastre
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - Stylianos Bournazos
- Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Jonathan Du
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - E Josephine Boder
- Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Julia E Edgar
- Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Tala Azzam
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nazneen Sultana
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Maros Huliciak
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Maria Flowers
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Lea Yoza
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ting Xu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Tatiana A Chernova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jeffrey V Ravetch
- Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Eric J Sundberg
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.
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Pipatpadungsin N, Chao K, Rouse SL. Coarse-Grained Simulations of Adeno-Associated Virus and Its Receptor Reveal Influences on Membrane Lipid Organization and Curvature. J Phys Chem B 2024; 128:10139-10153. [PMID: 39356546 PMCID: PMC11492248 DOI: 10.1021/acs.jpcb.4c03087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 08/21/2024] [Accepted: 09/17/2024] [Indexed: 10/03/2024]
Abstract
Adeno-associated virus (AAV) is a well-known gene delivery tool with a wide range of applications, including as a vector for gene therapies. However, the molecular mechanism of its cell entry remains unknown. Here, we performed coarse-grained molecular dynamics simulations of the AAV serotype 2 (AAV2) capsid and the universal AAV receptor (AAVR) in a model plasma membrane environment. Our simulations show that binding of the AAV2 capsid to the membrane induces membrane curvature, along with the recruitment and clustering of GM3 lipids around the AAV2 capsid. We also found that the AAVR binds to the AAV2 capsid at the VR-I loops using its PKD2 and PKD3 domains, whose binding poses differs from previous structural studies. These first molecular-level insights into AAV2 membrane interactions suggest a complex process during the initial phase of AAV2 capsid internalization.
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Affiliation(s)
- Nichakorn Pipatpadungsin
- Department
of Life Sciences, South Kensington Campus, Imperial College London, London SW7 5NH, U.K.
| | - Kin Chao
- Department
of Chemistry, Imperial College London, London W12 7TA, U.K.
| | - Sarah L. Rouse
- Department
of Life Sciences, South Kensington Campus, Imperial College London, London SW7 5NH, U.K.
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Tripp A, Braun M, Wieser F, Oberdorfer G, Lechner H. Click, Compute, Create: A Review of Web-based Tools for Enzyme Engineering. Chembiochem 2024; 25:e202400092. [PMID: 38634409 DOI: 10.1002/cbic.202400092] [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: 01/31/2024] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 04/19/2024]
Abstract
Enzyme engineering, though pivotal across various biotechnological domains, is often plagued by its time-consuming and labor-intensive nature. This review aims to offer an overview of supportive in silico methodologies for this demanding endeavor. Starting from methods to predict protein structures, to classification of their activity and even the discovery of new enzymes we continue with describing tools used to increase thermostability and production yields of selected targets. Subsequently, we discuss computational methods to modulate both, the activity as well as selectivity of enzymes. Last, we present recent approaches based on cutting-edge machine learning methods to redesign enzymes. With exception of the last chapter, there is a strong focus on methods easily accessible via web-interfaces or simple Python-scripts, therefore readily useable for a diverse and broad community.
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Affiliation(s)
- Adrian Tripp
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Markus Braun
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Florian Wieser
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Gustav Oberdorfer
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
- BioTechMed, Graz, Austria
| | - Horst Lechner
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
- BioTechMed, Graz, Austria
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69
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Li Y, Li F, Duan Z, Liu R, Jiao W, Wu H, Zhu F, Xue W. SYNBIP 2.0: epitopes mapping, sequence expansion and scaffolds discovery for synthetic binding protein innovation. Nucleic Acids Res 2024:gkae893. [PMID: 39413165 DOI: 10.1093/nar/gkae893] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Revised: 09/18/2024] [Accepted: 09/26/2024] [Indexed: 10/18/2024] Open
Abstract
Synthetic binding proteins (SBPs) represent a pivotal class of artificially engineered proteins, meticulously crafted to exhibit targeted binding properties and specific functions. Here, the SYNBIP database, a comprehensive resource for SBPs, has been significantly updated. These enhancements include (i) featuring 3D structures of 899 SBP-target complexes to illustrate the binding epitopes of SBPs, (ii) using the structures of SBPs in the monomer or complex forms with target proteins, their sequence space has been expanded five times to 12 025 by integrating a structure-based protein generation framework and a protein property prediction tool, (iii) offering detailed information on 78 473 newly identified SBP-like scaffolds from the RCSB Protein Data Bank, and an additional 16 401 555 ones from the AlphaFold Protein Structure Database, and (iv) the database is regularly updated, incorporating 153 new SBPs. Furthermore, the structural models of all SBPs have been enhanced through the application of the AlphaFold2, with their clinical statuses concurrently refreshed. Additionally, the design methods employed for each SBP are now prominently featured in the database. In sum, SYNBIP 2.0 is designed to provide researchers with essential SBP data, facilitating their innovation in research, diagnosis and therapy. SYNBIP 2.0 is now freely accessible at https://idrblab.org/synbip/.
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Affiliation(s)
- Yanlin Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, No. 55 South University Town Road, High-tech Zone, Chongqing 401331, China
| | - Fengcheng Li
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Hangzhou, Zhejiang 310052, China
- College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Zixin Duan
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, No. 55 South University Town Road, High-tech Zone, Chongqing 401331, China
| | - Ruihan Liu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, No. 55 South University Town Road, High-tech Zone, Chongqing 401331, China
| | - Wantong Jiao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, No. 55 South University Town Road, High-tech Zone, Chongqing 401331, China
| | - Haibo Wu
- School of Life Sciences, Chongqing University, No. 55 South University Town Road, High-tech Zone, Chongqing 401331, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Weiwei Xue
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, No. 55 South University Town Road, High-tech Zone, Chongqing 401331, China
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Km Rakhi, Bhati R, Jain M, Singh AK, Muthukumaran J. Unveiling MurM inhibitors in Enterococcus faecalis V583: a promising approach to tackle antibiotic resistance. J Biomol Struct Dyn 2024:1-17. [PMID: 39413038 DOI: 10.1080/07391102.2024.2415686] [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: 05/26/2023] [Accepted: 04/12/2024] [Indexed: 10/18/2024]
Abstract
Enterococcus faecalis is commonly found in the GI tract of humans and animals. It causes various infections, especially in hospital environments, and shows growing antibiotic resistance. This study utilized a subtractive proteomics approach to find out the potential drug targets in E. faecalis. Unique metabolic pathways were analysed and compared to the host to minimize adverse effects. Among twenty nine pathogenic specific and seventy three host-pathogen common pathways identified using the KEGG database, sixty seven essential proteins were found through the DEG BLAST search. PSORTB predicted that forty cytoplasmic proteins could be suitable as druggable targets. Further analysis identified fourteen proteins with virulence properties using the VFDB BLAST. Among these, seven proteins with more than ten antigenic sites were subjected to DrugBank BLAST, identifying three novel and four existing drug targets. One of the crucial drug targets, MurM, was selected due to its critical role in peptidoglycan biosynthesis. The reason for selecting MurM is crucial for addressing antibiotic resistance, disrupting bacterial cell wall synthesis, and attaining selective antimicrobial activity. MurM belongs to the mixed αβ class with two functional domains. The possible binding site residues of MurM are Trp31, Lys35, Trp38, Arg215, and Tyr219. Virtual screening identified potential lead candidates for MurM, and four were selected based on their physiochemical, pharmacokinetic, and structural properties. This study provides valuable insights into identifying and analysing a potential drug target, the MurM protein, and its inhibitors in E. faecalis V583.
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Affiliation(s)
- Km Rakhi
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Rittik Bhati
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Monika Jain
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Amit Kumar Singh
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Jayaraman Muthukumaran
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, India
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Maclean AE, Sloan MA, Renaud EA, Argyle BE, Lewis WH, Ovciarikova J, Demolombe V, Waller RF, Besteiro S, Sheiner L. The Toxoplasma gondii mitochondrial transporter ABCB7L is essential for the biogenesis of cytosolic and nuclear iron-sulfur cluster proteins and cytosolic translation. mBio 2024; 15:e0087224. [PMID: 39207139 PMCID: PMC11481526 DOI: 10.1128/mbio.00872-24] [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: 03/21/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024] Open
Abstract
Iron-sulfur (Fe-S) clusters are ubiquitous inorganic cofactors required for numerous essential cellular pathways. Since they cannot be scavenged from the environment, Fe-S clusters are synthesized de novo in cellular compartments such as the apicoplast, mitochondrion, and cytosol. The cytosolic Fe-S cluster biosynthesis pathway relies on the transport of an intermediate from the mitochondrial pathway. An ATP-binding cassette (ABC) transporter called ABCB7 is responsible for this role in numerous commonly studied organisms, but its role in the medically important apicomplexan parasites has not yet been studied. Here we identify and characterize a Toxoplasma gondii ABCB7 homolog, which we name ABCB7-like (ABCB7L). Genetic depletion shows that it is essential for parasite growth and that its disruption triggers partial stage conversion. Characterization of the knock-down line highlights a defect in the biogenesis of cytosolic and nuclear Fe-S proteins leading to defects in protein translation and other pathways including DNA and RNA replication and metabolism. Our work provides support for a broad conservation of the connection between mitochondrial and cytosolic pathways in Fe-S cluster biosynthesis and reveals its importance for parasite survival. IMPORTANCE Iron-sulfur (Fe-S) clusters are inorganic cofactors of proteins that play key roles in numerous essential biological processes, for example, respiration and DNA replication. Cells possess dedicated biosynthetic pathways to assemble Fe-S clusters, including a pathway in the mitochondrion and cytosol. A single transporter, called ABCB7, connects these two pathways, allowing an essential intermediate generated by the mitochondrial pathway to be used in the cytosolic pathway. Cytosolic and nuclear Fe-S proteins are dependent on the mitochondrial pathway, mediated by ABCB7, in numerous organisms studied to date. Here, we study the role of a homolog of ABCB7, which we name ABCB7-like (ABCB7L), in the ubiquitous unicellular apicomplexan parasite Toxoplasma gondii. We generated a depletion mutant of Toxoplasma ABCB7L and showed its importance for parasite fitness. Using comparative quantitative proteomic analysis and experimental validation of the mutants, we show that ABCB7L is required for cytosolic and nuclear, but not mitochondrial, Fe-S protein biogenesis. Our study supports the conservation of a protein homologous to ABCB7 and which has a similar function in apicomplexan parasites and provides insight into an understudied aspect of parasite metabolism.
