1
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Fernández FJ, Vega MC. Decoding anaphylatoxins: unveiling the molecular mechanisms of complement receptor activation and signaling. Trends Biochem Sci 2024; 49:280-282. [PMID: 38233283 DOI: 10.1016/j.tibs.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/19/2024]
Abstract
Recent advances in cryo-electron microscopy (Cryo-EM) have revolutionized our understanding of the complement C5a/C3a receptors that are crucial in inflammation. A recent report by Yadav et al. has elucidated the activation, ligand binding, selectivity, and signaling bias of these receptors, thereby enhancing structure-guided drug discovery. This paves the way for more effective anti-inflammatory therapies that target these receptors with unprecedented precision.
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Affiliation(s)
- Francisco J Fernández
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; Abvance Biotech SL, 28003 Madrid, Spain
| | - M Cristina Vega
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain.
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2
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Fernández FJ, Querol-García J, Navas-Yuste S, Martino F, Vega MC. X-Ray Crystallography for Macromolecular Complexes. Adv Exp Med Biol 2024; 3234:125-140. [PMID: 38507204 DOI: 10.1007/978-3-031-52193-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
X-ray crystallography has for most of the last century been the standard technique to determine the high-resolution structure of biological macromolecules, including multi-subunit protein-protein and protein-nucleic acids as large as the ribosome and viruses. As such, the successful application of X-ray crystallography to many biological problems revolutionized biology and biomedicine by solving the structures of small molecules and vitamins, peptides and proteins, DNA and RNA molecules, and many complexes-affording a detailed knowledge of the structures that clarified biological and chemical mechanisms, conformational changes, interactions, catalysis and the biological processes underlying DNA replication, translation, and protein synthesis. Now reaching well into the first quarter of the twenty-first century, X-ray crystallography shares the structural biology stage with cryo-electron microscopy and other innovative structure determination methods, as relevant and central to our understanding of biological function and structure as ever. In this chapter, we provide an overview of modern X-ray crystallography and how it interfaces with other mainstream structural biology techniques, with an emphasis on macromolecular complexes.
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Affiliation(s)
| | | | - Sergio Navas-Yuste
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain
| | - Fabrizio Martino
- Structural Biology Research Centre, Human Technopole, Milan, Italy
| | - M Cristina Vega
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain.
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3
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Santos-López J, Gómez S, Fernández FJ, Vega MC. Protein-Protein Binding Kinetics by Biolayer Interferometry. Adv Exp Med Biol 2024; 3234:73-88. [PMID: 38507201 DOI: 10.1007/978-3-031-52193-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
The specific kinetics and thermodynamics of protein-protein interactions underlie the molecular mechanisms of cellular functions; hence the characterization of these interaction parameters is central to the quantitative understanding of physiological and pathological processes. Many methods have been developed to study protein-protein interactions, which differ in various features including the interaction detection principle, the sensitivity, whether the method operates in vivo, in vitro, or in silico, the temperature control, the use of labels, immobilization, the amount of sample required, the number of measurements that can be accomplished simultaneously, or the cost. Bio-Layer Interferometry (BLI) is a label-free biophysical method to measure the kinetics of protein-protein interactions. Label-free interaction assays are a broad family of methods that do not require protein modifications (other than immobilization) or labels such as fusions with fluorescent proteins or transactivating domains or chemical modifications like biotinylation or reaction with radionuclides. Besides BLI, other label-free techniques that are widely used for determining protein-protein interactions include surface plasmon resonance (SPR), thermophoresis, and isothermal titration calorimetry (ITC), among others.
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Affiliation(s)
- Jorge Santos-López
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain
| | - Sara Gómez
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain
- Universidad Europea de Madrid, Madrid, Spain
| | | | - M Cristina Vega
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain.
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4
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López-Pérez M, Aguirre-Garrido F, Herrera-Zúñiga L, Fernández FJ. Gene as a dynamical notion: An extensive and integrative vision. Redefining the gene concept, from traditional to genic-interaction, as a new dynamical version. Biosystems 2023; 234:105060. [PMID: 37844827 DOI: 10.1016/j.biosystems.2023.105060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/08/2023] [Accepted: 10/10/2023] [Indexed: 10/18/2023]
Abstract
The current concept of gene has been very useful during the 20th and 21st centuries. However, recent advances in molecular biology and bioinformatics, which have further diversified the functional and adaptive profile of genetic information and its integration with cell physiology and environmental response, have contributed to focusing on additional new gene properties besides the traditional definition. Considering the inherent complexity of gene expression, whose adaptive objective must be referred to the Tortoise-Hare model, in which two tendencies converge, one focused on rapid adaptation to achieve survival, and the other that prevents an over-adaptation effect. In this context, a revision of the gene concept must be made, which must include these new mechanisms and approaches. In this paper, we propose a new conception of the idea of a gene that moves from a static and defined version of hereditary information to a dynamic idea that preponderates gene interaction (circumscribed to that established between protein-protein, protein-nucleic acid, and nucleic acid-nucleic acid) and the selection it exerts, as the irreducible element that works in a coordinated way in a genomic regulatory network (GRN).
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Affiliation(s)
- Marcos López-Pérez
- Environmental Sciences Department, Universidad Autónoma Metropolitana (Lerma Unit) Av. de las Garzas N° 10, Col. El Panteón, Municipio de Lerma de Villada, Estado de México, C.P. 52005, Mexico.
| | - Félix Aguirre-Garrido
- Environmental Sciences Department, Universidad Autónoma Metropolitana (Lerma Unit) Av. de las Garzas N° 10, Col. El Panteón, Municipio de Lerma de Villada, Estado de México, C.P. 52005, Mexico
| | - Leonardo Herrera-Zúñiga
- Chemistry Department, Universidad Autónoma Metropolitana (Iztapalapa Unit), C.P. 09340, Mexico City, Mexico
| | - Francisco J Fernández
- Biotechnology Department, Universidad Autónoma Metropolitana (Iztapalapa Unit), C.P. 09340, Mexico City, Mexico.
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5
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Cajamarca G, Proust V, Herskovic V, Cádiz RF, Verdezoto N, Fernández FJ. Technologies for Managing the Health of Older Adults with Multiple Chronic Conditions: A Systematic Literature Review. Healthcare (Basel) 2023; 11:2897. [PMID: 37958041 PMCID: PMC10648176 DOI: 10.3390/healthcare11212897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Multimorbidity is defined as the presence of two or more chronic medical conditions in a person, whether physical, mental or long-term infectious diseases. This is especially common in older populations, affecting their quality of life and emotionally impacting their caregivers and family. Technology can allow for monitoring, managing, and motivating older adults in their self-care, as well as supporting their caregivers. However, when several conditions are present at once, it may be necessary to manage several types of technologies, or for technology to manage the interaction between conditions. This work aims to understand and describe the technologies that are used to support the management of multimorbidity for older adults. We conducted a systematic review of ten years of scientific literature from four online databases. We reviewed a corpus of 681 research papers, finally including 25 in our review. The technologies used most frequently by older adults with multimorbidity are mobile applications and websites, and they are mostly focused on communication and connectivity. We then propose opportunities for future research on addressing the challenges in the management of several simultaneous health conditions, potentially creating a better approach than managing each condition as if it were independent.
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Affiliation(s)
- Gabriela Cajamarca
- School of Mathematical and Computational Sciences, Yachay Tech University, San Miguel de Urcuquí 100119, Ecuador;
| | - Valentina Proust
- Annenberg School for Communication, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Valeria Herskovic
- Department of Computer Science, School of Engineering, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Rodrigo F. Cádiz
- Department of Electrical Engineering, School of Engineering, and Music Institute, Faculty of Arts, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile;
| | - Nervo Verdezoto
- School of Computer Science and Informatics, Cardiff University, Cardiff CF24 4AG, UK;
| | - Francisco J. Fernández
- Faculty of Communication, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile;
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6
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Serrano I, Luque A, Ruiz-Cerulla A, Navas S, Blom AM, Rodríguez de Córdoba S, Fernández FJ, Cristina Vega M, Rodríguez-Moranta F, Guardiola J, Aran JM. C4BP(β-)-mediated immunomodulation attenuates inflammation in DSS-induced murine colitis and in myeloid cells from IBD patients. Pharmacol Res 2023; 197:106948. [PMID: 37806602 DOI: 10.1016/j.phrs.2023.106948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/10/2023]
Abstract
The most recent and promising therapeutic strategies for inflammatory bowel disease (IBD) have engaged biologics targeting single effector components involved in major steps of the immune-inflammatory processes, such as tumor necrosis factor, interleukins or integrins. Nevertheless, these molecules have not yet met expectations regarding efficacy and safety, resulting in a significant percentage of refractory or relapsing patients. Thus, novel treatment options are urgently needed. The minor isoform of the complement inhibitor C4b-binding protein, C4BP(β-), has been shown to confer a robust anti-inflammatory and immunomodulatory phenotype over inflammatory myeloid cells. Here we show that C4BP(β-)-mediated immunomodulation can significantly attenuate the histopathological traits and preserve the intestinal epithelial integrity in dextran sulfate sodium (DSS)-induced murine colitis. C4BP(β-) downregulated inflammatory transcripts, notably those related to neutrophil activity, mitigated circulating inflammatory effector cytokines and chemokines such as CXCL13, key in generating ectopic lymphoid structures, and, overall, prevented inflammatory immune cell infiltration in the colon of colitic mice. PRP6-HO7, a recombinant curtailed analogue with only immunomodulatory activity, achieved a similar outcome as C4BP(β-), indicating that the therapeutic effect is not due to the complement inhibitory activity. Furthermore, both C4BP(β-) and PRP6-HO7 significantly reduced, with comparable efficacy, the intrinsic and TLR-induced inflammatory markers in myeloid cells from both ulcerative colitis and Crohn's disease patients, regardless of their medication. Thus, the pleiotropic anti-inflammatory and immunomodulatory activity of PRP6-HO7, able to "reprogram" myeloid cells from the complex inflammatory bowel environment and to restore immune homeostasis, might constitute a promising therapeutic option for IBD.
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Affiliation(s)
- Inmaculada Serrano
- Immune-inflammatory Processes and Gene Therapeutics Group, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Ana Luque
- Immune-inflammatory Processes and Gene Therapeutics Group, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Alexandra Ruiz-Cerulla
- Department of Digestive Diseases, Bellvitge University Hospital, L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Sergio Navas
- Structural Biology of Host-Pathogen Interactions Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040 Madrid, Spain
| | - Anna M Blom
- Lund University, Department of Translational Medicine, Section of Medical Protein Chemistry, 21428 Malmö, Sweden
| | - Santiago Rodríguez de Córdoba
- Molecular Pathology/Genetics of Complement Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC) and Ciber de Enfermedades Raras (CIBERER), 28040 Madrid, Spain
| | | | - M Cristina Vega
- Structural Biology of Host-Pathogen Interactions Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040 Madrid, Spain
| | - Francisco Rodríguez-Moranta
- Department of Digestive Diseases, Bellvitge University Hospital, L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Jordi Guardiola
- Department of Digestive Diseases, Bellvitge University Hospital, L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Josep M Aran
- Immune-inflammatory Processes and Gene Therapeutics Group, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, 08908 Barcelona, Spain.
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7
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Fernández FJ, Vásquez-Lavín F, Ponce RD, Garreaud R, Hernández F, Link O, Zambrano F, Hanemann M. The economics impacts of long-run droughts: Challenges, gaps, and way forward. J Environ Manage 2023; 344:118726. [PMID: 37573693 DOI: 10.1016/j.jenvman.2023.118726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/04/2023] [Accepted: 07/27/2023] [Indexed: 08/15/2023]
Abstract
Quantifying drought's economic impacts has been key for decision-making to build future strategies and improve the development and implementation of proactive plans. However, climate change is changing drought frequency, intensity, and durability. These changes imply modifications of their economic impact, as longer droughts result in greater cumulative economic losses for water users. Though the longer the drought lasts, other factors also play a crucial role in its economic outcomes, such as Infrastructure capacity (IC), the Amount of Water in Storage (AWS) in reservoirs and aquifers, and short- and long-term responses to it. This study proposes and applies an analytical framework for the economic assessment of long-run droughts, assessing and explaining central Chile megadrought economic effects through the factors that begin to influence the economic impact level in this setting. High levels of both IC and the AWS, as well as short- and long-term responses of water users, allow for high resilience to long-run droughts, tolerating extraordinary water disruption in its society with relatively low total economic impacts. Despite this adaptability, long-term droughts bring places to a water-critical threshold where long-term adaptation strategies may be less flexible than short-term strategies, escalating the adverse economic effects. This fact suggests that the economic evaluation of megadrought needs to focus on future tipping points (substantial water scarcity). The tipping point depends on the IC, how water users manage the AWS, and adaptation strategies. Establishing the tipping point should be a priority for future interdisciplinary research.
