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Jiang C, Kong D, Li Y, Sun J, Chen Z, Yang M, Cao S, Yu C, Wang Z, Jiang J, Zhu C, Zhang N, Sun G, Zhang Q. Degradation and mechanism analysis of protein macromolecules by functional bacteria in tobacco leaves. Front Microbiol 2024; 15:1416734. [PMID: 39035444 PMCID: PMC11258012 DOI: 10.3389/fmicb.2024.1416734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 05/27/2024] [Indexed: 07/23/2024] Open
Abstract
Tobacco, a crop of significant economic importance, was greatly influenced in leaf quality by protein content. However, current processing parameters fail to adequately meet the requirements for protein degradation. Microorganisms possess potential advantages for degrading proteins and enhancing the quality of tobacco leaves, and hold substantial potential in the process of curing. To effectively reduce the protein content in tobacco leaves, thereby improving the quality and safety of the tobacco leaves. In this study, tobacco leaf were used as experimental material. From these, the BSP1 strain capable of effectively degrading proteins was isolated and identified as Bacillus subtilis by 16S rDNA analysis. Furthermore, the mechanisms were analyzed by integrating microbiome, transcriptome, and metabolome. Before curing, BSP1 was applied to the surface of tobacco leaves. The results indicated that BSP1 effectively improves the activity of key enzymes and the content of related substances, thereby enhancing protein degradation. Additionally, protein degradation was achieved by regulating the diversity of the microbial community on the surface of the tobacco leaves and the ubiquitin-proteasome pathway. This study provided new strategies for extracting and utilizing functional strains from tobacco leaves, opening new avenues for enhancing the quality of tobacco leaves.
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Affiliation(s)
- Chuandong Jiang
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Decai Kong
- Shandong China Tobacco Industry Co., Ltd., Jinan, China
| | - Yangyang Li
- Hunan Tobacco Research Institute, Changsha, China
| | - Jingguo Sun
- Hubei Provincial Tobacco Research Institute, Wuhan, China
| | - Zhenguo Chen
- Hubei Provincial Tobacco Research Institute, Wuhan, China
| | - Mingfeng Yang
- Shandong China Tobacco Industry Co., Ltd., Jinan, China
| | - Shoutao Cao
- Shandong China Tobacco Industry Co., Ltd., Jinan, China
| | - Cunfeng Yu
- Shandong China Tobacco Industry Co., Ltd., Jinan, China
| | - Zengyu Wang
- Shandong China Tobacco Industry Co., Ltd., Jinan, China
| | - Jiazhu Jiang
- Shandong China Tobacco Industry Co., Ltd., Jinan, China
| | | | - Nan Zhang
- Shandong China Tobacco Industry Co., Ltd., Jinan, China
| | - Guangwei Sun
- Hubei Provincial Tobacco Research Institute, Wuhan, China
| | - Qiang Zhang
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
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Shestakova A, Fatkulin A, Surkova D, Osmolovskiy A, Popova E. First Insight into the Degradome of Aspergillus ochraceus: Novel Secreted Peptidases and Their Inhibitors. Int J Mol Sci 2024; 25:7121. [PMID: 39000228 PMCID: PMC11241649 DOI: 10.3390/ijms25137121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/07/2024] [Accepted: 06/14/2024] [Indexed: 07/16/2024] Open
Abstract
Aspergillus fungi constitute a pivotal element within ecosystems, serving as both contributors of biologically active compounds and harboring the potential to cause various diseases across living organisms. The organism's proteolytic enzyme complex, termed the degradome, acts as an intermediary in its dynamic interaction with the surrounding environment. Using techniques such as genome and transcriptome sequencing, alongside protein prediction methodologies, we identified putative extracellular peptidases within Aspergillus ochraceus VKM-F4104D. Following manual annotation procedures, a total of 11 aspartic, 2 cysteine, 2 glutamic, 21 serine, 1 threonine, and 21 metallopeptidases were attributed to the extracellular degradome of A. ochraceus VKM-F4104D. Among them are enzymes with promising applications in biotechnology, potential targets and agents for antifungal therapy, and microbial antagonism factors. Thus, additional functionalities of the extracellular degradome, extending beyond mere protein substrate digestion for nutritional purposes, were demonstrated.
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Affiliation(s)
- Anna Shestakova
- Department of Microbiology, Lomonosov MSU, Moscow 119234, Russia; (A.S.); (A.O.)
| | - Artem Fatkulin
- Laboratory of Molecular Physiology, HSE University, Moscow 101000, Russia
| | - Daria Surkova
- Department of Microbiology, Lomonosov MSU, Moscow 119234, Russia; (A.S.); (A.O.)
| | | | - Elizaveta Popova
- Department of Microbiology, Lomonosov MSU, Moscow 119234, Russia; (A.S.); (A.O.)
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3
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Tong L, Li Y, Lou X, Wang B, Jin C, Fang W. Powerful cell wall biomass degradation enzymatic system from saprotrophic Aspergillus fumigatus. Cell Surf 2024; 11:100126. [PMID: 38827922 PMCID: PMC11143905 DOI: 10.1016/j.tcsw.2024.100126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 06/05/2024] Open
Abstract
Cell wall biomass, Earth's most abundant natural resource, holds significant potential for sustainable biofuel production. Composed of cellulose, hemicellulose, lignin, pectin, and other polymers, the plant cell wall provides essential structural support to diverse organisms in nature. In contrast, non-plant species like insects, crustaceans, and fungi rely on chitin as their primary structural polysaccharide. The saprophytic fungus Aspergillus fumigatus has been widely recognized for its adaptability to various environmental conditions. It achieves this by secreting different cell wall biomass degradation enzymes to obtain essential nutrients. This review compiles a comprehensive collection of cell wall degradation enzymes derived from A. fumigatus, including cellulases, hemicellulases, various chitin degradation enzymes, and other polymer degradation enzymes. Notably, these enzymes exhibit biochemical characteristics such as temperature tolerance or acid adaptability, indicating their potential applications across a spectrum of industries.
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Affiliation(s)
- Lige Tong
- National Key Laboratory of Non-food Biomass Energy Technology, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, Guangxi, China
| | - Yunaying Li
- National Key Laboratory of Non-food Biomass Energy Technology, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, Guangxi, China
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Baoding, Hebei, China
| | - Xinke Lou
- National Key Laboratory of Non-food Biomass Energy Technology, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, Guangxi, China
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Baoding, Hebei, China
| | - Bin Wang
- National Key Laboratory of Non-food Biomass Energy Technology, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, Guangxi, China
| | - Cheng Jin
- National Key Laboratory of Non-food Biomass Energy Technology, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, Guangxi, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wenxia Fang
- National Key Laboratory of Non-food Biomass Energy Technology, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, Guangxi, China
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Zheng L, Wang R, Fei Y, Pan Y, Zhou P, Shen R, Lan P. Fungal Secretomics Through iTRAQ-Based Analysis. Methods Mol Biol 2024; 2820:139-153. [PMID: 38941021 DOI: 10.1007/978-1-0716-3910-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Our understanding of how fungi respond and adapt to external environments can be increased by the comprehensive data sets of fungal-secreted proteins. Fungi produce a variety of secreted proteins, and environmental conditions can easily influence the fungal secretome. However, the low abundance of secreted proteins and their post-translational modifications make protein extraction more challenging. Hence, the enrichment of secreted proteins is a crucial procedure for secretome analysis. This chapter illustrates a protocol for iTRAQ-based quantitative secretome analysis describing the example of fungi exposed to different environmental conditions. The fungal-secreted proteins can be extracted by combining ultrafiltration and TCA-acetone precipitation. Subsequently, the secreted proteins can be identified and quantified by the iTRAQ-based quantitative proteomics approach.
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Affiliation(s)
- Lu Zheng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Ruonan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuchen Fei
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yilin Pan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peijun Zhou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Renfang Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.
- University of Chinese Academy of Sciences, Nanjing, China.
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5
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Silva NMD, Reis GF, Costa FDF, Grisolia ME, Geraldo MR, Lustosa BPR, Lima BJFDS, Weiss VA, de Souza EM, Li R, Song Y, Nascimento MMF, Robl D, Gomes RR, de Hoog GS, Vicente VA. Genome sequencing of Cladophialophora exuberans, a novel candidate for bioremediation of hydrocarbon and heavy metal polluted habitats. Fungal Biol 2023; 127:1032-1042. [PMID: 37142362 DOI: 10.1016/j.funbio.2023.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/23/2023] [Accepted: 03/26/2023] [Indexed: 05/06/2023]
Abstract
Cladophialophora exuberans is a filamentous fungus related to black yeasts in the order Chaetothyriales. These melanized fungi are known for their 'dual ecology', often occurring in toxic environments and also being frequently involved in human infection. Particularly Cladophialophora exuberans, C. immunda, C. psammophila, and Exophiala mesophila have been described with a pronounced ability to degrade aromatic compounds and xenobiotic volatiles, such as benzene, toluene, ethyl-benzene, and xylene, and are candidates for bioremediation applications. The objective of the present study is the sequencing, assembly, and description of the whole genome of C. exuberans focusing on genes and pathways related to carbon and toxin management, assessing the tolerance and bioremediation of lead and copper, and verifying the presence of genes for metal homeostasis. Genomic evaluations were carried out through a comparison with sibling species including clinical and environmental strains. Tolerance of metals was evaluated via a microdilution method establishing minimum inhibitory (MIC) and fungicidal concentrations (MFC), and agar diffusion assays. Heavy metal bioremediation was evaluated via graphite furnace atomic absorption spectroscopy (GFAAS). The final assembly of C. exuberans comprised 661 contigs, with genome size of 38.10 Mb, coverage of 89.9X and a GC content of 50.8%. In addition, inhibition of growth was shown at concentrations of 1250 ppm for copper and at 625 ppm for lead, using the MIC method. In the agar tests, the strain grew at 2500 ppm of copper and lead. In GFAAS tests, uptake capacities were observed of 89.2% and 95.7% for copper and lead, respectively, after 21 experimental days. This study enabled the annotation of genes involved in heavy metal homeostasis and also contributed to a better understanding of the mechanisms used in tolerance of and adaptation to extreme conditions.
