Methodologies and Perspectives of Proteomics Applied to Filamentous Fungi: From Sample Preparation to Secretome Analysis

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.

Microbial function and genital inflammation in young South African women at high risk of HIV infection

“…Candida proteins were detected, the curated dataset (following removal of taxa that had only 1 protein detected or 2 proteins detected in only a single sample) did not include any Candida species. This may be due to the relative rarity of fungal cells in these samples and it would be interesting to evaluate alternative methodology for sample processing to better resolve this population in the future [31]. A limitation of microbial functional analysis using metaproteomics is that, at present, there is generally sparse population of functional information in the databases for the majority of the microbiome.…”

Condiciones para el análisis de proteínas del micelio de Lentinula edodes obtenido por fermentación en estado líquido

“…Precipitación con TCA -acetona: en el primer protocolo se usó la precipitación con ácido tricloroacético (TCA) y acetona reportado por [21,31] con algunas modificaciones. El micelio liofilizado se maceró con nitrógeno líquido y se tomaron 20 mg del macerado en un tubo eppendorf de 2 mL.…”

“…Con estas necesidades se han desarrollado un conjunto de metodologías que permiten obtener extractos proteicos con buena calidad para la aplicación de dichas aproximaciones. Dentro de estas se destacan las que incluyen la precipitación con ácido tricloroacético (TCA) y acetona y la de TCA -acetona con un paso adicional de separación con fenol [21][22][23]. La separación electroforética tanto en 1D (SDS-PAGE) como en 2D (IEF-SDS PAGE) es la técnica de separación más aplicada en estudios proteómicos [24,25], usándose de manera previa a los análisis de identificación con espectrometría de masas.…”

Review Paper: Data Mining of Fungal Secondary Metabolites Using Genomics and Proteomics

“…Ascomycetes and basidiomycetes fungi, both are capable of secreting large amounts of lignocelluloses degrading enzymes; they are extremely useful in the biofuel industry [19]. Apart from food and pharmaceutical drugs such as antibiotics (namely penicillin, cephalosporine and griseofulvin) many immunosuppressant (cyclosporine A and gliotoxin) are also produced from these fungi [20] The Lae A factor, for instance from the Aspergillus nidulans genome, which is an important anti-tumor compound [1]. White rot fungi utilize their high redox potential to oxidize an array of environmental pollutants such as pesticides, organo chlorines, poly chlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), synthetic dyes, wood preservatives and synthetic polymers [21].…”