Genome-based engineering of ligninolytic enzymes in fungi

Abstract

Background Many fungi grow as saprobic organisms and obtain nutrients from a wide range of dead organic materials. Among saprobes, fungal species that grow on wood or in polluted environments have evolved prolific mechanisms for the production of degrading compounds, such as ligninolytic enzymes. These enzymes include arrays of intense redox-potential oxidoreductase, such as laccase, catalase, and peroxidases. The ability to produce ligninolytic enzymes makes a variety of fungal species suitable for application in many industries, including the production of biofuels and antibiotics, bioremediation, and biomedical application as biosensors. However, fungal ligninolytic enzymes are produced naturally in small quantities that may not meet the industrial or market demands. Over the last decade, combined synthetic biology and computational designs have yielded significant results in enhancing the synthesis of natural compounds in fungi. Main body of the abstract In this review, we gave insights into different protein engineering methods, including rational, semi-rational, and directed evolution approaches that have been employed to enhance the production of some important ligninolytic enzymes in fungi. We described the role of metabolic pathway engineering to optimize the synthesis of chemical compounds of interest in various fields. We highlighted synthetic biology novel techniques for biosynthetic gene cluster (BGC) activation in fungo and heterologous reconstruction of BGC in microbial cells. We also discussed in detail some recombinant ligninolytic enzymes that have been successfully enhanced and expressed in different heterologous hosts. Finally, we described recent advance in CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas (CRISPR associated) protein systems as the most promising biotechnology for large-scale production of ligninolytic enzymes. Short conclusion Aggregation, expression, and regulation of ligninolytic enzymes in fungi require very complex procedures with many interfering factors. Synthetic and computational biology strategies, as explained in this review, are powerful tools that can be combined to solve these puzzles. These integrated strategies can lead to the production of enzymes with special abilities, such as wide substrate specifications, thermo-stability, tolerance to long time storage, and stability in different substrate conditions, such as pH and nutrients.

Directed Evolution of a Glutathione Transferase for the Development of a Biosensor for Alachlor Determination

“…Increasingly, directed evolution has been applied to create enzymes catalyzing reactions either in a more efficient way or reactions that have not been observed in nature by taking advance of the promiscuous nature of enzymes [30]. A range of different methods and techniques have been developed that have enabled the evolution of any protein [29,30], pathway [31], network [32], or entire organism of interest [33].…”

Biosynthesis Pathways, Transport Mechanisms and Biotechnological Applications of Fungal Siderophores

“…Analytical pipelines linking genomics with other omics data have been developed and can reveal much information on the synthesis of such natural products. Computational tools coupled with genome mining provide efficient methods to identify and characterize biosynthetic gene clusters BGCs [223]. Natural product research and siderophore research have been concentrated on bacterial species, and there is an obvious bias in data availability and algorithm development for fungal research.…”

Effect of Nutritional Factors and Copper on the Regulation of Laccase Enzymes Production in <em>Pleurotus ostreatus</em>

“…2 Laccase activity was measured using 2, 2-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) as substrate. 3 Laccase activity was measured using syringaldazine as substrate.…”

“…Fungal laccases are glycosylated, multi-copper oxidases that catalyze the oxidation of hydroxyl functional groups on various substrates and the molecular oxygen reduction to water [1][2][3]. As laccases can oxidize phenolic and non-phenolic compounds, these enzymes are attractive in many processes or biotechnological applications, such as bioremediation, wastewater treatment, nanobiotechnology, biofuel production, pharmaceutical, and food industry [4,5].…”