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Affiliation(s)
- Nickolas Menezes da Silva
- Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Paraná, Brazil; Center of Expertise in Mycology of Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, the Netherlands
| | - Guilherme Fonseca Reis
- Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Flávia de Fátima Costa
- Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Maria Eduarda Grisolia
- Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Paraná, Brazil; Center of Expertise in Mycology of Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, the Netherlands
| | - Marlon Roger Geraldo
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Bruno Paulo Rodrigues Lustosa
- Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Bruna Jacomel Favoreto de Souza Lima
- Center of Expertise in Mycology of Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, the Netherlands; Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Vinicius Almir Weiss
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Ruoyu Li
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China; Research Center for Medical Mycology, Peking University, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China
| | - Yinggai Song
- Center of Expertise in Mycology of Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, the Netherlands; Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China; Research Center for Medical Mycology, Peking University, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China
| | | | - Diogo Robl
- Microbiology, Immunology and Parasitology Department, Federal University of Santa Catarina, Florianopolis, Santa Catarina, Brazil
| | - Renata Rodrigues Gomes
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - G Sybren de Hoog
- Center of Expertise in Mycology of Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, the Netherlands; Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Vania Aparecida Vicente
- Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Paraná, Brazil; Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil.
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6
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Genome-wide identification and functional analysis of circRNAs in Trichophyton mentagrophytes spores and hyphae. Microb Pathog 2023; 176:106003. [PMID: 36702368 DOI: 10.1016/j.micpath.2023.106003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023]
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Oda K, Wlodawer A. Overview of the Properties of Glutamic Peptidases That Are Present in Plant and Bacterial Pathogens and Play a Role in Celiac Disease and Cancer. Biochemistry 2023; 62:672-694. [PMID: 36705990 DOI: 10.1021/acs.biochem.2c00622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Seven peptidase (proteinase) families─aspartic, cysteine, metallo, serine, glutamic, threonine, and asparagine─are in the peptidase database MEROPS, version 12.4 (https://www.ebi.ac.uk/merops/). The glutamic peptidase family is assigned two clans, GA and GB, and comprises six subfamilies. This perspective summarizes the unique features of their representatives. (1) G1, scytalidoglutamic peptidase, has a β-sandwich structure containing catalytic residues glutamic acid (E) and glutamine (Q), thus the name eqolisin. Most family members are pepstatin-insensitive and act as plant pathogens. (2) G2, preneck appendage protein, originates in phages, is a transmembrane protein, and its catalytic residues consist of glutamic and aspartic acids. (3) G3, strawberry mottle virus glutamic peptidase, originates in viruses and has a β-sandwich structure with catalytic residues E and Q. Neprosin has propyl endopeptidase activity, is associated with celiac disease, has a β-sandwich structure, and contains catalytic residues E-E and Q-tryptophan. (4) G4, Tiki peptidase, of the erythromycin esterase family, is a transmembrane protein, and its catalytic residues are E-histidine pairs. (5) G5, RCE1 peptidase, is associated with cancer, is a transmembrane protein, and its catalytic residues are E-histidine and asparagine-histidine. Microcystinase, a bacterial toxin, is a transmembrane protein with catalytic residues E-histidine and asparagine-histidine. (6) G6, Ras/Rap1-specific peptidase, is a bacterial pathogen, a transmembrane protein, and its catalytic residues are E-histidine pairs. This family's common features are that their catalytic residues consist of a glutamic acid and another (variable) amino acid and that they exhibit a diversity of biological functions─plant and bacterial pathogens and involvement in celiac disease and cancer─that suggests they are viable drug targets.
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Affiliation(s)
- Kohei Oda
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-Ku, Kyoto 606-8585, Japan
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, Maryland 21702, United States
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Lim JY, Jung YE, Hwang HE, Kim CH, Basaran-Akgul N, Goli SH, Templeton SP, Park HM. Survival Factor A (SvfA) Contributes to Aspergillus nidulans Pathogenicity. J Fungi (Basel) 2023; 9:143. [PMID: 36836258 PMCID: PMC9962611 DOI: 10.3390/jof9020143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/02/2023] [Accepted: 01/19/2023] [Indexed: 01/25/2023] Open
Abstract
Survival factor A (SvfA) in Aspergillus nidulans plays multiple roles in growth and developmental processes. It is a candidate for a novel VeA-dependent protein involved in sexual development. VeA is a key developmental regulator in Aspergillus species that can interact with other velvet-family proteins and enter into the nucleus to function as a transcription factor. In yeast and fungi, SvfA-homologous proteins are required for survival under oxidative and cold-stress conditions. To assess the role of SvfA in virulence in A. nidulans, cell wall components, biofilm formation, and protease activity were evaluated in a svfA-gene-deletion or an AfsvfA-overexpressing strain. The svfA-deletion strain showed decreased production of β-1,3-glucan in conidia, a cell wall pathogen-associated molecular pattern, with a decrease in gene expression for chitin synthases and β-1,3-glucan synthase. The ability to form biofilms and produce proteases was reduced in the svfA-deletion strain. We hypothesized that the svfA-deletion strain was less virulent than the wild-type strain; therefore, we performed in vitro phagocytosis assays using alveolar macrophages and analyzed in vivo survival using two vertebrate animal models. While phagocytosis was reduced in mouse alveolar macrophages challenged with conidia from the svfA-deletion strain, the killing rate showed a significant increase with increased extracellular signal-regulated kinase ERK activation. The svfA-deletion conidia infection reduced host mortality in both T-cell-deficient zebrafish and chronic granulomatous disease mouse models. Taken together, these results indicate that SvfA plays a significant role in the pathogenicity of A. nidulans.
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Affiliation(s)
- Joo-Yeon Lim
- Department of Microbiology and Immunology, Indiana University School of Medicine-Terre Haute, Terre Haute, IN 47807, USA
| | - Ye-Eun Jung
- Laboratory of Cellular Differentiation, Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Hye-Eun Hwang
- Laboratory of Developmental Genetics Department of Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Cheol-Hee Kim
- Laboratory of Developmental Genetics Department of Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Nese Basaran-Akgul
- Department of Microbiology and Immunology, Indiana University School of Medicine-Terre Haute, Terre Haute, IN 47807, USA
| | - Sri Harshini Goli
- Department of Microbiology and Immunology, Indiana University School of Medicine-Terre Haute, Terre Haute, IN 47807, USA
| | - Steven P. Templeton
- Department of Microbiology and Immunology, Indiana University School of Medicine-Terre Haute, Terre Haute, IN 47807, USA
| | - Hee-Moon Park
- Laboratory of Cellular Differentiation, Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea
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Oda K, Dunn BM, Wlodawer A. Serine-Carboxyl Peptidases, Sedolisins: From Discovery to Evolution. Biochemistry 2022; 61:1643-1664. [PMID: 35862020 DOI: 10.1021/acs.biochem.2c00239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sedolisin is a proteolytic enzyme, listed in the peptidase database MEROPS as a founding member of clan SB, family S53. This enzyme, although active at low pH, was originally shown not to be inhibited by an aspartic peptidase specific inhibitor, S-PI (pepstatin Ac). In this Perspective, the S53 family is described from the moment of original identification to evolution. The representative enzymes of the family are sedolisin, kumamolisin, and TPP-1. They exhibit the following unique features. (1) The fold of the molecule is similar to that of subtilisin, but the catalytic residues consist of a triad, Ser/Glu/Asp, that is unlike the Ser/His/Asp triad of subtilisin. (2) The molecule is expressed as a pro-form composed of the amino-terminal prosegment and the active domain. Additionally, some members of this family have an additional, carboxy-terminal prosegment. (3) Their optimum pH for activity is in the acidic region, not in the neutral to alkaline region where subtilisin is active. (4) Their distribution in nature is very broad across the three kingdoms of life. (5) Some of these enzymes from fungi and bacteria are pathogens to plants. (6) Some of them have significant potential applications for industry. (7) The lack of a TPP-1 gene in human brain is the cause of incurable juvenile neuronal ceroid lipofuscinosis (Batten's disease).
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Affiliation(s)
- Kohei Oda
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Ben M Dunn
- Department of Biochemistry & Molecular Biology, University of Florida College of Medicine, Gainesville, Florida 32610-0245, United States
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, Maryland 21702, United States
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Lim JY, Kim YJ, Woo SA, Jeong JW, Lee YR, Kim CH, Park HM. The LAMMER Kinase, LkhA, Affects Aspergillus fumigatus Pathogenicity by Modulating Reproduction and Biosynthesis of Cell Wall PAMPs. Front Cell Infect Microbiol 2021; 11:756206. [PMID: 34722342 PMCID: PMC8548842 DOI: 10.3389/fcimb.2021.756206] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/27/2021] [Indexed: 02/01/2023] Open
Abstract
The LAMMER kinase in eukaryotes is a well-conserved dual-specificity kinase. Aspergillus species cause a wide spectrum of diseases called aspergillosis in humans, depending on the underlying immune status of the host, such as allergy, aspergilloma, and invasive aspergillosis. Aspergillus fumigatus is the most common opportunistic fungal pathogen that causes invasive aspergillosis. Although LAMMER kinase has various functions in morphology, development, and cell cycle regulation in yeast and filamentous fungi, its function in A. fumigatus is not known. We performed molecular studies on the function of the A. fumigatus LAMMER kinase, AfLkhA, and reported its involvement in multiple cellular processes, including development and virulence. Deletion of AflkhA resulted in defects in colonial growth, production of conidia, and sexual development. Transcription and genetic analyses indicated that AfLkhA modulates the expression of key developmental regulatory genes. The AflkhA-deletion strain showed increased production of gliotoxins and protease activity. When conidia were challenged with alveolar macrophages, enodocytosis of conidia by macrophages was increased in the AflkhA-deletion strain, resulting from changes in expression of the cell wall genes and thus content of cell wall pathogen-associated molecular patterns, including β-1,3-glucan and GM. While T cell-deficient zebrafish larvae were significantly susceptible to wild-type A. fumigatus infection, AflkhA-deletion conidia infection reduced host mortality. A. fumigatus AfLkhA is required for the establishment of virulence factors, including conidial production, mycotoxin synthesis, protease activity, and interaction with macrophages, which ultimately affect pathogenicity at the organismal level.
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Affiliation(s)
- Joo-Yeon Lim
- Laboratory of Cellular Differentiation, Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, South Korea.,Institute of Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Yeon Ju Kim
- Laboratory of Cellular Differentiation, Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Seul Ah Woo
- Laboratory of Cellular Differentiation, Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Jae Wan Jeong
- Laboratory of Cellular Differentiation, Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Yu-Ri Lee
- Laboratory of Developmental Genetics, Department of Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Cheol-Hee Kim
- Laboratory of Developmental Genetics, Department of Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Hee-Moon Park
- Laboratory of Cellular Differentiation, Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, South Korea
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Machata S, Müller MM, Lehmann R, Sieber P, Panagiotou G, Carvalho A, Cunha C, Lagrou K, Maertens J, Slevogt H, Jacobsen ID. Proteome analysis of bronchoalveolar lavage fluids reveals host and fungal proteins highly expressed during invasive pulmonary aspergillosis in mice and humans. Virulence 2021; 11:1337-1351. [PMID: 33043780 PMCID: PMC7549978 DOI: 10.1080/21505594.2020.1824960] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Invasive pulmonary aspergillosis (IPA) is a severe infection that is difficult to diagnose due to the ubiquitous presence of fungal spores, the underlying diseases of risk patients, and limitations of currently available markers. In this study, we performed a comprehensive liquid chromatography tandem mass spectrometry (LC-MS/MS)-based identification of host and fungal proteins expressed during IPA in mice and humans. The proteomic analysis of bronchoalveolar lavage samples of individual IPA and control cases allowed the description of common host factors that had significantly increased abundance in both infected animals and IPA patients compared to their controls. Although increased levels of these individual host proteins might not be sufficient to distinguish bacterial from fungal infection, a combination of these markers might be beneficial to improve diagnosis. We also identified 16 fungal proteins that were specifically detected during infection and may be valuable candidates for biomarker evaluation.