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Affiliation(s)
- Andrew E. Maclean
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
- School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
| | - Megan A. Sloan
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
- School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
| | - Eléa A. Renaud
- LPHI, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Blythe E. Argyle
- School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
| | - William H. Lewis
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jana Ovciarikova
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
- School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
| | - Vincent Demolombe
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Ross F. Waller
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Lilach Sheiner
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
- School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
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72
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Bhowmick S, Viveros RP, Latoscha A, Commichau FM, Wrede C, Al-Bassam MM, Tschowri N. Cell shape and division septa positioning in filamentous Streptomyces require a functional cell wall glycopolymer ligase CglA. mBio 2024; 15:e0149224. [PMID: 39248520 PMCID: PMC11481543 DOI: 10.1128/mbio.01492-24] [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: 05/15/2024] [Accepted: 08/01/2024] [Indexed: 09/10/2024] Open
Abstract
The cell wall of monoderm bacteria consists of peptidoglycan and glycopolymers in roughly equal proportions and is crucial for cellular integrity, cell shape, and bacterial vitality. Despite the immense value of Streptomyces in biotechnology and medicine as antibiotic producers, we know very little about their cell wall biogenesis, composition, and functions. Here, we have identified the LCP-LytR_C domain protein CglA (Vnz_13690) as a key glycopolymer ligase, which specifically localizes in zones of cell wall biosynthesis in S. venezuelae. Reduced amount of glycopolymers in the cglA mutant results in enlarged vegetative hyphae and failures in FtsZ-rings formation and positioning. Consequently, division septa are misplaced leading to the formation of aberrant cell compartments, misshaped spores, and reduced cell vitality. In addition, we report our discovery that c-di-AMP signaling and decoration of the cell wall with glycopolymers are physiologically linked in Streptomyces since the deletion of cglA restores growth of the S. venezuelae disA mutant at high salt. Altogether, we have identified and characterized CglA as a novel component of cell wall biogenesis in Streptomyces, which is required for cell shape maintenance and cellular vitality in filamentous, multicellular bacteria.IMPORTANCEStreptomyces are our key producers of antibitiotics and other bioactive molecules and are, therefore, of high value for medicine and biotechnology. They proliferate by apical extension and branching of hyphae and undergo complex cell differentiation from filaments to spores during their life cycle. For both, growth and sporulation, coordinated cell wall biogenesis is crucial. However, our knowledge about cell wall biosynthesis, functions, and architecture in Streptomyces and in other Actinomycetota is still very limited. Here, we identify CglA as the key enzyme needed for the attachment of glycopolymers to the cell wall of S. venezuelae. We demonstrate that defects in the cell wall glycopolymer content result in loss of cell shape in these filamentous bacteria and show that division-competent FtsZ-rings cannot assemble properly and fail to be positioned correctly. As a consequence, cell septa placement is disturbed leading to the formation of misshaped spores with reduced viability.
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Affiliation(s)
- Sukanya Bhowmick
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | - Ruth P. Viveros
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | - Andreas Latoscha
- Institute of Biology/Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Fabian M. Commichau
- Institute of Biology, FG Molecular Microbiology 190 h, Universität Hohenheim, Stuttgart, Germany
| | - Christoph Wrede
- Institute of Functional and Applied Anatomy, Research Core Unit Electron Microscopy, Hannover Medical School, Hannover, Germany
| | | | - Natalia Tschowri
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
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73
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Caulat LC, Lotoux A, Martins MC, Kint N, Anjou C, Teixeira M, Folgosa F, Morvan C, Martin-Verstraete I. Physiological role and complex regulation of O 2-reducing enzymes in the obligate anaerobe Clostridioides difficile. mBio 2024; 15:e0159124. [PMID: 39189748 PMCID: PMC11481553 DOI: 10.1128/mbio.01591-24] [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: 06/05/2024] [Accepted: 07/22/2024] [Indexed: 08/28/2024] Open
Abstract
Clostridioides difficile, the major cause of antibiotic-associated diarrhea, is a strict anaerobic, sporulating Firmicutes. However, during its infectious cycle, this anaerobe is exposed to low oxygen (O2) tensions, with a longitudinal decreasing gradient along the gastrointestinal tract and a second lateral gradient with higher O2 tensions in the vicinity of the cells. A plethora of enzymes involved in oxidative stress detoxication has been identified in C. difficile, including four O2-reducing enzymes: two flavodiiron proteins (FdpA and FdpF) and two reverse rubrerythrins (revRbr1 and revRbr2). Here, we investigated the role of the four O2-reducing enzymes in the tolerance to increasing physiological O2 tensions and air. The four enzymes have different, yet overlapping, spectra of activity. revRbr2 is specific to low O2 tensions (<0.4%), FdpA to low and intermediate O2 tensions (0.4%-1%), revRbr1 has a wider spectrum of activity (0.1%-4%), and finally FdpF is more specific to tensions > 4% and air. These different O2 ranges of action partly arise from differences in regulation of expression of the genes encoding those enzymes. Indeed, we showed that revrbr2 is under the dual control of σA and σB. We also identified a regulator of the Spx family that plays a role in the induction of fdp and revrbr genes upon O2 exposure. Finally, fdpF is regulated by Rex, a regulator sensing the NADH/NAD+ ratio. Our results demonstrate that the multiplicity of O2-reducing enzymes of C. difficile is associated with different roles depending on the environmental conditions, stemming from a complex multi-leveled network of regulation. IMPORTANCE The gastrointestinal tract is a hypoxic environment, with the existence of two gradients of O2 along the gut, one longitudinal anteroposterior decreasing gradient and one proximodistal increasing from the lumen to the epithelial cells. O2 is a major source of stress for an obligate anaerobe such as the enteropathogen C. difficile. This bacterium possesses a plethora of enzymes capable of scavenging O2 and reducing it to H2O. In this work, we identified the role of the four O2-reducing enzymes in the tolerance to the physiological O2 tensions faced by C. difficile during its infectious cycle. These four enzymes have different spectra of action and protect the vegetative cells over a large range of O2 tensions. These differences are associated with a distinct regulation of each gene encoding those enzymes. The complex network of regulation is crucial for C. difficile to adapt to the various O2 tensions encountered during infection.
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Affiliation(s)
- Léo C. Caulat
- Institut Pasteur, Université de Paris, CNRS UMR6047, Laboratoire Pathogenèse des Bactéries Anaérobies, Paris, France
| | - Aurélie Lotoux
- Institut Pasteur, Université de Paris, CNRS UMR6047, Laboratoire Pathogenèse des Bactéries Anaérobies, Paris, France
| | - Maria C. Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Nicolas Kint
- Institut Pasteur, Université de Paris, CNRS UMR6047, Laboratoire Pathogenèse des Bactéries Anaérobies, Paris, France
| | - Cyril Anjou
- Institut Pasteur, Université de Paris, CNRS UMR6047, Laboratoire Pathogenèse des Bactéries Anaérobies, Paris, France
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Filipe Folgosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Claire Morvan
- Institut Pasteur, Université de Paris, CNRS UMR6047, Laboratoire Pathogenèse des Bactéries Anaérobies, Paris, France
| | - Isabelle Martin-Verstraete
- Institut Pasteur, Université de Paris, CNRS UMR6047, Laboratoire Pathogenèse des Bactéries Anaérobies, Paris, France
- Institut Universitaire de France, Paris, France
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74
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Chandrasekaran FP, Nelson EJR. Molecular dynamics simulations involving different β-propeller mutations reported in Swiss and French patients correlate with their disease phenotypes. Sci Rep 2024; 14:24133. [PMID: 39406775 PMCID: PMC11480402 DOI: 10.1038/s41598-024-75070-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 10/01/2024] [Indexed: 10/19/2024] Open
Abstract
Integrin αIIbβ3 is the predominant receptor for fibrinogen which mediates platelet aggregation, an important step in hemostasis and thrombosis. Several mutations have been reported in the genes encoding αIIb and β3 subunits among patients with Glanzmann thrombasthenia, of which 177 are in the β-propeller domain. The two subunits form a heterodimer at the interface between β-propeller and β-I domains of αIIb and β3, respectively with their stability critical for intracellular trafficking, surface expression, and ligand binding. Our study was aimed at retrieving the β-propeller mutations from various databases and studying structural variations due to select mutations upon interaction with fibrinogen using molecular docking and molecular dynamics. Mutations were studied for their impact on phenotypic severity, structural stability, and evolutionary conservation. Molecular docking analysis and molecular dynamics simulations were carried out for αIIb-β3 complexes as well as αIIbβ3-fibrinogen complexes; in particular, E355K structure had more deviations, fluctuations, and other changes which compromised its structural stability and binding affinity when compared to both wild-type and G401C structures. Our comprehensive in silico analysis clearly reiterates that mutations in the β-propeller are not only responsible for structural changes in this domain but also have implications on the overall structure and function of integrin αIIbβ3.
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Affiliation(s)
- Finola Priyadharshini Chandrasekaran
- Gene Therapy Laboratory, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, 632 014, India
| | - Everette Jacob Remington Nelson
- Gene Therapy Laboratory, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, 632 014, India.