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Affiliation(s)
- Francisco J Fernández
- Escuela de Negocios, Facultad de Economía y Gobierno, Universidad San Sebastián, Santiago, Chile; Center for Climate and Resilience Research, Chile; Center of Applied Ecology and Sustainability (CAPES), Chile.
| | - Felipe Vásquez-Lavín
- Center for Climate and Resilience Research, Chile; Center of Applied Ecology and Sustainability (CAPES), Chile; School of Economics and Management, Universidad del Desarrollo, Concepción, Chile
| | - Roberto D Ponce
- Center for Climate and Resilience Research, Chile; Center of Applied Ecology and Sustainability (CAPES), Chile; School of Economics and Management, Universidad del Desarrollo, Concepción, Chile
| | | | - Francisco Hernández
- Center for Climate and Resilience Research, Chile; Departamento de Economía y Finanzas, Facultad de Ciencias Empresariales, Universidad del Bío-Bío, Concepción, Chile
| | - Oscar Link
- Departamento de Ingeniería Civil, Facultad de Ingeniería, Universidad de Concepción, Concepción, Chile
| | - Francisco Zambrano
- Hémera Centro de Observación de la Tierra, Facultad de Ciencias, Escuela de Ingeniería en Medio Ambiente y Sustentabilidad, Santiago, Chile
| | - Michael Hanemann
- Julia Ann Wrigley Global Institute of Sustainability, Arizona State University, Tempe, AZ, USA; Department of Economics, Arizona State University, Tempe, AZ, USA
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Abstract
The complement system plays crucial roles in a wide breadth of immune and inflammatory processes and is frequently cited as an etiological or aggravating factor in many human diseases, from asthma to cancer. Complement receptors encompass at least eight proteins from four structural classes, orchestrating complement-mediated humoral and cellular effector responses and coordinating the complex cross-talk between innate and adaptive immunity. The progressive increase in understanding of the structural features of the main complement factors, activated proteolytic fragments, and their assemblies have spurred a renewed interest in deciphering their receptor complexes. In this review, we describe what is currently known about the structural biology of the complement receptors and their complexes with natural agonists and pharmacological antagonists. We highlight the fundamental concepts and the gray areas where issues and problems have been identified, including current research gaps. We seek to offer guidance into the structural biology of the complement system as structural information underlies fundamental and therapeutic research endeavors. Finally, we also indicate what we believe are potential developments in the field.
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Affiliation(s)
- Jorge Santos-López
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Karla de la Paz
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Research & Development, Abvance Biotech SL, Madrid, Spain
| | | | - M. Cristina Vega
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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9
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Rossi E, Pericacho M, Kauskot A, Gamella-Pozuelo L, Reboul E, Leuci A, Egido-Turrion C, El Hamaoui D, Marchelli A, Fernández FJ, Margaill I, Vega MC, Gaussem P, Pasquali S, Smadja DM, Bachelot-Loza C, Bernabeu C. Soluble endoglin reduces thrombus formation and platelet aggregation via interaction with αIIbβ3 integrin. J Thromb Haemost 2023; 21:1943-1956. [PMID: 36990159 DOI: 10.1016/j.jtha.2023.03.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023]
Abstract
BACKGROUND The circulating form of human endoglin (sEng) is a cleavage product of membrane-bound endoglin present on endothelial cells. Because sEng encompasses an RGD motif involved in integrin binding, we hypothesized that sEng would be able to bind integrin αIIbβ3, thereby compromising platelet binding to fibrinogen and thrombus stability. METHODS In vitro human platelet aggregation, thrombus retraction, and secretion-competition assays were performed in the presence of sEng. Surface plasmon resonance (SPR) binding and computational (docking) analyses were carried out to evaluate protein-protein interactions. A transgenic mouse overexpressing human sEng (hsEng+) was used to measure bleeding/rebleeding, prothrombin time (PT), blood stream, and embolus formation after FeCl3-induced injury of the carotid artery. RESULTS Under flow conditions, supplementation of human whole blood with sEng led to a smaller thrombus size. sEng inhibited platelet aggregation and thrombus retraction, interfering with fibrinogen binding, but did not affect platelet activation. SPR binding studies demonstrated that the specific interaction between αIIbβ3 and sEng and molecular modeling showed a good fitting between αIIbβ3 and sEng structures involving the endoglin RGD motif, suggesting the possible formation of a highly stable αIIbβ3/sEng. hsEng+ mice showed increased bleeding time and number of rebleedings compared to wild-type mice. No differences in PT were denoted between genotypes. After FeCl3 injury, the number of released emboli in hsEng+ mice was higher and the occlusion was slower compared to controls. CONCLUSIONS Our results demonstrate that sEng interferes with thrombus formation and stabilization, likely via its binding to platelet αIIbβ3, suggesting its involvement in primary hemostasis control.
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Affiliation(s)
- Elisa Rossi
- Innovative Therapies in Hemostasis, INSERM U1140, Université Paris Cité, Paris, France.
| | - Miguel Pericacho
- Department of Physiology and Pharmacology, Universidad de Salamanca, Salamanca, Spain
| | - Alexandre Kauskot
- HITh, INSERM UMR-S 1176, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Luis Gamella-Pozuelo
- Department of Physiology and Pharmacology, Universidad de Salamanca, Salamanca, Spain; Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Etienne Reboul
- Innovative Therapies in Hemostasis, INSERM U1140, Université Paris Cité, Paris, France
| | - Alexandre Leuci
- Innovative Therapies in Hemostasis, INSERM U1140, Université Paris Cité, Paris, France
| | | | - Divina El Hamaoui
- Innovative Therapies in Hemostasis, INSERM U1140, Université Paris Cité, Paris, France
| | - Aurore Marchelli
- Innovative Therapies in Hemostasis, INSERM U1140, Université Paris Cité, Paris, France
| | - Francisco J Fernández
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Isabelle Margaill
- Innovative Therapies in Hemostasis, INSERM U1140, Université Paris Cité, Paris, France
| | - M Cristina Vega
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Pascale Gaussem
- Innovative Therapies in Hemostasis, INSERM U1140, Université Paris Cité, Paris, France; Service d'hématologie biologique, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - Samuela Pasquali
- Cibles Thérapeutiques et Conception de Médicaments (CiTCoM), UMR8038 CNRS, Paris, France
| | - David M Smadja
- Innovative Therapies in Hemostasis, INSERM U1140, Université Paris Cité, Paris, France; Service d'hématologie biologique, Hôpital Européen Georges Pompidou, AP-HP, Paris, France; Laboratory of Biosurgical Research, Carpentier Foundation, Paris, France
| | | | - Carmelo Bernabeu
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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10
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Navas-Yuste S, de la Paz K, Querol-García J, Gómez-Quevedo S, Rodríguez de Córdoba S, Fernández FJ, Vega MC. The structure of Leptospira interrogans GAPDH sheds light into an immunoevasion factor that can target the anaphylatoxin C5a of innate immunity. Front Immunol 2023; 14:1190943. [PMID: 37409124 PMCID: PMC10318897 DOI: 10.3389/fimmu.2023.1190943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/30/2023] [Indexed: 07/07/2023] Open
Abstract
Leptospirosis is a neglected worldwide zoonosis involving farm animals and domestic pets caused by the Gram-negative spirochete Leptospira interrogans. This bacterium deploys a variety of immune evasive mechanisms, some of them targeted at the complement system of the host's innate immunity. In this work, we have solved the X-ray crystallographic structure of L. interrogans glyceraldehyde-3-phosphate dehydrogenase (GAPDH) to 2.37-Å resolution, a glycolytic enzyme that has been shown to exhibit moonlighting functions that potentiate infectivity and immune evasion in various pathogenic organisms. Besides, we have characterized the enzyme's kinetic parameters toward the cognate substrates and have proven that the two natural products anacardic acid and curcumin are able to inhibit L. interrogans GAPDH at micromolar concentration through a noncompetitive inhibition modality. Furthermore, we have established that L. interrogans GAPDH can interact with the anaphylatoxin C5a of human innate immunity in vitro using bio-layer interferometry and a short-range cross-linking reagent that tethers free thiol groups in protein complexes. To shed light into the interaction between L. interrogans GAPDH and C5a, we have also carried out cross-link guided protein-protein docking. These results suggest that L. interrogans could be placed in the growing list of bacterial pathogens that exploit glycolytic enzymes as extracellular immune evasive factors. Analysis of the docking results indicates a low affinity interaction that is consistent with previous evidence, including known binding modes of other α-helical proteins with GAPDH. These findings allow us to propose L. interrogans GAPDH as a potential immune evasive factor targeting the complement system.
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Affiliation(s)
- Sergio Navas-Yuste
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Karla de la Paz
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Abvance Biotech Srl, Madrid, Spain
| | - Javier Querol-García
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Abvance Biotech Srl, Madrid, Spain
| | - Sara Gómez-Quevedo
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Universidad Europea, Madrid, Spain
| | - Santiago Rodríguez de Córdoba
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomedica en Red sobre Enfermedades Raras (CIBERER), Madrid, Spain
| | - Francisco J. Fernández
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Abvance Biotech Srl, Madrid, Spain
| | - M. Cristina Vega
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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11
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Torres-García JL, Ahuactzin-Pérez M, Fernández FJ, Cortés-Espinosa DV. Bisphenol A in the environment and recent advances in biodegradation by fungi. Chemosphere 2022; 303:134940. [PMID: 35588877 DOI: 10.1016/j.chemosphere.2022.134940] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/03/2022] [Accepted: 05/08/2022] [Indexed: 06/15/2023]
Abstract
Bisphenol A (BPA) is a compound used in the manufacture of a wide variety of everyday materials that, when released into the environment, causes multiple detrimental effects on humans and other organisms. The reason for this review is to provide an overview of the presence, distribution, and concentration of BPA in water, soil, sediment, and air, as well as the process of release and migration, biomagnification, and exposure mechanisms that cause various toxic effects in humans. Therefore, it is important to seek efficient and economic strategies that allow its removal from the environment and prevent it from reaching humans through food chains. Likewise, the main removal techniques are analyzed, focusing on biological treatments, particularly the most recent advances in the degradation of BPA in different environmental matrices through the use of ligninolytic fungi, non-ligninolytic fungi and yeasts, as well as the possible routes of metabolic processes that allow their biotransformation or biodegradation due to their efficient extracellular enzyme systems. This review supports the importance of the application of new biotechnological tools for the degradation of BPA.
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Affiliation(s)
- J L Torres-García
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Vicentina, 09340, Ciudad de México, México
| | - M Ahuactzin-Pérez
- Facultad de Agrobiología, Universidad Autónoma de Tlaxcala, Autopista Tlaxcala-San Martín Km 10.5, 90120, San Felipe Ixtacuixtla, Tlaxcala, Mexico
| | - F J Fernández
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Vicentina, 09340, Ciudad de México, México
| | - Diana V Cortés-Espinosa
- Instituto Politécnico Nacional, Centro de Investigación en Biotecnología Aplicada. Carretera Estatal San Inés Tecuexcomac-Tepetitla Km 1.5, 90700, Tepetitla de Lardizabal, Tlaxcala, Mexico.
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12
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Galindo-Solís JM, Fernández FJ. Endophytic Fungal Terpenoids: Natural Role and Bioactivities. Microorganisms 2022; 10:microorganisms10020339. [PMID: 35208794 PMCID: PMC8875210 DOI: 10.3390/microorganisms10020339] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 02/01/2023] Open
Abstract
Endophytic fungi are a highly diverse group of fungi that intermittently colonize all plants without causing symptoms of the disease. They sense and respond to physiological and environmental changes of their host plant and microbiome. The inter-organism interactions are largely driven by chemical networks mediated by specialized metabolites. The balance of these complex interactions leads to healthy and strong host plants. Endophytic strains have particular machinery to produce a plethora of secondary metabolites with a variety of bioactivities and unknown functions in an ecological niche. Terpenoids play a key role in endophytism and represent an important source of bioactive molecules for human health and agriculture. In this review, we describe the role of endophytic fungi in plant health, fungal terpenoids in multiple interactions, and bioactive fungal terpenoids recently reported from endophytes, mainly from plants used in traditional medicine, as well as from algae and mangroves. Additionally, we highlight endophytic fungi as producers of important chemotherapeutic terpenoids, initially discovered in plants. Despite advances in understanding endophytism, we still have much to learn in this field. The study of the role, the evolution of interactions of endophytic fungi and their terpenoids provide an opportunity for better applications in human health and agriculture.