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Affiliation(s)
- Silke Machata
- Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute , Jena, Germany
| | - Mario M Müller
- Septomics Research Centre, Jena University Hospital , Jena, Germany
| | - Roland Lehmann
- Septomics Research Centre, Jena University Hospital , Jena, Germany
| | - Patricia Sieber
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute , Jena, Germany
| | - Gianni Panagiotou
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute , Jena, Germany.,School of the Biological Sciences, Faculty of Sciences, The University of Hong Kong , Hong Kong, China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong , Hong Kong, China
| | - Agostinho Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho , Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory , Braga/Guimarães, Portugal
| | - Cristina Cunha
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho , Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory , Braga/Guimarães, Portugal
| | - Katrien Lagrou
- Department of Microbiology, Immunology and Transplantation, KU Leuven , Leuven, Belgium.,Clinical Department of Laboratory Medicine and National Reference Center for Mycosis, University Hospitals Leuven , Leuven, Belgium
| | - Johan Maertens
- Department of Microbiology, Immunology and Transplantation, KU Leuven , Leuven, Belgium.,Department of Hematology, University Hospitals Leuven , Leuven, Belgium
| | - Hortense Slevogt
- Septomics Research Centre, Jena University Hospital , Jena, Germany
| | - Ilse D Jacobsen
- Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute , Jena, Germany.,Institute for Microbiology, Friedrich-Schiller-University Jena , Jena, Germany
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12
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Bombassaro A, Schneider GX, Costa FF, Leão ACR, Soley BS, Medeiros F, da Silva NM, Lima BJFS, Castro RJA, Bocca AL, Baura VA, Balsanelli E, Pankievicz VCS, Hrysay NMC, Scola RH, Moreno LF, Azevedo CMPS, Souza EM, Gomes RR, de Hoog S, Vicente VA. Genomics and Virulence of Fonsecaea pugnacius, Agent of Disseminated Chromoblastomycosis. Front Genet 2020; 11:822. [PMID: 32849816 PMCID: PMC7417343 DOI: 10.3389/fgene.2020.00822] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 07/08/2020] [Indexed: 11/16/2022] Open
Abstract
Among agents of chromoblastomycosis, Fonsecaea pugnacius presents a unique type of infection because of its secondary neurotropic dissemination from a chronic cutaneous case in an immunocompetent patient. Neurotropism occurs with remarkable frequency in the fungal family Herpotrichiellaceae, possibly associated with the ability of some species to metabolize aromatic hydrocarbons. In an attempt to understand this new disease pattern, were conducted genomic analysis of Fonsecaea pugnacius (CBS 139214) performed with de novo assembly, gene prediction, annotation and mitochondrial genome assembly, supplemented with animal infection models performed with Tenebrio molitor in Mus musculus lineages BALB/c and C57BL/6. The genome draft of 34.8 Mb was assembled with a total of 12,217 protein-coding genes. Several proteins, enzymes and metabolic pathways related to extremotolerance and virulence were recognized. The enzyme profiles of black fungi involved in chromoblastomycosis and brain infection were analyzed with the Carbohydrate-Active Enzymes (CAZY) and peptidases database (MEROPS). The capacity of the fungus to survive inside Tenebrio molitor animal model was confirmed by histopathological analysis and by presence of melanin and hyphae in host tissue. Although F. pugnacius was isolated from brain in a murine model following intraperitoneal infection, cytokine levels were not statistically significant, indicating a profile of an opportunistic agent. A dual ecological ability can be concluded from presence of metabolic pathways for nutrient scavenging and extremotolerance, combined with a capacity to infect human hosts.
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Affiliation(s)
- Amanda Bombassaro
- Microbiology, Parasitology and Pathology Post-graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Gabriela X Schneider
- Microbiology, Parasitology and Pathology Post-graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Flávia F Costa
- Engineering Bioprocess and Biotechnology Post-graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| | - Aniele C R Leão
- Engineering Bioprocess and Biotechnology Post-graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| | - Bruna S Soley
- Pharmacology Post-graduation Program, Department of Pharmacology, Federal University of Paraná, Curitiba, Brazil
| | - Fernanda Medeiros
- Graduation in Biology Sciences, Federal University of Paraná, Curitiba, Brazil
| | - Nickolas M da Silva
- Engineering Bioprocess and Biotechnology Post-graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| | - Bruna J F S Lima
- Microbiology, Parasitology and Pathology Post-graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
| | | | - Anamélia L Bocca
- Department of Cell Biology, University of Brasilia, Brasilia, Brazil
| | - Valter A Baura
- Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | - Eduardo Balsanelli
- Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | | | - Nyvia M C Hrysay
- Service of Neuromuscular and Demyelinating Diseases, Complex Histochemistry-Immunity Laboratory, Hospital of Clinics, Federal University of Paraná, Curitiba, Brazil
| | - Rosana H Scola
- Service of Neuromuscular and Demyelinating Diseases, Complex Histochemistry-Immunity Laboratory, Hospital of Clinics, Federal University of Paraná, Curitiba, Brazil
| | - Leandro F Moreno
- Engineering Bioprocess and Biotechnology Post-graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| | | | - Emanuel M Souza
- Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | - Renata R Gomes
- Microbiology, Parasitology and Pathology Post-graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Sybren de Hoog
- Microbiology, Parasitology and Pathology Post-graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil.,Center of Expertise in Mycology of Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, Netherlands
| | - Vânia A Vicente
- Microbiology, Parasitology and Pathology Post-graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil.,Engineering Bioprocess and Biotechnology Post-graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
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13
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Wiesner DL, Merkhofer RM, Ober C, Kujoth GC, Niu M, Keller NP, Gern JE, Brockman-Schneider RA, Evans MD, Jackson DJ, Warner T, Jarjour NN, Esnault SJ, Feldman MB, Freeman M, Mou H, Vyas JM, Klein BS. Club Cell TRPV4 Serves as a Damage Sensor Driving Lung Allergic Inflammation. Cell Host Microbe 2020; 27:614-628.e6. [PMID: 32130954 DOI: 10.1016/j.chom.2020.02.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/28/2019] [Accepted: 02/12/2020] [Indexed: 12/12/2022]
Abstract
Airway epithelium is the first body surface to contact inhaled irritants and report danger. Here, we report how epithelial cells recognize and respond to aeroallergen alkaline protease 1 (Alp1) of Aspergillus sp., because proteases are critical components of many allergens that provoke asthma. In a murine model, Alp1 elicits helper T (Th) cell-dependent lung eosinophilia that is initiated by the rapid response of bronchiolar club cells to Alp1. Alp1 damages bronchiolar cell junctions, which triggers a calcium flux signaled through calcineurin within club cells of the bronchioles, inciting inflammation. In two human cohorts, we link fungal sensitization and/or asthma with SNP/protein expression of the mechanosensitive calcium channel, TRPV4. TRPV4 is also necessary and sufficient for club cells to sensitize mice to Alp1. Thus, club cells detect junction damage as mechanical stress, which signals danger via TRPV4, calcium, and calcineurin to initiate allergic sensitization.
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Affiliation(s)
- Darin L Wiesner
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Richard M Merkhofer
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Gregory C Kujoth
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Mengyao Niu
- Department of Medical Microbiology and Immunology University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology University of Wisconsin-Madison, Madison, WI 53706, USA; School of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - James E Gern
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Michael D Evans
- Clinical and Translational Science Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Thomas Warner
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nizar N Jarjour
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Stephane J Esnault
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Michael B Feldman
- Division of Pulmonary and Critical Care Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Freeman
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hongmei Mou
- The Mucosal Immunology & Biology Research Center, Harvard Medical School, Boston, MA 02115, USA; Division of Pediatric Pulmonary Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jatin M Vyas
- Division of Infectious Disease, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Bruce S Klein
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Medical Microbiology and Immunology University of Wisconsin-Madison, Madison, WI 53706, USA.
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14
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Abstract
Aspergillus fumigatus is a saprotrophic fungus; its primary habitat is the soil. In its ecological niche, the fungus has learned how to adapt and proliferate in hostile environments. This capacity has helped the fungus to resist and survive against human host defenses and, further, to be responsible for one of the most devastating lung infections in terms of morbidity and mortality. In this review, we will provide (i) a description of the biological cycle of A. fumigatus; (ii) a historical perspective of the spectrum of aspergillus disease and the current epidemiological status of these infections; (iii) an analysis of the modes of immune response against Aspergillus in immunocompetent and immunocompromised patients; (iv) an understanding of the pathways responsible for fungal virulence and their host molecular targets, with a specific focus on the cell wall; (v) the current status of the diagnosis of different clinical syndromes; and (vi) an overview of the available antifungal armamentarium and the therapeutic strategies in the clinical context. In addition, the emergence of new concepts, such as nutritional immunity and the integration and rewiring of multiple fungal metabolic activities occurring during lung invasion, has helped us to redefine the opportunistic pathogenesis of A. fumigatus.
