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Abu Bakar N, Chung BLY, Smykla J, Karsani SA, Alias SA. Proteomic characterization of Pseudogymnoascus spp. isolates from polar and temperate regions. Mycologia 2024; 116:449-463. [PMID: 38484286 DOI: 10.1080/00275514.2024.2313429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/30/2024] [Indexed: 05/01/2024]
Abstract
Proteomics has been used extensively in the field of mycology, mainly in trying to understand the complex network of protein-protein interactions that has been implicated in the molecular functions of fungi. It is also a useful tool to compare metabolic differences within a genus. Species of Pseudogymnoascus, a genus under the phyla Ascomycota, have been shown to play an important role in the soil environment. They have been found in both polar and temperate regions and are a known producer of many extracellular hydrolases that contribute to soil decomposition. Despite the apparent importance of Pseudogymnoascus spp. in the soil ecosystem, investigations into their molecular functions are still very limited. In the present study, proteomic characterization of six Pseudogymnoascus spp. isolated from three biogeographic regions (the Arctic, Antarctic, and temperate regions) was carried out using tandem mass spectrometry. Prior to proteomic analysis, the optimization for protein extraction was carried out. Trichloroacetic acid‑acetone‑phenol was found to be the best extraction method to be used for proteomic profiling of Pseudogymnoascus spp. The proteomic analysis identified 2003 proteins that were successfully mapped to the UniProtKB database. The identified proteins were clustered according to their biological processes and molecular functions. The shared proteins found in all Pseudogymnoascus spp. (1201 proteins) showed a significantly close relationship in their basic cellular functions, despite differences in morphological structures. Analysis of Pseudogymnoascus spp. proteome also identified proteins that were unique to each region. However, a high number of these proteins belonged to protein families of similar molecular functions, namely, transferases and hydrolases. Our proteomic data can be used as a reference for Pseudogymnoascus spp. across different global regions and a foundation for future soil ecosystem function research.
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Affiliation(s)
- Nurlizah Abu Bakar
- Institute of Ocean and Earth Sciences, Universiti Malaya, C308, Institute of Advanced Studies Building, Kuala Lumpur 50603, Malaysia
- National Antarctic Research Centre, Universiti Malaya, B303, Institute of Advanced Studies Building, Kuala Lumpur 50603, Malaysia
| | - Benjamin Lau Yii Chung
- Advanced Biotechnology and Breeding Centre, Persiaran Institusi, Malaysian Palm Oil Board, No. 6, Bandar Baru Bangi, Kajang, Selangor 43000, Malaysia
| | - Jerzy Smykla
- Department of Biodiversity, Institute of Nature Conservation, Polish Academy of Sciences, Mickiewicza 33, Krakow 31-120, Poland
| | - Saiful Anuar Karsani
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Siti Aisyah Alias
- Institute of Ocean and Earth Sciences, Universiti Malaya, C308, Institute of Advanced Studies Building, Kuala Lumpur 50603, Malaysia
- National Antarctic Research Centre, Universiti Malaya, B303, Institute of Advanced Studies Building, Kuala Lumpur 50603, Malaysia
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Neto OBS, Valladão R, Coelho GR, Dias R, Pimenta DC, Lopes AR. Spiders' digestive system as a source of trypsin inhibitors: functional activity of a member of atracotoxin structural family. Sci Rep 2023; 13:2389. [PMID: 36765114 PMCID: PMC9918498 DOI: 10.1038/s41598-023-29576-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
Spiders are important predators of insects and their venoms play an essential role in prey capture. Spider venoms have several potential applications as pharmaceutical compounds and insecticides. However, transcriptomic and proteomic analyses of the digestive system (DS) of spiders show that DS is also a rich source of new peptidase inhibitor molecules. Biochemical, transcriptomic and proteomic data of crude DS extracts show the presence of molecules with peptidase inhibitor potential in the spider Nephilingis cruentata. Therefore, the aims of this work were to isolate and characterize molecules with trypsin inhibitory activity. The DS of fasting adult females was homogenized under acidic conditions and subjected to heat treatment. After that, samples were submitted to ion exchange batch and high-performance reverse-phase chromatography. The fractions with trypsin inhibitory activity were confirmed by mass spectrometry, identifying six molecules with inhibitory potential. The inhibitor NcTI (Nephilingis cruentata trypsin inhibitor) was kinetically characterized, showing a KD value of 30.25 nM ± 8.13. Analysis of the tertiary structure by molecular modeling using Alpha-Fold2 indicates that the inhibitor NcTI structurally belongs to the MIT1-like atracotoxin family. This is the first time that a serine peptidase inhibitory function is attributed to this structural family and the inhibitor reactive site residue is identified. Sequence analysis indicates that these molecules may be present in the DS of other spiders and could be associated to the inactivation of prey trypsin (serine peptidase) ingested by the spiders.
