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.
Highlights
The widespread use of fungi in different biotechnological processes can be attributed to their intrinsic characteristics
As an example of the progress in fungal proteomics research supported by fungal genome sequencing, here we report the case of Penicillium chrysogenum [23,61,62]
Proteomics in particular, appear to be an outstanding way to decipher the enzymatic toolbox of lignocellulose degrading fungi
Summary
The widespread use of fungi in different biotechnological processes can be attributed to their intrinsic characteristics. They can use diverse mechanisms distinguishable by the way they make lignocellulose accessible for degradation, by the enzymes involved, and by their behaviour during attack and wood decomposition These different mechanisms are generally classified as soft-, brown- and white-rot degradations [3]. The extracellular oxidative enzymes involved in lignin depolymerisation include a wide range of oxidases and peroxidases, responsible for the generation of highly reactive and nonspecific free radicals that cleave a variety of carbon–carbon and ether inter-unit bonds. Enzymes such as lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP) and dye-decolorizing peroxidase (DyP) are considered the most common and representative oxidative enzymes of the ligninolytic system [14]. Special attention will be given to lignocellulose degrading fungi; representative examples of their secretomes will be discussed in relation to their involvement in bio-based processes, such as biomass deconstruction and bioremediation
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