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Affiliation(s)
- Jean-Paul Latgé
- School of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Georgios Chamilos
- School of Medicine, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece
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15
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Adhikari S, Leissa JA, Karlsson AJ. Beyond function: Engineering improved peptides for therapeutic applications. AIChE J 2019. [DOI: 10.1002/aic.16776] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Sayanee Adhikari
- Department of Chemical and Biomolecular Engineering University of Maryland College Park Maryland
| | - Jesse A. Leissa
- Department of Chemical and Biomolecular Engineering University of Maryland College Park Maryland
| | - Amy J. Karlsson
- Department of Chemical and Biomolecular Engineering University of Maryland College Park Maryland
- Fischell Department of Bioengineering University of Maryland College Park Maryland
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16
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Valsecchi I, Lai JI, Stephen-Victor E, Pillé A, Beaussart A, Lo V, Pham CLL, Aimanianda V, Kwan AH, Duchateau M, Gianetto QG, Matondo M, Lehoux M, Sheppard DC, Dufrene YF, Bayry J, Guijarro JI, Sunde M, Latgé JP. Assembly and disassembly of Aspergillus fumigatus conidial rodlets. ACTA ACUST UNITED AC 2019; 5:100023. [PMID: 32743139 PMCID: PMC7389560 DOI: 10.1016/j.tcsw.2019.100023] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 02/22/2019] [Accepted: 02/23/2019] [Indexed: 11/27/2022]
Abstract
The rodlet structure present on the Aspergillus fumigatus conidial surface hides conidia from immune recognition. In spite of the essential biological role of the rodlets, the molecular basis for their self-assembly and disaggregation is not known. Analysis of the soluble forms of conidia-extracted and recombinant RodA by NMR spectroscopy has indicated the importance of disulfide bonds and identified two dynamic regions as likely candidates for conformational change and intermolecular interactions during conversion of RodA into the amyloid rodlet structure. Point mutations introduced into the RODA sequence confirmed that (1) mutation of a single cysteine was sufficient to block rodlet formation on the conidial surface and (2) both presumed amyloidogenic regions were needed for proper rodlet assembly. Mutations in the two putative amyloidogenic regions retarded and disturbed, but did not completely inhibit, the formation of the rodlets in vitro and on the conidial surface. Even in a disturbed form, the presence of rodlets on the surface of the conidia was sufficient to immunosilence the conidium. However, in contrast to the parental conidia, long exposure of mutant conidia lacking disulfide bridges within RodA or expressing RodA carrying the double (I115S/I146G) mutation activated dendritic cells with the subsequent secretion of proinflammatory cytokines. The immune reactivity of the RodA mutant conidia was not due to a modification in the RodA structure, but to the exposure of different pathogen-associated molecular patterns on the surface as a result of the modification of the rodlet surface layer. The full degradation of the rodlet layer, which occurs during early germination, is due to a complex array of cell wall bound proteases. As reported earlier, this loss of the rodlet layer lead to a strong anti-fumigatus host immune response in mouse lungs.
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Affiliation(s)
- Isabel Valsecchi
- Unité des Aspergillus, Institut Pasteur, Paris, France.,Biological NMR Technological Platform, Institut Pasteur, CNRS UMR 3528, Paris, France
| | - Jennifer I Lai
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia
| | - Emmanuel Stephen-Victor
- Institut National de la Santé et de la Recherche Médicale, Centre de Recherche des Cordeliers, Sorbonne Université, Paris, France
| | - Ariane Pillé
- Biological NMR Technological Platform, Institut Pasteur, CNRS UMR 3528, Paris, France
| | - Audrey Beaussart
- Institute of Life Sciences, Université Catholique de Louvain, Croix du Sud, 4-5, bte L7.07.06, B-1348 Louvain-la-Neuve, Belgium.,Walloon Excellence in Life Sciences and Biotechnology, Belgium
| | - Victor Lo
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia
| | - Chi L L Pham
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia
| | | | - Ann H Kwan
- School of Life and Environmental Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia
| | - Magalie Duchateau
- Pasteur Proteomics Platform, Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS USR 2000, Paris, France
| | - Quentin Giai Gianetto
- Pasteur Proteomics Platform, Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS USR 2000, Paris, France.,Bioinformatics and Biostatistics Hub, C3BI, CNRS USR 3756, Institut Pasteur, Paris, France
| | - Mariette Matondo
- Pasteur Proteomics Platform, Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS USR 2000, Paris, France
| | - Melanie Lehoux
- Departments of Medicine, Microbiology and Immunology, McGill University, Montréal, QC, Canada
| | - Donald C Sheppard
- Departments of Medicine, Microbiology and Immunology, McGill University, Montréal, QC, Canada
| | - Yves F Dufrene
- Institute of Life Sciences, Université Catholique de Louvain, Croix du Sud, 4-5, bte L7.07.06, B-1348 Louvain-la-Neuve, Belgium.,Walloon Excellence in Life Sciences and Biotechnology, Belgium
| | - Jagadeesh Bayry
- Institut National de la Santé et de la Recherche Médicale, Centre de Recherche des Cordeliers, Sorbonne Université, Paris, France
| | - J Iñaki Guijarro
- Biological NMR Technological Platform, Institut Pasteur, CNRS UMR 3528, Paris, France
| | - Margaret Sunde
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia
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17
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Gräser Y, Monod M, Bouchara JP, Dukik K, Nenoff P, Kargl A, Kupsch C, Zhan P, Packeu A, Chaturvedi V, de Hoog S. New insights in dermatophyte research. Med Mycol 2018. [PMID: 29538740 DOI: 10.1093/mmy/myx141] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Dermatophyte research has renewed interest because of changing human floras with changing socioeconomic conditions, and because of severe chronic infections in patients with congenital immune disorders. Main taxonomic traits at the generic level have changed considerably, and now fine-tuning at the species level with state-of-the-art technology has become urgent. Research on virulence factors focuses on secreted proteases now has support in genome data. It is speculated that most protease families are used for degrading hard keratin during nitrogen recycling in the environment, while others, such as Sub6 may have emerged as a result of ancestral gene duplication, and are likely to have specific roles during infection. Virulence may differ between mating partners of the same species and concepts of zoo- and anthropophily may require revision in some recently redefined species. Many of these questions benefit from international cooperation and exchange of materials. The aim of the ISHAM Working Group Dermatophytes aims to stimulate and coordinate international networking on these fungi.
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Affiliation(s)
- Yvonne Gräser
- Nationales Konsiliarlabor für Dermatophyten, Institut für Mikrobiologie und Hygiene, Berlin, Germany
| | - Michel Monod
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | | | - Karolina Dukik
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Pietro Nenoff
- Labor für Medizinische Mikrobiologie, Mölbis, Germany
| | | | - Christiane Kupsch
- Nationales Konsiliarlabor für Dermatophyten, Institut für Mikrobiologie und Hygiene, Berlin, Germany
| | - Ping Zhan
- Jiangxi Dermatology Hospital and Jiangxi Dermatology Institute, Nanchang, China
| | - Ann Packeu
- Mycologie & Aerobiologie Scientific Institute of Public Health, Brussels, Belgium
| | | | - Sybren de Hoog
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
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18
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Growth and protease secretion of Scedosporium aurantiacum under conditions of hypoxia. Microbiol Res 2018; 216:23-29. [PMID: 30269853 DOI: 10.1016/j.micres.2018.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/02/2018] [Accepted: 08/03/2018] [Indexed: 12/19/2022]
Abstract
One of the micro-environmental stresses that fungal pathogens, such as Scedosporium aurantiacum, colonising human lungs encounter in vivo is hypoxia, or deficiency of oxygen. In this work, we studied the impacts of a hypoxic micro-environment (oxygen levels ≤1%) on the growth of a clinical S. aurantiacum isolate (WM 06.482; CBS 136046) and an environmental strain (S. aurantiacum WM 10.136; CBS 136049) on mucin-containing synthetic cystic fibrosis sputum medium. Additionally, profiles of secreted proteases were compared between the two isolates and protease activity was assessed using class-specific substrates and inhibitors. Overall, both isolates grew slower and produced less biomass under hypoxia compared to normoxic conditions. The pH of the medium decreased to 4.0 over the cultivation time, indicating that S. aurantiacum released acidic compounds into the medium. Accordingly, secreted proteases of the two isolates were dominated by acidic proteases, including aspartic and cysteine proteases, with optimal protease activity at pH 4.0 and 6.0 respectively. The clinical isolate produced higher aspartic and cysteine protease activities. Conversely, all serine proteases, including elastase-like, trypsin-like, chymotrypsin-like and subtilisin-like proteases had higher activities in the environmental isolate. Sequence similarities to 13 secreted proteases were identified by mass spectrometry (MS) by searching against other fungal proteases in the NCBI database. Results from MS analysis were consistent with those from activity assays. The clinical highly-virulent, and environmental low-virulence S. aurantiacum isolates responded differently to hypoxia in terms of the type of proteases secreted, which may reflect their different virulence properties.
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19
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Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species. Sci Rep 2018; 8:6617. [PMID: 29700415 PMCID: PMC5919931 DOI: 10.1038/s41598-018-25016-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/13/2018] [Indexed: 12/11/2022] Open
Abstract
Aspergillus fumigatus and multiple other Aspergillus species cause a wide range of lung infections, collectively termed aspergillosis. Aspergilli are ubiquitous in environment with healthy immune systems routinely eliminating inhaled conidia, however, Aspergilli can become an opportunistic pathogen in immune-compromised patients. The aspergillosis mortality rate and emergence of drug-resistance reveals an urgent need to identify novel targets. Secreted and cell membrane proteins play a critical role in fungal-host interactions and pathogenesis. Using a computational pipeline integrating data from high-throughput experiments and bioinformatic predictions, we have identified secreted and cell membrane proteins in ten Aspergillus species known to cause aspergillosis. Small secreted and effector-like proteins similar to agents of fungal-plant pathogenesis were also identified within each secretome. A comparison with humans revealed that at least 70% of Aspergillus secretomes have no sequence similarity with the human proteome. An analysis of antigenic qualities of Aspergillus proteins revealed that the secretome is significantly more antigenic than cell membrane proteins or the complete proteome. Finally, overlaying an expression dataset, four A. fumigatus proteins upregulated during infection and with available structures, were found to be structurally similar to known drug target proteins in other organisms, and were able to dock in silico with the respective drug.
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20
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Abstract
Humans are exceptional among vertebrates in that their living tissue is directly exposed to the outside world. In the absence of protective scales, feathers, or fur, the skin has to be highly effective in defending the organism against the gamut of opportunistic fungi surrounding us. Most (sub)cutaneous infections enter the body by implantation through the skin barrier. On intact skin, two types of fungal expansion are noted: (A) colonization by commensals, i.e., growth enabled by conditions prevailing on the skin surface without degradation of tissue, and (B) infection by superficial pathogens that assimilate epidermal keratin and interact with the cellular immune system. In a response-damage framework, all fungi are potentially able to cause disease, as a balance between their natural predilection and the immune status of the host. For this reason, we will not attribute a fixed ecological term to each species, but rather describe them as growing in a commensal state (A) or in a pathogenic state (B).
