1
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Spizzichino S, Di Fonzo F, Marabelli C, Tramonti A, Chaves-Sanjuan A, Parroni A, Boumis G, Liberati FR, Paone A, Montemiglio LC, Ardini M, Jakobi AJ, Bharadwaj A, Swuec P, Tartaglia GG, Paiardini A, Contestabile R, Mai A, Rotili D, Fiorentino F, Macone A, Giorgi A, Tria G, Rinaldo S, Bolognesi M, Giardina G, Cutruzzolà F. Structure-based mechanism of riboregulation of the metabolic enzyme SHMT1. Mol Cell 2024; 84:2682-2697.e6. [PMID: 38996576 DOI: 10.1016/j.molcel.2024.06.016] [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: 04/05/2023] [Revised: 01/26/2024] [Accepted: 06/18/2024] [Indexed: 07/14/2024]
Abstract
RNA can directly control protein activity in a process called riboregulation; only a few mechanisms of riboregulation have been described in detail, none of which have been characterized on structural grounds. Here, we present a comprehensive structural, functional, and phylogenetic analysis of riboregulation of cytosolic serine hydroxymethyltransferase (SHMT1), the enzyme interconverting serine and glycine in one-carbon metabolism. We have determined the cryoelectron microscopy (cryo-EM) structure of human SHMT1 in its free- and RNA-bound states, and we show that the RNA modulator competes with polyglutamylated folates and acts as an allosteric switch, selectively altering the enzyme's reactivity vs. serine. In addition, we identify the tetrameric assembly and a flap structural motif as key structural elements necessary for binding of RNA to eukaryotic SHMT1. The results presented here suggest that riboregulation may have played a role in evolution of eukaryotic SHMT1 and in compartmentalization of one-carbon metabolism. Our findings provide insights for RNA-based therapeutic strategies targeting this cancer-linked metabolic pathway.
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Affiliation(s)
- Sharon Spizzichino
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Federica Di Fonzo
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Chiara Marabelli
- Department of Molecular Medicine, University of Pavia, Via Forlanini 3, 27100 Pavia, Italy
| | - Angela Tramonti
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185 Rome, Italy
| | - Antonio Chaves-Sanjuan
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milano, Italy; Fondazione Romeo e Enrica Invernizzi and NOLIMITS, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Alessia Parroni
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185 Rome, Italy
| | - Giovanna Boumis
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Francesca Romana Liberati
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Alessio Paone
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy; Department of Biochemical Sciences, Sapienza University of Rome, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, P.le A. Moro 5, 00185 Rome, Italy
| | - Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185 Rome, Italy
| | - Matteo Ardini
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Arjen J Jakobi
- Department of Bionanoscience, Kavli Institute of Nanoscience Deft, Delft University of Technology, Van der Maasweg, 92629 HZ Delft, the Netherlands
| | - Alok Bharadwaj
- Department of Bionanoscience, Kavli Institute of Nanoscience Deft, Delft University of Technology, Van der Maasweg, 92629 HZ Delft, the Netherlands
| | - Paolo Swuec
- CryoElectron Microscopy Facility, Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Gian Gaetano Tartaglia
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152 Genova, Italy; Department of Biology "Charles Darwin", Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Alessandro Paiardini
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Roberto Contestabile
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Alberto Macone
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Alessandra Giorgi
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Giancarlo Tria
- CNR Institute of Crystallography - URT Caserta c/o Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Serena Rinaldo
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milano, Italy; Fondazione Romeo e Enrica Invernizzi and NOLIMITS, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Giorgio Giardina
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy.
| | - Francesca Cutruzzolà
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy; Department of Biochemical Sciences, Sapienza University of Rome, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, P.le A. Moro 5, 00185 Rome, Italy.
