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Minjárez-Sáenz M, Martínez-Júlvez M, Yruela I, Medina M. Mining the Flavoproteome of Brucella ovis, the Brucellosis Causing Agent in Ovis aries. Microbiol Spectr 2022; 10:e0229421. [PMID: 35315701 PMCID: PMC9045290 DOI: 10.1128/spectrum.02294-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/19/2022] [Indexed: 11/20/2022] Open
Abstract
Flavoproteins are a diverse class of proteins that are mostly enzymes and contain as cofactors flavin mononucleotide (FMN) and/or flavin adenine dinucleotide (FAD), which enable them to participate in a wide range of physiological reactions. We have compiled 78 potential proteins building the flavoproteome of Brucella ovis (B. ovis), the causative agent of ovine brucellosis. The curated list of flavoproteins here reported is based on (i) the analysis of sequence, structure and function of homologous proteins, and their classification according to their structural domains, clans, and expected enzymatic functions; (ii) the constructed phylogenetic trees of enzyme functional classes using 19 Brucella strains and 26 pathogenic and/or biotechnological relevant alphaproteobacteria together with B. ovis; and (iii) the evaluation of the genetic context for each entry. Candidates account for ∼2.7% of the B. ovis proteome, and 75% of them use FAD as cofactor. Only 55% of these flavoproteins belong to the core proteome of Brucella and contribute to B. ovis processes involved in maintenance activities, survival and response to stress, virulence, and/or infectivity. Several of the predicted flavoproteins are highly divergent in Brucella genus from revised proteins and for them it is difficult to envisage a clear function. This might indicate modified catalytic activities or even divergent processes and mechanisms still not identified. We have also detected the lack of some functional flavoenzymes in B. ovis, which might contribute to it being nonzoonotic. Finally, potentiality of B. ovis flavoproteome as the source of antimicrobial targets or biocatalyst is discussed. IMPORTANCE Some microorganisms depend heavily on flavin-dependent activities, but others maintain them at a minimum. Knowledge about flavoprotein content and functions in different microorganisms will help to identify their metabolic requirements, as well as to benefit either industry or health. Currently, most flavoproteins from the sheep pathogen Brucella ovis are only automatically annotated in databases, and only two have been experimentally studied. Indeed, certain homologues with unknown function are not characterized, and they might relate to still not identified mechanisms or processes. Our research has identified 78 members that comprise its flavoproteome, 76 of them flavoenzymes, which mainly relate to bacteria survival, virulence, and/or infectivity. The list of flavoproteins here presented allows us to better understand the peculiarities of Brucella ovis and can be applied as a tool to search for candidates as new biocatalyst or antimicrobial targets.
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Affiliation(s)
- Martha Minjárez-Sáenz
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain
| | - Marta Martínez-Júlvez
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain
- Group of Biochemistry, Biophysics and Computational Biology “GBsC” (BIFI, Unizar) Joint Unit to CSIC, Zaragoza, Spain
| | - Inmaculada Yruela
- Estación Experimental de Aula Dei, CSIC, Zaragoza, Spain
- Group of Biochemistry, Biophysics and Computational Biology “GBsC” (BIFI, Unizar) Joint Unit to CSIC, Zaragoza, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain
- Group of Biochemistry, Biophysics and Computational Biology “GBsC” (BIFI, Unizar) Joint Unit to CSIC, Zaragoza, Spain
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Hagen F, Lumbsch HT, Arsic Arsenijevic V, Badali H, Bertout S, Billmyre RB, Bragulat MR, Cabañes FJ, Carbia M, Chakrabarti A, Chaturvedi S, Chaturvedi V, Chen M, Chowdhary A, Colom MF, Cornely OA, Crous PW, Cuétara MS, Diaz MR, Espinel-Ingroff A, Fakhim H, Falk R, Fang W, Herkert PF, Ferrer Rodríguez C, Fraser JA, Gené J, Guarro J, Idnurm A, Illnait-Zaragozi MT, Khan Z, Khayhan K, Kolecka A, Kurtzman CP, Lagrou K, Liao W, Linares C, Meis JF, Nielsen K, Nyazika TK, Pan W, Pekmezovic M, Polacheck I, Posteraro B, de Queiroz Telles F, Romeo O, Sánchez M, Sampaio A, Sanguinetti M, Sriburee P, Sugita T, Taj-Aldeen SJ, Takashima M, Taylor JW, Theelen B, Tomazin R, Verweij PE, Wahyuningsih R, Wang P, Boekhout T. Importance of Resolving Fungal Nomenclature: the Case of Multiple Pathogenic Species in the Cryptococcus Genus. mSphere 2017; 2:e00238-17. [PMID: 28875175 PMCID: PMC5577652 DOI: 10.1128/msphere.00238-17] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cryptococcosis is a major fungal disease caused by members of the Cryptococcus gattii and Cryptococcus neoformans species complexes. After more than 15 years of molecular genetic and phenotypic studies and much debate, a proposal for a taxonomic revision was made. The two varieties within C. neoformans were raised to species level, and the same was done for five genotypes within C. gattii. In a recent perspective (K. J. Kwon-Chung et al., mSphere 2:e00357-16, 2017, https://doi.org/10.1128/mSphere.00357-16), it was argued that this taxonomic proposal was premature and without consensus in the community. Although the authors of the perspective recognized the existence of genetic diversity, they preferred the use of the informal nomenclature "C. neoformans species complex" and "C. gattii species complex." Here we highlight the advantage of recognizing these seven species, as ignoring these species will impede deciphering further biologically and clinically relevant differences between them, which may in turn delay future clinical advances.