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21
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Vicente VA, Weiss VA, Bombassaro A, Moreno LF, Costa FF, Raittz RT, Leão AC, Gomes RR, Bocca AL, Fornari G, de Castro RJA, Sun J, Faoro H, Tadra-Sfeir MZ, Baura V, Balsanelli E, Almeida SR, Dos Santos SS, Teixeira MDM, Soares Felipe MS, do Nascimento MMF, Pedrosa FO, Steffens MB, Attili-Angelis D, Najafzadeh MJ, Queiroz-Telles F, Souza EM, De Hoog S. Comparative Genomics of Sibling Species of Fonsecaea Associated with Human Chromoblastomycosis. Front Microbiol 2017; 8:1924. [PMID: 29062304 PMCID: PMC5640708 DOI: 10.3389/fmicb.2017.01924] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/21/2017] [Indexed: 01/16/2023] Open
Abstract
Fonsecaea and Cladophialophora are genera of black yeast-like fungi harboring agents of a mutilating implantation disease in humans, along with strictly environmental species. The current hypothesis suggests that those species reside in somewhat adverse microhabitats, and pathogenic siblings share virulence factors enabling survival in mammal tissue after coincidental inoculation driven by pathogenic adaptation. A comparative genomic analysis of environmental and pathogenic siblings of Fonsecaea and Cladophialophora was undertaken, including de novo assembly of F. erecta from plant material. The genome size of Fonsecaea species varied between 33.39 and 35.23 Mb, and the core genomes of those species comprises almost 70% of the genes. Expansions of protein domains such as glyoxalases and peptidases suggested ability for pathogenicity in clinical agents, while the use of nitrogen and degradation of phenolic compounds was enriched in environmental species. The similarity of carbohydrate-active vs. protein-degrading enzymes associated with the occurrence of virulence factors suggested a general tolerance to extreme conditions, which might explain the opportunistic tendency of Fonsecaea sibling species. Virulence was tested in the Galleria mellonella model and immunological assays were performed in order to support this hypothesis. Larvae infected by environmental F. erecta had a lower survival. Fungal macrophage murine co-culture showed that F. erecta induced high levels of TNF-α contributing to macrophage activation that could increase the ability to control intracellular fungal growth although hyphal death were not observed, suggesting a higher level of extremotolerance of environmental species.
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Affiliation(s)
- Vania A Vicente
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil.,Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| | - Vinícius A Weiss
- Laboratory of Bioinformatics, Sector of Technological and Professional Education, Federal University of Paraná, Curitiba, Brazil.,Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | - Amanda Bombassaro
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Leandro F Moreno
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil.,CBS-KNAW Fungal Biodiversity Centre, Utrecht, Netherlands.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Flávia F Costa
- Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| | - Roberto T Raittz
- Laboratory of Bioinformatics, Sector of Technological and Professional Education, Federal University of Paraná, Curitiba, Brazil
| | - Aniele C Leão
- Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil.,Laboratory of Bioinformatics, Sector of Technological and Professional Education, Federal University of Paraná, Curitiba, Brazil.,Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | - Renata R Gomes
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Anamelia L Bocca
- Department of Cell Biology, University of Brasília, Brasilia, Brazil
| | - Gheniffer Fornari
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
| | | | - Jiufeng Sun
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Helisson Faoro
- Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | | | - Valter Baura
- Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | - Eduardo Balsanelli
- Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | - Sandro R Almeida
- Department of Clinical and Toxicological Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Suelen S Dos Santos
- Department of Clinical and Toxicological Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Marcus de Melo Teixeira
- Department of Cell Biology, University of Brasília, Brasilia, Brazil.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Maria S Soares Felipe
- Department of Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasilia, Brazil
| | | | - Fabio O Pedrosa
- Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | - Maria B Steffens
- Laboratory of Bioinformatics, Sector of Technological and Professional Education, Federal University of Paraná, Curitiba, Brazil.,Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | | | - Mohammad J Najafzadeh
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Flávio Queiroz-Telles
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil.,Clinical Hospital of the Federal University of Paraná, Curitiba, Brazil
| | - Emanuel M Souza
- Laboratory of Bioinformatics, Sector of Technological and Professional Education, Federal University of Paraná, Curitiba, Brazil.,Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | - Sybren De Hoog
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil.,CBS-KNAW Fungal Biodiversity Centre, Utrecht, Netherlands.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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22
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Zhu Y, Liang X, Zhang H, Feng W, Liu Y, Zhang F, Linhardt RJ. A comparative secretome analysis of industrial Aspergillus oryzae and its spontaneous mutant ZJGS-LZ-21. Int J Food Microbiol 2017; 248:1-9. [PMID: 28237882 DOI: 10.1016/j.ijfoodmicro.2017.02.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 01/24/2017] [Accepted: 02/05/2017] [Indexed: 10/20/2022]
Abstract
Aspergillus oryzae koji plays a crucial role in fermented food products due to the hydrolytic activities of secreted enzymes. In the present study, we performed a comparative secretome analysis of the industrial strain of Aspergillus oryzae 3.042 and its spontaneous mutantZJGS-LZ-21. One hundred and fifty two (152) differential protein spots were excised (p<0.05), and 25 proteins were identified. Of the identified proteins, 91.3% belonged to hydrolytic enzymes acting on carbohydrates or proteins. Consistent with their enzyme activities, the expression of 14 proteins involved in the degradation of cellulose, hemicellulose, starch and proteins, increased in the ZJGS-LZ-21isolate. In particular, increased levels of acid protease (Pep) may favor the degradation of soy proteins in acidic environments and promote the cleavage of allergenic soybean proteins in fermentation, resulting in improvements of product safety and quality. The ZJGS-LZ-21 isolate showed higher protein secretion and increased hydrolytic activities than did strain 3.042, indicating its promising application in soybean paste fermentation.
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Affiliation(s)
- Yuanyuan Zhu
- Department of Biochemical Engineering, Zhejiang Gongshang University, Hangzhou 310025, China
| | - Xinle Liang
- Department of Biochemical Engineering, Zhejiang Gongshang University, Hangzhou 310025, China.
| | - Hong Zhang
- Department of Biochemical Engineering, Zhejiang Gongshang University, Hangzhou 310025, China
| | - Wei Feng
- Zhejiang Wuweihe Food Co. Ltd, Huzhou 313213, China
| | - Ye Liu
- Zhejiang Wuweihe Food Co. Ltd, Huzhou 313213, China
| | - Fuming Zhang
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Robert J Linhardt
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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23
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AoS28D, a proline-Xaa carboxypeptidase secreted by Aspergillus oryzae. Appl Microbiol Biotechnol 2017; 101:4129-4137. [PMID: 28229206 DOI: 10.1007/s00253-017-8186-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/30/2017] [Accepted: 02/07/2017] [Indexed: 10/20/2022]
Abstract
Prolyl peptidases of the MEROPS S28 family are of particular interest because they are key enzymes in the digestion of proline-rich peptides. A BLAST analysis of the Aspergillus oryzae genome revealed sequences coding for four proteases of the S28 family. Three of these proteases, AoS28A, AoS28B, and AoS28C, were previously characterized as acidic prolyl endopeptidases. The fourth protease, AoS28D, showed high sequence divergence with other S28 proteases and belongs to a phylogenetically distinct cluster together with orthologous proteases from other Aspergillus species. The objective of the present paper was to characterize AoS28D protease in terms of substrate specificity and activity. AoS28D produced by gene overexpression in A. oryzae and in Pichia pastoris was a 70-kDa glycoprotein with a 10-kDa sugar moiety. In contrast with other S28 proteases, AoS28D did not hydrolyze internal Pro-Xaa bonds of several tested peptides. Similarly, to human lysosomal Pro-Xaa carboxypeptidase, AoS28D demonstrated selectivity for cleaving C-terminal Pro-Xaa bonds which are resistant to carboxypeptidases of the S10 family concomitantly secreted by A. oryzae. Therefore, AoS28D could act in synergy with these enzymes during sequential degradation of a peptide from its C-terminus.
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24
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Kuan CS, Cham CY, Singh G, Yew SM, Tan YC, Chong PS, Toh YF, Atiya N, Na SL, Lee KW, Hoh CC, Yee WY, Ng KP. Genomic Analyses of Cladophialophora bantiana, a Major Cause of Cerebral Phaeohyphomycosis Provides Insight into Its Lifestyle, Virulence and Adaption in Host. PLoS One 2016; 11:e0161008. [PMID: 27570972 PMCID: PMC5003357 DOI: 10.1371/journal.pone.0161008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/28/2016] [Indexed: 11/18/2022] Open
Abstract
Cladophialophora bantiana is a dematiaceous fungus with a predilection for causing central nervous system (CNS) infection manifesting as brain abscess in both immunocompetent and immunocompromised patients. In this paper, we report comprehensive genomic analyses of C. bantiana isolated from the brain abscess of an immunocompetent man, the first reported case in Malaysia and Southeast Asia. The identity of the fungus was determined using combined morphological analysis and multilocus phylogeny. The draft genome sequence of a neurotrophic fungus, C. bantiana UM 956 was generated using Illumina sequencing technology to dissect its genetic fundamental and basic biology. The assembled 37.1 Mb genome encodes 12,155 putative coding genes, of which, 1.01% are predicted transposable elements. Its genomic features support its saprophytic lifestyle, renowned for its versatility in decomposing hemicellulose and pectin components. The C. bantiana UM 956 was also found to carry some important putative genes that engaged in pathogenicity, iron uptake and homeostasis as well as adaptation to various stresses to enable the organism to survive in hostile microenvironment. This wealth of resource will further catalyse more downstream functional studies to provide better understanding on how this fungus can be a successful and persistent pathogen in human.
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Affiliation(s)
- Chee Sian Kuan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Chun Yoong Cham
- Department of Neurosurgery, Hospital Pulau Pinang, Jalan Residensi, Georgetown, Pulau Pinang, Malaysia
- Department of Surgery, Neurosurgical Division, University of Malaya, Kuala Lumpur, Malaysia
| | - Gurmit Singh
- Department of Neurosurgery, Hospital Pulau Pinang, Jalan Residensi, Georgetown, Pulau Pinang, Malaysia
| | - Su Mei Yew
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | | | - Yue Fen Toh
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Nadia Atiya
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Shiang Ling Na
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok Wei Lee
- Codon Genomics SB, Selangor Darul Ehsan, Malaysia
| | | | - Wai-Yan Yee
- Codon Genomics SB, Selangor Darul Ehsan, Malaysia
| | - Kee Peng Ng
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail:
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25
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Insight into different environmental niches adaptation and allergenicity from the Cladosporium sphaerospermum genome, a common human allergy-eliciting Dothideomycetes. Sci Rep 2016; 6:27008. [PMID: 27243961 PMCID: PMC4886633 DOI: 10.1038/srep27008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/10/2016] [Indexed: 11/09/2022] Open
Abstract
Cladosporium sphaerospermum, a dematiaceous saprophytic fungus commonly found in diverse environments, has been reported to cause allergy and other occasional diseases in humans. However, its basic biology and genetic information are largely unexplored. A clinical isolate C. sphaerospermum genome, UM 843, was re-sequenced and combined with previously generated sequences to form a model 26.89 Mb genome containing 9,652 predicted genes. Functional annotation on predicted genes suggests the ability of this fungus to degrade carbohydrate and protein complexes. Several putative peptidases responsible for lung tissue hydrolysis were identified. These genes shared high similarity with the Aspergillus peptidases. The UM 843 genome encodes a wide array of proteins involved in the biosynthesis of melanin, siderophores, cladosins and survival in high salinity environment. In addition, a total of 28 genes were predicted to be associated with allergy. Orthologous gene analysis together with 22 other Dothideomycetes showed genes uniquely present in UM 843 that encode four class 1 hydrophobins which may be allergens specific to Cladosporium. The mRNA of these hydrophobins were detected by RT-PCR. The genomic analysis of UM 843 contributes to the understanding of the biology and allergenicity of this widely-prevalent species.