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75
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Liang JJ, Pitsillou E, Karagiannis TC. Investigation of RNA-binding protein NOVA1 in silico: Comparison of the modern human V197 with the archaic I197 variant present in Neanderthals. Comput Biol Med 2024; 183:109278. [PMID: 39413624 DOI: 10.1016/j.compbiomed.2024.109278] [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: 07/30/2024] [Revised: 09/25/2024] [Accepted: 10/14/2024] [Indexed: 10/18/2024]
Abstract
By comparing the high-coverage archaic genome sequences to those of modern humans, specific genetic differences have been identified. For example, a human-specific substitution has been found in neuro-oncological ventral antigen 1 (NOVA1) - an RNA-binding protein that regulates the alternative splicing of neuronal pre-mRNA. The amino acid substitution results in an isoleucine-to-valine change at position 197 in NOVA1 (archaic: I197, modern human: V197). Previous studies have utilised gene editing technology to compare the archaic and modern human forms of NOVA1 in cortical organoids, however, the structural and molecular details require further investigation. Using an in silico approach, the modern human (WT) and archaic (V197I) structures of NOVA1 were generated. Moreover, the structure of NOVA1 containing a glycine-to-valine substitution at position 68 (G68V), which occurs at the RNA-binding interface, was examined for comparison. Protein-RNA docking was subsequently performed to model the interaction of NOVA1 variants with RNA and the complexes were evaluated further using classical molecular dynamics (MD) simulations. Based on the MM-PBSA analysis, the binding free energies were similar between the WT (-956.8 ± 32.6 kcal/mol), V197I (-975.4 ± 65.6 kcal/mol), and G68V (-946.7 ± 34.3 kcal/mol) complexes. The findings highlight the binding and stability of protein-RNA complexes with only modest structural changes observed in the archaic and G68V variants compared to the WT NOVA1 protein. Further clarification is required to enhance our understanding of the impact of NOVA1 mutations on alternative splicing and disease development. In particular, delineating the effect of multiple mutations in the NOVA1 gene is of importance.
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Affiliation(s)
- Julia J Liang
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC, 3004, Australia; yΘμ Study Group, ProspED Polytechnic, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Eleni Pitsillou
- yΘμ Study Group, ProspED Polytechnic, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Tom C Karagiannis
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC, 3004, Australia; yΘμ Study Group, ProspED Polytechnic, Carlton, VIC, 3053, Australia; Baker Department of Cardiometabolic Health, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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76
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de Crécy-Lagard V, Dias R, Friedberg I, Yuan Y, Swairjo MA. Limitations of Current Machine-Learning Models in Predicting Enzymatic Functions for Uncharacterized Proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601547. [PMID: 39005379 PMCID: PMC11244979 DOI: 10.1101/2024.07.01.601547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Thirty to seventy percent of proteins in any given genome have no assigned function and have been labeled as the protein "unknome". This large knowledge gap prevents the biological community from fully leveraging the plethora of genomic data that is now available. Machine-learning approaches are showing some promise in propagating functional knowledge from experimentally characterized proteins to the correct set of isofunctional orthologs. However, they largely fail to predict enzymatic functions unseen in the training set, as shown by dissecting the predictions made for over 450 enzymes of unknown function from the model bacteria Escherichia coli uxgsing the DeepECTransformer platform. Lessons from these failures can help the community develop machine-learning methods that assist domain experts in making testable functional predictions for more members of the uncharacterized proteome. Article Summary Many proteins in any genome, ranging from 30 to 70%, lack an assigned function. This knowledge gap limits the full use of the vast available genomic data. Machine learning has shown promise in transferring functional knowledge from proteins of known functions to similar ones, but largely fails to predict novel functions not seen in its training data. Understanding these failures can guide the development of better machine-learning methods to help experts make accurate functional predictions for uncharacterized proteins.
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77
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Chow CFW, Ghosh S, Hadarovich A, Toth-Petroczy A. SHARK enables sensitive detection of evolutionary homologs and functional analogs in unalignable and disordered sequences. Proc Natl Acad Sci U S A 2024; 121:e2401622121. [PMID: 39383002 PMCID: PMC11494347 DOI: 10.1073/pnas.2401622121] [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: 01/24/2024] [Accepted: 08/30/2024] [Indexed: 10/11/2024] Open
Abstract
Intrinsically disordered regions (IDRs) are structurally flexible protein segments with regulatory functions in multiple contexts, such as in the assembly of biomolecular condensates. Since IDRs undergo more rapid evolution than ordered regions, identifying homology of such poorly conserved regions remains challenging for state-of-the-art alignment-based methods that rely on position-specific conservation of residues. Thus, systematic functional annotation and evolutionary analysis of IDRs have been limited, despite them comprising ~21% of proteins. To accurately assess homology between unalignable sequences, we developed an alignment-free sequence comparison algorithm, SHARK (Similarity/Homology Assessment by Relating K-mers). We trained SHARK-dive, a machine learning homology classifier, which achieved superior performance to standard alignment-based approaches in assessing evolutionary homology in unalignable sequences. Furthermore, it correctly identified dissimilar but functionally analogous IDRs in IDR-replacement experiments reported in the literature, whereas alignment-based tools were incapable of detecting such functional relationships. SHARK-dive not only predicts functionally similar IDRs at a proteome-wide scale but also identifies cryptic sequence properties and motifs that drive remote homology and analogy, thereby providing interpretable and experimentally verifiable hypotheses of the sequence determinants that underlie such relationships. SHARK-dive acts as an alternative to alignment to facilitate systematic analysis and functional annotation of the unalignable protein universe.
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Affiliation(s)
- Chi Fung Willis Chow
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden01307, Germany
- Center for Systems Biology Dresden, Dresden01307, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden01062, Germany
| | - Soumyadeep Ghosh
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden01307, Germany
- Center for Systems Biology Dresden, Dresden01307, Germany
| | - Anna Hadarovich
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden01307, Germany
- Center for Systems Biology Dresden, Dresden01307, Germany
| | - Agnes Toth-Petroczy
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden01307, Germany
- Center for Systems Biology Dresden, Dresden01307, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden01062, Germany
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78
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Crowley LM, Wawman DC. The genome sequence of the Large Red Damselfly Pyrrhosoma nymphula (Sulzer, 1776). Wellcome Open Res 2024; 9:367. [PMID: 39184129 PMCID: PMC11342034 DOI: 10.12688/wellcomeopenres.22586.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2024] [Indexed: 08/27/2024] Open
Abstract
We present a genome assembly from an individual male Pyrrhosoma nymphula (the Large Red Damselfly; Arthropoda; Insecta; Odonata; Coenagrionidae). The genome sequence is 2,117.2 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.78 kilobases in length.
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Affiliation(s)
- Liam M. Crowley
- Department of Biology, University of Oxford, Oxford, England, UK
| | - Denise C. Wawman
- Department of Biology, University of Oxford, Oxford, England, UK
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79
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Harrison PM. Intrinsically Disordered Compositional Bias in Proteins: Sequence Traits, Region Clustering, and Generation of Hypothetical Functional Associations. Bioinform Biol Insights 2024; 18:11779322241287485. [PMID: 39417089 PMCID: PMC11481073 DOI: 10.1177/11779322241287485] [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: 05/20/2024] [Accepted: 08/27/2024] [Indexed: 10/19/2024] Open
Abstract
Compositionally biased regions (CBRs), ie, tracts that are dominated by a subset of residue types, are common features of eukaryotic proteins. These are often found bounded within or almost coterminous with intrinsically disordered or 'natively unfolded' parts. Here, it is investigated how the function of such intrinsically disordered compositionally biased regions (ID-CBRs) is directly linked to their compositional traits, focusing on the well-characterized yeast (Saccharomyces cerevisiae) proteome as a test case. The ID-CBRs that are clustered together using compositional distance are discovered to have clear functional linkages at various levels of diversity. The specific case of the Sup35p and Rnq1p proteins that underlie causally linked prion phenomena ([PSI+] and [RNQ+]) is highlighted. Their prion-forming ID-CBRs are typically clustered very close together indicating some compositional engendering for [RNQ+] seeding of [PSI+] prions. Delving further, ID-CBRs with distinct types of residue patterning such as 'blocking' or relative segregation of residues into homopeptides are found to have significant functional trends. Specific examples of such ID-CBR functional linkages that are discussed are: Q/N-rich ID-CBRs linked to transcriptional coactivation, S-rich to transcription-factor binding, R-rich to DNA-binding, S/E-rich to protein localization, and D-rich linked to chromatin remodelling. These data may be useful in informing experimental hypotheses for proteins containing such regions.
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Affiliation(s)
- Paul M Harrison
- Department of Biology, McGill University, Montreal, QC, Canada
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80
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He H, Gómez-Coronado PA, Zarzycki J, Barthel S, Kahnt J, Claus P, Klein M, Klose M, de Crécy-Lagard V, Schindler D, Paczia N, Glatter T, Erb TJ. Adaptive laboratory evolution recruits the promiscuity of succinate semialdehyde dehydrogenase to repair different metabolic deficiencies. Nat Commun 2024; 15:8898. [PMID: 39406738 PMCID: PMC11480449 DOI: 10.1038/s41467-024-53156-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 10/03/2024] [Indexed: 10/19/2024] Open
Abstract
Promiscuous enzymes often serve as the starting point for the evolution of novel functions. Yet, the extent to which the promiscuity of an individual enzyme can be harnessed several times independently for different purposes during evolution is poorly reported. Here, we present a case study illustrating how NAD(P)+-dependent succinate semialdehyde dehydrogenase of Escherichia coli (Sad) is independently recruited through various evolutionary mechanisms for distinct metabolic demands, in particular vitamin biosynthesis and central carbon metabolism. Using adaptive laboratory evolution (ALE), we show that Sad can substitute for the roles of erythrose 4-phosphate dehydrogenase in pyridoxal 5'-phosphate (PLP) biosynthesis and glyceraldehyde 3-phosphate dehydrogenase in glycolysis. To recruit Sad for PLP biosynthesis and glycolysis, ALE employs various mechanisms, including active site mutation, copy number amplification, and (de)regulation of gene expression. Our study traces down these different evolutionary trajectories, reports on the surprising active site plasticity of Sad, identifies regulatory links in amino acid metabolism, and highlights the potential of an ordinary enzyme as innovation reservoir for evolution.