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Affiliation(s)
- Ferry Hagen
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Centre of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
| | | | | | - Hamid Badali
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, Iran
| | - Sebastien Bertout
- Unité Mixte Internationale Recherches Translationnelles sur l’Infection à VIH et les Maladies Infectieuses, Laboratoire de Parasitologie et Mycologie Médicale, UFR Pharmacie, Université Montpellier, Montpellier, France
| | - R. Blake Billmyre
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - M. Rosa Bragulat
- Veterinary Mycology Group, Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - F. Javier Cabañes
- Veterinary Mycology Group, Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Mauricio Carbia
- Departamento de Parasitología y Micología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sudha Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Vishnu Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Min Chen
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai, China
- Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Anuradha Chowdhary
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | | | - Oliver A. Cornely
- CECAD Cluster of Excellence, University of Cologne, Cologne, Germany
- Department I for Internal Medicine, University Hospital of Cologne, Cologne, Germany
- Center for Clinical Trials, University Hospital Cologne, Cologne, Germany
| | - Pedro W. Crous
- Phytopathology Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Maria S. Cuétara
- Department of Microbiology, Hospital Severo Ochoa, Madrid, Spain
| | - Mara R. Diaz
- University of Miami, NSF NIEHS Oceans and Human Health Center, Miami, Florida, USA
- Rosentiel School of Marine and Atmospheric Science, Division of Marine Biology and Fisheries, University of Miami, Miami, Florida, USA
| | | | - Hamed Fakhim
- Department of Medical Parasitology and Mycology/Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, Iran
| | - Rama Falk
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel
- Department of Fisheries and Aquaculture, Ministry of Agriculture and Rural Development, Nir-David, Israel
| | - Wenjie Fang
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai, China
- Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Patricia F. Herkert
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Postgraduate Program in Microbiology, Parasitology and Pathology, Biological Sciences, Department of Basic Pathology, Federal University of Parana, Curitiba, Brazil
| | | | - James A. Fraser
- Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, University of Queensland, Brisbane, Australia
| | - Josepa Gené
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Josep Guarro
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Alexander Idnurm
- School of BioSciences, BioSciences 2, University of Melbourne, Melbourne, Australia
| | | | - Ziauddin Khan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Kantarawee Khayhan
- Department of Microbiology and Parasitology, Faculty of Medical Sciences, University of Phayao, Phayao, Thailand
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Anna Kolecka
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Cletus P. Kurtzman
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois, USA
| | - Katrien Lagrou
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium
| | - Wanqing Liao
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai, China
- Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Carlos Linares
- Medical School, Universidad Miguel Hernández, Alicante, Spain
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Centre of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
| | - Kirsten Nielsen
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Tinashe K. Nyazika
- Department of Medical Microbiology, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
- Malawi-Liverpool-Wellcome Trust, College of Medicine, University of Malawi, Blantyre, Malawi
- School of Tropical Medicine, Liverpool, United Kingdom
| | - Weihua Pan
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai, China
- Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | | | - Itzhack Polacheck
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel
| | - Brunella Posteraro
- Institute of Public Health (Section of Hygiene), Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Flavio de Queiroz Telles
- Department of Communitarian Health, Hospital de Clínicas, Federal University of Parana, Curitiba, Brazil
| | - Orazio Romeo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
- IRCCS Centro Neurolesi Bonino-Pulejo, Messina, Italy
| | - Manuel Sánchez
- Medical School, Universidad Miguel Hernández, Alicante, Spain
| | - Ana Sampaio
- Centro de Investigação e de Tecnologias Agro-ambientais e Biológicas (CITAB), Universidade de Trás-os-Montes e Alto Douro (UTAD), Quinta dos Prados, Vila Real, Portugal
| | - Maurizio Sanguinetti
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Pojana Sriburee
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Takashi Sugita