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26
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Merz M, Claaßen W, Appel D, Berends P, Rabe S, Blank I, Stressler T, Fischer L. Characterization of commercially available peptidases in respect of the production of protein hydrolysates with defined compositions using a three-step methodology. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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27
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Batch-to-batch variation and storage stability of the commercial peptidase preparation Flavourzyme in respect of key enzyme activities and its influence on process reproducibility. Eur Food Res Technol 2015. [DOI: 10.1007/s00217-015-2606-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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28
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Eugster PJ, Grouzmann E, Salamin K, Monod M. Production and characterization of two major Aspergillus oryzae secreted prolyl endopeptidases able to efficiently digest proline-rich peptides of gliadin. Microbiology (Reading) 2015; 161:2277-88. [DOI: 10.1099/mic.0.000198] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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29
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Comparative Secretome Analysis of Aspergillus niger, Trichoderma reesei, and Penicillium oxalicum During Solid-State Fermentation. Appl Biochem Biotechnol 2015; 177:1252-71. [DOI: 10.1007/s12010-015-1811-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 08/17/2015] [Indexed: 10/23/2022]
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30
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Merz M, Eisele T, Berends P, Appel D, Rabe S, Blank I, Stressler T, Fischer L. Flavourzyme, an Enzyme Preparation with Industrial Relevance: Automated Nine-Step Purification and Partial Characterization of Eight Enzymes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:5682-5693. [PMID: 25996918 DOI: 10.1021/acs.jafc.5b01665] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Flavourzyme is sold as a peptidase preparation from Aspergillus oryzae. The enzyme preparation is widely and diversely used for protein hydrolysis in industrial and research applications. However, detailed information about the composition of this mixture is still missing due to the complexity. The present study identified eight key enzymes by mass spectrometry and partially by activity staining on native polyacrylamide gels or gel zymography. The eight enzymes identified were two aminopeptidases, two dipeptidyl peptidases, three endopeptidases, and one α-amylase from the A. oryzae strain ATCC 42149/RIB 40 (yellow koji mold). Various specific marker substrates for these Flavourzyme enzymes were ascertained. An automated, time-saving nine-step protocol for the purification of all eight enzymes within 7 h was designed. Finally, the purified Flavourzyme enzymes were biochemically characterized with regard to pH and temperature profiles and molecular sizes.
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Affiliation(s)
- Michael Merz
- †Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, University of Hohenheim, Garbenstrasse 25, D-70599 Stuttgart, Germany
| | - Thomas Eisele
- †Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, University of Hohenheim, Garbenstrasse 25, D-70599 Stuttgart, Germany
| | - Pieter Berends
- §Nestlé Product Technology Centre, Lange Strasse 21, D-78224 Singen, Germany
| | - Daniel Appel
- §Nestlé Product Technology Centre, Lange Strasse 21, D-78224 Singen, Germany
| | - Swen Rabe
- §Nestlé Product Technology Centre, Lange Strasse 21, D-78224 Singen, Germany
| | - Imre Blank
- §Nestlé Product Technology Centre, Lange Strasse 21, D-78224 Singen, Germany
| | - Timo Stressler
- †Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, University of Hohenheim, Garbenstrasse 25, D-70599 Stuttgart, Germany
| | - Lutz Fischer
- †Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, University of Hohenheim, Garbenstrasse 25, D-70599 Stuttgart, Germany
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31
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Budak SO, Zhou M, Brouwer C, Wiebenga A, Benoit I, Di Falco M, Tsang A, de Vries RP. A genomic survey of proteases in Aspergilli. BMC Genomics 2014; 15:523. [PMID: 24965873 PMCID: PMC4102723 DOI: 10.1186/1471-2164-15-523] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 06/18/2014] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Proteases can hydrolyze peptides in aqueous environments. This property has made proteases the most important industrial enzymes by taking up about 60% of the total enzyme market. Microorganisms are the main sources for industrial protease production due to their high yield and a wide range of biochemical properties. Several Aspergilli have the ability to produce a variety of proteases, but no comprehensive comparative study has been carried out on protease productivity in this genus so far. RESULTS We have performed a combined analysis of comparative genomics, proteomics and enzymology tests on seven Aspergillus species grown on wheat bran and sugar beet pulp. Putative proteases were identified by homology search and Pfam domains. These genes were then clusters based on orthology and extracellular proteases were identified by protein subcellular localization prediction. Proteomics was used to identify the secreted enzymes in the cultures, while protease essays with and without inhibitors were performed to determine the overall protease activity per protease class. All this data was then integrated to compare the protease productivities in Aspergilli. CONCLUSIONS Genomes of Aspergillus species contain a similar proportion of protease encoding genes. According to comparative genomics, proteomics and enzymatic experiments serine proteases make up the largest group in the protease spectrum across the species. In general wheat bran gives higher induction of proteases than sugar beet pulp. Interesting differences of protease activity, extracellular enzyme spectrum composition, protein occurrence and abundance were identified for species. By combining in silico and wet-lab experiments, we present the intriguing variety of protease productivity in Aspergilli.
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Affiliation(s)
- Sebnem Ozturkoglu Budak
- />CBS-KNAW Fungal Biodiversity Center, Uppsalalaan 8, Utrecht, 3584 CT The Netherlands
- />Faculty of Agriculture, Department of Dairy Technology, University of Ankara, Ankara, Turkey
- />Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Miaomiao Zhou
- />CBS-KNAW Fungal Biodiversity Center, Uppsalalaan 8, Utrecht, 3584 CT The Netherlands
- />Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Carlo Brouwer
- />CBS-KNAW Fungal Biodiversity Center, Uppsalalaan 8, Utrecht, 3584 CT The Netherlands
| | - Ad Wiebenga
- />CBS-KNAW Fungal Biodiversity Center, Uppsalalaan 8, Utrecht, 3584 CT The Netherlands
- />Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Isabelle Benoit
- />CBS-KNAW Fungal Biodiversity Center, Uppsalalaan 8, Utrecht, 3584 CT The Netherlands
- />Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Marcos Di Falco
- />Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| | - Adrian Tsang
- />Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| | - Ronald P de Vries
- />CBS-KNAW Fungal Biodiversity Center, Uppsalalaan 8, Utrecht, 3584 CT The Netherlands
- />Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
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32
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Surface structure characterization of Aspergillus fumigatus conidia mutated in the melanin synthesis pathway and their human cellular immune response. Infect Immun 2014; 82:3141-53. [PMID: 24818666 DOI: 10.1128/iai.01726-14] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Aspergillus fumigatus, the conidial surface contains dihydroxynaphthalene (DHN)-melanin. Six-clustered gene products have been identified that mediate sequential catalysis of DHN-melanin biosynthesis. Melanin thus produced is known to be a virulence factor, protecting the fungus from the host defense mechanisms. In the present study, individual deletion of the genes involved in the initial three steps of melanin biosynthesis resulted in an altered conidial surface with masked surface rodlet layer, leaky cell wall allowing the deposition of proteins on the cell surface and exposing the otherwise-masked cell wall polysaccharides at the surface. Melanin as such was immunologically inert; however, deletion mutant conidia with modified surfaces could activate human dendritic cells and the subsequent cytokine production in contrast to the wild-type conidia. Cell surface defects were rectified in the conidia mutated in downstream melanin biosynthetic pathway, and maximum immune inertness was observed upon synthesis of vermelone onward. These observations suggest that although melanin as such is an immunologically inert material, it confers virulence by facilitating proper formation of the A. fumigatus conidial surface.
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33
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Beauvais A, Bozza S, Kniemeyer O, Formosa C, Balloy V, Henry C, Roberson RW, Dague E, Chignard M, Brakhage AA, Romani L, Latgé JP. Deletion of the α-(1,3)-glucan synthase genes induces a restructuring of the conidial cell wall responsible for the avirulence of Aspergillus fumigatus. PLoS Pathog 2013; 9:e1003716. [PMID: 24244155 PMCID: PMC3828178 DOI: 10.1371/journal.ppat.1003716] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 08/22/2013] [Indexed: 01/12/2023] Open
Abstract
α-(1,3)-Glucan is a major component of the cell wall of Aspergillus fumigatus, an opportunistic human fungal pathogen. There are three genes (AGS1, AGS2 and AGS3) controlling the biosynthesis of α-(1,3)-glucan in this fungal species. Deletion of all the three AGS genes resulted in a triple mutant that was devoid of α-(1,3)-glucan in its cell wall; however, its growth and germination was identical to that of the parental strain in vitro. In the experimental murine aspergillosis model, this mutant was less pathogenic than the parental strain. The AGS deletion resulted in an extensive structural modification of the conidial cell wall, especially conidial surface where the rodlet layer was covered by an amorphous glycoprotein matrix. This surface modification was responsible for viability reduction of conidia in vivo, which explains decrease in the virulence of triple agsΔ mutant. Aspergillus fumigatus is the predominant mold pathogen of humans, responsible for life-threatening systemic infections in patients with depressed immunity. Because of its external localization and specific composition, the fungal cell wall represents a target for recognition by and interaction with the host immune cells. In A. fumigatus, α-(1,3)-glucan is a key component of the extracellular matrix, which encloses the cell wall β-(1,3)-glucan-chitin fibrillar core. Interestingly, the deletion of the genes responsible for α-(1,3)-glucan synthesis resulted in a mutant that exhibited wild type phenotype in vitro; while the altered cell wall organization resulted in this fungus being avirulent in vivo. This study confirms that any modification in the cell wall components is associated with compensatory reactions developed by the fungus to counteract stress on the cell wall that may result in unexpected fungal response when challenged with the host immune system.