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Affiliation(s)
- Juan M. Galindo-Solís
- Posgrado en Biotecnología, Universidad Autonoma Metropolitana, Unidad Iztapalapa, Mexico City CP 09340, Mexico;
| | - Francisco J. Fernández
- Departamento de Biotecnología, Universidad Autónoma Metropolitana, Unidad Iztapalapa, San Rafael Atlixco No. 186, Col. Vicentina, Mexico City CP 09340, Mexico
- Correspondence: ; Tel.: +52-(55)-5804-6453
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13
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Mateu-Borrás M, González-Alsina A, Doménech-Sánchez A, Querol-García J, Fernández FJ, Vega MC, Albertí S. Pseudomonas aeruginosa adaptation in cystic fibrosis patients increases C5a levels and promotes neutrophil recruitment. Virulence 2022; 13:215-224. [PMID: 35094639 PMCID: PMC8802900 DOI: 10.1080/21505594.2022.2028484] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cystic fibrosis (CF) disease is characterized by an intense airway inflammatory response mediated by neutrophils and chronic respiratory infections caused by P. aeruginosa. High levels of the complement component C5a, the strongest neutrophil chemoattractant molecule, are commonly found in the CF lung and have been associated with a worsening of the disease. In this study, we investigated how the isolates from CF patients modulate the levels of C5a and identified the bacterial factors involved. We demonstrated that most isolates from airway chronic infections induce the production and accumulation of C5a, an effect attributable to the loss of C5a cleavage by the exoproteases alkaline protease (AprA) and elastase B (LasB). Furthermore, we found that lack of the bacterial protease-dependent C5a degradation is due to mutations in the master regulator LasR. Thus, complementation of a non-C5a-cleaving CF isolate with a functional wild-type LasR restored its ability to express both proteases, cleave C5a and reduce neutrophil recruitment in vitro. These findings suggest that the non-cleaving C5a phenotype acquired by the LasR variants frequently isolated in CF patients may account for the strong neutrophilia and general neutrophil dysfunction predisposing toward increased inflammation and reduced bacterial clearance described in CF patients.
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Affiliation(s)
- Margalida Mateu-Borrás
- Instituto Universitario de Investigación En Ciencias de La Salud, Universidad de Las Islas Baleares and Instituto de Investigación Sanitaria de Les Illes Balears, Palma de Mallorca, Spain
| | - Alex González-Alsina
- Instituto Universitario de Investigación En Ciencias de La Salud, Universidad de Las Islas Baleares and Instituto de Investigación Sanitaria de Les Illes Balears, Palma de Mallorca, Spain
| | - Antonio Doménech-Sánchez
- Instituto Universitario de Investigación En Ciencias de La Salud, Universidad de Las Islas Baleares and Instituto de Investigación Sanitaria de Les Illes Balears, Palma de Mallorca, Spain
| | - Javier Querol-García
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Francisco J. Fernández
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Mª Cristina Vega
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Sebastián Albertí
- Instituto Universitario de Investigación En Ciencias de La Salud, Universidad de Las Islas Baleares and Instituto de Investigación Sanitaria de Les Illes Balears, Palma de Mallorca, Spain
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14
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Campos C, Ruiz LAM, Fragoso‐Soriano R, Sato‐Berrú RY, Hernández‐Pérez E, Fernández FJ. Surface‐enhanced Raman spectroscopy and ultrastructural analysis of penicillin‐producing
Penicillium rubens
strains. J Microsc 2022; 286:22-30. [DOI: 10.1111/jmi.13085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Carolina Campos
- Department of Health Sciences Universidad Autónoma Metropolitana‐Iztapalapa, Av. San Rafael Atlixco 186, Col. Vicentina Mexico City Iztapalapa 09340 Mexico
| | - Luis Alberto Moreno Ruiz
- Centro de Nanociencias y Micro y Nanotecnologías del Instituto Politécnico Nacional Av. Luis Enrique Erro S/N, Unidad Profesional Adolfo López Mateos, Zacatenco, Delegación Gustavo A. Madero, C.P. Mexico City 07738 Mexico
| | - Rogelio Fragoso‐Soriano
- Department of Physics CINVESTAV‐IPN Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Mexico City Mexico
| | - Roberto Y. Sato‐Berrú
- Instituto de Ciencias Aplicadas y Tecnología Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria A.P. 70–186, Delegación Coyoacán, C.P. Mexico City 04510 Mexico
| | - Elizabeth Hernández‐Pérez
- Department of Health Sciences Universidad Autónoma Metropolitana‐Iztapalapa, Av. San Rafael Atlixco 186, Col. Vicentina Mexico City Iztapalapa 09340 Mexico
| | - Francisco J. Fernández
- Department of Biotechnology Universidad Autónoma Metropolitana‐Iztapalapa Av. San Rafael Atlixco 186, Col. Vicentina Iztapalapa 09340 Mexico
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15
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Valdez-Salazar HA, Ares MA, Fernández FJ, Ibarra JA, Torres J, Bustamante VH, De la Cruz MA. Long-chain fatty acids alter transcription of Helicobacter pylori virulence and regulatory genes. PeerJ 2021; 9:e12270. [PMID: 34760355 PMCID: PMC8567857 DOI: 10.7717/peerj.12270] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/17/2021] [Indexed: 12/18/2022] Open
Abstract
Infection with Helicobacter pylori is one of the most important risk factors for developing gastric cancer (GC). The type IV secretion system (T4SS) encoded in the cag pathogenicity island is the main virulence factor of H. pylori associated with GC. Additionally, other virulence factors have been shown to play a role in the H. pylori virulence, such as vacuolizing cytotoxin (VacA), urease, flagella, and adhesins. Long-chain fatty acids (LCFAs) are signaling molecules that affect the transcription of virulence genes in several pathogenic bacteria such as Salmonella enterica, Vibrio cholerae, Pseudomonas aeruginosa and Mycobacterium tuberculosis. However, the effect of LCFAs on the transcription of H. pylori virulence and regulatory genes remains unknown. Here we analyzed whether the transcription of virulence genes that encode T4SS and cellular envelope components, flagellins, adhesins, toxins, urease, as well as the transcription of different regulatory genes of the H. pylori strain 26695, are altered by the presence of five distinct LCFAs: palmitic, stearic, oleic, linoleic, and linolenic acids. Palmitic and oleic acids up-regulated the transcription of most of the virulence genes tested, including cagL, cagM, flaB, sabA, mraY and vacA, as well as that of the genes encoding the transcriptional regulators NikR, Fur, CheY, ArsR, FlgR, HspR, HsrA, Hup, and CrdR. In contrast, the other LCFAs differentially affected the transcription of the virulence and regulatory genes assessed. Our data show that LCFAs can act as signaling molecules that control the transcription of the H. pylori virulome.
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Affiliation(s)
- Hilda A Valdez-Salazar
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Instituto Mexicano del Seguro Social, Mexico City, Mexico.,Posgrado en Biología Experimental, DCBS., Universidad Autónoma Metropolitana (UAM) Iztapalapa, Mexico City, Mexico
| | - Miguel A Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Instituto Mexicano del Seguro Social, Mexico City, Mexico.,Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Francisco J Fernández
- Laboratorio de Ingeniería Genética y Metabolismo Secundario, Departamento de Biotecnología, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - J Antonio Ibarra
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Javier Torres
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Víctor H Bustamante
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Miguel A De la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Instituto Mexicano del Seguro Social, Mexico City, Mexico
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16
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Ruiz-Llorente L, Vega MC, Fernández FJ, Langa C, Morrell NW, Upton PD, Bernabeu C. Generation of a Soluble Form of Human Endoglin Fused to Green Fluorescent Protein. Int J Mol Sci 2021; 22:ijms222011282. [PMID: 34681942 PMCID: PMC8539536 DOI: 10.3390/ijms222011282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 10/08/2021] [Accepted: 10/15/2021] [Indexed: 01/06/2023] Open
Abstract
Endoglin (Eng, CD105) is a type I membrane glycoprotein that functions in endothelial cells as an auxiliary receptor for transforming growth factor β (TGF-β)/bone morphogenetic protein (BMP) family members and as an integrin ligand, modulating the vascular pathophysiology. Besides the membrane-bound endoglin, there is a soluble form of endoglin (sEng) that can be generated by the action of the matrix metalloproteinase (MMP)-14 or -12 on the juxtamembrane region of its ectodomain. High levels of sEng have been reported in patients with preeclampsia, hypercholesterolemia, atherosclerosis and cancer. In addition, sEng is a marker of cardiovascular damage in patients with hypertension and diabetes, plays a pathogenic role in preeclampsia, and inhibits angiogenesis and tumor proliferation, migration, and invasion in cancer. However, the mechanisms of action of sEng have not yet been elucidated, and new tools and experimental approaches are necessary to advance in this field. To this end, we aimed to obtain a fluorescent form of sEng as a new tool for biological imaging. Thus, we cloned the extracellular domain of endoglin in the pEGFP-N1 plasmid to generate a fusion protein with green fluorescent protein (GFP), giving rise to pEGFP-N1/Eng.EC. The recombinant fusion protein was characterized by transient and stable transfections in CHO-K1 cells using fluorescence microscopy, SDS-PAGE, immunodetection, and ELISA techniques. Upon transfection with pEGFP-N1/Eng.EC, fluorescence was readily detected in cells, indicating that the GFP contained in the recombinant protein was properly folded into the cytosol. Furthermore, as evidenced by Western blot analysis, the secreted fusion protein yielded the expected molecular mass and displayed a specific fluorescent signal. The fusion protein was also able to bind to BMP9 and BMP10 in vitro. Therefore, the construct described here could be used as a tool for functional in vitro studies of the extracellular domain of endoglin.
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Affiliation(s)
- Lidia Ruiz-Llorente
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (L.R.-L.); (M.C.V.); (F.J.F.); (C.L.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28040 Madrid, Spain
- Biochemistry and Molecular Biology Unit, Department of System Biology, School of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, 28871 Madrid, Spain
| | - M. Cristina Vega
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (L.R.-L.); (M.C.V.); (F.J.F.); (C.L.)
| | - Francisco J. Fernández
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (L.R.-L.); (M.C.V.); (F.J.F.); (C.L.)
| | - Carmen Langa
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (L.R.-L.); (M.C.V.); (F.J.F.); (C.L.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28040 Madrid, Spain
| | - Nicholas W. Morrell
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK; (N.W.M.); (P.D.U.)
| | - Paul D. Upton
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK; (N.W.M.); (P.D.U.)
| | - Carmelo Bernabeu
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (L.R.-L.); (M.C.V.); (F.J.F.); (C.L.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28040 Madrid, Spain
- Correspondence:
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17
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Fernández FJ, Muñoz M, Ponce Oliva RD, Vásquez-Lavín F, Gelcich S. Gaps, biases, and future directions in research on the impacts of anthropogenic land-use change on aquatic ecosystems: a topic-based bibliometric analysis. Environ Sci Pollut Res Int 2021; 28:43173-43189. [PMID: 34165733 DOI: 10.1007/s11356-021-15010-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 06/15/2021] [Indexed: 06/13/2023]
Abstract
Anthropogenic land use change (ALUC) satisfies human needs but also impacts aquatic ecosystems. Aquatic ecosystems are intrinsically linked with terrestrial landscapes, an association that is already recognized as a key factor to address future research and effective governance. However, the complexity and range of the impact of ALUC in aquatic ecosystems have been fundamental challenges and have implicitly routed the analysis to particular segments, drivers, management, or effects of the theme. In this study, we present an attempt to frame the subject in a broader context through a topic-based bibliometric analysis. Our aim is to identify possible biases and gaps in the current scientific literature and detect the main topics that have characterized the theme. Our results show an unequal distribution of articles by country when we analyzed the authors' affiliation and also a slight increase in contributions from social and economic disciplines, although they are still underrepresented. Moreover, we distinguish topics whose prevalence seems to change, especially those topics where the use of scenario analysis and multi-stressors are considered. We discuss the main biases and gaps revealed by our results, concluding that future studies on the impact of ALUC on aquatic ecosystems should better integrate social and economic disciplines and expand geographic frontiers.
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Affiliation(s)
- Francisco J Fernández
- School of Agronomy, Faculty of Sciences, Universidad Mayor, Santiago, Chile.
- Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biologicas, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Manuel Muñoz
- Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biologicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Roberto D Ponce Oliva
- Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biologicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Instituto Milenio en Socio-Ecologia Costera (SECOS), Pontificia Universidad Católica de Chile, Santiago, Chile
- School of Business and Economics , Universidad del Desarrollo , Concepción, Chile
- Water Research Center for Agriculture and Mining (CRHIAM) , Concepción, Chile
| | - Felipe Vásquez-Lavín
- Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biologicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Instituto Milenio en Socio-Ecologia Costera (SECOS), Pontificia Universidad Católica de Chile, Santiago, Chile
- School of Business and Economics , Universidad del Desarrollo , Concepción, Chile
| | - Stefan Gelcich
- Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biologicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Instituto Milenio en Socio-Ecologia Costera (SECOS), Pontificia Universidad Católica de Chile, Santiago, Chile
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18
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Fàbrega-Ferrer M, Cuervo A, Fernández FJ, Machón C, Pérez-Luque R, Pous J, Vega MC, Carrascosa JL, Coll M. Using a partial atomic model from medium-resolution cryo-EM to solve a large crystal structure. Acta Crystallogr D Struct Biol 2021; 77:11-18. [PMID: 33404521 PMCID: PMC7787105 DOI: 10.1107/s2059798320015156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 11/13/2020] [Indexed: 11/21/2022] Open
Abstract
Medium-resolution cryo-electron microscopy maps, in particular when they include a significant number of α-helices, may allow the building of partial models that are useful for molecular-replacement searches in large crystallographic structures when the structures of homologs are not available and experimental phasing has failed. Here, as an example, the solution of the structure of a bacteriophage portal using a partial 30% model built into a 7.8 Å resolution cryo-EM map is shown. Inspection of the self-rotation function allowed the correct oligomerization state to be determined, and density-modification procedures using rotation matrices and a mask based on the cryo-EM structure were critical for solving the structure. A workflow is described that may be applicable to similar cases and this strategy is compared with direct use of the cryo-EM map for molecular replacement.
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Affiliation(s)
- Montserrat Fàbrega-Ferrer
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (IBMB–CSIC), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Ana Cuervo
- Centro Nacional de Biotecnología (CNB–CSIC), Darwin 3, 28049 Madrid, Spain
| | - Francisco J. Fernández
- Centro de Investigaciones Biológicas (CIB–CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Cristina Machón
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (IBMB–CSIC), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Rosa Pérez-Luque
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (IBMB–CSIC), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Joan Pous
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - M. Cristina Vega
- Centro de Investigaciones Biológicas (CIB–CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - José L. Carrascosa
- Centro Nacional de Biotecnología (CNB–CSIC), Darwin 3, 28049 Madrid, Spain
| | - Miquel Coll
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (IBMB–CSIC), Baldiri Reixac 10, 08028 Barcelona, Spain
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19
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Alegria-Lertxundi I, Aguirre C, Bujanda L, Fernández FJ, Polo F, Ordovás JM, Etxezarraga MC, Zabalza I, Larzabal M, Portillo I, M. de Pancorbo M, Palencia-Madrid L, Garcia-Etxebarria K, Rocandio AM, Arroyo-Izaga M. Gene-Diet Interactions in Colorectal Cancer: Survey Design, Instruments, Participants and Descriptive Data of a Case-Control Study in the Basque Country. Nutrients 2020; 12:nu12082362. [PMID: 32784647 PMCID: PMC7468855 DOI: 10.3390/nu12082362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 02/07/2023] Open
Abstract
Epidemiologic studies have revealed inconsistent evidence of gene-diet interaction in relation to colorectal cancer (CRC). The aim of this study was to analyze them in a sample of cases and controls from the population-based bowel cancer screening program of the Osakidetza/Basque Health Service. This study analyzed dietetic, genetic, demographic, socioeconomic factors and lifestyles. In the present manuscript, the survey design, sampling, instruments, measurements and related quality management were presented. Moreover, we analyze differences between cases and controls in some data, especially those related to diet. The participants were 308 cases and 308 age- and sex-matched subjects as controls. Cases were more likely than controls to have overweight/obesity (67.5% vs. 58.1%, p < 0.05), a lower intake of vitamin B2 (0.86 ± 0.23 vs. 0.92 ± 0.23 mg/1000 kcal, p < 0.01) and calcium:phosphorus ratio (0.62 ± 0.12 vs. 0.65 ± 0.13, p < 0.01). A higher proportion of cases than controls did not meet the Nutritional Objectives for saturated fatty acids (85.7% vs. 67.5%, p < 0.001) or cholesterol (35.4% vs. 25.0%, p < 0.01). In conclusion, the present study provides valuable data for analyzing the complexity of gene-diet interaction in relation to CRC. The results presented here suggest that overweight/obesity and a high intake of certain dietary components, especially saturated fatty acids and cholesterol, are more frequent in cases than in controls.
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Affiliation(s)
- Iker Alegria-Lertxundi
- Department of Pharmacy and Food Sciences. Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain; (I.A.-L.); (A.M.R.)
| | - Carmelo Aguirre
- Pharmacovigilance Unit, Galdakao-Usansolo University Hospital, Osakidetza, 48960 Galdakao, Spain;
| | - Luis Bujanda
- Department of Gastroenterology, Donostia University Hospital/Biodonostia Health Research Institute, University of the Basque Country UPV/EHU, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 20014 San Sebastian, Spain;
| | - Francisco J. Fernández
- Department of Gastroenterology, Galdakao-Usansolo University Hospital, Osakidetza, 48960 Galdakao, Spain;
| | - Francisco Polo
- Department of Gastroenterology, Basurto University Hospital, Osakidetza, 48013 Bilbao, Spain;
| | - José M. Ordovás
- Nutrition and Genomics Laboratory, Jean Mayer Human Nutrition Research Center on Aging, Tufts University, Boston, MA 02111, USA;
- Institute IMDEA Food, Institutos Madrileños de Estudios Avanzados (IMDEA), 28049 Madrid, Spain
| | - M. Carmen Etxezarraga
- Department of Pathology, Basurto University Hospital, Osakidetza, 48013 Bilbao, Spain;
- Department of Physician and Surgeon Specialities, University of the Basque Country UPV/EHU, 48940 Leioa, Spain
| | - Iñaki Zabalza
- Department of Pathology, Galdakao-Usansolo University Hospital, Osakidetza, 48960 Galdakao, Spain;
| | - Mikel Larzabal
- Department of Pathology, Donostia Hospital/Biodonostia Health Research Institute, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 20014 San Sebastian, Spain;
| | - Isabel Portillo
- Central Coordinating Center of the Bowel Cancer Screening Program, Healthcare subdirectorate, Osakidetza, 48011 Bilbao, Spain;
| | - Marian M. de Pancorbo
- BIOMICs Research Group, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain; (M.M.d.P.); (L.P.-M.)
| | - Leire Palencia-Madrid
- BIOMICs Research Group, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain; (M.M.d.P.); (L.P.-M.)
| | - Koldo Garcia-Etxebarria
- Biodonostia Health Research Institute, Gastrointestional genetics group, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 20014 San Sebastian, Spain;
| | - Ana M. Rocandio
- Department of Pharmacy and Food Sciences. Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain; (I.A.-L.); (A.M.R.)
- BIOMICs Research Group, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain; (M.M.d.P.); (L.P.-M.)
| | - Marta Arroyo-Izaga
- Department of Pharmacy and Food Sciences. Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain; (I.A.-L.); (A.M.R.)
- Correspondence:
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20
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Alegria-Lertxundi I, Aguirre C, Bujanda L, Fernández FJ, Polo F, Ordovás JM, Etxezarraga MC, Zabalza I, Larzabal M, Portillo I, de Pancorbo MM, Garcia-Etxebarria K, Rocandio AM, Arroyo-Izaga M. Food groups, diet quality and colorectal cancer risk in the Basque Country. World J Gastroenterol 2020; 26:4108-4125. [PMID: 32821073 PMCID: PMC7403796 DOI: 10.3748/wjg.v26.i28.4108] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/03/2020] [Accepted: 07/16/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The results obtained to date concerning food groups, diet quality and colorectal cancer (CRC) risk vary according to criteria used and the study populations. AIM To study the relationships between food groups, diet quality and CRC risk, in an adult population of the Basque Country (North of Spain). METHODS This observational study included 308 patients diagnosed with CRC and 308 age- and sex-matched subjects as controls. During recruitment, dietary, anthropometric, lifestyle, socioeconomic, demographic and health status information was collected. Adherence to the dietary recommendations was evaluated utilizing the Healthy Eating Index for the Spanish Diet and the MedDietScore. Conditional logistic regressions were used to evaluate the associations of food group intakes, diet quality scores, categorized in tertiles, with CRC risk. RESULTS The adjusted models for potential confounding factors showed a direct association between milk and dairy products consumption, in particular high-fat cheeses [odds ratio (OR) third tertile vs first tertile = 1.87, 95% confidence intervals (CI): 1.11-3.16], and CRC risk. While the consumption of fiber-containing foods, especially whole grains (OR third tertile vs first tertile = 0.62, 95%CI: 0.39-0.98), and fatty fish (OR third tertile vs first tertile = 0.53, 95%CI: 0.27-0.99) was associated with a lower risk for CRC. Moreover, higher MD adherence was associated with a reduced CRC risk in adjusted models (OR third tertile vs first tertile = 0.40, 95%CI: 0.20-0.80). CONCLUSION Direct associations were found for high-fat cheese, whereas an inverse relation was reported for fiber-containing foods and fatty fish, as well as adherence to a Mediterranean dietary pattern.
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Affiliation(s)
- Iker Alegria-Lertxundi
- Department of Pharmacy and Food Sciences, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz 01006, Spain
| | - Carmelo Aguirre
- Pharmacovigilance Unit, Galdakao-Usansolo University Hospital, Osakidetza, Galdakao 48960, Spain
| | - Luis Bujanda
- Department of Gastroenterology, Donostia University Hospital / Biodonostia, University of the Basque Country UPV/EHU, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), San Sebastian 20014, Spain
| | - Francisco J Fernández
- Department of Gastroenterology, Galdakao-Usansolo University Hospital, Osakidetza, Galdakao 48960, Spain
| | - Francisco Polo
- Department of Gastroenterology, Basurto University Hospital, Osakidetza, Bilbao 48013, Spain
| | - José Mª Ordovás
- Nutrition and Genomics Laboratory, Jean Mayer Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts 02111, United States of America; IMDEA Food, Madrid 28049, Spain
| | - Mª Carmen Etxezarraga
- Department of Pathology, Basurto University Hospital, Osakidetza, Bilbao 48013, Spain; Department of Physician and Surgeon Specialities, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | - Iñaki Zabalza
- Department of Pathology, Galdakao-Usansolo University Hospital, Osakidetza, Galdakao 48960, Spain
| | - Mikel Larzabal
- Department of Pathology, Donostia Hospital / Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), San Sebastian 20014, Spain
| | - Isabel Portillo
- Colorectal cancer screening programme, Osakidetza, Bilbao 48011, Spain
| | - Marian M de Pancorbo
- BIOMICs Research Group, University of the Basque Country UPV/EHU, Vitoria-Gasteiz 01006, Spain
| | - Koldo Garcia-Etxebarria
- Biodonostia, Gastrointestinal genetics group, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), San Sebastian 20014, Spain
| | - Ana Mª Rocandio
- BIOMICs Research Group, University of the Basque Country UPV/EHU, Vitoria-Gasteiz 01006, Spain
| | - Marta Arroyo-Izaga
- Department of Pharmacy and Food Sciences, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz 01006, Spain
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21
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Roca M, Navas-Yuste S, Zinovjev K, López-Estepa M, Gómez S, Fernández FJ, Vega MC, Tuñón I. Elucidating the Catalytic Reaction Mechanism of Orotate Phosphoribosyltransferase by Means of X-ray Crystallography and Computational Simulations. ACS Catal 2020. [DOI: 10.1021/acscatal.9b05294] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maite Roca
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Sergio Navas-Yuste
- Structural and Chemical Biology, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
| | - Kirill Zinovjev
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
| | - Miguel López-Estepa
- Structural and Chemical Biology, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
| | - Sara Gómez
- Structural and Chemical Biology, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
| | - Francisco J. Fernández
- Structural and Chemical Biology, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
| | - M. Cristina Vega
- Structural and Chemical Biology, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
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22
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Gómez S, Navas-Yuste S, Payne AM, Rivera W, López-Estepa M, Brangbour C, Fullà D, Juanhuix J, Fernández FJ, Vega MC. Peroxisomal catalases from the yeasts Pichia pastoris and Kluyveromyces lactis as models for oxidative damage in higher eukaryotes. Free Radic Biol Med 2019; 141:279-290. [PMID: 31238127 DOI: 10.1016/j.freeradbiomed.2019.06.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/13/2019] [Accepted: 06/21/2019] [Indexed: 01/14/2023]
Abstract
Catalases are among the main scavengers of reactive oxygen species (ROS) present in the peroxisome, thereby preventing oxidative cellular and tissular damage. In human, multiple diseases are associated with malfunction of these organelles, which causes accumulation of ROS species and consequently the inefficient detoxification of cells. Despite intense research, much remains to be clarified about the precise molecular role of catalase in cellular homeostasis. Yeast peroxisomes and their peroxisomal catalases have been used as eukaryotic models for oxidative metabolism, ROS generation and detoxification, and associated pathologies. In order to provide reliable models for oxidative metabolism research, we have determined the high-resolution crystal structures of peroxisomal catalase from two important biotechnology and basic biology yeast models, Pichia pastoris and Kluyveromyces lactis. We have performed an extensive functional, biochemical and stability characterization of both enzymes in order to establish their differential activity profiles. Furthermore, we have analyzed the role of the peroxisomal catalase under study in the survival of yeast to oxidative burst challenges combining methanol, water peroxide, and sodium chloride. Interestingly, whereas catalase activity was induced 200-fold upon challenging the methylotrophic P. pastoris cells with methanol, the increase in catalase activity in the non-methylotrophic K. lactis was only moderate. The inhibitory effect of sodium azide and β-mercaptoethanol over both catalases was analyzed, establishing IC50 values for both compounds that are consistent with an elevated resistance of both enzymes toward these inhibitors. Structural comparison of these two novel catalase structures allows us to rationalize the differential susceptibility to inhibitors and oxidative bursts. The inherent worth and validity of the P. pastoris and K. lactis yeast models for oxidative damage will be strengthened by the availability of reliable structural-functional information on these enzymes, which are central to our understanding of peroxisomal response toward oxidative stress.