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Affiliation(s)
- Hai He
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
| | - Paul A Gómez-Coronado
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jan Zarzycki
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Sebastian Barthel
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jörg Kahnt
- Mass Spectrometry and Proteomics Facility, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Peter Claus
- Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Moritz Klein
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Melanie Klose
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
- Genetic Institute, University of Florida, Gainesville, FL, USA
| | - Daniel Schindler
- MaxGENESYS Biofoundry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Nicole Paczia
- Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Timo Glatter
- Mass Spectrometry and Proteomics Facility, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany.
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81
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Casado-Fernández L, Laso-García F, Piniella D, Gómez-de Frutos MC, Otero-Ortega L, Bravo SB, Fuentes-Gimeno B, Docando F, Alonso-López E, Ruiz-Ares G, Rodríguez-Pardo J, Rigual R, de Celis-Ruiz E, Hervás C, Díez-Tejedor E, Gutiérrez-Fernández M, Alonso de Leciñana M. The proteomic signature of circulating extracellular vesicles following intracerebral hemorrhage: Novel insights into mechanisms underlying recovery. Neurobiol Dis 2024; 201:106665. [PMID: 39277144 DOI: 10.1016/j.nbd.2024.106665] [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: 03/24/2024] [Revised: 05/19/2024] [Accepted: 09/11/2024] [Indexed: 09/17/2024] Open
Abstract
Circulating extracellular vesicles (EVs) can participate in innate repair processes triggered after intracerebral hemorrhage (ICH). We aimed to describe changes in the proteomic profile of circulating EVs between the acute and subacute phases of ICH and to compare the findings depending on outcomes, as an approach to unraveling such repair mechanisms. This was a prospective observational study including patients with non-traumatic supratentorial ICH. Exclusion criteria were previous disability, signs of herniation on baseline computed tomography, or limited life expectancy. EVs were isolated from blood samples at 24 h and 7 days after symptom onset. After 6-months' follow-up, patients were dichotomized into poor and good outcomes, defining good as an improvement of >10 points or > 50 % on the National Institutes of Health Stroke Scale and a modified Rankin Scale of 0-2. The protein cargo was analyzed by quantitative mass spectrometry and compared according to outcomes. Forty-four patients completed follow-up, 16 (35.5 %) having good outcomes. We identified 1321 proteins in EVs, 37 with differential abundance. In patients with good outcomes, proteins related to stress response (DERA, VNN2, TOMM34) and angiogenesis (RHG01) had increased abundance at 7 days. EVs from patients with poor outcomes showed higher levels of acute-phase reactants (CRP, SAA2) at 7 days compared with 24 h. In conclusion, the protein content of circulating EVs in patients with ICH changes over time, the changes varying depending on the clinical outcome, with greater abundance of proteins potentially involved in the repair processes of patients with good outcomes.
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Affiliation(s)
- Laura Casado-Fernández
- Neurological Sciences and Cerebrovascular Research Laboratory, Department of Neurology and Stroke Center, Neurology and Cerebrovascular Disease Group, Neuroscience Area Hospital La Paz Institute for Health Research - IdiPAZ (La Paz University Hospital - Universidad Autónoma de Madrid), Madrid, Spain
| | - Fernando Laso-García
- Neurological Sciences and Cerebrovascular Research Laboratory, Department of Neurology and Stroke Center, Neurology and Cerebrovascular Disease Group, Neuroscience Area Hospital La Paz Institute for Health Research - IdiPAZ (La Paz University Hospital - Universidad Autónoma de Madrid), Madrid, Spain
| | - Dolores Piniella
- Neurological Sciences and Cerebrovascular Research Laboratory, Department of Neurology and Stroke Center, Neurology and Cerebrovascular Disease Group, Neuroscience Area Hospital La Paz Institute for Health Research - IdiPAZ (La Paz University Hospital - Universidad Autónoma de Madrid), Madrid, Spain; Faculty of Medicine, Universidad Alfonso X el Sabio, Villanueva de la Cañada, Madrid, Spain
| | - Mari Carmen Gómez-de Frutos
- Neurological Sciences and Cerebrovascular Research Laboratory, Department of Neurology and Stroke Center, Neurology and Cerebrovascular Disease Group, Neuroscience Area Hospital La Paz Institute for Health Research - IdiPAZ (La Paz University Hospital - Universidad Autónoma de Madrid), Madrid, Spain; Faculty of Health Sciences - HM Hospitals, University Camilo José Cela. Villanueva de la Cañada, Madrid, España; Instituto de Investigación Sanitaria HM Hospitales, 28015 Madrid, Spain
| | - Laura Otero-Ortega
- Neurological Sciences and Cerebrovascular Research Laboratory, Department of Neurology and Stroke Center, Neurology and Cerebrovascular Disease Group, Neuroscience Area Hospital La Paz Institute for Health Research - IdiPAZ (La Paz University Hospital - Universidad Autónoma de Madrid), Madrid, Spain
| | - Susana-Belén Bravo
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Blanca Fuentes-Gimeno
- Neurological Sciences and Cerebrovascular Research Laboratory, Department of Neurology and Stroke Center, Neurology and Cerebrovascular Disease Group, Neuroscience Area Hospital La Paz Institute for Health Research - IdiPAZ (La Paz University Hospital - Universidad Autónoma de Madrid), Madrid, Spain
| | - Félix Docando
- Electron Microscopy Unit, Scientific-Technical Central Units, Institute of Health Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain
| | - Elisa Alonso-López
- Neurological Sciences and Cerebrovascular Research Laboratory, Department of Neurology and Stroke Center, Neurology and Cerebrovascular Disease Group, Neuroscience Area Hospital La Paz Institute for Health Research - IdiPAZ (La Paz University Hospital - Universidad Autónoma de Madrid), Madrid, Spain
| | - Gerardo Ruiz-Ares
- Neurological Sciences and Cerebrovascular Research Laboratory, Department of Neurology and Stroke Center, Neurology and Cerebrovascular Disease Group, Neuroscience Area Hospital La Paz Institute for Health Research - IdiPAZ (La Paz University Hospital - Universidad Autónoma de Madrid), Madrid, Spain
| | - Jorge Rodríguez-Pardo
- Neurological Sciences and Cerebrovascular Research Laboratory, Department of Neurology and Stroke Center, Neurology and Cerebrovascular Disease Group, Neuroscience Area Hospital La Paz Institute for Health Research - IdiPAZ (La Paz University Hospital - Universidad Autónoma de Madrid), Madrid, Spain
| | - Ricardo Rigual
- Neurological Sciences and Cerebrovascular Research Laboratory, Department of Neurology and Stroke Center, Neurology and Cerebrovascular Disease Group, Neuroscience Area Hospital La Paz Institute for Health Research - IdiPAZ (La Paz University Hospital - Universidad Autónoma de Madrid), Madrid, Spain
| | - Elena de Celis-Ruiz
- Neurological Sciences and Cerebrovascular Research Laboratory, Department of Neurology and Stroke Center, Neurology and Cerebrovascular Disease Group, Neuroscience Area Hospital La Paz Institute for Health Research - IdiPAZ (La Paz University Hospital - Universidad Autónoma de Madrid), Madrid, Spain
| | - Carlos Hervás
- Neurological Sciences and Cerebrovascular Research Laboratory, Department of Neurology and Stroke Center, Neurology and Cerebrovascular Disease Group, Neuroscience Area Hospital La Paz Institute for Health Research - IdiPAZ (La Paz University Hospital - Universidad Autónoma de Madrid), Madrid, Spain
| | - Exuperio Díez-Tejedor
- Neurological Sciences and Cerebrovascular Research Laboratory, Department of Neurology and Stroke Center, Neurology and Cerebrovascular Disease Group, Neuroscience Area Hospital La Paz Institute for Health Research - IdiPAZ (La Paz University Hospital - Universidad Autónoma de Madrid), Madrid, Spain
| | - María Gutiérrez-Fernández
- Neurological Sciences and Cerebrovascular Research Laboratory, Department of Neurology and Stroke Center, Neurology and Cerebrovascular Disease Group, Neuroscience Area Hospital La Paz Institute for Health Research - IdiPAZ (La Paz University Hospital - Universidad Autónoma de Madrid), Madrid, Spain.
| | - María Alonso de Leciñana
- Neurological Sciences and Cerebrovascular Research Laboratory, Department of Neurology and Stroke Center, Neurology and Cerebrovascular Disease Group, Neuroscience Area Hospital La Paz Institute for Health Research - IdiPAZ (La Paz University Hospital - Universidad Autónoma de Madrid), Madrid, Spain.
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82
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Wang C, Yang Y, Song J, Nan X. Research Progresses and Applications of Knowledge Graph Embedding Technique in Chemistry. J Chem Inf Model 2024; 64:7189-7213. [PMID: 39302256 DOI: 10.1021/acs.jcim.4c00791] [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] [Indexed: 09/22/2024]
Abstract
A knowledge graph (KG) is a technique for modeling entities and their interrelations. Knowledge graph embedding (KGE) translates these entities and relationships into a continuous vector space to facilitate dense and efficient representations. In the domain of chemistry, applying KG and KGE techniques integrates heterogeneous chemical information into a coherent and user-friendly framework, enhances the representation of chemical data features, and is beneficial for downstream tasks, such as chemical property prediction. This paper begins with a comprehensive review of classical and contemporary KGE methodologies, including distance-based models, semantic matching models, and neural network-based approaches. We then catalogue the primary databases employed in chemistry and biochemistry that furnish the KGs with essential chemical data. Subsequently, we explore the latest applications of KG and KGE in chemistry, focusing on risk assessment, property prediction, and drug discovery. Finally, we discuss the current challenges to KG and KGE techniques and provide a perspective on their potential future developments.
