Strategies for the Development of Industrial Fungal Producing Strains

Abstract

The use of microorganisms in industry has enabled the (over)production of various compounds (e.g., primary and secondary metabolites, proteins and enzymes) that are relevant for the production of antibiotics, food, beverages, cosmetics, chemicals and biofuels, among others. Industrial strains are commonly obtained by conventional (non-GMO) strain improvement strategies and random screening and selection. However, recombinant DNA technology has made it possible to improve microbial strains by adding, deleting or modifying specific genes. Techniques such as genetic engineering and genome editing are contributing to the development of industrial production strains. Nevertheless, there is still significant room for further strain improvement. In this review, we will focus on classical and recent methods, tools and technologies used for the development of fungal production strains with the potential to be applied at an industrial scale. Additionally, the use of functional genomics, transcriptomics, proteomics and metabolomics together with the implementation of genetic manipulation techniques and expression tools will be discussed.

Small GTPase Rab7 is involved in stress adaptation to carbon starvation to ensure the induced cellulase biosynthesis in Trichoderma reesei

“…The filamentous fungus T. reesei is well known for its high capacity to secrete large amounts of (hemi)cellulases [ 46 ]. Dissecting the molecular mechanism of the efficient cellulase secretion by T. reesei is crucial for developing it into a protein cell factory [ 47 ]. Whereas the anterograde trafficking of vesicles containing protein cargoes derived from the Golgi to the plasma membrane has been deemed to be responsible for extracellular protein secretion, the endosomal/vacuolar pathway has been reported to affect this process although the exact mechanism remains largely unknown [ 48 , 49 ].…”

Using Fungi in Artificial Microbial Consortia to Solve Bioremediation Problems

“…The economic viability and attractiveness of using artificial consortia containing fungi for bioremediation determines the cost-effectiveness of cultivating individual strains and their availability for commercial application. The availability can be satisfied by searching for and isolating the necessary fungi from natural sources or by creating genetically modified strains [ 116 , 117 ]. Whereas the costs of obtaining the necessary amounts of biomass of fungal cells are, according to the economic estimates just conducted, considered low enough [ 116 , 134 ].…”

“…Since there are no globally accepted regulatory documents that concern the spread of genetically modified organisms, the regulation of the development and release of genetically modified organisms varies in different countries, depending on the purposes of their use, extending from a complete ban on their import, release or use to allowing their use, subject to varying degrees of regulation. However, despite this, methods of genetically engineering filamentous fungi continue to be actively developed and used in research around the world, making it possible to overcome many of the shortcomings of classical methods for improving strains [ 115 , 116 , 117 ]. To eliminate the negative effect of such cells, it is possible to use several genetic tools, including cell self-destruction systems [ 118 ].…”

Secretome Analysis of Thermothelomyces thermophilus LMBC 162 Cultivated with Tamarindus indica Seeds Reveals CAZymes for Degradation of Lignocellulosic Biomass

“…Based on their protein sequence similarities and three-dimensional folding structure, CAZymes are classified into several hundred different enzyme protein families [16]. These enzymes are involved in many biological processes, and they are responsible for the degradation, synthesis, and modification of carbohydrates [17,18].…”