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Choudhary H, Kaur H, Singh S, Singh R, Muthu V, Verma R, Rudramurthy SM, Agarwal R, Jain S, Bal A, Ghosh AK, Chakrabarti A. A novel indirect ELISA for serodiagnosis of mucormycosis using antigens from Rhizopus arrhizus. Mycoses 2024; 67:e13730. [PMID: 38712824 DOI: 10.1111/myc.13730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/08/2024]
Abstract
BACKGROUND Due to a delay in diagnosis by conventional techniques and high mortality, the development of a standardised and rapid non-culture-based technique is an unmet need in pulmonary, gastrointestinal, and disseminated forms of mucormycosis. Though limited studies have been conducted for molecular diagnosis, there are no established serologic tests for this highly fatal infection. OBJECTIVE To develop and evaluate an indirect in-house enzyme-linked immunosorbent assay (ELISA) utilising antigens of Rhizopus arrhizus for detecting anti-Rhizopus antibodies (IgG and IgM) in sera of patients with mucormycosis. METHODS We extracted both secretory and mycelial Rhizopus antigens using standardised protocols. Bradford assay was used for protein quantification. We then standardised an indirect ELISA using R. arrhizus mycelial and secretory antigens (10.0 μg/mL in bicarbonate buffer pH 9.2) for detecting anti-Rhizopus IgG and IgM antibodies in patient sera. We included patients with mucormycosis, other fungal infections, and healthy controls. Antibody index value (E-value) was calculated for each patient sample. RESULTS Asparagine broth culture filtrate utilising 85% ammonium sulphate salt fractionation and mycelial homogenate grown in yeast extract peptone dextrose (YPD) broth precipitated with trichloroacetic acid (TCA) yielded a large amount of good-quality protein for the assay. We included 55 patients with mucormycosis (rhino-orbito-cerebral mucormycosis [ROCM, n = 39], pulmonary [n = 15], gastrointestinal [n = 1]), 24 with other fungal infections (probable aspergillosis [n = 14], candidiasis [n = 10]), and healthy controls (n = 16). The sensitivity of the antibody test for diagnosing mucormycosis ranged from 83.6-92.7% for IgG and 72.7-87.3% for IgM, with a specificity of 91.7-92.5% for IgG and 80-82.5% for IgM. The sera from patients with other fungal infections and healthy individuals did not show significant cross-reactivity. CONCLUSION The detection of anti-Rhizopus IgG antibody performed significantly better in comparison to IgM-based ELISA for diagnosing both ROCM (sensitivity of 84.6% vs. 69.2%) and pulmonary cases (86.6% vs. 80.0%). More extensive studies are required to confirm our findings.
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Affiliation(s)
| | - Harsimran Kaur
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research (PGIMER), Chandigarh, India
| | - Shreya Singh
- Department of Medical Microbiology, Dr. B. R. Ambedkar Institute of Medical Sciences, Mohali, Punjab, India
| | - Rachna Singh
- Department of Microbial Biotechnology, Panjab University, Chandigarh, India
| | - Valliappan Muthu
- Department of Pulmonary Medicine, Postgraduate Institute of Medical Education & Research (PGIMER), Chandigarh, India
| | - Roshan Verma
- Department of Otolaryngology (ENT), Postgraduate Institute of Medical Education & Research (PGIMER), Chandigarh, India
| | - Shivaprakash M Rudramurthy
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research (PGIMER), Chandigarh, India
| | - Ritesh Agarwal
- Department of Pulmonary Medicine, Postgraduate Institute of Medical Education & Research (PGIMER), Chandigarh, India
| | - Sanjay Jain
- Department of Internal Medicine, Postgraduate Institute of Medical Education & Research (PGIMER), Chandigarh, India
| | - Amanjit Bal
- Department of Histopathology, Postgraduate Institute of Medical Education & Research (PGIMER), Chandigarh, India
| | - Anup K Ghosh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research (PGIMER), Chandigarh, India
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Nogueira-López G, Padilla-Arizmendi F, Inwood S, Lyne S, Steyaert JM, Nieto-Jacobo MF, Stewart A, Mendoza-Mendoza A. TrichoGate: An Improved Vector System for a Large Scale of Functional Analysis of Trichoderma Genes. Front Microbiol 2019; 10:2794. [PMID: 31921006 PMCID: PMC6915037 DOI: 10.3389/fmicb.2019.02794] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 11/18/2019] [Indexed: 11/13/2022] Open
Abstract
Species of the genus Trichoderma are ubiquitous in the environment and are widely used in agriculture, as biopesticides, and in the industry for the production of plant cell wall-degrading enzymes. Trichoderma represents an important genus of endophytes, and several Trichoderma species have become excellent models for the study of fungal biology and plant–microbe interactions; moreover, are exceptional biotechnological factories for the production of bioactive molecules useful in agriculture and medicine. Next-generation sequencing technology coupled with systematic construction of recombinant DNA molecules provides powerful tools that contribute to the functional analysis of Trichoderma genetics, thus allowing for a better understanding of the underlying factors determining its biology. Here, we present the creation of diverse vectors containing (i) promoter-specific vectors for Trichoderma, (ii) gene deletions (using hygromycin phosphotransferase as selection marker), (iii) protein localization (mCherry and eGFP, which were codon-optimized for Trichoderma), (iv) gene complementation (neomycin phosphotransferase) and (v) overexpression of encoding gene proteins fused to fluorescent markers, by using the Golden Gate cloning technology. Furthermore, we present the design and implementation of a binary vector for Agrobacterium-mediated transformation in Trichoderma to increase the homologous recombination rate and the generation of a novel selection marker based on carboxin resistance.