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Affiliation(s)
- Chuanghui Wang
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou 450001, China
| | - Yunqing Yang
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou 450001, China
| | - Jinshuai Song
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Xiaofei Nan
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou 450001, China
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83
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Rouse I, Power D, Subbotina J, Lobaskin V. NPCoronaPredict: A Computational Pipeline for the Prediction of the Nanoparticle-Biomolecule Corona. J Chem Inf Model 2024; 64:7525-7543. [PMID: 39324861 PMCID: PMC11480982 DOI: 10.1021/acs.jcim.4c00434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 08/02/2024] [Accepted: 09/12/2024] [Indexed: 09/27/2024]
Abstract
The corona of a nanoparticle immersed in a biological fluid is of key importance to its eventual fate and bioactivity in the environment or inside live tissues. It is critical to have insight into both the underlying bionano interactions and the corona composition to ensure biocompatibility of novel engineered nanomaterials. A prediction of these properties in silico requires the successful spanning of multiple orders of magnitude of both time and physical dimensions to produce results in a reasonable amount of time, necessitating the development of a multiscale modeling approach. Here, we present the NPCoronaPredict open-source software package: a suite of software tools to enable this prediction for complex multicomponent nanomaterials in essentially arbitrary biological fluids, or more generally any medium containing organic molecules. The package integrates several recent physics-based computational models and a library of both physics-based and data-driven parametrizations for nanomaterials and organic molecules. We describe the underlying theoretical background and the package functionality from the design of multicomponent NPs through to the evaluation of the corona.
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Affiliation(s)
- Ian Rouse
- University College Dublin, Belfield, Dublin 4, Ireland
| | - David Power
- University College Dublin, Belfield, Dublin 4, Ireland
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84
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Salcedo-Tacuma D, Howells GD, McHose C, Gutierrez-Diaz A, Schupp J, Smith DM. ProEnd: a comprehensive database for identifying HbYX motif-containing proteins across the tree of life. BMC Genomics 2024; 25:951. [PMID: 39396964 PMCID: PMC11475706 DOI: 10.1186/s12864-024-10864-4] [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: 07/29/2024] [Accepted: 10/03/2024] [Indexed: 10/15/2024] Open
Abstract
The proteasome plays a crucial role in cellular homeostasis by degrading misfolded, damaged, or unnecessary proteins. Understanding the regulatory mechanisms of proteasome activity is vital, particularly the interaction with activators containing the hydrophobic-tyrosine-any amino acid (HbYX) motif. Here, we present ProEnd, a comprehensive database designed to identify and catalog HbYX motif-containing proteins across the tree of life. Using a simple bioinformatics pipeline, we analyzed approximately 73 million proteins from 22,000 reference proteomes in the UniProt/SwissProt database. Our findings reveal the widespread presence of HbYX motifs in diverse organisms, highlighting their evolutionary conservation and functional significance. Notably, we observed an interesting prevalence of these motifs in viral proteomes, suggesting strategic interactions with the host proteasome. As validation two novel HbYX proteins found in this database were experimentally tested by pulldowns, confirming that they directly interact with the proteasome, with one of them directly activating it. ProEnd's extensive dataset and user-friendly interface enable researchers to explore the potential proteasomal regulator landscape, generating new hypotheses to advance proteasome biology. This resource is set to facilitate the discovery of novel therapeutic targets, enhancing our approach to treating diseases such as neurodegenerative disorders and cancer.
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Affiliation(s)
- David Salcedo-Tacuma
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr, Morgantown, WV, USA
| | - Giovanni D Howells
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr, Morgantown, WV, USA
| | - Coleman McHose
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr, Morgantown, WV, USA
| | - Aimer Gutierrez-Diaz
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Jane Schupp
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr, Morgantown, WV, USA
| | - David M Smith
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr, Morgantown, WV, USA.
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV, USA.
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85
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Blackwell AM, Jami-Alahmadi Y, Nasamu AS, Kudo S, Senoo A, Slam C, Tsumoto K, Wohlschlegel JA, Caaveiro JMM, Goldberg DE, Sigala PA. Malaria parasites require a divergent heme oxygenase for apicoplast gene expression and biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596652. [PMID: 38853871 PMCID: PMC11160694 DOI: 10.1101/2024.05.30.596652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Malaria parasites have evolved unusual metabolic adaptations that specialize them for growth within heme-rich human erythrocytes. During blood-stage infection, Plasmodium falciparum parasites internalize and digest abundant host hemoglobin within the digestive vacuole. This massive catabolic process generates copious free heme, most of which is biomineralized into inert hemozoin. Parasites also express a divergent heme oxygenase (HO)-like protein (PfHO) that lacks key active-site residues and has lost canonical HO activity. The cellular role of this unusual protein that underpins its retention by parasites has been unknown. To unravel PfHO function, we first determined a 2.8 Å-resolution X-ray structure that revealed a highly α-helical fold indicative of distant HO homology. Localization studies unveiled PfHO targeting to the apicoplast organelle, where it is imported and undergoes N-terminal processing but retains most of the electropositive transit peptide. We observed that conditional knockdown of PfHO was lethal to parasites, which died from defective apicoplast biogenesis and impaired isoprenoid-precursor synthesis. Complementation and molecular-interaction studies revealed an essential role for the electropositive N-terminus of PfHO, which selectively associates with the apicoplast genome and enzymes involved in nucleic acid metabolism and gene expression. PfHO knockdown resulted in a specific deficiency in levels of apicoplast-encoded RNA but not DNA. These studies reveal an essential function for PfHO in apicoplast maintenance and suggest that Plasmodium repurposed the conserved HO scaffold from its canonical heme-degrading function in the ancestral chloroplast to fulfill a critical adaptive role in organelle gene expression.
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86
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Chen M, Xia L, Tan X, Gao S, Wang S, Li M, Zhang Y, Xu T, Cheng Y, Chu Y, Hu S, Wu S, Zhang Z. Seeing the unseen in characterizing RNA editome during rice endosperm development. Commun Biol 2024; 7:1314. [PMID: 39397073 PMCID: PMC11471866 DOI: 10.1038/s42003-024-07032-5] [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: 02/19/2024] [Accepted: 10/07/2024] [Indexed: 10/15/2024] Open
Abstract
Rice (Oryza sativa L.) endosperm is essential to provide nutrients for seed germination and determine grain yield. RNA editing, a post-transcriptional modification essential for plant development, unfortunately, is not fully characterized during rice endosperm development. Here, we perform systematic analyses to characterize RNA editome during rice endosperm development. We find that most editing sites are C-to-U CDS-recoding in mitochondria, leading to increased hydrophobic amino acids and changed structures of mitochondrial proteins. Comparative analysis of RNA editome reveals that CDS-recoding sites present higher editing frequencies with lower variabilities and their resultant recoded amino acids tend to exhibit stronger evolutionary conservation across many land plants. Furthermore, we classify mitochondrial genes into three groups, presenting distinct patterns in terms of CDS-recoding events. Besides, we conduct genome-wide screening to detect pentatricopeptide repeat (PPR) proteins and construct PPR-RNA binding profiles, yielding candidate PPR editing factors related to rice endosperm development. Taken together, our findings provide valuable insights for deciphering fundamental mechanisms of rice endosperm development underlying RNA editing machinery.
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Affiliation(s)
- Ming Chen
- National Genomics Data Center, China National Center for Bioinformation, Beijing, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lin Xia
- National Genomics Data Center, China National Center for Bioinformation, Beijing, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, China
| | - Xinyu Tan
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shenghan Gao
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Sen Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Man Li
- National Genomics Data Center, China National Center for Bioinformation, Beijing, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuansheng Zhang
- National Genomics Data Center, China National Center for Bioinformation, Beijing, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tianyi Xu
- National Genomics Data Center, China National Center for Bioinformation, Beijing, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yuanyuan Cheng
- National Genomics Data Center, China National Center for Bioinformation, Beijing, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuan Chu
- National Genomics Data Center, China National Center for Bioinformation, Beijing, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Songnian Hu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Shuangyang Wu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
| | - Zhang Zhang
- National Genomics Data Center, China National Center for Bioinformation, Beijing, China.
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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87
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Haas N, Thompson JD, Renaud JP, Chennen K, Poch O. StopKB: a comprehensive knowledgebase for nonsense suppression therapies. Database (Oxford) 2024; 2024:baae108. [PMID: 39395187 PMCID: PMC11470752 DOI: 10.1093/database/baae108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 09/13/2024] [Accepted: 10/03/2024] [Indexed: 10/14/2024]
Abstract
Nonsense variations, characterized by premature termination codons, play a major role in human genetic diseases as well as in cancer susceptibility. Despite their high prevalence, effective therapeutic strategies targeting premature termination codons remain a challenge. To understand and explore the intricate mechanisms involved, we developed StopKB, a comprehensive knowledgebase aggregating data from multiple sources on nonsense variations, associated genes, diseases, and phenotypes. StopKB identifies 637 317 unique nonsense variations, distributed across 18 022 human genes and linked to 3206 diseases and 7765 phenotypes. Notably, ∼32% of these variations are classified as nonsense-mediated mRNA decay-insensitive, potentially representing suitable targets for nonsense suppression therapies. We also provide an interactive web interface to facilitate efficient and intuitive data exploration, enabling researchers and clinicians to navigate the complex landscape of nonsense variations. StopKB represents a valuable resource for advancing research in precision medicine and more specifically, the development of targeted therapeutic interventions for genetic diseases associated with nonsense variations. Database URL: https://lbgi.fr/stopkb/.