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Affiliation(s)
- Oscar Bento Silva Neto
- Laboratory of Biochemistry, Instituto Butantan, São Paulo, 05503900, Brazil.,Programa Interunidades (USP, Instituto Butantan, IPT) de pós-graduação em Biotecnologia, Universidade de São Paulo, São Paulo, 05508000, Brazil
| | - Rodrigo Valladão
- Laboratory of Biochemistry, Instituto Butantan, São Paulo, 05503900, Brazil.,Programa Interunidades (USP, Instituto Butantan, IPT) de pós-graduação em Biotecnologia, Universidade de São Paulo, São Paulo, 05508000, Brazil
| | | | - Renata Dias
- Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiás, Brazil
| | | | - Adriana Rios Lopes
- Laboratory of Biochemistry, Instituto Butantan, São Paulo, 05503900, Brazil. .,Programa Interunidades (USP, Instituto Butantan, IPT) de pós-graduação em Biotecnologia, Universidade de São Paulo, São Paulo, 05508000, Brazil.
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Zhang ZY, Han YF, Chen WH, Tao G. Additions to Thelebolales (Leotiomycetes, Ascomycota): Pseudogeomyces lindneri gen. et sp. nov. and Pseudogymnoascus campensis sp. nov. MycoKeys 2023; 95:47-60. [DOI: 10.3897/mycokeys.95.97474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 01/22/2023] [Indexed: 02/09/2023] Open
Abstract
Thelebolales are globally distributed fungi with diverse ecological characteristics. The classification of Thelebolales remains controversial to date and this study introduces two new taxa, based on morphological and phylogenetic analyses. The results of phylogenetic analyses indicated that the new taxa formed distinct lineages with strong support that were separated from the other members of Thelebolales. The new taxa described herein did not form sexual structures. The phylogenetic relationships of the new taxa and the morphological differences between these taxa and the other species under Thelebolales are also discussed.
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Urbanek AK, Arroyo M, de la Mata I, Mirończuk AM. Identification of novel extracellular putative chitinase and hydrolase from Geomyces sp. B10I with the biodegradation activity towards polyesters. AMB Express 2022; 12:12. [PMID: 35122534 PMCID: PMC8818076 DOI: 10.1186/s13568-022-01352-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/22/2022] [Indexed: 11/10/2022] Open
Abstract
Cold-adapted filamentous fungal strain Geomyces sp. B10I has been reported to decompose polyesters such as poly(e-caprolactone) (PCL), poly(butylene succinate) (PBS) and poly(butylene succinate-co-butylene adipate) (PBSA). Here, we identified the enzymes of Geomyces sp. B10I, which appear to be responsible for its biodegradation activity. We compared their amino acid sequences with sequences of well-studied fungal enzymes. Partial purification of an extracellular mixture of the two enzymes, named hydrGB10I and chitGB10I, using ammonium sulfate precipitation and ionic exchange chromatography gave 14.16-fold purity. The amino acid sequence of the proteins obtained from the MALDI-TOF analysis determined the molecular mass of 77.2 kDa and 46.5 kDa, respectively. Conserved domain homology analysis revealed that both proteins belong to the class of hydrolases; hydrGB10I belongs to the glycosyl hydrolase 81 superfamily, while chitGB10I contains the domain of the glycosyl hydrolase 18 superfamily. Phylogenetic analysis suggests a distinct nature of the hydrGB10I and chitGB10I of Geomyces sp. B10I when compared with other fungal polyester-degrading enzymes described to date.