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Affiliation(s)
- Sara Gómez
- Structural and Chemical Biology Department, Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Sergio Navas-Yuste
- Structural and Chemical Biology Department, Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Asia M Payne
- Structural and Chemical Biology Department, Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Wilmaris Rivera
- Structural and Chemical Biology Department, Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Miguel López-Estepa
- Structural and Chemical Biology Department, Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Clotilde Brangbour
- Structural and Chemical Biology Department, Center for Biological Research (CIB-CSIC), Madrid, Spain
| | | | | | - Francisco J Fernández
- Structural and Chemical Biology Department, Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - M Cristina Vega
- Structural and Chemical Biology Department, Center for Biological Research (CIB-CSIC), Madrid, Spain.
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23
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Cuervo A, Fàbrega-Ferrer M, Machón C, Conesa JJ, Fernández FJ, Pérez-Luque R, Pérez-Ruiz M, Pous J, Vega MC, Carrascosa JL, Coll M. Structures of T7 bacteriophage portal and tail suggest a viral DNA retention and ejection mechanism. Nat Commun 2019; 10:3746. [PMID: 31431626 PMCID: PMC6702177 DOI: 10.1038/s41467-019-11705-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 07/18/2019] [Indexed: 12/31/2022] Open
Abstract
Double-stranded DNA bacteriophages package their genome at high pressure inside a procapsid through the portal, an oligomeric ring protein located at a unique capsid vertex. Once the DNA has been packaged, the tail components assemble on the portal to render the mature infective virion. The tail tightly seals the ejection conduit until infection, when its interaction with the host membrane triggers the opening of the channel and the viral genome is delivered to the host cell. Using high-resolution cryo-electron microscopy and X-ray crystallography, here we describe various structures of the T7 bacteriophage portal and fiber-less tail complex, which suggest a possible mechanism for DNA retention and ejection: a portal closed conformation temporarily retains the genome before the tail is assembled, whereas an open portal is found in the tail. Moreover, a fold including a seven-bladed β-propeller domain is described for the nozzle tail protein.
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Affiliation(s)
- Ana Cuervo
- Centro Nacional de Biotecnología, (CNB-CSIC), Darwin 3, 28049, Madrid, Spain
| | - Montserrat Fàbrega-Ferrer
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Cristina Machón
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Baldiri Reixac 10, 08028, Barcelona, Spain
| | - José Javier Conesa
- Centro Nacional de Biotecnología, (CNB-CSIC), Darwin 3, 28049, Madrid, Spain
| | - Francisco J Fernández
- Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
- Abvance Biotech srl, Ave. Reina Victoria 32, 28003, Madrid, Spain
| | - Rosa Pérez-Luque
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Mar Pérez-Ruiz
- Centro Nacional de Biotecnología, (CNB-CSIC), Darwin 3, 28049, Madrid, Spain
| | - Joan Pous
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - M Cristina Vega
- Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - José L Carrascosa
- Centro Nacional de Biotecnología, (CNB-CSIC), Darwin 3, 28049, Madrid, Spain.
| | - Miquel Coll
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain.
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Baldiri Reixac 10, 08028, Barcelona, Spain.
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24
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Gómez S, Querol-García J, Sánchez-Barrón G, Subias M, González-Alsina À, Franco-Hidalgo V, Albertí S, Rodríguez de Córdoba S, Fernández FJ, Vega MC. The Antimicrobials Anacardic Acid and Curcumin Are Not-Competitive Inhibitors of Gram-Positive Bacterial Pathogenic Glyceraldehyde-3-Phosphate Dehydrogenase by a Mechanism Unrelated to Human C5a Anaphylatoxin Binding. Front Microbiol 2019; 10:326. [PMID: 30863383 PMCID: PMC6400076 DOI: 10.3389/fmicb.2019.00326] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 02/07/2019] [Indexed: 12/12/2022] Open
Abstract
The ubiquitous and highly abundant glycolytic enzyme D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is pivotal for the energy and carbon metabolism of most organisms, including human pathogenic bacteria. For bacteria that depend mostly on glycolysis for survival, GAPDH is an attractive target for inhibitor discovery. The availability of high-resolution structures of GAPDH from various pathogenic bacteria is central to the discovery of new antibacterial compounds. We have determined the X-ray crystal structures of two new GAPDH enzymes from Gram-positive bacterial pathogens, Streptococcus pyogenes and Clostridium perfringens. These two structures, and the recent structure of Atopobium vaginae GAPDH, reveal details in the active site that can be exploited for the design of novel inhibitors based on naturally occurring molecules. Two such molecules, anacardic acid and curcumin, have been found to counter bacterial infection in clinical settings, although the cellular targets responsible for their antimicrobial properties remain unknown. We show that both anacardic acid and curcumin inhibit GAPDH from two bacterial pathogens through uncompetitive and non-competitive mechanisms, suggesting GAPDH as a relevant pharmaceutical target for antibacterial development. Inhibition of GAPDH by anacardic acid and curcumin seems to be unrelated to the immune evasion function of pathogenic bacterial GAPDH, since neither natural compound interfere with binding to the human C5a anaphylatoxin.
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Affiliation(s)
- Sara Gómez
- Center for Biological Research, Spanish National Research Council, Madrid, Spain
| | - Javier Querol-García
- Center for Biological Research, Spanish National Research Council, Madrid, Spain
| | - Gara Sánchez-Barrón
- Center for Biological Research, Spanish National Research Council, Madrid, Spain
| | - Marta Subias
- Center for Biological Research, Spanish National Research Council, Madrid, Spain.,CIBER de Enfermedades Raras, Madrid, Spain
| | - Àlex González-Alsina
- Institut Universitari d'Investigació en Ciències de la Salut, University of the Balearic Islands, Mallorca, Spain
| | | | - Sebastián Albertí
- Institut Universitari d'Investigació en Ciències de la Salut, University of the Balearic Islands, Mallorca, Spain
| | - Santiago Rodríguez de Córdoba
- Center for Biological Research, Spanish National Research Council, Madrid, Spain.,CIBER de Enfermedades Raras, Madrid, Spain
| | | | - M Cristina Vega
- Center for Biological Research, Spanish National Research Council, Madrid, Spain
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25
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Mejía A, Luna D, Fernández FJ, Barrios-González J, H. Gutierrez L, Reyes AG, Absalón AE, Kelly S. Improving rifamycin production in Amycolatopsis mediterranei by expressing a Vitreoscilla hemoglobin ( vhb) gene fused to a cytochrome P450 monooxygenase domain. 3 Biotech 2018; 8:456. [PMID: 30370197 DOI: 10.1007/s13205-018-1472-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 10/09/2018] [Indexed: 10/28/2022] Open
Abstract
Expression of the vhb gene encoding hemoglobin from Vitreoscilla stercoraria in several organisms, clearly enhances oxygen-dependent product formation. In a previous work, we expressed the vhb gene that encodes hemoglobin from V. stercoraria in Amycolatopsis mediterranei, resulting in an increase (oxygen-dependent formation) in rifamycin B production. In the present work, we first confirm; by heterologous expression in Escherichia coli, that rif-orf5 from the rifamycin biosynthetic gene cluster, really encodes a cytochrome P450 enzyme, which is the key step for oxygen incorporation in the final biosynthetic product. Likewise, we fused rif-orf5 to the vhb gene, as part of a genetic engineering strategy. The fused genes were used to generate an Amycolatopsis mediterranei transformant (Msb-HbCYP5). Interestingly, the fermentation of Msb-HbCYP5 manifested 1.5-fold higher rifamicin B production than the transformant with only the hemoglobin gene, and 2.2-fold higher than the parental strain.
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26
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Herrera-Morande A, Castro-Fernández V, Merino F, Ramírez-Sarmiento CA, Fernández FJ, Vega MC, Guixé V. Protein topology determines substrate-binding mechanism in homologous enzymes. Biochim Biophys Acta Gen Subj 2018; 1862:2869-2878. [PMID: 30251675 DOI: 10.1016/j.bbagen.2018.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/21/2018] [Accepted: 09/11/2018] [Indexed: 10/28/2022]
Abstract
During evolution, some homologs proteins appear with different connectivity between secondary structures (different topology) but conserving the tridimensional arrangement of them (same architecture). These events can produce two types of arrangements; circular permutation or non-cyclic permutations. The first one results in the N and C terminus transferring to a different position on a protein sequence while the second refers to a more complex arrangement of the structural elements. In ribokinase superfamily, two different topologies can be identified, which are related to each other as a non-cyclic permutation occurred during the evolution. Interestingly, this change in topology is correlated with the nucleotide specificity of its members. Thereby, the connectivity of the secondary elements allows us to distinguish an ATP-dependent and an ADP-dependent topology. Here we address the impact of introducing the topology of a homologous ATP-dependent kinase in an ADP-dependent kinase (Thermococcus litoralis glucokinase) in the structure, nucleotide specificity, and substrate binding order of the engineered enzyme. Structural evidence demonstrates that rewiring the topology of TlGK leads to an active and soluble enzyme without modifications on its three-dimensional architecture. The permuted enzyme (PerGK) retains the nucleotide preference of the parent TlGK enzyme but shows a change in the substrate binding order. Our results illustrate how the rearrangement of the protein folding topology during the evolution of the ribokinase superfamily enzymes may have dictated the substrate-binding order in homologous enzymes of this superfamily.
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Affiliation(s)
| | | | - Felipe Merino
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | | | - Francisco J Fernández
- Centro de Investigaciones Biológicas (CIB-CSIC), Structural and Chemical Biology Dep., Madrid, Spain
| | - M Cristina Vega
- Centro de Investigaciones Biológicas (CIB-CSIC), Structural and Chemical Biology Dep., Madrid, Spain.
| | - Victoria Guixé
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
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27
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Affiliation(s)
- José R Regueiro
- Complutense University School of Medicine, Dept. of Immunology, Ophthalmology and ENT, 12 de Octubre Health Research Institute (imas12), 28040, Madrid, Spain.
| | | | - M Cristina Vega
- Center for Biological Research, Spanish National Research Council (CIB-CSIC), 28040 Madrid, Spain.
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28
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García-Martín E, Pueyo V, Martin J, Almarcegui C, Ara JR, Dolz I, Honrubia FM, Fernández FJ. Progressive Changes in the Retinal Nerve Fiber Layer in Patients with Multiple Sclerosis. Eur J Ophthalmol 2018; 20:167-73. [DOI: 10.1177/112067211002000123] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Purpose To quantify changes in the retinal nerve fiber layer (RNFL) of patients with multiple sclerosis (MS) over a 1-year time period and to compare the ability of noninvasive diagnostic imaging devices and visual evoked potentials (VEP) to detect axonal loss in these patients. Methods Eighty-one patients with MS underwent a complete ophthalmic examination that included assessment of visual acuity and color vision, refractive evaluation, visual field examination, optical coherence tomography (OCT), scanning laser polarimetry (GDx), and measurement of VEP. All the patients were re-evaluated after a period of 12 months in order to quantify any change in the RNFL. Only one randomly chosen eye from each patient was included in the study. Results Statistically significant differences between the 2 examinations were recorded for the overall mean and inferior RNFL thickness and the macular volume, as assessed by OCT, as well as for the temporal-superior-nasal-inferior-temporal average standard deviation provided by GDx. The greatest differences were obtained for the mean RNFL thickness (90.46 μm vs 85.96 μm). Changes in the optic nerve were detected by structural measurements but not by functional assessments. Conclusions Axonal loss in the optic nerve of patients with MS is greater than that expected in healthy subjects, regardless of the presence of a previous optic neuritis.