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Völkers M, Preiss T, Hentze MW. RNA-binding proteins in cardiovascular biology and disease: the beat goes on. Nat Rev Cardiol 2024; 21:361-378. [PMID: 38163813 DOI: 10.1038/s41569-023-00958-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/06/2023] [Indexed: 01/03/2024]
Abstract
Cardiac development and function are becoming increasingly well understood from different angles, including signalling, transcriptional and epigenetic mechanisms. By contrast, the importance of the post-transcriptional landscape of cardiac biology largely remains to be uncovered, building on the foundation of a few existing paradigms. The discovery during the past decade of hundreds of additional RNA-binding proteins in mammalian cells and organs, including the heart, is expected to accelerate progress and has raised intriguing possibilities for better understanding the intricacies of cardiac development, metabolism and adaptive alterations. In this Review, we discuss the progress and new concepts on RNA-binding proteins and RNA biology and appraise them in the context of common cardiovascular clinical conditions, from cell and organ-wide perspectives. We also discuss how a better understanding of cardiac RNA-binding proteins can fill crucial knowledge gaps in cardiology and might pave the way to developing better treatments to reduce cardiovascular morbidity and mortality.
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Affiliation(s)
- Mirko Völkers
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg and Mannheim, Germany
| | - Thomas Preiss
- Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Matthias W Hentze
- European Molecular Biology Laboratory, Heidelberg, Germany.
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.
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3
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Yang Y, Zhang M, Zhao Y, Deng T, Zhou X, Qian H, Wang M, Zhang C, Huo Z, Mao Z, Shao Z, Liu M, Yang C, Lin C, Xu F, Tian G, Zhang Y. HOXD8 suppresses renal cell carcinoma growth by upregulating SHMT1 expression. Cancer Sci 2023; 114:4583-4595. [PMID: 37752684 PMCID: PMC10728000 DOI: 10.1111/cas.15982] [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: 04/12/2023] [Revised: 09/11/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
Amplification of amino acids synthesis is reported to promote tumorigenesis. The serine/glycine biosynthesis pathway is a reversible conversion of serine and glycine catalyzed by cytoplasmic serine hydroxymethyltransferase (SHMT)1 and mitochondrial SHMT2; however, the role of SHTM1 in renal cell carcinoma (RCC) is still unclear. We found that low SHMT1 expression is correlated with poor survival of RCC patients. The in vitro study showed that overexpression of SHMT1 suppressed RCC proliferation and migration. In the mouse tumor model, SHMT1 significantly retarded RCC tumor growth. Furthermore, by gene network analysis, we found several SHMT1-related genes, among which homeobox D8 (HOXD8) was identified as the SHMT1 regulator. Knockdown of HOXD8 decreased SHMT1 expression, resulting in faster RCC growth, and rescued the SHMT1 overexpression-induced cell migration defects. Additionally, ChIP assay found the binding site of HOXD8 to SHMT1 promoter was at the -456~-254 bp region. Taken together, SHMT1 functions as a tumor suppressor in RCC. The transcription factor HOXD8 can promote SHMT1 expression and suppress RCC cell proliferation and migration, which provides new mechanisms of SHMT1 in RCC tumor growth and might be used as a potential therapeutic target candidate for clinical treatment.