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Villanueva P, Vásquez G, Gil-Durán C, Oliva V, Díaz A, Henríquez M, Álvarez E, Laich F, Chávez R, Vaca I. Description of the First Four Species of the Genus Pseudogymnoascus From Antarctica. Front Microbiol 2021; 12:713189. [PMID: 34867840 PMCID: PMC8640180 DOI: 10.3389/fmicb.2021.713189] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 10/18/2021] [Indexed: 12/03/2022] Open
Abstract
The genus Pseudogymnoascus represents a diverse group of fungi widely distributed in different cold regions on Earth. Our current knowledge of the species of Pseudogymnoascus is still very limited. Currently, there are only 15 accepted species of Pseudogymnoascus that have been isolated from different environments in the Northern Hemisphere. In contrast, species of Pseudogymnoascus from the Southern Hemisphere have not yet been described. In this work, we characterized four fungal strains obtained from Antarctic marine sponges. Based on multilocus phylogenetic analyses and morphological characterizations we determined that these strains are new species, for which the names Pseudogymnoascus antarcticus sp. nov., Pseudogymnoascus australis sp. nov., Pseudogymnoascus griseus sp. nov., and Pseudogymnoascus lanuginosus sp. nov. are proposed. Phylogenetic analyses indicate that the new species form distinct lineages separated from other species of Pseudogymnoascus with strong support. The new species do not form sexual structures and differ from the currently known species mainly in the shape and size of their conidia, the presence of chains of arthroconidia, and the appearance of their colonies. This is the first report of new species of Pseudogymnoascus not only from Antarctica but also from the Southern Hemisphere.
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Affiliation(s)
- Pablo Villanueva
- Department of Chemistry, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Ghislaine Vásquez
- Department of Chemistry, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Carlos Gil-Durán
- Department of Chemistry, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Vicente Oliva
- Department of Chemistry, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Anaí Díaz
- Department of Chemistry, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Marlene Henríquez
- Department of Chemistry, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Eduardo Álvarez
- Institute of Biomedical Sciences (ICBM), Mycology Unit, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Federico Laich
- Departamento de Protección Vegetal, Instituto Canario de Investigaciones Agrarias, Santa Cruz de Tenerife, Islas Canarias, Spain
| | - Renato Chávez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Inmaculada Vaca
- Department of Chemistry, Faculty of Sciences, University of Chile, Santiago, Chile
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Green Oxidation of Amines by a Novel Cold-Adapted Monoamine Oxidase MAO P3 from Psychrophilic Fungi Pseudogymnoascus sp. P3. Molecules 2021; 26:molecules26206237. [PMID: 34684818 PMCID: PMC8538783 DOI: 10.3390/molecules26206237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 11/17/2022] Open
Abstract
The use of monoamine oxidases (MAOs) in amine oxidation is a great example of how biocatalysis can be applied in the agricultural or pharmaceutical industry and manufacturing of fine chemicals to make a shift from traditional chemical synthesis towards more sustainable green chemistry. This article reports the screening of fourteen Antarctic fungi strains for MAO activity and the discovery of a novel psychrozyme MAOP3 isolated from the Pseudogymnoascus sp. P3. The activity of the native enzyme was 1350 ± 10.5 U/L towards a primary (n-butylamine) amine, and 1470 ± 10.6 U/L towards a secondary (6,6-dimethyl-3-azabicyclohexane) amine. MAO P3 has the potential for applications in biotransformations due to its wide substrate specificity (aliphatic and cyclic amines, pyrrolidine derivatives). The psychrozyme operates at an optimal temperature of 30 °C, retains 75% of activity at 20 °C, and is rather thermolabile, which is beneficial for a reduction in the overall costs of a bioprocess and offers a convenient way of heat inactivation. The reported biocatalyst is the first psychrophilic MAO; its unique biochemical properties, substrate specificity, and effectiveness predispose MAO P3 for use in environmentally friendly, low-emission biotransformations.
