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      Characterization of the Paracoccidioides Hypoxia Response Reveals New Insights into Pathogenesis Mechanisms of This Important Human Pathogenic Fungus

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          Abstract

          Background

          Hypoxic microenvironments are generated during fungal infection. It has been described that to survive in the human host, fungi must also tolerate and overcome in vivo microenvironmental stress conditions including low oxygen tension; however nothing is known how Paracoccidioides species respond to hypoxia. The genus Paracoccidioides comprises human thermal dimorphic fungi and are causative agents of paracoccidioidomycosis (PCM), an important mycosis in Latin America.

          Methodology/Principal Findings

          In this work, a detailed hypoxia characterization was performed in Paracoccidioides. Using NanoUPLC-MS E proteomic approach, we obtained a total of 288 proteins differentially regulated in 12 and 24 h of hypoxia, providing a global view of metabolic changes during this stress. In addition, a functional characterization of the homologue to the most important molecule involved in hypoxia responses in other fungi, the SREBP (sterol regulatory element binding protein) was performed. We observed that Paracoccidioides species have a functional homologue of SREBP, named here as SrbA, detected by using a heterologous genetic approach in the srbA null mutant in Aspergillus fumigatus. Paracoccidioides srbA ( PbsrbA), in addition to involvement in hypoxia, is probable involved in iron adaptation and azole drug resistance responses.

          Conclusions/Significance

          In this study, the hypoxia was characterized in Paracoccidioides. The first results can be important for a better understanding of the fungal adaptation to the host and improve the arsenal of molecules for the development of alternative treatment options in future, since molecules related to fungal adaptation to low oxygen levels are important to virulence and pathogenesis in human pathogenic fungi.

          Author Summary

          The genus Paracoccidioides is composed of species that are causative agents of paracoccidioidomycosis (PCM), a neglected human granulomatous mycosis, endemic in Latin America. To survive in the human host, fungi must tolerate and overcome in vivo micro environmental stress conditions, including low oxygen levels. Paracoccidioides spp. depicts differential responses to several stresses such as iron/zinc deprivation, oxidative and nitrosative stresses and carbon starvation. In addition, Paracoccidioides yeast cells recovered from liver of infected mice demonstrated adaptability to the host conditions. Mechanisms by which fungi sense oxygen levels have been characterized, although this is the first description in Paracoccidioides spp. Little is known about hypoxia in thermally dimorphic fungi and nothing has been studied in Paracoccidioides genus, one of the representatives of this group of pathogens. A detailed characterization of the hypoxia responses was performed using proteomic and heterologous genetics approaches. Paracoccidioides genus have a functional homologue of the key regulator of hypoxia adaptation in fungi, SrbA, a SREBP (sterol regulatory element binding protein) orthologue. The proteome during hypoxia provided a global view of metabolic changes during this stress and species of the Paracoccidioides genus have a functional SrbA. Our study provides a better understanding of the fungal adaptation to the host and it can improve the arsenal of molecules for the development of alternative treatment options to paracoccidioidomycosis, since molecules related to fungal adaptation to low oxygen levels are important to virulence and pathogenesis in human pathogenic fungi.

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          Most cited references87

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          SMART, a simple modular architecture research tool: identification of signaling domains.

          Accurate multiple alignments of 86 domains that occur in signaling proteins have been constructed and used to provide a Web-based tool (SMART: simple modular architecture research tool) that allows rapid identification and annotation of signaling domain sequences. The majority of signaling proteins are multidomain in character with a considerable variety of domain combinations known. Comparison with established databases showed that 25% of our domain set could not be deduced from SwissProt and 41% could not be annotated by Pfam. SMART is able to determine the modular architectures of single sequences or genomes; application to the entire yeast genome revealed that at least 6.7% of its genes contain one or more signaling domains, approximately 350 greater than previously annotated. The process of constructing SMART predicted (i) novel domain homologues in unexpected locations such as band 4.1-homologous domains in focal adhesion kinases; (ii) previously unknown domain families, including a citron-homology domain; (iii) putative functions of domain families after identification of additional family members, for example, a ubiquitin-binding role for ubiquitin-associated domains (UBA); (iv) cellular roles for proteins, such predicted DEATH domains in netrin receptors further implicating these molecules in axonal guidance; (v) signaling domains in known disease genes such as SPRY domains in both marenostrin/pyrin and Midline 1; (vi) domains in unexpected phylogenetic contexts such as diacylglycerol kinase homologues in yeast and bacteria; and (vii) likely protein misclassifications exemplified by a predicted pleckstrin homology domain in a Candida albicans protein, previously described as an integrin.
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            Pathogenesis of Aspergillus fumigatus in Invasive Aspergillosis.