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Affiliation(s)
- Yang Yang
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Minghui Zhang
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Yaxuan Zhao
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Tingzhi Deng
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Xiang Zhou
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Hanxu Qian
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Mengxuan Wang
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Chuanchuan Zhang
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Zhengjin Huo
- The First School of Clinical MedicineBinzhou Medical UniversityYantaiChina
| | - Zijun Mao
- The First School of Clinical MedicineBinzhou Medical UniversityYantaiChina
| | - Zhufeng Shao
- School of PharmacyBinzhou Medical UniversityYantaiChina
| | - Mengxue Liu
- School of PharmacyBinzhou Medical UniversityYantaiChina
| | - Chunhua Yang
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Chunhua Lin
- Department of UrologyThe Affiliated Yantai Yuhuangding Hospital of Qingdao UniversityYantaiChina
| | - Fuyi Xu
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Geng Tian
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Yin Zhang
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
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Shi M, Han S, Klier K, Fobo G, Montrone C, Yu S, Harada M, Henning AK, Friedrich N, Bahls M, Dörr M, Nauck M, Völzke H, Homuth G, Grabe HJ, Prehn C, Adamski J, Suhre K, Rathmann W, Ruepp A, Hertel J, Peters A, Wang-Sattler R. Identification of candidate metabolite biomarkers for metabolic syndrome and its five components in population-based human cohorts. Cardiovasc Diabetol 2023; 22:141. [PMID: 37328862 PMCID: PMC10276453 DOI: 10.1186/s12933-023-01862-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/20/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND Metabolic Syndrome (MetS) is characterized by risk factors such as abdominal obesity, hypertriglyceridemia, low high-density lipoprotein cholesterol (HDL-C), hypertension, and hyperglycemia, which contribute to the development of cardiovascular disease and type 2 diabetes. Here, we aim to identify candidate metabolite biomarkers of MetS and its associated risk factors to better understand the complex interplay of underlying signaling pathways. METHODS We quantified serum samples of the KORA F4 study participants (N = 2815) and analyzed 121 metabolites. Multiple regression models adjusted for clinical and lifestyle covariates were used to identify metabolites that were Bonferroni significantly associated with MetS. These findings were replicated in the SHIP-TREND-0 study (N = 988) and further analyzed for the association of replicated metabolites with the five components of MetS. Database-driven networks of the identified metabolites and their interacting enzymes were also constructed. RESULTS We identified and replicated 56 MetS-specific metabolites: 13 were positively associated (e.g., Val, Leu/Ile, Phe, and Tyr), and 43 were negatively associated (e.g., Gly, Ser, and 40 lipids). Moreover, the majority (89%) and minority (23%) of MetS-specific metabolites were associated with low HDL-C and hypertension, respectively. One lipid, lysoPC a C18:2, was negatively associated with MetS and all of its five components, indicating that individuals with MetS and each of the risk factors had lower concentrations of lysoPC a C18:2 compared to corresponding controls. Our metabolic networks elucidated these observations by revealing impaired catabolism of branched-chain and aromatic amino acids, as well as accelerated Gly catabolism. CONCLUSION Our identified candidate metabolite biomarkers are associated with the pathophysiology of MetS and its risk factors. They could facilitate the development of therapeutic strategies to prevent type 2 diabetes and cardiovascular disease. For instance, elevated levels of lysoPC a C18:2 may protect MetS and its five risk components. More in-depth studies are necessary to determine the mechanism of key metabolites in the MetS pathophysiology.
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Affiliation(s)
- Mengya Shi
- TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Partner Neuherberg, Munich-Neuherberg, Germany
| | - Siyu Han
- TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Partner Neuherberg, Munich-Neuherberg, Germany
| | - Kristin Klier
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Gisela Fobo
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Corinna Montrone
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Shixiang Yu
- TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Makoto Harada
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Partner Neuherberg, Munich-Neuherberg, Germany
| | - Ann-Kristin Henning
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Nele Friedrich
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany
| | - Martin Bahls
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Marcus Dörr
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany
| | - Henry Völzke