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Affiliation(s)
- Nicolas Haas
- Complex Systems and Translational Bioinformatics (CSTB), ICube laboratory—CNRS, University of Strasbourg, CRBS, 1 rue Eugène Boeckel, Strasbourg 67000, France
| | - Julie Dawn Thompson
- Complex Systems and Translational Bioinformatics (CSTB), ICube laboratory—CNRS, University of Strasbourg, CRBS, 1 rue Eugène Boeckel, Strasbourg 67000, France
| | | | - Kirsley Chennen
- Complex Systems and Translational Bioinformatics (CSTB), ICube laboratory—CNRS, University of Strasbourg, CRBS, 1 rue Eugène Boeckel, Strasbourg 67000, France
| | - Olivier Poch
- Complex Systems and Translational Bioinformatics (CSTB), ICube laboratory—CNRS, University of Strasbourg, CRBS, 1 rue Eugène Boeckel, Strasbourg 67000, France
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88
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Breunig K, Lei X, Montalbano M, Guardia GDA, Ostadrahimi S, Alers V, Kosti A, Chiou J, Klein N, Vinarov C, Wang L, Li M, Song W, Kraus WL, Libich DS, Tiziani S, Weintraub ST, Galante PAF, Penalva LOF. SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586270. [PMID: 38585848 PMCID: PMC10996453 DOI: 10.1101/2024.03.22.586270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
RNA binding proteins (RBPs) containing intrinsically disordered regions (IDRs) are present in diverse molecular complexes where they function as dynamic regulators. Their characteristics promote liquid-liquid phase separation (LLPS) and the formation of membraneless organelles such as stress granules and nucleoli. IDR-RBPs are particularly relevant in the nervous system and their dysfunction is associated with neurodegenerative diseases and brain tumor development. Serpine1 mRNA-binding protein 1 (SERBP1) is a unique member of this group, being mostly disordered and lacking canonical RNA-binding domains. We defined SERBP1's interactome, uncovered novel roles in splicing, cell division and ribosomal biogenesis, and showed its participation in pathological stress granules and Tau aggregates in Alzheimer's brains. SERBP1 preferentially interacts with other G-quadruplex (G4) binders, implicated in different stages of gene expression, suggesting that G4 binding is a critical component of SERBP1 function in different settings. Similarly, we identified important associations between SERBP1 and PARP1/polyADP-ribosylation (PARylation). SERBP1 interacts with PARP1 and its associated factors and influences PARylation. Moreover, protein complexes in which SERBP1 participates contain mostly PARylated proteins and PAR binders. Based on these results, we propose a feedback regulatory model in which SERBP1 influences PARP1 function and PARylation, while PARylation modulates SERBP1 functions and participation in regulatory complexes.
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89
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Vazquez JM, Lauterbur ME, Mottaghinia S, Bucci M, Fraser D, Gray-Sandoval G, Gaucherand L, Haidar ZR, Han M, Kohler W, Lama TM, Corf AL, Maesen S, McMillan D, Li S, Lo J, Rey C, Capel SL, Singer M, Slocum K, Thomas W, Tyburec JD, Villa S, Miller R, Buchalski M, Vazquez-Medina JP, Pfeffer S, Etienne L, Enard D, Sudmant PH. Extensive longevity and DNA virus-driven adaptation in nearctic Myotis bats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.10.617725. [PMID: 39416019 PMCID: PMC11482938 DOI: 10.1101/2024.10.10.617725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
The rich species diversity of bats encompasses extraordinary adaptations, including extreme longevity and tolerance to infectious disease. While traditional approaches using genetic screens in model organisms have uncovered some fundamental processes underlying these traits, model organisms do not possess the variation required to understand the evolution of traits with complex genetic architectures. In contrast, the advent of genomics at tree-of-life scales enables us to study the genetic interactions underlying these processes by leveraging millions of years of evolutionary trial-and-error. Here, we use the rich species diversity of the genus Myotis - one of the longest-living clades of mammals - to study the evolution of longevity-associated traits and infectious disease using functional evolutionary genomics. We generated reference genome assemblies and cell lines for 8 closely-related (∼11 MYA) species of Myotis rich in phenotypic and life history diversity. Using genome-wide screens of positive selection, analysis of structural variation and copy number variation, and functional experiments in primary cell lines, we identify new patterns of adaptation in longevity, cancer resistance, and viral interactions both within Myotis and across bats. We find that the rapid evolution of lifespan in Myotis has some of the most significant variations in cancer risk across mammals, and demonstrate a unique DNA damage response in the long-lived M. lucifugus using primary cell culture models. Furthermore, we find evidence of abundant adaptation in response to DNA viruses, but not RNA viruses, in Myotis and other bats. This is in contrast to these patterns of adaptation in humans, which might contribute to the importance of bats as a reservoir of zoonotic viruses. Together, our results demonstrate the utility of leveraging natural variation to understand the genomics of traits with implications for human health and suggest important pleiotropic relationships between infectious disease tolerance and cancer resistance.
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90
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Blanco P, Trigo da Roza F, Toribio-Celestino L, García-Pastor L, Caselli N, Morón Á, Ojeda F, Darracq B, Vergara E, Amaro F, San Millán Á, Skovgaard O, Mazel D, Loot C, Escudero JA. Chromosomal integrons are genetically and functionally isolated units of genomes. Nucleic Acids Res 2024:gkae866. [PMID: 39385642 DOI: 10.1093/nar/gkae866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 09/17/2024] [Accepted: 09/23/2024] [Indexed: 10/12/2024] Open
Abstract
Integrons are genetic elements that increase the evolvability of bacteria by capturing new genes and stockpiling them in arrays. Sedentary chromosomal integrons (SCIs) can be massive and highly stabilized structures encoding hundreds of genes, whose function remains generally unknown. SCIs have co-evolved with the host for aeons and are highly intertwined with their physiology from a mechanistic point of view. But, paradoxically, other aspects, like their variable content and location within the genome, suggest a high genetic and functional independence. In this work, we have explored the connection of SCIs to their host genome using as a model the Superintegron (SI), a 179-cassette long SCI in the genome of Vibrio cholerae N16961. We have relocated and deleted the SI using SeqDelTA, a novel method that allows to counteract the strong stabilization conferred by toxin-antitoxin systems within the array. We have characterized in depth the impact in V. cholerae's physiology, measuring fitness, chromosome replication dynamics, persistence, transcriptomics, phenomics, natural competence, virulence and resistance against protist grazing. The deletion of the SI did not produce detectable effects in any condition, proving that-despite millions of years of co-evolution-SCIs are genetically and functionally isolated units of genomes.
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Affiliation(s)
- Paula Blanco
- Molecular Basis of Adaptation, Departamento de Sanidad Animal, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Filipa Trigo da Roza
- Molecular Basis of Adaptation, Departamento de Sanidad Animal, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Laura Toribio-Celestino
- Departamento de Microbiología Microbiana, Centro Nacional de Biotecnología-CSIC, Madrid 28049, Spain
| | - Lucía García-Pastor
- Molecular Basis of Adaptation, Departamento de Sanidad Animal, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Niccolò Caselli
- Departamento de Química Física, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Álvaro Morón
- Departamento de Genética, Fisiología y Microbiología, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Francisco Ojeda
- Molecular Basis of Adaptation, Departamento de Sanidad Animal, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Baptiste Darracq
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
- Sorbonne Université, ED515, F-75005 Paris, France
| | - Ester Vergara
- Molecular Basis of Adaptation, Departamento de Sanidad Animal, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Francisco Amaro
- Departamento de Genética, Fisiología y Microbiología, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Álvaro San Millán
- Departamento de Microbiología Microbiana, Centro Nacional de Biotecnología-CSIC, Madrid 28049, Spain
| | - Ole Skovgaard
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Céline Loot
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - José Antonio Escudero
- Molecular Basis of Adaptation, Departamento de Sanidad Animal, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
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Li ZL, Pei S, Chen Z, Huang TY, Wang XD, Shen L, Chen X, Wang QQ, Wang DX, Ao YF. Machine learning-assisted amidase-catalytic enantioselectivity prediction and rational design of variants for improving enantioselectivity. Nat Commun 2024; 15:8778. [PMID: 39389964 PMCID: PMC11467325 DOI: 10.1038/s41467-024-53048-0] [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: 02/26/2024] [Accepted: 09/30/2024] [Indexed: 10/12/2024] Open
Abstract
Biocatalysis is an attractive approach for the synthesis of chiral pharmaceuticals and fine chemicals, but assessing and/or improving the enantioselectivity of biocatalyst towards target substrates is often time and resource intensive. Although machine learning has been used to reveal the underlying relationship between protein sequences and biocatalytic enantioselectivity, the establishment of substrate fitness space is usually disregarded by chemists and is still a challenge. Using 240 datasets collected in our previous works, we adopt chemistry and geometry descriptors and build random forest classification models for predicting the enantioselectivity of amidase towards new substrates. We further propose a heuristic strategy based on these models, by which the rational protein engineering can be efficiently performed to synthesize chiral compounds with higher ee values, and the optimized variant results in a 53-fold higher E-value comparing to the wild-type amidase. This data-driven methodology is expected to broaden the application of machine learning in biocatalysis research.
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Affiliation(s)
- Zi-Lin Li
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuxin Pei
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Ziying Chen
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Teng-Yu Huang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xu-Dong Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Lin Shen
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China.
- Yantai-Jingshi Institute of Material Genome Engineering, Yantai, China.
| | - Xuebo Chen
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China.
- Yantai-Jingshi Institute of Material Genome Engineering, Yantai, China.