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Landscape Genetic Connectivity and Evidence for Recombination in the North American Population of the White-Nose Syndrome Pathogen, Pseudogymnoascus destructans. J Fungi (Basel) 2021; 7:jof7030182. [PMID: 33802538 PMCID: PMC8001231 DOI: 10.3390/jof7030182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 11/28/2022] Open
Abstract
White-Nose Syndrome is an ongoing fungal epizootic caused by epidermal infections of the fungus, Pseudogymnoascus destructans (P. destructans), affecting hibernating bat species in North America. Emerging early in 2006 in New York State, infections of P. destructans have spread to 38 US States and seven Canadian Provinces. Since then, clonal isolates of P. destructans have accumulated genotypic and phenotypic variations in North America. Using microsatellite and single nucleotide polymorphism markers, we investigated the population structure and genetic relationships among P. destructans isolates from diverse regions in North America to understand its pattern of spread, and to test hypotheses about factors that contribute to transmission. We found limited support for genetic isolation of P. destructans populations by geographic distance, and instead identified evidence for gene flow among geographic regions. Interestingly, allelic association tests revealed evidence for recombination in the North American P. destructans population. Our landscape genetic analyses revealed that the population structure of P. destructans in North America was significantly influenced by anthropogenic impacts on the landscape. Our results have important implications for understanding the mechanism(s) of P. destructans spread.
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Muggia L, Ametrano CG, Sterflinger K, Tesei D. An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota. Life (Basel) 2020; 10:E356. [PMID: 33348904 PMCID: PMC7765829 DOI: 10.3390/life10120356] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 12/26/2022] Open
Abstract
Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.
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Affiliation(s)
- Lucia Muggia
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Claudio G. Ametrano
- Grainger Bioinformatics Center, Department of Science and Education, The Field Museum, Chicago, IL 60605, USA;
| | - Katja Sterflinger
- Academy of Fine Arts Vienna, Institute of Natual Sciences and Technology in the Arts, 1090 Vienna, Austria;
| | - Donatella Tesei
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria;
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da Silva TH, Silva DAS, de Oliveira FS, Schaefer CEGR, Rosa CA, Rosa LH. Diversity, distribution, and ecology of viable fungi in permafrost and active layer of Maritime Antarctica. Extremophiles 2020; 24:565-576. [PMID: 32405812 DOI: 10.1007/s00792-020-01176-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/27/2020] [Indexed: 01/20/2023]
Abstract
We evaluated the diversity and distribution of viable fungi present in permafrost and active layers obtained from three islands of Maritime Antarctica. A total of 213 fungal isolates were recovered from the permafrost, and 351 from the active layer, which were identified in 58 taxa; 27 from permafrost and 31 from the active layer. Oidiodendron, Penicillium, and Pseudogymnoascus taxa were the most abundant in permafrost. Bionectriaceae, Helotiales, Mortierellaceae, and Pseudeurotium were the most abundant in the active layer. Only five shared both substrates. The yeast Mrakia blollopis represented is the first reported on Antarctic permafrost. The fungal diversity detected was moderate to high, and composed of cosmopolitan, cold-adapted, and endemic taxa, reported as saprobic, mutualistic, and parasitic species. Our results demonstrate that permafrost shelters viable fungi across the Maritime Antarctica, and that they are contrasting to the overlying active layer. We detected important fungal taxa represented by potential new species, particularly, those genetically close to Pseudogymnoascus destructans, which can cause extinction of bats in North America and Eurasia. The detection of viable fungi trapped in permafrost deserves further studies on the extension of its fungal diversity and its capability to expand from permafrost to other habitats in Antarctica, and elsewhere.
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Affiliation(s)
- Thamar Holanda da Silva
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Fábio Soares de Oliveira
- Departamento de Geografia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | | | - Luiz Henrique Rosa
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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Phylogenomic analysis supports a recent change in nitrate assimilation in the White-nose Syndrome pathogen, Pseudogymnoascus destructans. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2016.04.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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