            Aspergillus species are globally ubiquitous saprophytes found in a variety of ecological niches. Almost 200 species of aspergilli have been identified, less than 20 of which are known to cause human disease. Among them, Aspergillus fumigatus is the most prevalent and is largely responsible for the increased incidence of invasive aspergillosis (IA) in the immunocompromised patient population. IA is a devastating illness, with mortality rates in some patient groups reaching as high as 90%. Studies identifying and assessing the roles of specific factors of A. fumigatus that contribute to the pathogenesis of IA have traditionally focused on single-gene deletion and mutant characterization. In combination with recent large-scale approaches analyzing global fungal responses to distinct environmental or host conditions, these studies have identified many factors that contribute to the overall pathogenic potential of A. fumigatus. Here, we provide an overview of the significant findings regarding A. fumigatus pathogenesis as it pertains to invasive disease.
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              Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures.

              A novel database search algorithm is presented for the qualitative identification of proteins over a wide dynamic range, both in simple and complex biological samples. The algorithm has been designed for the analysis of data originating from data independent acquisitions, whereby multiple precursor ions are fragmented simultaneously. Measurements used by the algorithm include retention time, ion intensities, charge state, and accurate masses on both precursor and product ions from LC-MS data. The search algorithm uses an iterative process whereby each iteration incrementally increases the selectivity, specificity, and sensitivity of the overall strategy. Increased specificity is obtained by utilizing a subset database search approach, whereby for each subsequent stage of the search, only those peptides from securely identified proteins are queried. Tentative peptide and protein identifications are ranked and scored by their relative correlation to a number of models of known and empirically derived physicochemical attributes of proteins and peptides. In addition, the algorithm utilizes decoy database techniques for automatically determining the false positive identification rates. The search algorithm has been tested by comparing the search results from a four-protein mixture, the same four-protein mixture spiked into a complex biological background, and a variety of other "system" type protein digest mixtures. The method was validated independently by data dependent methods, while concurrently relying on replication and selectivity. Comparisons were also performed with other commercially and publicly available peptide fragmentation search algorithms. The presented results demonstrate the ability to correctly identify peptides and proteins from data independent acquisition strategies with high sensitivity and specificity. They also illustrate a more comprehensive analysis of the samples studied; providing approximately 20% more protein identifications, compared to a more conventional data directed approach using the same identification criteria, with a concurrent increase in both sequence coverage and the number of modified peptides.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS Negl Trop Dis
                PLoS Negl Trop Dis
                plos
                plosntds
                PLoS Neglected Tropical Diseases
                Public Library of Science (San Francisco, CA USA )
                1935-2727
                1935-2735
                10 December 2015
                December 2015
                : 9
                : 12
                : e0004282
                Affiliations
                [1 ]Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
                [2 ]Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
                University of California San Diego School of Medicine, UNITED STATES
                Author notes

                The authors have declared that no competing interests exist.

                Conceived and designed the experiments: PdSL RAC CMdAS. Performed the experiments: PdSL DC. Analyzed the data: PdSL AMB RAC CMdAS. Contributed reagents/materials/analysis tools: RAC CMdAS. Wrote the paper: PdSL CMdAS.

                Article
                PNTD-D-15-01407
                10.1371/journal.pntd.0004282
                4686304
                26659387
                2d1f540d-a024-447c-bf92-5f5a26626ecb
                © 2015 Lima et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

                History
                : 11 August 2015
                : 16 November 2015
                Page count
                Figures: 9, Tables: 1, Pages: 25
                Funding
                This work at Universidade Federal de Goiás was supported by grants from Conselho Nacional de Desenvolvimento Científico e Tecnológico, [CNPq] ( http://www.cnpq.br), grant numbers: 442213/2014-0 and 304810/2014-2; Fundação de Amparo à Pesquisa do Estado de Goiás [FAPEG] ( http://www.fapeg.go.gov.br/sitefapeg), grant numbers: 201210267001055 and 201410267001224; National Institute Of General Medical Sciences of the National Institutes of Health [NIH],( http://www.nigms.nih.gov/Pages/default.aspx), grant number: P30GM106394 (Stanton, Bruce PI, pilot project RAC) and NIH/National Institute of Allergy and Infectious Diseases, ( http://www.niaid.nih.gov/Pages/default.aspx), grant number R01AI81838 (RAC PI). PdSL was supported by a fellowship from Coordenação de Aperfeiçoamento de Pessoal de Nível Superior [CAPES], ( http://www.capes.gov.br). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Custom metadata
                All relevant data are within the paper and its Supporting Information files.

                Infectious disease & Microbiology
                Infectious disease & Microbiology

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