- Shandong Laboratory of Yantai Advanced Materials and Green Manufacturing, Yantai, China.
| | - Qi-Qiang Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - De-Xian Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Fei Ao
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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92
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Han W, Yang K, Tan X, Gao L, Qu S, Zhang G, Fan W, Liu M, Wang E, Li P, Ling F, Wang G, Liu T. Curcumin is an efficacious therapeutic agent against Chilodonella uncinata via interaction with tubulin alpha chain as protein target. FISH & SHELLFISH IMMUNOLOGY 2024; 154:109961. [PMID: 39395598 DOI: 10.1016/j.fsi.2024.109961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Revised: 09/26/2024] [Accepted: 10/09/2024] [Indexed: 10/14/2024]
Abstract
Chilodonella, a parasitic ciliate that infects both cold water and warm water fish, can impede the growth of juvenile fish and cause considerable economic losses globally to freshwater aquaculture. In this study, the parasite was collected from both the gills and zygotes of largemouth bass (Micropterus salmoides). Isolated from diseased fish, the parasites were identified as Chilodonella uncinata based on morphological features and genetical diagnostic characterization using the partial small subunit ribosomal RNA gene. To develop an effective approach to treat chilodonellosis caused by C. uncinata in largemouth bass farming, we first developed an in vivo culture model for propagating C. uncinate and thus could use for morphological characterization, molecular analyses and antiparasitic drug screening. Curcumin was successfully identified as an efficacious anti-C. uncinata agent from 26 phytochemical compounds. When administered at a concentration of 6 mg/L, curcumin not only completely cured infected largemouth bass but also shielded uninfected fish from C. uncinata infections. The 24 h median effective concentration (EC50) of curcumin against C. uncinata was 3.098 mg/L. Remarkably, the 96 h median lethal concentration (LC50) of curcumin against largemouth bass was determined to be 17.143 mg/L, approximately 5.533 times higher than EC50. The mechanism of action of curcumin was investigated by the cellular thermal shift assay, demonstrating that tubulin alpha chain was the binding target for curcumin. Moreover, SEM investigations further provided morphological evidence suggesting that curcumin induces parasite demise by disrupting the parasite's body surface and subsequently infiltrating its interior. These findings collectively emphasize the potential of curcumin as a safe and effective therapeutic agent for controlling C. uncinata in aquaculture.
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Affiliation(s)
- Wenjia Han
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China
| | - Kechen Yang
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China; Engineering Research Center of the Innovation and Development of Green Fishery Drugs, Universities of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaoping Tan
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China; Engineering Research Center of the Innovation and Development of Green Fishery Drugs, Universities of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Longkun Gao
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China; Northwest A&F University Shenzhen Research Institute, 518057, Shenzhen, Guangdong, China; Engineering Research Center of the Innovation and Development of Green Fishery Drugs, Universities of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shenye Qu
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China; Engineering Research Center of the Innovation and Development of Green Fishery Drugs, Universities of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Gengrong Zhang
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China; Northwest A&F University Shenzhen Research Institute, 518057, Shenzhen, Guangdong, China; Engineering Research Center of the Innovation and Development of Green Fishery Drugs, Universities of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Wenqi Fan
- College of Chemistry and Pharmacy, Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China
| | - Mingzhu Liu
- Guangxi Key Laboratory of Aquatic Biotechnology and Modern Ecological Aquaculture, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, Nanning, Guangxi, China
| | - Erlong Wang
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China; Northwest A&F University Shenzhen Research Institute, 518057, Shenzhen, Guangdong, China; Engineering Research Center of the Innovation and Development of Green Fishery Drugs, Universities of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Pengfei Li
- Guangxi Key Laboratory of Aquatic Biotechnology and Modern Ecological Aquaculture, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, Nanning, Guangxi, China
| | - Fei Ling
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China; Northwest A&F University Shenzhen Research Institute, 518057, Shenzhen, Guangdong, China
| | - Gaoxue Wang
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China; Northwest A&F University Shenzhen Research Institute, 518057, Shenzhen, Guangdong, China.
| | - Tianqiang Liu
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China; Northwest A&F University Shenzhen Research Institute, 518057, Shenzhen, Guangdong, China; Engineering Research Center of the Innovation and Development of Green Fishery Drugs, Universities of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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93
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Voßen S, Xerxa E, Bajorath J. Assessing Darkness of the Human Kinome from a Medicinal Chemistry Perspective. J Med Chem 2024; 67:17919-17928. [PMID: 39320975 DOI: 10.1021/acs.jmedchem.4c01992] [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: 09/27/2024]
Abstract
In drug discovery, human protein kinases (PKs) represent one of the major target classes due to their central role in cellular signaling, implication in various diseases as a consequence of deregulated signaling, and notable druggability. Individual PKs and their disease biology have been explored to different degrees, giving rise to heterogeneous functional knowledge and disease associations across the human kinome. The U.S. National Institutes of Health previously designated 162 understudied ("dark") human PKs and lipid kinases due to the lack of functional annotations and high-quality molecular probes for functional investigations. Given the large volumes of available PK inhibitors (PKIs) and activity data, we have systematically analyzed the distribution of PKIs and associated data at different confidence levels across the human kinome and distinguished between chemically explored, underexplored, and unexplored PKs. The analysis provides a medicinal chemistry-centric view of PK exploration and further extends prior assessment of the dark kinome.
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Affiliation(s)
- Selina Voßen
- B-IT, Department of Life Science Informatics and Data Science, Rheinische Friedrich-Wilhelms-Universität, Bonn D-53115, Germany
| | - Elena Xerxa
- B-IT, Department of Life Science Informatics and Data Science, Rheinische Friedrich-Wilhelms-Universität, Bonn D-53115, Germany
- Lamarr Institute for Machine Learning and Artificial Intelligence, Bonn D-53115, Germany
| | - Jürgen Bajorath
- B-IT, Department of Life Science Informatics and Data Science, Rheinische Friedrich-Wilhelms-Universität, Bonn D-53115, Germany
- Lamarr Institute for Machine Learning and Artificial Intelligence, Bonn D-53115, Germany
- LIMES Institute, Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 5/6, Bonn D-53115, Germany
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94
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Tan C, Lanz MC, Swaffer M, Skotheim J, Chang F. Intracellular diffusion in the cytoplasm increases with cell size in fission yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.21.613766. [PMID: 39386641 PMCID: PMC11463555 DOI: 10.1101/2024.09.21.613766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Diffusion in the cytoplasm can greatly impact cellular processes, yet regulation of macromolecular diffusion remains poorly understood. There is increasing evidence that cell size affects the density and macromolecular composition of the cytoplasm. Here, we studied whether cell size affects diffusion at the scale of macromolecules tens of microns in diameter. We analyzed the diffusive motions of intracellular genetically-encoded multimeric 40 nm nanoparticles (cytGEMs) in the cytoplasm of the fission yeast Schizosaccharomyces pombe . Using cell size mutants, we showed that cytGEMs diffusion coefficients decreased in smaller cells and increased in larger cells. This increase in diffusion in large cells may be due to a decrease in the DNA-to-Cytoplasm ratio, as diffusion was not affected in large multinucleate cytokinesis mutants. In investigating the underlying causes of altered cytGEMs diffusion, we found that the proteomes of large and small cells exhibited size-specific changes, including the sub-scaling of ribosomal proteins in large cells. Comparison with a similar dataset from human cells revealed that features of size-dependent proteome remodeling were conserved. These studies demonstrate that cell size is an important parameter in determining the biophysical properties and the composition of the cytoplasm.
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95
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Kuzma A, Valladares O, Greenfest-Allen E, Nicaretta H, Kirsch M, Ren Y, Katanic Z, White H, Wilk A, Bass L, Brettschneider J, Carter L, Cifello J, Chuang WH, Clark K, Gangadharan P, Haut J, Ho PC, Horng W, Iqbal T, Jin Y, Keskinen P, Rose AL, Moon MK, Manuel J, Qu L, Robbins F, Saravanan N, Sha J, Tate S, Zhao Y, Cantwell L, Gardner J, Chou SY, Tzeng JY, Bush W, Naj A, Kuksa P, Lee WP, Leung YY, Schellenberg G, Wang LS. NIAGADS: A Comprehensive National Data Repository for Alzheimer's Disease and Related Dementia Genetics and Genomics Research. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.10.07.24315029. [PMID: 39417134 PMCID: PMC11483014 DOI: 10.1101/2024.10.07.24315029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
NIAGADS is the National Institute on Aging (NIA) designated national data repository for human genetics research on Alzheimer's Disease and related dementia (ADRD). NIAGADS maintains a high-quality data collection for ADRD genetic/genomic research and supports genetics data production and analysis. NIAGADS hosts whole genome and exome sequence data from the Alzheimer's Disease Sequencing Project (ADSP) and other genotype/phenotype data, encompassing 209,000 samples. NIAGADS shares these data with hundreds of research groups around the world via the Data Sharing Service, a FISMA moderate compliant cloud-based platform that fully supports the NIH Genome Data Sharing Policy. NIAGADS Open Access consists of multiple knowledge bases with genome-wide association summary statistics and rich annotations on the biological significance of genetic variants and genes across the human genome. NIAGADS stands as a keystone in promoting collaborations to advance the understanding and treatment of Alzheimer's disease.