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Affiliation(s)
| | - Victoria Pueyo
- Ophthalmology Department, Miguel Servet University Hospital, Zaragoza
| | - Jesus Martin
- Neurology Department, Miguel Servet University Hospital, Zaragoza
| | - Carmen Almarcegui
- Neurophysiology Department, Miguel Servet University Hospital, Zaragoza - Spain
| | - Jose R. Ara
- Neurology Department, Miguel Servet University Hospital, Zaragoza
| | - Isabel Dolz
- Neurophysiology Department, Miguel Servet University Hospital, Zaragoza - Spain
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29
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Fernández FJ, Gómez S, Vega MC. Pathogens' toolbox to manipulate human complement. Semin Cell Dev Biol 2017; 85:98-109. [PMID: 29221973 DOI: 10.1016/j.semcdb.2017.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 11/30/2017] [Accepted: 12/03/2017] [Indexed: 12/15/2022]
Abstract
The surveillance and pathogen fighting functions of the complement system have evolved to protect mammals from life-threatening infections. In turn, pathogens have developed complex molecular mechanisms to subvert, divert and evade the effector functions of the complement. The study of complement immunoevasion by pathogens sheds light on their infection drivers, knowledge that is essential to implement therapies. At the same time, complement evasion also acts as a discovery ground that reveals important aspects of how complement works under physiological conditions. In recent years, complex interrelationships between infection insults and the onset of autoimmune and complement dysregulation diseases have led to propose that encounters with pathogens can act as triggering factors for disease. The correct management of these diseases involves the recognition of their triggering factors and the development and administration of complement-associated molecular therapies. Even more recently, unsuspected proteins from pathogens have been shown to possess moonlighting functions as virulence factors, raising the possibility that behind the first line of virulence factors there be many more pathogen proteins playing secondary, helping and supporting roles for the pathogen to successfully establish infections. In an era where antibiotics have a progressively reduced effect on the management and control of infectious diseases worldwide, knowledge on the mechanisms of pathogenic invasion and evasion look more necessary and pressing than ever.
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Affiliation(s)
| | - Sara Gómez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - M Cristina Vega
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
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30
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Escamilla-Martínez EE, Cisneros YMÁ, Fernández FJ, Quirasco-Baruch M, Ponce-Alquicira E. Identification of Structural and Immunity Genes of a Class IIb Bacteriocin Encoded in the Enterocin A Operon of Enterococcus faecium Strain MXVK29. J Food Prot 2017; 80:1851-1856. [PMID: 28990822 DOI: 10.4315/0362-028x.jfp-17-039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 05/31/2017] [Indexed: 11/11/2022]
Abstract
The Enterococcus faecium strain MXVK29, isolated from fermented sausages, produces a bacteriocin with a molecular mass of 3.5 kDa that belongs to the class of enterocins II.1, according to the terminal amino acid sequence, and has been identified as enterocin A. This bacteriocin is active against selected strains of Listeria, Staphylococcus, Pediococcus, and Enterococcus. In this study, we identified the genes adjacent to the structural gene for this bacteriocin, such as the immunity gene (entI) and the inducer gene (entF). Accessory genes for this bacteriocin, such as entK, entR, and entT, were identified as well, in addition to the orf2 and orf3, showing a high identity with class IIb peptides bacteriocins. The orf2 shows the consensus motif GxxxG, similar to those shown by bacteriocins such as PlnNC8α, EntCα, and Ent1071A, whereas orf3 shows a consensus motif SxxxS similar to that present in PlnNC8β (AxxxA). PlnNC8 is expressed only in bacterial cocultures, so there is the possibility that the expression of this two-peptide bacteriocin can be induced by a similar mechanism. So far, only the expression of enterocin A has been found in this strain; however, the presence of the genes ent29α and ent29β opens the possibility for further research on its induction, functionality, and origin. Although there are reports on this type of bacteriocin (EntX, EntC, and Ent1071) in other strains of E. faecium, no report exists yet on an Enterococcus strain producing two different classes of bacteriocin.
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Affiliation(s)
- E E Escamilla-Martínez
- Division de Ciencias Biológicas y de la Salud, UAM Iztapalapa, Avenida San Rafael Atlixco No. 186, Col. Vicentina, Iztapalapa, 09340, Mexico City (ORCID: http://orcid.org/0000-0003-4676-1828 [F.J.F.])
| | - Y M Álvarez Cisneros
- Division de Ciencias Biológicas y de la Salud, UAM Iztapalapa, Avenida San Rafael Atlixco No. 186, Col. Vicentina, Iztapalapa, 09340, Mexico City (ORCID: http://orcid.org/0000-0003-4676-1828 [F.J.F.])
| | - F J Fernández
- Division de Ciencias Biológicas y de la Salud, UAM Iztapalapa, Avenida San Rafael Atlixco No. 186, Col. Vicentina, Iztapalapa, 09340, Mexico City (ORCID: http://orcid.org/0000-0003-4676-1828 [F.J.F.])
| | - M Quirasco-Baruch
- Facultad de Química UNAM, Avenida Universidad No. 3000, Universidad Nacional Autónoma de México, C. U. Coyoacán, 04510, Mexico City, Mexico
| | - E Ponce-Alquicira
- Division de Ciencias Biológicas y de la Salud, UAM Iztapalapa, Avenida San Rafael Atlixco No. 186, Col. Vicentina, Iztapalapa, 09340, Mexico City (ORCID: http://orcid.org/0000-0003-4676-1828 [F.J.F.])
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Peña-Soler E, Aranda J, López-Estepa M, Gómez S, Garces F, Coll M, Fernández FJ, Tuñon I, Vega MC. Insights into the inhibited form of the redox-sensitive SufE-like sulfur acceptor CsdE. PLoS One 2017; 12:e0186286. [PMID: 29045454 PMCID: PMC5646864 DOI: 10.1371/journal.pone.0186286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/28/2017] [Indexed: 11/18/2022] Open
Abstract
Sulfur trafficking in living organisms relies on transpersulfuration reactions consisting in the enzyme-catalyzed transfer of S atoms via activated persulfidic S across protein-protein interfaces. The recent elucidation of the mechanistic basis for transpersulfuration in the CsdA-CsdE model system has paved the way for a better understanding of its role under oxidative stress. Herein we present the crystal structure of the oxidized, inactivated CsdE dimer at 2.4 Å resolution. The structure sheds light into the activation of the Cys61 nucleophile on its way from a solvent-secluded position in free CsdE to a fully extended conformation in the persulfurated CsdA-CsdE complex. Molecular dynamics simulations of available CsdE structures allow to delineate the sequence of conformational changes underwent by CsdE and to pinpoint the key role played by the deprotonation of the Cys61 thiol. The low-energy subunit orientation in the disulfide-bridged CsdE dimer demonstrates the likely physiologic relevance of this oxidative dead-end form of CsdE, suggesting that CsdE could act as a redox sensor in vivo.
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Affiliation(s)
- Esther Peña-Soler
- Chemical and Physical Biology Department, Center for Biological Research (CIB-CSIC), Madrid, Spain
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
- Institute for Biomedical Research (IRB Barcelona), Barcelona, Spain
| | - Juan Aranda
- Departamento de Química Física, Universitat de València, Burjassot, Spain
| | - Miguel López-Estepa
- Chemical and Physical Biology Department, Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Sara Gómez
- Chemical and Physical Biology Department, Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Fernando Garces
- The Scripps Research Institute, La Jolla, California, United States of America
| | - Miquel Coll
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
- Institute for Biomedical Research (IRB Barcelona), Barcelona, Spain
| | - Francisco J. Fernández
- Chemical and Physical Biology Department, Center for Biological Research (CIB-CSIC), Madrid, Spain
- Abvance Biotech srl, Madrid, Spain
| | - Iñaki Tuñon
- Departamento de Química Física, Universitat de València, Burjassot, Spain
- * E-mail: , (MCV); (IT)
| | - M. Cristina Vega
- Chemical and Physical Biology Department, Center for Biological Research (CIB-CSIC), Madrid, Spain
- * E-mail: , (MCV); (IT)
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Fernández FJ, Gómez S, Navas-Yuste S, López-Estepa M, Vega MC. Protein-tRNA Agarose Gel Retardation Assays for the Analysis of the N 6-threonylcarbamoyladenosine TcdA Function. J Vis Exp 2017. [PMID: 28671653 DOI: 10.3791/55638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
We demonstrate methods for the expression and purification of tRNA(UUU) in Escherichia coli and the analysis by gel retardation assays of the binding of tRNA(UUU) to TcdA, an N6-threonylcarbamoyladenosine (t6A) dehydratase, which cyclizes the threonylcarbamoyl side chain attached to A37 in the anticodon stem loop (ASL) of tRNAs to cyclic t6A (ct6A). Transcription of the synthetic gene encoding tRNA(UUU) is induced in E. coli with 1 mM isopropyl β-D-1-thiogalactopyranoside (IPTG) and the cells containing tRNA are harvested 24 h post-induction. The RNA fraction is purified using the acid phenol extraction method. Pure tRNA is obtained by a gel filtration chromatography that efficiently separates the small-sized tRNA molecules from larger intact or fragmented nucleic acids. To analyze TcdA binding to tRNA(UUU), TcdA is mixed with tRNA(UUU) and separated on a native agarose gel at 4 °C. The free tRNA(UUU) migrates faster, while the TcdA-tRNA(UUU) complexes undergo a mobility retardation that can be observed upon staining of the gel. We demonstrate that TcdA is a tRNA(UUU)-binding enzyme. This gel retardation assay can be used to study TcdA mutants and the effects of additives and other proteins on binding.
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Affiliation(s)
- Francisco J Fernández
- Department of Physical Chemical Biology, Center for Biological Research (CIB-CSIC), Spanish National Research Council (CSIC); Department of Immunology, Complutense University School of Medicine; Abvance Biotech srl
| | - Sara Gómez
- Department of Physical Chemical Biology, Center for Biological Research (CIB-CSIC), Spanish National Research Council (CSIC)
| | - Sergio Navas-Yuste
- Department of Physical Chemical Biology, Center for Biological Research (CIB-CSIC), Spanish National Research Council (CSIC)
| | - Miguel López-Estepa
- Department of Physical Chemical Biology, Center for Biological Research (CIB-CSIC), Spanish National Research Council (CSIC)
| | - M Cristina Vega
- Department of Physical Chemical Biology, Center for Biological Research (CIB-CSIC), Spanish National Research Council (CSIC);
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Alvarez-Cisneros YM, Fernández FJ, Sainz-Espuñez T, Ponce-Alquicira E. Assessment of virulence factors, antibiotic resistance and amino-decarboxylase activity in Enterococcus faecium MXVK29 isolated from Mexican chorizo. Lett Appl Microbiol 2017; 64:171-176. [PMID: 27930817 DOI: 10.1111/lam.12699] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/22/2016] [Accepted: 11/28/2016] [Indexed: 11/29/2022]
Abstract
Enterococcus faecium MXVK29 has the ability to produce an antimicrobial compound that belongs to Class IIa of the Klaenhammer classification, and could be used as part of a biopreservation technology through direct inoculation of the strain as a starter or protective culture. However, Enterococcus is considered as an opportunistic pathogen, hence, the purpose of this work was to study the food safety determinants of E. faecium MXVK29. The strain was sensitive to all of the antibiotics tested (penicillin, tetracycline, vancomycin, erythromycin, chloramphenicol, gentamicin, neomycin, kanamycin and netilmicin) and did not demonstrate histamine, cadaverine or putrescine formation. Furthermore, tyrosine-decarboxylase activity was detected by qualitative assays and PCR. Among the virulence factors analysed for the strain, only the genes encoding the sexual pheromone cCF10 precursor lipoprotein (ccf) and cell-wall adhesion (efaAfm ) were amplified. The presence of these genes has low impact on pathogenesis, as there are no other genes encoding for virulence factors, such as aggregation proteins. Therefore, Enterococcus faecium could be employed as part of a bioconservation method, because it does not produce risk factors for consumer's health; in addition, it could be used as part of the hurdle technology in foods. SIGNIFICANCE AND IMPACT OF THE STUDY The use of molecular techniques has allowed, in recent years, to detect pathogenicity genes present in the genome of starter cultures used in food processing and preservation. The presence of these genes is undesirable, because horizontal transfer may occur with the natural biota of consumers. For this reason, it is important to analyse the presence of pathogenicity genes in such cultures. In this work, virulence factors and antibiotic resistance of Enterococcus faecium strain MXVK29, producing an antimicrobial compound with high antilisterial activity, were analysed. The results indicate that the strain is safe to be used in food processing as starter culture.