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Affiliation(s)
- Anne Beauvais
- Unité des Aspergillus, Institut Pasteur, Paris, France
- * E-mail:
| | - Silvia Bozza
- Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy
| | - Olaf Kniemeyer
- Molecular and Applied Microbiology, Leibniz-Institute for Natural Product Research and Infection Biology (HKI), University of Jena, Jena, Germany
- Integrated Research and Treatment Center, Center for Sepsis Control and Care Jena, University Hospital (CSCC), Jena, Germany
| | | | - Viviane Balloy
- Unité de Défence Innée et Inflammation, Institut Pasteur, Inserm U874, Paris, France
| | | | - Robert W. Roberson
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | | | - Michel Chignard
- Unité de Défence Innée et Inflammation, Institut Pasteur, Inserm U874, Paris, France
| | - Axel A. Brakhage
- Molecular and Applied Microbiology, Leibniz-Institute for Natural Product Research and Infection Biology (HKI), University of Jena, Jena, Germany
| | - Luigina Romani
- Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy
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Shah F, Rineau F, Canbäck B, Johansson T, Tunlid A. The molecular components of the extracellular protein-degradation pathways of the ectomycorrhizal fungus Paxillus involutus. THE NEW PHYTOLOGIST 2013; 200:875-887. [PMID: 23902518 PMCID: PMC4282482 DOI: 10.1111/nph.12425] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 06/25/2013] [Indexed: 05/20/2023]
Abstract
Proteins contribute to a major part of the organic nitrogen (N) in forest soils. This N is mobilized and becomes available to trees as a result of the depolymerizing activities of symbiotic ectomycorrhizal fungi. The mechanisms by which these fungi depolymerize proteins and assimilate the released N are poorly characterized. Biochemical analysis and transcriptome profiling were performed to examine the proteolytic machinery and the uptake system of the ectomycorrhizal basidiomycete Paxillus involutus during the assimilation of organic N from various protein sources and extracts of organic matter. All substrates induced secretion of peptidase activity with an acidic pH optimum, mostly contributed by aspartic peptidases. The peptidase activity was transiently repressed by ammonium. Transcriptional analysis revealed a large number of extracellular endo- and exopeptidases. The expression levels of these peptidases were regulated in parallel with transporters and enzymes involved in the assimilation and metabolism of the released peptides and amino acids. For the first time the molecular components of the protein degradation pathways of an ectomycorrhizal fungus are described. The data suggest that the transcripts encoding these components are regulated in response to the chemical properties and the availability of the protein substrates.
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Affiliation(s)
- Firoz Shah
- Department of Biology, Microbial Ecology Group, Lund UniversityEcology Building, SE-223 62, Lund, Sweden
| | - Francois Rineau
- Department of Biology, Microbial Ecology Group, Lund UniversityEcology Building, SE-223 62, Lund, Sweden
| | - Björn Canbäck
- Department of Biology, Microbial Ecology Group, Lund UniversityEcology Building, SE-223 62, Lund, Sweden
| | - Tomas Johansson
- Department of Biology, Microbial Ecology Group, Lund UniversityEcology Building, SE-223 62, Lund, Sweden
| | - Anders Tunlid
- Department of Biology, Microbial Ecology Group, Lund UniversityEcology Building, SE-223 62, Lund, Sweden
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35
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Xiang Q, Wang Z, Zhang Y, Wang H. An oligopeptide transporter gene family in Phanerochaete chrysosporium. Gene 2013; 522:133-41. [DOI: 10.1016/j.gene.2013.03.069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 02/21/2013] [Accepted: 03/16/2013] [Indexed: 10/27/2022]
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Girard V, Dieryckx C, Job C, Job D. Secretomes: The fungal strike force. Proteomics 2013; 13:597-608. [DOI: 10.1002/pmic.201200282] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 10/01/2012] [Accepted: 10/05/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Vincent Girard
- Bayer CropScience Joint Laboratory (UMR5240); CNRS, University Lyon1; Lyon; France
| | - Cindy Dieryckx
- Bayer CropScience Joint Laboratory (UMR5240); CNRS, University Lyon1; Lyon; France
| | - Claudette Job
- Bayer CropScience Joint Laboratory (UMR5240); CNRS, University Lyon1; Lyon; France
| | - Dominique Job
- Bayer CropScience Joint Laboratory (UMR5240); CNRS, University Lyon1; Lyon; France
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Farnell E, Rousseau K, Thornton DJ, Bowyer P, Herrick SE. Expression and secretion of Aspergillus fumigatus proteases are regulated in response to different protein substrates. Fungal Biol 2012; 116:1003-12. [PMID: 22954343 PMCID: PMC3605576 DOI: 10.1016/j.funbio.2012.07.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 07/06/2012] [Accepted: 07/09/2012] [Indexed: 01/12/2023]
Abstract
The ubiquitous filamentous fungus Aspergillus fumigatus secretes a number of allergens with protease activity and has been linked to a variety of allergic conditions such as Severe Asthma with Fungal Sensitization (SAFS) and Allergic Bronchopulmonary Aspergillosis (ABPA). However, it is unclear which allergen proteases are being secreted during fungal invasion and whether the local biological environment regulates their expression. Understanding the dynamic expression of allergen proteases during growth of A. fumigatus may lead to further characterisation of the pathogenesis of these disorders as well as improved standardisation in the commercial production of these allergens. Secretion of proteases during germination and early growth of A. fumigatus was investigated in response to various complex protein sources (pig lung homogenate, mucin or casein). Protease inhibitor studies demonstrated that A. fumigatus (AF293 strain) secretes predominately serine proteases during growth in pig lung based medium and mainly metalloproteases during growth in casein based medium but suppressed protease secretion in unmodified Vogel's minimal medium and secreted both types in mucin based medium. Analysis of gene transcription and protein identification by mass spectrometry showed that the matrix metalloprotease, Mep/Asp f 5 and the serine protease, Alp1/Asp f 13, were upregulated and secreted during growth in pig lung medium, whereas Alp1 was predominately expressed and secreted in mucin based medium. In casein medium, the matrix metalloprotease, Lap1, was also upregulated and secreted in addition to Mep and Alp1. These findings suggest that A. fumigatus is able to detect different complex proteins available as substrates in its environment and regulate protease secretion accordingly. There is a requirement for the standardisation of A. fumigatus allergen extracts used both in clinical diagnosis of A. fumigatus allergy and in research studies.
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Affiliation(s)
- Edward Farnell
- Respiratory Research Group, School of Translational Medicine, Faculty of Medical and Human Sciences, University of Manchester, Stopford Building, Manchester M13 9PT, UK
| | - Karine Rousseau
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester M13 9PT, UK
| | - David J. Thornton
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester M13 9PT, UK
| | - Paul Bowyer
- Respiratory Research Group, School of Translational Medicine, Faculty of Medical and Human Sciences, University of Manchester, Education and Research Centre, Wythenshawe Hospital, Manchester M23 9LT, UK
| | - Sarah E. Herrick
- Respiratory Research Group, School of Translational Medicine, Faculty of Medical and Human Sciences, University of Manchester, Stopford Building, Manchester M13 9PT, UK
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Millon L, Roussel S, Rognon B, Quadroni M, Salamin K, Reboux G, Barrera C, Fellrath JM, Aubert JD, Dalphin JC, Monod M. Aspergillus species recombinant antigens for serodiagnosis of farmer's lung disease. J Allergy Clin Immunol 2012; 130:803-805.e6. [DOI: 10.1016/j.jaci.2012.03.039] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Revised: 03/21/2012] [Accepted: 03/30/2012] [Indexed: 12/01/2022]
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Zhu L, Nemoto T, Yoon J, Maruyama JI, Kitamoto K. Improved heterologous protein production by a tripeptidyl peptidase gene (AosedD) disruptant of the filamentous fungus Aspergillus oryzae. J GEN APPL MICROBIOL 2012; 58:199-209. [PMID: 22878738 DOI: 10.2323/jgam.58.199] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Proteolytic degradation is one of the serious bottlenecks limiting the yields of heterologous protein production by Aspergillus oryzae. In this study, we selected a tripeptidyl peptidase gene AosedD (AO090166000084) as a candidate potentially degrading the heterologous protein, and performed localization analysis of the fusion protein AoSedD-EGFP in A. oryzae. As a result, the AoSedD-EGFP was observed in the septa and cell walls as well as in the culture medium, suggesting that AoSedD is a secretory enzyme. An AosedD disruptant was constructed to investigate an effect of AoSedD on the production level of heterologous proteins and protease activity. Both of the total protease and tripeptidyl peptidase activities in the culture medium of the AosedD disruptant were decreased as compared to those of the control strain. The maximum yields of recombinant bovine chymosin (CHY) and human lysozyme (HLY) produced by the AosedD disruptants showed approximately 2.9- and 1.7-fold increases, respectively, as compared to their control strains. These results suggest that AoSedD is one of the major proteases involved in the proteolytic degradation of recombinant proteins in A. oryzae.
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Affiliation(s)
- Lin Zhu
- Department of Biotechnology, The University of Tokyo, Japan
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40
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Hagag S, Kubitschek-Barreira P, Neves GWP, Amar D, Nierman W, Shalit I, Shamir R, Lopes-Bezerra L, Osherov N. Transcriptional and proteomic analysis of the Aspergillus fumigatus ΔprtT protease-deficient mutant. PLoS One 2012; 7:e33604. [PMID: 22514608 PMCID: PMC3326020 DOI: 10.1371/journal.pone.0033604] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 02/13/2012] [Indexed: 01/21/2023] Open
Abstract
Aspergillus fumigatus is the most common opportunistic mold pathogen of humans, infecting immunocompromised patients. The fungus invades the lungs and other organs, causing severe damage. Penetration of the pulmonary epithelium is a key step in the infectious process. A. fumigatus produces extracellular proteases to degrade the host structural barriers. The A. fumigatus transcription factor PrtT controls the expression of multiple secreted proteases. PrtT shows similarity to the fungal Gal4-type Zn(2)-Cys(6) DNA-binding domain of several transcription factors. In this work, we further investigate the function of this transcription factor by performing a transcriptional and a proteomic analysis of the ΔprtT mutant. Unexpectedly, microarray analysis revealed that in addition to the expected decrease in protease expression, expression of genes involved in iron uptake and ergosterol synthesis was dramatically decreased in the ΔprtT mutant. A second finding of interest is that deletion of prtT resulted in the upregulation of four secondary metabolite clusters, including genes for the biosynthesis of toxic pseurotin A. Proteomic analysis identified reduced levels of three secreted proteases (ALP1 protease, TppA, AFUA_2G01250) and increased levels of three secreted polysaccharide-degrading enzymes in the ΔprtT mutant possibly in response to its inability to derive sufficient nourishment from protein breakdown. This report highlights the complexity of gene regulation by PrtT, and suggests a potential novel link between the regulation of protease secretion and the control of iron uptake, ergosterol biosynthesis and secondary metabolite production in A. fumigatus.