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Affiliation(s)
| | | | - Sarah Inwood
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand.,Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Sarah Lyne
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand
| | - Johanna M Steyaert
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand.,Lincoln Agritech Ltd, Lincoln, New Zealand
| | - Maria Fernanda Nieto-Jacobo
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand.,Plant & Food Research Gerald St, Lincoln, New Zealand
| | - Alison Stewart
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand.,Foundation For Arable Research, Templeton, New Zealand
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Krishnaswamy A, Barnes N, Lotlikar NP, Damare SR. An Improved Method for Protein Extraction from Minuscule Quantities of Fungal Biomass. Indian J Microbiol 2019; 59:100-104. [PMID: 30728637 PMCID: PMC6328415 DOI: 10.1007/s12088-018-0752-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 06/20/2018] [Indexed: 11/30/2022] Open
Abstract
Filamentous fungi are ubiquitous eukaryotes having chitin as a major constituent of the cell wall. Chitin is tough to lyse due to which the intracellular fungal proteins are not readily accessible. The problem is further enhanced when the biomass to be analyzed for protein studies is too little due to the extreme experimental parameters under consideration such as increased or lowered pH, temperature, hydrostatic pressure, nutrients, etc. The method described here is capable of obtaining proteins from minuscule quantities of biomass (~5 mg lyophilized biomass). In this study, different lysing conditions and varied composition of extraction buffers were tried to obtain maximum protein of high quality. Lysis with zirconium beads in a combination buffer system (Tris-MgCl2 buffer, urea buffer I and urea buffer II) was best for extracting proteins from the fungal isolates used. The protocol described here provides for a simple and quick method for extraction of high-quality proteins from very less biomass that could be extended to other tough to lyse biological material also.
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Affiliation(s)
- Akhila Krishnaswamy
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403004 India
| | - Natasha Barnes
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403004 India
- Present Address: Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Nikita P. Lotlikar
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403004 India
| | - Samir R. Damare
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403004 India
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Uranga CC, Ghassemian M, Hernández-Martínez R. Novel proteins from proteomic analysis of the trunk disease fungus Lasiodiplodia theobromae (Botryosphaeriaceae). BIOCHIMIE OPEN 2017; 4:88-98. [PMID: 29450146 PMCID: PMC5802045 DOI: 10.1016/j.biopen.2017.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/02/2017] [Indexed: 11/21/2022]
Abstract
Many basic science questions remain regarding protein functions in the pathogen: host interaction, especially in the trunk disease fungi family, the Botryosphaeriaceae, which are a global problem for economically important plants, especially fruiting trees. Proteomics is a highly useful technology for studying protein expression and for discovering novel proteins in unsequenced and poorly annotated organisms. Current fungal proteomics approaches involve 2D SDS-PAGE and extensive, complex, protein extraction methodologies. In this work, a modified Folch extraction was applied to protein extraction to perform both de novo peptide sequencing and peptide fragmentation analysis/protein identification of the plant and human fungal pathogen Lasiodiplodia theobromae. Both bioinformatics approaches yielded novel peptide sequences from proteins produced by L. theobromae in the presence of exogenous triglycerides and glucose. These proteins and the functions they may possess could be targeted for further functional characterization and validation efforts, due to their potential uses in biotechnology and as new paradigms for understanding fungal biochemistry, such as the finding of allergenic enolases, as well as various novel proteases, including zinc metalloproteinases homologous to those found in snake venom. This work contributes to genomic annotation efforts, which, hand in hand with genomic sequencing, will help improve fungal bioinformatics databases for future studies of Botryosphaeriaceae. All data, including raw data, are available via the ProteomeXchange data repository with identifier PXD005283. This is the first study of its kind in Botryosphaeriaceae.