- Department of Microbiology, Meiji Pharmaceutical University, Noshio, Kiyose, Tokyo, Japan
| | - Saad J. Taj-Aldeen
- Mycology Unit, Microbiology Division, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Masako Takashima
- Japan Collection of Microorganisms, RIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki, Japan
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Bart Theelen
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Rok Tomazin
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Paul E. Verweij
- Centre of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Retno Wahyuningsih
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Department of Parasitology, School of Medicine, Universitas Kristen Indonesia, Jakarta, Indonesia
| | - Ping Wang
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
- Department of Pediatrics, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Teun Boekhout
- Institute of Biodiversity and Ecosystems Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
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9
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Martho KFC, de Melo AT, Takahashi JPF, Guerra JM, Santos DCDS, Purisco SU, Melhem MDSC, Fazioli RDA, Phanord C, Sartorelli P, Vallim MA, Pascon RC. Amino Acid Permeases and Virulence in Cryptococcus neoformans. PLoS One 2016; 11:e0163919. [PMID: 27695080 PMCID: PMC5047642 DOI: 10.1371/journal.pone.0163919] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/17/2016] [Indexed: 11/19/2022] Open
Abstract
Fungal opportunistic pathogens colonize various environments, from plants and wood to human and animal tissue. Regarding human pathogens, one great challenge during contrasting niche occupation is the adaptation to different conditions, such as temperature, osmolarity, salinity, pressure, oxidative stress and nutritional availability, which may constitute sources of stress that need to be tolerated and overcome. As an opportunistic pathogen, C. neoformans faces exactly these situations during the transition from the environment to the human host, encountering nutritional constraints. Our previous and current research on amino acid biosynthetic pathways indicates that amino acid permeases are regulated by the presence of the amino acids, nitrogen and temperature. Saccharomyces cerevisiae and Candida albicans have twenty-four and twenty-seven genes encoding amino acid permeases, respectively; conversely, they are scarce in number in Basidiomycetes (C. neoformans, Coprinopsis cinerea and Ustilago maydis), where nine to ten permease genes can be found depending on the species. In this study, we have demonstrated that two amino acid permeases are essential for virulence in C. neoformans. Our data showed that C. neoformans uses two global and redundant amino acid permeases, Aap4 and Aap5 to respond correctly to thermal and oxidative stress. Double deletion of these permeases causes growth arrest in C. neoformans at 37°C and in the presence of hydrogen peroxide. The inability to uptake amino acid at a higher temperature and under oxidative stress also led to virulence attenuation in vivo. Our data showed that thermosensitivity caused by the lack of permeases Aap4 and Aap5 can be remedied by alkaline conditions (higher pH) and salinity. Permeases Aap4 and Aap5 are also required during fluconazole stress and they are the target of the plant secondary metabolite eugenol, a potent antifungal inhibitor that targets amino acid permeases. In summary, our work unravels (i) interesting physiological property of C. neoformans regarding its amino acid uptake system; (ii) an important aspect of virulence, which is the need for amino acid permeases during thermal and oxidative stress resistance and, hence, host invasion and colonization; and (iii) provides a convenient prototype for antifungal development, which are the amino acid permeases Aap4/Aap5 and their inhibitor.
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Affiliation(s)
- Kevin Felipe Cruz Martho
- Instituto de Ciências Ambientais, Química e Farmacêuticas, Universidade Federal de São Paulo, Rua Arthur Ridel, 275, Diadema, SP, Brazil
| | - Amanda Teixeira de Melo
- Instituto de Ciências Ambientais, Química e Farmacêuticas, Universidade Federal de São Paulo, Rua Arthur Ridel, 275, Diadema, SP, Brazil
| | | | | | | | - Sônia Ueda Purisco
- Mycology Unit, Adolfo Lutz Institute, Secretary of Health, São Paulo, Brazil
| | | | | | - Clerlune Phanord
- Instituto de Ciências Ambientais, Química e Farmacêuticas, Universidade Federal de São Paulo, Rua Arthur Ridel, 275, Diadema, SP, Brazil
| | - Patrícia Sartorelli
- Instituto de Ciências Ambientais, Química e Farmacêuticas, Universidade Federal de São Paulo, Rua Arthur Ridel, 275, Diadema, SP, Brazil
| | - Marcelo A. Vallim
- Instituto de Ciências Ambientais, Química e Farmacêuticas, Universidade Federal de São Paulo, Rua Arthur Ridel, 275, Diadema, SP, Brazil
| | - Renata C. Pascon
- Instituto de Ciências Ambientais, Química e Farmacêuticas, Universidade Federal de São Paulo, Rua Arthur Ridel, 275, Diadema, SP, Brazil
- * E-mail:
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