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Affiliation(s)
- Shelly Hagag
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine Ramat-Aviv, Tel-Aviv, Israel
| | - Paula Kubitschek-Barreira
- Department of Cellular Biology, The Roberto Alcantara Gomes Institute of Biology, University of Estado Rio de Janeiro, Brazil
| | - Gabriela W. P. Neves
- Department of Cellular Biology, The Roberto Alcantara Gomes Institute of Biology, University of Estado Rio de Janeiro, Brazil
| | - David Amar
- Department of Computer Science, Tel-Aviv University, Ramat-Aviv, Tel-Aviv, Israel
| | - William Nierman
- The J. CraigVenter Institute, Rockville, Maryland, United States of America
| | - Itamar Shalit
- Sackler School of Medicine, Ramat Aviv, Tel-Aviv, Israel
| | - Ron Shamir
- Department of Computer Science, Tel-Aviv University, Ramat-Aviv, Tel-Aviv, Israel
| | - Leila Lopes-Bezerra
- Department of Cellular Biology, The Roberto Alcantara Gomes Institute of Biology, University of Estado Rio de Janeiro, Brazil
| | - Nir Osherov
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine Ramat-Aviv, Tel-Aviv, Israel
- * E-mail:
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Sriranganadane D, Waridel P, Salamin K, Feuermann M, Mignon B, Staib P, Neuhaus JM, Quadroni M, Monod M. Identification of novel secreted proteases during extracellular proteolysis by dermatophytes at acidic pH. Proteomics 2011; 11:4422-33. [PMID: 21919205 DOI: 10.1002/pmic.201100234] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 08/18/2011] [Accepted: 08/29/2011] [Indexed: 02/04/2023]
Abstract
The dermatophytes are a group of closely related fungi which are responsible for the great majority of superficial mycoses in humans and animals. Among various potential virulence factors, their secreted proteolytic activity attracts a lot of attention. Most dermatophyte-secreted proteases which have so far been isolated in vitro are neutral or alkaline enzymes. However, inspection of the recently decoded dermatophyte genomes revealed many other hypothetical secreted proteases, in particular acidic proteases similar to those characterized in Aspergillus spp. The validation of such genome predictions instigated the present study on two dermatophyte species, Microsporum canis and Arthroderma benhamiae. Both fungi were found to grow well in a protein medium at acidic pH, accompanied by extracellular proteolysis. Shotgun MS analysis of secreted protein revealed fundamentally different protease profiles during fungal growth in acidic versus neutral pH conditions. Most notably, novel dermatophyte-secreted proteases were identified at acidic pH such as pepsins, sedolisins and acidic carboxypeptidases. Therefore, our results not only support genome predictions, but demonstrate for the first time the secretion of acidic proteases by dermatophytes. Our findings also suggest the existence of different pathways of protein degradation into amino acids and short peptides in these highly specialized pathogenic fungi.
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Affiliation(s)
- Dev Sriranganadane
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
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Kniemeyer O. Proteomics of eukaryotic microorganisms: The medically and biotechnologically important fungal genus Aspergillus. Proteomics 2011; 11:3232-43. [DOI: 10.1002/pmic.201100087] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 03/26/2011] [Accepted: 04/05/2011] [Indexed: 11/09/2022]
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Watson DS, Feng X, Askew DS, Jambunathan K, Kodukula K, Galande AK. Substrate specifity profiling of the Aspergillus fumigatus proteolytic secretome reveals consensus motifs with predominance of Ile/Leu and Phe/Tyr. PLoS One 2011; 6:e21001. [PMID: 21695046 PMCID: PMC3117871 DOI: 10.1371/journal.pone.0021001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Accepted: 05/16/2011] [Indexed: 01/12/2023] Open
Abstract
Background The filamentous fungus Aspergillus fumigatus (AF) can cause devastating infections in immunocompromised individuals. Early diagnosis improves patient outcomes but remains challenging because of the limitations of current methods. To augment the clinician's toolkit for rapid diagnosis of AF infections, we are investigating AF secreted proteases as novel diagnostic targets. The AF genome encodes up to 100 secreted proteases, but fewer than 15 of these enzymes have been characterized thus far. Given the large number of proteases in the genome, studies focused on individual enzymes may overlook potential diagnostic biomarkers. Methodology and Principal Findings As an alternative, we employed a combinatorial library of internally quenched fluorogenic probes (IQFPs) to profile the global proteolytic secretome of an AF clinical isolate in vitro. Comparative protease activity profiling revealed 212 substrate sequences that were cleaved by AF secreted proteases but not by normal human serum. A central finding was that isoleucine, leucine, phenylalanine, and tyrosine predominated at each of the three variable positions of the library (44.1%, 59.1%, and 57.0%, respectively) among substrate sequences cleaved by AF secreted proteases. In contrast, fewer than 10% of the residues at each position of cleaved sequences were cationic or anionic. Consensus substrate motifs were cleaved by thermostable serine proteases that retained activity up to 50°C. Precise proteolytic cleavage sites were reliably determined by a simple, rapid mass spectrometry-based method, revealing predominantly non-prime side specificity. A comparison of the secreted protease activities of three AF clinical isolates revealed consistent protease substrate specificity fingerprints. However, secreted proteases of A. flavus, A. nidulans, and A. terreus strains exhibited striking differences in their proteolytic signatures. Conclusions This report provides proof-of-principle for the use of protease substrate specificity profiling to define the proteolytic secretome of Aspergillus fumigatus. Expansion of this technique to protease secretion during infection could lead to development of novel approaches to fungal diagnosis.
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Affiliation(s)
- Douglas S. Watson
- Center for Advanced Drug Research, Biosciences Division, SRI International, Harrisonburg, Virginia, United States of America
| | - Xizhi Feng
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - David S. Askew
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Kalyani Jambunathan
- Center for Advanced Drug Research, Biosciences Division, SRI International, Harrisonburg, Virginia, United States of America
| | - Krishna Kodukula
- Center for Advanced Drug Research, Biosciences Division, SRI International, Harrisonburg, Virginia, United States of America
| | - Amit K. Galande
- Center for Advanced Drug Research, Biosciences Division, SRI International, Harrisonburg, Virginia, United States of America
- * E-mail:
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Wartenberg D, Lapp K, Jacobsen ID, Dahse HM, Kniemeyer O, Heinekamp T, Brakhage AA. Secretome analysis of Aspergillus fumigatus reveals Asp-hemolysin as a major secreted protein. Int J Med Microbiol 2011; 301:602-11. [PMID: 21658997 DOI: 10.1016/j.ijmm.2011.04.016] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 04/07/2011] [Accepted: 04/10/2011] [Indexed: 11/28/2022] Open
Abstract
Surface-associated and secreted proteins represent primarily exposed components of Aspergillus fumigatus during host infection. Several secreted proteins are known to be involved in defense mechanisms or immune evasion, thus, probably contributing to pathogenicity. Furthermore, several secreted antigens were identified as possible biomarkers for the verification of diseases caused by Aspergillus species. Nevertheless, there is only limited knowledge about the composition of the secretome and about molecular functions of particular proteins. To identify secreted proteins potentially essential for virulence, the core secretome of A. fumigatus grown in minimal medium was determined. Two-dimensional gel electrophoretic separation and subsequent MALDI-TOF-MS/MS analyses resulted in the identification of 64 different proteins. Additionally, secretome analyses of A. fumigatus utilizing elastin, collagen or keratin as main carbon and nitrogen source were performed. Thereby, the alkaline serine protease Alp1 was identified as the most abundant protein and hence presumably represents an important protease during host infection. Interestingly, the Asp-hemolysin (Asp-HS), which belongs to the protein family of aegerolysins and which was often suggested to be involved in fungal virulence, was present in the secretome under all growth conditions tested. In addition, a second, non-secreted protein with an aegerolysin domain annotated as Asp-hemolysin-like (HS-like) protein can be found to be encoded in the genome of A. fumigatus. Generation and analysis of Asp-HS and HS-like deletion strains revealed no differences in phenotype compared to the corresponding wild-type strain. Furthermore, hemolysis and cytotoxicity was not altered in both single-deletion and double-deletion mutants lacking both aegerolysin genes. All mutant strains showed no attenuation in virulence in a mouse infection model for invasive pulmonary aspergillosis. Overall, this study provides a comprehensive analysis of secreted proteins of A. fumigatus and a detailed characterization of hemolysin mutants.
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Affiliation(s)
- Dirk Wartenberg
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany
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A novel protein family mediates Casparian strip formation in the endodermis. Nature 2011; 473:380-3. [DOI: 10.1038/nature10070] [Citation(s) in RCA: 283] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2010] [Accepted: 03/24/2011] [Indexed: 01/19/2023]
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Sriranganadane D, Reichard U, Salamin K, Fratti M, Jousson O, Waridel P, Quadroni M, Neuhaus JM, Monod M. Secreted glutamic protease rescues aspartic protease Pep deficiency in Aspergillus fumigatus during growth in acidic protein medium. MICROBIOLOGY-SGM 2011; 157:1541-1550. [PMID: 21349972 DOI: 10.1099/mic.0.048603-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In an acidic protein medium Aspergillus fumigatus secretes an aspartic endoprotease (Pep) as well as tripeptidyl-peptidases, a prolyl-peptidase and carboxypeptidases. In addition, LC-MS/MS revealed a novel glutamic protease, AfuGprA, homologous to Aspergillus niger aspergillopepsin II. The importance of AfuGprA in protein digestion was evaluated by deletion of its encoding gene in A. fumigatus wild-type D141 and in a pepΔ mutant. Either A. fumigatus Pep or AfuGprA was shown to be necessary for fungal growth in protein medium at low pH. Exoproteolytic activity is therefore not sufficient for complete protein hydrolysis and fungal growth in a medium containing proteins as the sole nitrogen source. Pep and AfuGprA constitute a pair of endoproteases active at low pH, in analogy to A. fumigatus alkaline protease (Alp) and metalloprotease I (Mep), where at least one of these enzymes is necessary for fungal growth in protein medium at neutral pH. Heterologous expression of AfuGprA in Pichia pastoris showed that the enzyme is synthesized as a preproprotein and that the propeptide is removed through an autoproteolytic reaction at low pH to generate the mature protease. In contrast to A. niger aspergillopepsin II, AfuGprA is a single-chain protein and is structurally more similar to G1 proteases characterized in other non-Aspergillus fungi.
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Affiliation(s)
- Dev Sriranganadane
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
| | - Utz Reichard
- Department of Medical Microbiology and National Reference Centre for Systemic Mycoses, University Hospital of Göttingen, Germany
| | - Karine Salamin
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
| | - Marina Fratti
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
| | - Olivier Jousson
- Centre for Integrative Biology (CIBIO), University of Trento, Italy
| | - Patrice Waridel
- Protein Analysis Facility, Centre for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Manfredo Quadroni
- Protein Analysis Facility, Centre for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jean-Marc Neuhaus
- Laboratory of Molecular and Cellular Biology, University of Neuchâtel, rue E-Argand 11, 2009 Neuchâtel, Switzerland
| | - Michel Monod
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
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