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Affiliation(s)
- Carla C. Uranga
- Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana 3918, Zona Playitas, 22860 Ensenada, B.C., Mexico
| | - Majid Ghassemian
- University of California, San Diego, Department of Chemistry and Biochemistry, 9500 Gilman Drive, La Jolla, CA 92093-0378, USA
| | - Rufina Hernández-Martínez
- Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana 3918, Zona Playitas, 22860 Ensenada, B.C., Mexico
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Kramer A, Beck HC, Kumar A, Kristensen LP, Imhoff JF, Labes A. Proteomic Analysis of Anti-Cancerous Scopularide Production by a Marine Microascus brevicaulis Strain and Its UV Mutant. PLoS One 2015; 10:e0140047. [PMID: 26460745 PMCID: PMC4603891 DOI: 10.1371/journal.pone.0140047] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 09/21/2015] [Indexed: 11/19/2022] Open
Abstract
The marine fungus Microascus brevicaulis strain LF580 is a non-model secondary metabolite producer with high yields of the two secondary metabolites scopularides A and B, which exhibit distinct activities against tumour cell lines. A mutant strain was obtained using UV mutagenesis, showing faster growth and differences in pellet formation besides higher production levels. Here, we show the first proteome study of a marine fungus. Comparative proteomics were applied to gain deeper understanding of the regulation of production and of the physiology of the wild type strain and its mutant. For this purpose, an optimised protein extraction protocol was established. In total, 4759 proteins were identified. The central metabolic pathway of strain LF580 was mapped using the KEGG pathway analysis and GO annotation. Employing iTRAQ labelling, 318 proteins were shown to be significantly regulated in the mutant strain: 189 were down- and 129 upregulated. Proteomics are a powerful tool for the understanding of regulatory aspects: The differences on proteome level could be attributed to limited nutrient availability in the wild type strain due to a strong pellet formation. This information can be applied for optimisation on strain and process level. The linkage between nutrient limitation and pellet formation in the non-model fungus M. brevicaulis is in consensus with the knowledge on model organisms like Aspergillus niger and Penicillium chrysogenum.
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Affiliation(s)
- Annemarie Kramer
- Research Unit Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Hans Christian Beck
- Centre for Clinical Proteomics, Department for Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - Abhishek Kumar
- Department for Botany and Molecular Biology, Institute of Botany, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Lars Peter Kristensen
- Centre for Clinical Proteomics, Department for Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - Johannes F. Imhoff
- Research Unit Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Antje Labes
- Research Unit Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
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Bianco L, Perrotta G. Methodologies and perspectives of proteomics applied to filamentous fungi: from sample preparation to secretome analysis. Int J Mol Sci 2015; 16:5803-29. [PMID: 25775160 PMCID: PMC4394507 DOI: 10.3390/ijms16035803] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/17/2015] [Accepted: 03/03/2015] [Indexed: 11/17/2022] Open
Abstract
Filamentous fungi possess the extraordinary ability to digest complex biomasses and mineralize numerous xenobiotics, as consequence of their aptitude to sensing the environment and regulating their intra and extra cellular proteins, producing drastic changes in proteome and secretome composition. Recent advancement in proteomic technologies offers an exciting opportunity to reveal the fluctuations of fungal proteins and enzymes, responsible for their metabolic adaptation to a large variety of environmental conditions. Here, an overview of the most commonly used proteomic strategies will be provided; this paper will range from sample preparation to gel-free and gel-based proteomics, discussing pros and cons of each mentioned state-of-the-art technique. The main focus will be kept on filamentous fungi. Due to the biotechnological relevance of lignocellulose degrading fungi, special attention will be finally given to their extracellular proteome, or secretome. Secreted proteins and enzymes will be discussed in relation to their involvement in bio-based processes, such as biomass deconstruction and mycoremediation.
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Affiliation(s)
- Linda Bianco
- UTTRI-GENER Genetics and Genomics for Energy and Environment Laboratory-ENEA TRISAIA Research Center, 75025 Rotondella (Matera), Italy.
| | - Gaetano Perrotta
- UTTRI-GENER Genetics and Genomics for Energy and Environment Laboratory-ENEA TRISAIA Research Center, 75025 Rotondella (Matera), Italy.
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