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Affiliation(s)
- Y M Alvarez-Cisneros
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, Mexico City, Mexico
| | - F J Fernández
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, Mexico City, Mexico
| | - T Sainz-Espuñez
- Universidad Autónoma Metropolitana-Xochimilco, Mexico City, Mexico
| | - E Ponce-Alquicira
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, Mexico City, Mexico
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Querol-García J, Fernández FJ, Marin AV, Gómez S, Fullà D, Melchor-Tafur C, Franco-Hidalgo V, Albertí S, Juanhuix J, Rodríguez de Córdoba S, Regueiro JR, Vega MC. Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from the Gram-Positive Bacterial Pathogen A. vaginae, an Immunoevasive Factor that Interacts with the Human C5a Anaphylatoxin. Front Microbiol 2017; 8:541. [PMID: 28443070 PMCID: PMC5385343 DOI: 10.3389/fmicb.2017.00541] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 03/14/2017] [Indexed: 01/05/2023] Open
Abstract
The Gram-positive anaerobic human pathogenic bacterium Atopobium vaginae causes most diagnosed cases of bacterial vaginosis as well as opportunistic infections in immunocompromised patients. In addition to its well-established role in carbohydrate metabolism, D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Streptococcus pyogenes and S. pneumoniae have been reported to act as extracellular virulence factors during streptococcal infections. Here, we report the crystal structure of GAPDH from A. vaginae (AvGAPDH) at 2.19 Å resolution. The refined model has a crystallographic Rfree of 22.6%. AvGAPDH is a homotetramer wherein each subunit is bound to a nicotinamide adenine dinucleotide (NAD+) molecule. The AvGAPDH enzyme fulfills essential glycolytic as well as moonlight (non-glycolytic) functions, both of which might be targets of chemotherapeutic intervention. We report that AvGAPDH interacts in vitro with the human C5a anaphylatoxin and inhibits C5a-specific granulocyte chemotaxis, thereby suggesting the participation of AvGAPDH in complement-targeted immunoevasion in a context of infection. The availability of high-quality structures of AvGAPDH and other homologous virulence factors from Gram-positive pathogens is critical for drug discovery programs. In this study, sequence and structural differences between AvGAPDH and related bacterial and eukaryotic GAPDH enzymes are reported in an effort to understand how to subvert the immunoevasive properties of GAPDH and evaluate the potential of AvGAPDH as a druggable target.
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Affiliation(s)
- Javier Querol-García
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
| | - Francisco J Fernández
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain.,Department of Immunology, Complutense University School of MedicineMadrid, Spain.,Hospital 12 de Octubre Health Research InstituteMadrid, Spain.,Abvance Biotech srlMadrid, Spain
| | - Ana V Marin
- Department of Immunology, Complutense University School of MedicineMadrid, Spain.,Hospital 12 de Octubre Health Research InstituteMadrid, Spain
| | - Sara Gómez
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
| | - Daniel Fullà
- ALBA Synchrotron, Cerdanyola del VallèsCatalonia, Spain
| | - Cecilia Melchor-Tafur
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
| | - Virginia Franco-Hidalgo
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
| | | | | | - Santiago Rodríguez de Córdoba
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
| | - José R Regueiro
- Department of Immunology, Complutense University School of MedicineMadrid, Spain.,Hospital 12 de Octubre Health Research InstituteMadrid, Spain
| | - M Cristina Vega
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
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Fernández FJ, Ardá A, López-Estepa M, Aranda J, Peña-Soler E, Garces F, Round A, Campos-Olivas R, Bruix M, Coll M, Tuñón I, Jiménez-Barbero J, Vega MC. Mechanism of Sulfur Transfer Across Protein–Protein Interfaces: The Cysteine Desulfurase Model System. ACS Catal 2016. [DOI: 10.1021/acscatal.6b00360] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Francisco J. Fernández
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
| | - Ana Ardá
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
- CIC bioGUNE, Bizkaia Technology
Park, Building 801A, 48170 Derio, Spain
| | - Miguel López-Estepa
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
| | - Juan Aranda
- Departamento
de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Esther Peña-Soler
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
| | - Fernando Garces
- The Scripps Research Institute, La
Jolla, 92037 California, United States
| | - Adam Round
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, France
- Unit for
Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 38042 Grenoble, France
| | | | - Marta Bruix
- Instituto de Química Física Rocasolano (IQFR-CSIC), 28006 Madrid, Spain
| | - Miquel Coll
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
- Institute for Biomedical Research (IRB Barcelona), 08028 Barcelona, Spain
| | - Iñaki Tuñón
- Departamento
de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Jesús Jiménez-Barbero
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
- CIC bioGUNE, Bizkaia Technology
Park, Building 801A, 48170 Derio, Spain
- Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 13, 48009 Bilbao, Spain
- Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, 48940 Leioa, Bizkaia, Spain
| | - M. Cristina Vega
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
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Gómez S, López-Estepa M, Fernández FJ, Suárez T, Vega MC. Alternative Eukaryotic Expression Systems for the Production of Proteins and Protein Complexes. Advanced Technologies for Protein Complex Production and Characterization 2016; 896:167-84. [DOI: 10.1007/978-3-319-27216-0_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Abstract
Research for multiprotein expression in nonconventional bacterial and archaeal expression systems aims to exploit particular properties of "alternative" prokaryotic hosts that might make them more efficient than E. coli for particular applications, especially in those areas where more conventional bacterial hosts traditionally do not perform well. Currently, a wide range of products with clinical or industrial application have to be isolated from their native source, often microorganisms whose growth present numerous problems owing to very slow growth phenotypes or because they are unculturable under laboratory conditions. In those cases, transfer of the gene pathway responsible for synthesizing the product of interest into a suitable recombinant host becomes an attractive alternative solution. Despite many efforts dedicated to improving E. coli systems due to low cost, ease of use, and its dominant position as a ubiquitous expression host model, many alternative prokaryotic systems have been developed for heterologous protein expression mostly for biotechnological applications. Continuous research has led to improvements in expression yield through these non-conventional models, including Pseudomonas, Streptomyces and Mycobacterium as alternative bacterial expression hosts. Advantageous properties shared by these systems include low costs, high levels of secreted protein products and their safety of use, with non-pathogenic strains been commercialized. In addition, the use of extremophilic and halotolerant archaea as expression hosts has to be considered as a potential tool for the production of mammalian membrane proteins such as GPCRs.
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Affiliation(s)
- Sara Gómez
- Center for Biological Research, Spanish National Research Council (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Miguel López-Estepa
- Center for Biological Research, Spanish National Research Council (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Francisco J Fernández
- Center for Biological Research, Spanish National Research Council (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - M Cristina Vega
- Center for Biological Research, Spanish National Research Council (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.
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Abstract
Recombinant overexpression of a protein or a protein complex using any specific heterologous host can be an overwhelming challenge. The reasons may range from low yield and poor solubility of a single-subunit enzyme to the wrong stoichiometry or the incomplete assembly of a multiprotein complex. Whatever the reason, overcoming the difficulties will take the researcher into a journey through the seemingly countless options that exist for protein expression. While some choices stand to reason fairly straightforwardly (e.g., using Escherichia coli for the production of bacterial enzymes), most other choices do not need to be so self-revealing. Here, we attempt to portrait the canvas of available hosts for heterologous expression of many different protein classes and complexes and offer guidance as to which expression host may be more suitable to the problem at hand. The guidance in this chapter must be taken only as a rough indication which will have to be checked against the available literature and corroborated by experiment. It is not only expected but also welcome that, as more knowledge is gathered about the performance of hosts and protein types and new expression systems develop, the information in this chapter will have to be updated and refined.
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Affiliation(s)
- Francisco J Fernández
- Center for Biological Research, Spanish National Research Council (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - M Cristina Vega
- Center for Biological Research, Spanish National Research Council (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.
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Fernández FJ, López-Estepa M, Querol-García J, Vega MC. Production of Protein Complexes in Non-methylotrophic and Methylotrophic Yeasts : Nonmethylotrophic and Methylotrophic Yeasts. Adv Exp Med Biol 2016; 896:137-53. [PMID: 27165323 DOI: 10.1007/978-3-319-27216-0_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Protein complexes can be produced in multimilligram quantities using nonmethylotrophic and methylotrophic yeasts such as Saccharomyces cerevisiae and Komagataella (Pichia) pastoris. Yeasts have distinct advantages as hosts for recombinant protein production owing to their cost efficiency, ease of cultivation and genetic manipulation, fast growth rates, capacity to introduce post-translational modifications, and high protein productivity (yield) of correctly folded protein products. Despite those advantages, yeasts have surprisingly lagged behind other eukaryotic hosts in their use for the production of multisubunit complexes. As our knowledge of the metabolic and genomic bottlenecks that yeast microorganisms face when overexpressing foreign proteins expands, new possibilities emerge for successfully engineering yeasts as superb expression hosts. In this chapter, we describe the current state of the art and discuss future possibilities for the development of yeast-based systems for the production of protein complexes.
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Affiliation(s)
- Francisco J Fernández
- Center for Biological Research, Spanish National Research Council (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Miguel López-Estepa
- Center for Biological Research, Spanish National Research Council (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Javier Querol-García
- Center for Biological Research, Spanish National Research Council (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - M Cristina Vega
- Center for Biological Research, Spanish National Research Council (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.
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López-Estepa M, Ardá A, Savko M, Round A, Shepard WE, Bruix M, Coll M, Fernández FJ, Jiménez-Barbero J, Vega MC. Correction: The Crystal Structure and Small-Angle X-Ray Analysis of CsdL/TcdA Reveal a New tRNA Binding Motif in the MoeB/E1 Superfamily. PLoS One 2015. [PMID: 26208179 PMCID: PMC4514599 DOI: 10.1371/journal.pone.0134070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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García-Saucedo C, Fernández FJ, Cuervo-López FM, Gómez J. Effect of sulfate and lactate loading rates on the respiration process and microbial population changes measured by ecological indices. Water Sci Technol 2015; 71:97-104. [PMID: 25607675 DOI: 10.2166/wst.2014.472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In a sulfate reducing process, increasing loading rates and sulfide accumulation may induce population changes resulting in decreasing effectiveness of the process. Thus, the relationship between microbial metabolism changes and population dynamics was studied. An upflow anaerobic sludge blanket reactor was operated at different sulfate loading rates (SLR), from 290 to 981 mg SO4-S/L d at a constant carbon/sulfur ratio of 0.75. When the SLR was increased, the total organic carbon and sulfate consumption efficiencies decreased to nearly 30% and 25%, respectively. The acetate and propionate yields increased with increasing SLR and 385±7 mg sulfide-S/L d was reached. The ecological indices, determined by random amplified polymorphic DNA and denaturing gradient gel electrophoresis techniques, diversity and evenness were found to be constant, and similarity coefficient values remained higher than 76%. The results suggest that the microbial population changes were negligible compared with metabolic changes when SLR was increased. The sulfide accumulation did not modify the microbial diversity. The sequencing of 16S rRNA genes showed strains related to sulfate reducing, fermentation, and methanogenesis processes. The results indicated that the decreasing of effectiveness, under the experimental conditions tested, was dependent more on operational parameters than microbial changes.
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Affiliation(s)
- C García-Saucedo
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Vicentina, C.P. 09340, México, D.F., México E-mail:
| | - F J Fernández
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Vicentina, C.P. 09340, México, D.F., México E-mail:
| | - F M Cuervo-López
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Vicentina, C.P. 09340, México, D.F., México E-mail:
| | - J Gómez
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Vicentina, C.P. 09340, México, D.F., México E-mail:
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Rocha-Pino Z, Vigueras G, Sepúlveda-Sánchez JD, Hernández-Guerrero M, Campos-Terán J, Fernández FJ, Shirai K. The hydrophobicity of the support in solid state culture affected the production of hydrophobins from Lecanicillium lecanii. Process Biochem 2015. [DOI: 10.1016/j.procbio.2014.10.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Rovatsos MT, Marchal JA, Romero-Fernández I, Cano-Linares M, Fernández FJ, Giagia-Athanasopoulou EB, Sánchez A. Molecular and physical characterization of the complex pericentromeric heterochromatin of the vole species Microtus thomasi. Cytogenet Genome Res 2014; 144:131-41. [PMID: 25402553 DOI: 10.1159/000368648] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2014] [Indexed: 11/19/2022] Open
Abstract
A new repeated DNA from Microtus thomasi, Mth-Alu2.2, was cloned and characterized and is presented here for the first time. Digestion of genomic DNA from M. thomasi with AluI restriction enzyme revealed a 2.2-kb repetitive DNA sequence with a high AT content (69%). This sequence consists of a tandemly repeated nonanucleotide of the consensus sequence CACAATGTA, which constitutes approximately 93-95% of the total unit length. The location of the Mth-Alu2.2 sequence in the karyotype was determined by FISH, demonstrating strong hybridization signals in the pericentromeric regions of all chromosomes and in the heterochromatin blocks of several X chromosome variants. In addition, the distribution of the 4 pericentromeric repeat sequences Msat-160, Mth-Alu900, Mth-Alu2.2, and interstitial telomeric repeats was analyzed by in situ hybridization in M. thomasi, in order to shed light on the complex composition of the chromosomal pericentromeric regions in this species. The order and organization of these sequences in the pericentromeric regions are conserved, with slight variations in both the degree of overlapping and the amount of each repeated DNA in the chromosomes. Specifically, Mth-Alu2.2 is localized in the terminal regions of the chromosomes, with Msat-160 occupying the immediately inner region, partially intermixed with Mth-Alu2.2. The sequence Mth-Alu900 is found in internal positions below Msat-160, and the interstitial telomeric repeats are located close to the long-arm euchromatin of the chromosomes.