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- German Centre for Diabetes Research (DZD), Partner Greifswald, Neuherberg, Germany
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Hans J. Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
- German Center for Neurodegenerative Diseases (DZNE), Greifswald, Germany
| | - Cornelia Prehn
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Jerzy Adamski
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine—Qatar, Education City—Qatar Foundation, Doha, Qatar
| | - Wolfgang Rathmann
- German Center for Diabetes Research (DZD), Partner Düsseldorf, Neuherberg, Germany
- Institute of Biometrics and Epidemiology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Andreas Ruepp
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Johannes Hertel
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany
| | - Annette Peters
- German Center for Diabetes Research (DZD), Partner Neuherberg, Munich-Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute for Medical Information Processing, Biometry, and Epidemiology, Pettenkofer School of Public Health, Ludwig Maximilian University of Munich (LMU), Munich, Germany
- Munich Heart Alliance, German Center for Cardiovascular Health (DZHK E.V., Partner-Site Munich), Munich, Germany
| | - Rui Wang-Sattler
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Partner Neuherberg, Munich-Neuherberg, Germany
- Institute for Medical Information Processing, Biometry, and Epidemiology, Pettenkofer School of Public Health, Ludwig Maximilian University of Munich (LMU), Munich, Germany
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Jin Q, Xie X, Zhai Y, Zhang H. Mechanisms of folate metabolism-related substances affecting Staphylococcus aureus infection. Int J Med Microbiol 2023; 313:151577. [PMID: 36841056 DOI: 10.1016/j.ijmm.2023.151577] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 01/28/2023] [Accepted: 02/15/2023] [Indexed: 02/18/2023] Open
Abstract
Staphylococcus aureus (S. aureus) is one of the critical clinical pathogens which can cause multiple diseases ranging from skin infections to fatal sepsis. S. aureus is generally considered to be an extracellular pathogen. However, more and more evidence has shown that S. aureus can survive inside various cells. Folate plays an essential role in multiple life activities, including the conversion of serine and glycine, the remethylation of homocysteine to methionine, and the de novo synthesis of purine /dTMP, et al. More and more studies reported that S. aureus intracellular infection requires the involvement of folate metabolism. This review focused on the mechanisms of folate metabolism and related substances affecting S. aureus infection. Loss of tetrahydrofolic acid (THF)-dependent dTMP directly inhibits the nucleotide synthesis pathway of the S. aureus due to pabA deficiency. Besides, trimethoprim-sulfamethoxazole (TMP/SMX), a potent antibiotic that treats S. aureus infections, interferes in the process of the folate mechanism and leads to the production of thymidine-dependent small-colony variants (TD-SCVs). In addition, S. aureus is resistant to lysostaphin in the presence of serine hydroxymethyltransferase (SHMT). We provide new insights for understanding the molecular pathogenesis of S. aureus infection.
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Affiliation(s)
- Qiyuan Jin
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaolu Xie
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yaxuan Zhai
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Haifang Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China.
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Brancato V, Brentari I, Coscujuela Tarrero L, Furlan M, Nicassio F, Denti MA. News from around the RNA world: new avenues in RNA biology, biotechnology and therapeutics from the 2022 SIBBM meeting. Biol Open 2022; 11:277240. [PMID: 36239357 PMCID: PMC9581514 DOI: 10.1242/bio.059597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Since the formalization of the Central Dogma of molecular biology, the relevance of RNA in modulating the flow of information from DNA to proteins has been clear. More recently, the discovery of a vast set of non-coding transcripts involved in crucial aspects of cellular biology has renewed the enthusiasm of the RNA community. Moreover, the remarkable impact of RNA therapies in facing the COVID19 pandemics has bolstered interest in the translational opportunities provided by this incredible molecule. For all these reasons, the Italian Society of Biophysics and Molecular Biology (SIBBM) decided to dedicate its 17th yearly meeting, held in June 2022 in Rome, to the many fascinating aspects of RNA biology. More than thirty national and international speakers covered the properties, modes of action and applications of RNA, from its role in the control of development and cell differentiation to its involvement in disease. Here, we summarize the scientific content of the conference, highlighting the take-home message of each presentation, and we stress the directions the community is currently exploring to push forward our comprehension of the RNA World 3.0.