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Affiliation(s)
- Amanda Kuzma
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Otto Valladares
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Emily Greenfest-Allen
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Heather Nicaretta
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Maureen Kirsch
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Youli Ren
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Zivadin Katanic
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Heather White
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Andrew Wilk
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Lauren Bass
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Jascha Brettschneider
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Luke Carter
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Jeffrey Cifello
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Wei-Hsuan Chuang
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Kaylyn Clark
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Prabhakaran Gangadharan
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Jacob Haut
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Pei-Chuan Ho
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Wenhwai Horng
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Taha Iqbal
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yumi Jin
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Peter Keskinen
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Alexis Lerro Rose
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Michelle K Moon
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Joseph Manuel
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Liming Qu
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Flawless Robbins
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Naveensri Saravanan
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Jin Sha
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sam Tate
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Yi Zhao
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Laura Cantwell
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Jake Gardner
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Shin-Yi Chou
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Economics, Lehigh University, Bethlehem, PA, United States
- National Bureau of Economic Research, Cambridge, MA, United States
| | - Jung-Ying Tzeng
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Bioinformatics Research Center, North Carolina State University, NC, USA
- Department of Statistics, North Carolina State University, NC, USA
| | - William Bush
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Adam Naj
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Pavel Kuksa
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Wan-Ping Lee
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Yuk Yee Leung
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Gerard Schellenberg
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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Zhao H, Zhao H, Tang Y, Li M, Cai Y, Xiao X, He F, Huang H, Zhang Y, Li J. Skin-permeable gold nanoparticles with modifications azelamide monoethanolamine ameliorate inflammatory skin diseases. Biomark Res 2024; 12:118. [PMID: 39385245 PMCID: PMC11465885 DOI: 10.1186/s40364-024-00663-0] [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: 07/20/2024] [Accepted: 09/27/2024] [Indexed: 10/12/2024] Open
Abstract
BACKGROUND Traditional topical drug delivery for treating inflammatory skin diseases suffers from poor skin penetration and long-term side effects. Metal nanoparticles show promising application in topical drug delivery for inflammatory skin diseases. METHODS Here, we synthesized a new type of nanoparticles, azelamide monoethanolamine-functionalized gold nanoparticles (Au-MEA NPs), based on citrate-capped gold nanoparticles (Au-CA NPs) via the ligand exchange method. The physical and chemical properties of Au-CA NPs and Au-MEA NPs were characterized. In vivo studies were performed using imiquimod-induced psoriasis and LL37-induced rosacea animal models, respectively. For in vitro studies, a model of cellular inflammation was established using HaCaT cells stimulated with TNF-α. In addition, proteomics, gelatin zymography, and other techniques were used to investigate the possible therapeutic mechanisms of the Au-MEA NPs. RESULTS We found that Au-MEA NPs exhibited better stability and permeation properties compared to conventional Au-CA NPs. Transcutaneously administered Au-MEA NPs exerted potent therapeutic efficacy against both rosacea-like and psoriasiform skin dermatitis in vivo without overt signs of toxicity. Mechanistically, Au-MEA NPs reduced the production of pro-inflammatory mediators in keratinocytes by promoting SOD activity and inhibiting the activity of MMP9. CONCLUSION Au-MEA NPs have the potential to be a topical nanomedicine for the effective and safe treatment of inflammatory skin diseases.
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Affiliation(s)
- He Zhao
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Han Zhao
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Yan Tang
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Mengfan Li
- College of Materials Science and Engineering, Hunan University, Changsha, Hunan, 410082, P. R. China
| | - Yisheng Cai
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Xin Xiao
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Fanping He
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Hongwen Huang
- College of Materials Science and Engineering, Hunan University, Changsha, Hunan, 410082, P. R. China.
| | - Yiya Zhang
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Ji Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
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Rojas J, Hose J, Dutcher HA, Place M, Wolters JF, Hittinger CT, Gasch AP. Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model. CELL GENOMICS 2024; 4:100656. [PMID: 39317188 DOI: 10.1016/j.xgen.2024.100656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/10/2024] [Accepted: 08/20/2024] [Indexed: 09/26/2024]
Abstract
Although implicated as deleterious in many organisms, aneuploidy can underlie rapid phenotypic evolution. However, aneuploidy will be maintained only if the benefit outweighs the cost, which remains incompletely understood. To quantify this cost and the molecular determinants behind it, we generated a panel of chromosome duplications in Saccharomyces cerevisiae and applied comparative modeling and molecular validation to understand aneuploidy toxicity. We show that 74%-94% of the variance in aneuploid strains' growth rates is explained by the cumulative cost of genes on each chromosome, measured for single-gene duplications using a genomic library, along with the deleterious contribution of small nucleolar RNAs (snoRNAs) and beneficial effects of tRNAs. Machine learning to identify properties of detrimental gene duplicates provided no support for the balance hypothesis of aneuploidy toxicity and instead identified gene length as the best predictor of toxicity. Our results present a generalized framework for the cost of aneuploidy with implications for disease biology and evolution.
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Affiliation(s)
- Julie Rojas
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - James Hose
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - H Auguste Dutcher
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Michael Place
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA; Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John F Wolters
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Chris Todd Hittinger
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA; Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA; Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA; J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Audrey P Gasch
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA; Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA; Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA; J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA.
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98
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Naser-Khdour S, Scheuber F, Fields PD, Ebert D. The Evolution of Extreme Genetic Variability in a Parasite-Resistance Complex. Genome Biol Evol 2024; 16:evae222. [PMID: 39391977 PMCID: PMC11500718 DOI: 10.1093/gbe/evae222] [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: 08/13/2024] [Revised: 09/27/2024] [Accepted: 10/04/2024] [Indexed: 10/12/2024] Open
Abstract
Genomic regions that play a role in parasite defense are often found to be highly variable, with the major histocompatibility complex serving as an iconic example. Single nucleotide polymorphisms may represent only a small portion of this variability, with Indel polymorphisms and copy number variation further contributing. In extreme cases, haplotypes may no longer be recognized as orthologous. Understanding the evolution of such highly divergent regions is challenging because the most extreme variation is not visible using reference-assisted genomic approaches. Here we analyze the case of the Pasteuria Resistance Complex in the crustacean Daphnia magna, a defense complex in the host against the common and virulent bacterium Pasteuria ramosa. Two haplotypes of this region have been previously described, with parts of it being nonhomologous, and the region has been shown to be under balancing selection. Using pan-genome analysis and tree reconciliation methods to explore the evolution of the Pasteuria Resistance Complex and its characteristics within and between species of Daphnia and other Cladoceran species, our analysis revealed a remarkable diversity in this region even among host species, with many nonhomologous hyper-divergent haplotypes. The Pasteuria Resistance Complex is characterized by extensive duplication and losses of Fucosyltransferase (FuT) and Galactosyltransferase (GalT) genes that are believed to play a role in parasite defense. The Pasteuria Resistance Complex region can be traced back to common ancestors over 250 million years. The unique combination of an ancient resistance complex and a dynamic, hyper-divergent genomic environment presents a fascinating opportunity to investigate the role of such regions in the evolution and long-term maintenance of resistance polymorphisms. Our findings offer valuable insights into the evolutionary forces shaping disease resistance and adaptation, not only in the genus Daphnia, but potentially across the entire Cladocera class.
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Affiliation(s)
- Suha Naser-Khdour
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
| | - Fabian Scheuber
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
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99
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Samuel B, Mittelman K, Croitoru SY, Ben Haim M, Burstein D. Diverse anti-defence systems are encoded in the leading region of plasmids. Nature 2024:10.1038/s41586-024-07994-w. [PMID: 39385022 DOI: 10.1038/s41586-024-07994-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 08/27/2024] [Indexed: 10/11/2024]
Abstract
Plasmids are major drivers of gene mobilization by means of horizontal gene transfer and play a key role in spreading antimicrobial resistance among pathogens1,2. Despite various bacterial defence mechanisms such as CRISPR-Cas, restriction-modification systems and SOS-response genes that prevent the invasion of mobile genetic elements3, plasmids robustly transfer within bacterial populations through conjugation4,5. Here we show that the leading region of plasmids, the first to enter recipient cells, is a hotspot for an extensive repertoire of anti-defence systems, encoding anti-CRISPR, anti-restriction, anti-SOS and other counter-defence proteins. We further identified in the leading region a prevalence of promoters known to allow expression from single-stranded DNA6, potentially facilitating rapid protection against bacterial immunity during the early stages of plasmid establishment. We demonstrated experimentally the importance of anti-defence gene localization in the leading region for efficient conjugation. These results indicate that focusing on the leading region of plasmids could lead to the discovery of diverse anti-defence genes. Combined, our findings show a new facet of plasmid dissemination and provide theoretical foundations for developing efficient conjugative delivery systems for natural microbial communities.
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Affiliation(s)
- Bruria Samuel
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Karin Mittelman
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Shirly Ynbal Croitoru
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Maya Ben Haim
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - David Burstein
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel.
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100
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Nijs M, Waelkens E, Moor BD. Hierarchical Biclustering of Mouse Pancreas Mass Spectrometry Imaging Data Using Recursive Rank-2 Non-negative Matrix Factorization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39383443 DOI: 10.1021/jasms.4c00268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/11/2024]
Abstract
One of the main challenges in mass spectrometry imaging data analysis remains the analysis of m/z-spectra displaying a low signal-to-noise ratio caused by their low abundance, sample preparation, matrix effects, fragmentation, and other artifacts. Additionally, we observe that molecules with a high abundance suppress those with lower intensities and misdirect classical tools for MSI data analysis, such as principal component analysis. As a result, the observed significance of a molecule may not always be directly related to its abundance. In this work, we present a recursive rank-2 non-negative matrix factorization (rr2-NMF) algorithm that automatically returns spectral and spatial visualization of colocalized molecules, both highly and lowly abundant. Using this hierarchical decomposition, our method finds spatial and spectral correlations on different levels of abundances. The quality of the analysis is evaluated on MALDI-TOF data of healthy mouse pancreatic tissue for the annotation of molecules of interest in the lower abundances. The results show interesting findings regarding the functioning and colocalization of certain molecules.
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Affiliation(s)
- Melanie Nijs
- STADIUS Center for Dynamical Systems, Signal Processing, and Data Analytics, Department of Electrical Engineering (ESAT), KU Leuven, 3001 Leuven, Belgium
| | - Etienne Waelkens
- Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Bart De Moor
- STADIUS Center for Dynamical Systems, Signal Processing, and Data Analytics, Department of Electrical Engineering (ESAT), KU Leuven, 3001 Leuven, Belgium
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