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Affiliation(s)
- Michalis T Rovatsos
- Department of Ecology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
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Pérez EA, Fernández FJ, Fierro F, Mejía A, Marcos AT, Martín JF, Barrios-González J. Yeast HXK2 gene reverts glucose regulation mutation of penicillin biosynthesis in P. chrysogenum. Braz J Microbiol 2014; 45:873-83. [PMID: 25477921 PMCID: PMC4204972 DOI: 10.1590/s1517-83822014000300017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 03/14/2014] [Indexed: 11/25/2022] Open
Abstract
The mutant Penicillium chrysogenum strain dogR5, derived from strain AS-P-78, does not respond to glucose regulation of penicillin biosynthesis and β-galactosidase, and is partially deficient in D-glucose phosphorilating activity. We have transformed strain dogR5 with the (hexokinase) hxk2 gene from Saccharomyces cerevisiae. Transformants recovered glucose control of penicillin biosynthesis in different degrees, and acquired a hexokinase (fructose phosphorylating) activity absent in strains AS- P-78 and dogR5. Interestingly, they also recovered glucose regulation of β-galactosidase. On the other hand, glucokinase activity was affected in different ways in the transformants; one of which showed a lower activity than the parental dogR5, but normal glucose regulation of penicillin biosynthesis. Our results show that Penicillium chrysogenum AS-P-78 and dogR5 strains lack hexokinase, and suggest that an enzyme with glucokinase activity is involved in glucose regulation of penicillin biosynthesis and β-galactosidase, thus signaling glucose in both primary and secondary metabolism; however, catalytic and signaling activities seem to be independent.
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Affiliation(s)
- Edmundo A. Pérez
- Laboratorio de Ingeniería Genética y Metabolitos SecundariosDepartamento de BiotecnologíaUniversidad Autónoma MetropolitanaMexico D.F.MexicoLaboratorio de Ingeniería Genética y Metabolitos Secundarios, Departamento de Biotecnología, Universidad Autónoma Metropolitana, Mexico D.F., Mexico.
| | - Francisco J. Fernández
- Laboratorio de Ingeniería Genética y Metabolitos SecundariosDepartamento de BiotecnologíaUniversidad Autónoma MetropolitanaMexico D.F.MexicoLaboratorio de Ingeniería Genética y Metabolitos Secundarios, Departamento de Biotecnología, Universidad Autónoma Metropolitana, Mexico D.F., Mexico.
| | - Francisco Fierro
- Laboratorio de Ingeniería Genética y Metabolitos SecundariosDepartamento de BiotecnologíaUniversidad Autónoma MetropolitanaMexico D.F.MexicoLaboratorio de Ingeniería Genética y Metabolitos Secundarios, Departamento de Biotecnología, Universidad Autónoma Metropolitana, Mexico D.F., Mexico.
| | - Armando Mejía
- Laboratorio de Ingeniería Genética y Metabolitos SecundariosDepartamento de BiotecnologíaUniversidad Autónoma MetropolitanaMexico D.F.MexicoLaboratorio de Ingeniería Genética y Metabolitos Secundarios, Departamento de Biotecnología, Universidad Autónoma Metropolitana, Mexico D.F., Mexico.
| | - Ana T. Marcos
- Instituto de Biotecnología de LeónLeónSpainInstituto de Biotecnología de León, León, Spain.
| | - Juan F. Martín
- Instituto de Biotecnología de LeónLeónSpainInstituto de Biotecnología de León, León, Spain.
- Área de MicrobiologíaFacultad de Ciencias Biológicas y AmbientalesUniversidad de LeónLeónSpainÁrea de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, León, Spain.
| | - Javier Barrios-González
- Laboratorio de Ingeniería Genética y Metabolitos SecundariosDepartamento de BiotecnologíaUniversidad Autónoma MetropolitanaMexico D.F.MexicoLaboratorio de Ingeniería Genética y Metabolitos Secundarios, Departamento de Biotecnología, Universidad Autónoma Metropolitana, Mexico D.F., Mexico.
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Úbeda JF, Maldonado M, Briones AI, Fernández FJ. Erratum to: Bio-prospecting of Distillery Yeasts as Bio-control and Bio-remediation Agents. Curr Microbiol 2014. [DOI: 10.1007/s00284-014-0546-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Coreño-Alonso A, Solé A, Diestra E, Esteve I, Gutiérrez-Corona JF, Reyna López GE, Fernández FJ, Tomasini A. Mechanisms of interaction of chromium with Aspergillus niger var tubingensis strain Ed8. Bioresour Technol 2014; 158:188-192. [PMID: 24607453 DOI: 10.1016/j.biortech.2014.02.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/07/2014] [Accepted: 02/10/2014] [Indexed: 06/03/2023]
Abstract
Experiments were conducted to determine the mechanisms of interaction with chromium of Aspergillus niger var tubingensis strain Ed8 in batch culture and in bioreactor experiments. Results obtained in this work showed that the interaction of A. niger var tubingensis Ed8 with Cr(VI) is based mainly in a reduction process and also, secondly, in a sorption process. Using electron microscopy techniques the ultrathin sections obtained from the mycelium biomass produced by the fungus in batch cultures showed the ability to incorporate Cr intracellulary, into low electron-dense inclusions, but not extracellularly. On the other hand, cultures without Cr(VI) of A. niger var tubingensis Ed8, grown in a bubble column bioreactor, reduced Cr(VI) immediately after repeated addition of this oxyanion; after six loads, 460 mg Cr(VI) was reduced to Cr(III) in 60 h, corresponding to a reduction rate of 2.62 mg Cr(VI)g(-1) dry biomass h(-1).
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Affiliation(s)
- A Coreño-Alonso
- Departamento de Biotecnología, Universidad Autónoma Metropolitana, Unidad Iztapalapa, Av. San Rafael Atlixco no. 186, Col Vicentina México, Del. Iztapalapa, A.P. 55-535, C.P. 09340 México D.F., Mexico
| | - A Solé
- Genetics and Microbiology Department, Biosciences Faculty, Universitat Autónoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - E Diestra
- Genetics and Microbiology Department, Biosciences Faculty, Universitat Autónoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - I Esteve
- Genetics and Microbiology Department, Biosciences Faculty, Universitat Autónoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - J F Gutiérrez-Corona
- Departamento de Biología, DCNyE, Universidad de Guanajuato, Apartado Postal 187, Guanajuato, Gto 36000, Mexico
| | - G E Reyna López
- Departamento de Biología, DCNyE, Universidad de Guanajuato, Apartado Postal 187, Guanajuato, Gto 36000, Mexico
| | - F J Fernández
- Departamento de Biotecnología, Universidad Autónoma Metropolitana, Unidad Iztapalapa, Av. San Rafael Atlixco no. 186, Col Vicentina México, Del. Iztapalapa, A.P. 55-535, C.P. 09340 México D.F., Mexico
| | - A Tomasini
- Departamento de Biotecnología, Universidad Autónoma Metropolitana, Unidad Iztapalapa, Av. San Rafael Atlixco no. 186, Col Vicentina México, Del. Iztapalapa, A.P. 55-535, C.P. 09340 México D.F., Mexico.
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Villaseñor J, Capilla P, Rodrigo MA, Cañizares P, Fernández FJ. Operation of a horizontal subsurface flow constructed wetland--microbial fuel cell treating wastewater under different organic loading rates. Water Res 2013; 47:6731-6738. [PMID: 24074815 DOI: 10.1016/j.watres.2013.09.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 08/23/2013] [Accepted: 09/02/2013] [Indexed: 06/02/2023]
Abstract
The aim of the present work is to determine whether a horizontal subsurface flow constructed wetland treating wastewater could act simultaneously as a microbial fuel cell (MFC). Specifically, and as the main variable under study, different organic loading rates were used, and the response of the system was monitored. The installation consisted of a synthetic domestic wastewater-feeding system and a pilot-scale constructed wetland for wastewater treatment, which also included coupled devices necessary to function as an MFC. The wetland worked under continuous operation for 180 d, treating three types of synthetic wastewater with increasing organic loading rates: 13.9 g COD m(-2) d(-1), 31.1 g COD m(-2) d(-1), and 61.1 g COD m(-2) d(-1). The COD removal efficiencies and the cell voltage generation were continuously monitored. The wetland worked simultaneously as an MFC generating electric power. Under low organic loading rates, the wastewater organic matter was completely oxidised in the lower anaerobic compartment, and there were slight aerobic conditions in the upper cathodic compartment, thus causing an electrical current. Under high organic loading rates, the organic matter could not be completely oxidised in the anodic compartment and flowed to the cathodic one, which entered into anaerobic conditions and caused the MFC to stop working. The system developed in this work offered similar cell voltage, power density, and current density values compared with the ones obtained in previous studies using photosynthetic MFCs, sediment-type MFCs, and plant-type MFCs. The light/darkness changes caused voltage fluctuations due to the photosynthetic activity of the macrophytes used (Phragmites australis), which affected the conditions in the cathodic compartment.
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Affiliation(s)
- J Villaseñor
- Chemical Engineering Department, Institute for Chemical and Environmental Technology (ITQUIMA), University of Castilla-La Mancha, Avenida Camilo José Cela S/N, 13071 Ciudad Real, Spain.
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Reyes-César A, Absalón ÁE, Fernández FJ, González JM, Cortés-Espinosa DV. Biodegradation of a mixture of PAHs by non-ligninolytic fungal strains isolated from crude oil-contaminated soil. World J Microbiol Biotechnol 2013; 30:999-1009. [PMID: 24132496 DOI: 10.1007/s11274-013-1518-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 10/08/2013] [Indexed: 11/27/2022]
Abstract
Nine native non-ligninolytic fungal strains were isolated from Maya crude oil-contaminated soil and selected based on their ability to grow and use crude oil and several polycyclic aromatic hydrocarbons (PAHs) as carbon source, for their application to PAH removal in soil. The fungi were identified by PCR amplification of intergenic transcribed sequences regions and microbiological techniques, and results showed them to be part of the genera Fusarium, Neurospora, Aspergillus, Scedosporium, Penicillium, Neosartorya and Talaromyces. A primary selection of fungi was made in minimal medium plates, considering the tolerance to different concentrations of PAHs for each strain. The radial extension rate exhibited significant differences (p < 0.05) from 200 to 1,000 mg of PAHs mixture l⁻¹. A secondary selection of Aspergillus terreus, Talaromyces spectabilis, and Fusarium sp. was achieved based on their tolerance to 2,000 mg of a mixture of Phenanathrene and Pyrene kg⁻¹ of soil in a solid-state microcosm system for 2 weeks. The percentage of PAH removal obtained by the three strains was approximately 21 % of the mixture.
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Affiliation(s)
- Anaisell Reyes-César
- Instituto Politécnico Nacional, Centro de Investigación en Biotecnología Aplicada, Carretera Federal Santa Inés Tecuexcomac-Tepetitla Km 1.5, C.P. 90700, Tepetitla de Lardizabal, Tlaxcala, Mexico
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Rodas-Suárez OR, Quiñones-Ramírez EI, Fernández FJ, Vázquez-Salinas C. Listeria monocytogenes strains isolated from dry milk samples in Mexico: occurrence and antibiotic sensitivity. J Environ Health 2013; 76:32-37. [PMID: 24073487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Dry milk is a particular concern in Mexico, as approximately 150,000 metric tons of dry milk are imported every year at a cost of around $250 million. Dry milk is used to make many products, most of which are dairy products widely distributed among the population covered by welfare programs. The purpose of the study described in this article was to determine the presence of Listeria spp. in imported dry milk samples in Mexico, and to determine the sensitivity of the Listeria monocytogenes isolates to different antimicrobial agents. Listeria isolates (7.8% of 550 bacterial isolates) were identified as L. monocytogenes (53.49%), L. innocua (30.23%), L. seeligeri (13.95%), and L. ivanovii (2.33%). L. monocytogenes strains isolated showed multiresistance to ampicillin, erythromycin, tetracycline, dicloxacillin, and trimethoprim-sulfamethoxazole (9%-14%). The results provide additional evidence of the emergence of multiresistant Listeria strains both in nature and in widely consumed dairy products, representing a potential threat to human health.
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Affiliation(s)
- O R Rodas-Suárez
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
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50
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Fernández FJ, Vega MC. Technologies to keep an eye on: alternative hosts for protein production in structural biology. Curr Opin Struct Biol 2013; 23:365-73. [DOI: 10.1016/j.sbi.2013.02.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 01/31/2013] [Accepted: 02/01/2013] [Indexed: 12/21/2022]
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