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Affiliation(s)
- Virginia Brancato
- Center for Genomic Science IIT@SEMM, Italian Institute of Technology, Milan 20139, Italy
| | - Ilaria Brentari
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | | | - Mattia Furlan
- Center for Genomic Science IIT@SEMM, Italian Institute of Technology, Milan 20139, Italy
| | - Francesco Nicassio
- Center for Genomic Science IIT@SEMM, Italian Institute of Technology, Milan 20139, Italy
| | - Michela A Denti
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
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7
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Prediction of Time Series Gene Expression and Structural Analysis of Gene Regulatory Networks Using Recurrent Neural Networks. ENTROPY 2022; 24:e24020141. [PMID: 35205437 PMCID: PMC8871363 DOI: 10.3390/e24020141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/14/2022] [Accepted: 01/15/2022] [Indexed: 11/17/2022]
Abstract
Methods for time series prediction and classification of gene regulatory networks (GRNs) from gene expression data have been treated separately so far. The recent emergence of attention-based recurrent neural network (RNN) models boosted the interpretability of RNN parameters, making them appealing for the understanding of gene interactions. In this work, we generated synthetic time series gene expression data from a range of archetypal GRNs and we relied on a dual attention RNN to predict the gene temporal dynamics. We show that the prediction is extremely accurate for GRNs with different architectures. Next, we focused on the attention mechanism of the RNN and, using tools from graph theory, we found that its graph properties allow one to hierarchically distinguish different architectures of the GRN. We show that the GRN responded differently to the addition of noise in the prediction by the RNN and we related the noise response to the analysis of the attention mechanism. In conclusion, this work provides a way to understand and exploit the attention mechanism of RNNs and it paves the way to RNN-based methods for time series prediction and inference of GRNs from gene expression data.
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8
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Spizzichino S, Boi D, Boumis G, Lucchi R, Liberati FR, Capelli D, Montanari R, Pochetti G, Piacentini R, Parisi G, Paone A, Rinaldo S, Contestabile R, Tramonti A, Paiardini A, Giardina G, Cutruzzolà F. Cytosolic localization and in vitro assembly of human de novo thymidylate synthesis complex. FEBS J 2021; 289:1625-1649. [PMID: 34694685 PMCID: PMC9299187 DOI: 10.1111/febs.16248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 10/21/2021] [Indexed: 11/27/2022]
Abstract
De novo thymidylate synthesis is a crucial pathway for normal and cancer cells. Deoxythymidine monophosphate (dTMP) is synthesized by the combined action of three enzymes: serine hydroxymethyltransferase (SHMT1), dihydrofolate reductase (DHFR) and thymidylate synthase (TYMS), with the latter two being targets of widely used chemotherapeutics such as antifolates and 5‐fluorouracil. These proteins translocate to the nucleus after SUMOylation and are suggested to assemble in this compartment into the thymidylate synthesis complex. We report the intracellular dynamics of the complex in cancer cells by an in situ proximity ligation assay, showing that it is also detected in the cytoplasm. This result indicates that the role of the thymidylate synthesis complex assembly may go beyond dTMP synthesis. We have successfully assembled the dTMP synthesis complex in vitro, employing tetrameric SHMT1 and a bifunctional chimeric enzyme comprising human thymidylate synthase and dihydrofolate reductase. We show that the SHMT1 tetrameric state is required for efficient complex assembly, indicating that this aggregation state is evolutionarily selected in eukaryotes to optimize protein–protein interactions. Lastly, our results regarding the activity of the complete thymidylate cycle in vitro may provide a useful tool with respect to developing drugs targeting the entire complex instead of the individual components.
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Affiliation(s)
- Sharon Spizzichino
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Dalila Boi
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Giovanna Boumis
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Roberta Lucchi
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Davide Capelli
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Roberta Montanari
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Giorgio Pochetti
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Roberta Piacentini
- Center for Life Nano & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Giacomo Parisi
- Center for Life Nano & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Alessio Paone
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Serena Rinaldo
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Angela Tramonti
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy.,Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy
| | | | - Giorgio Giardina
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Francesca Cutruzzolà
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy.,Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome, Italy
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