Abstract
Fungi from the Pleurotus genus secrete different enzymes, including laccases, manganese peroxidases, versatile peroxidases, glycosyl hydrolases, peptidases, and esterases/lipases. This genus contains white-rot fungi, which degrade the components of plant materials. The secreted enzymes have great application in the biotechnology field. The general conditions of a fungal culture have a direct effect on the regulation of protein expression, which changes the composition of the transcriptome, proteome, and secretome. Studies have shown that the culture type, either solid or submerged, also changes the transcriptional profiles. The knowledge of the transcriptome and proteome allows one to find valuable enzymes to obtain portable fuels from lignocellulosic materials and provide information oriented to improve the enzymes production through different culture conditions. Additionally, research has been conducted on the Pleurotus genus to better understand its biology. Numerous tools have been used for this purpose, such as classical recombination, genetic engineering, and omic tools. The information generated by the omic sciences (comparative genomics, transcriptomics, proteomics, and metabolomics) and through bioinformatics (massive data analysis), among other things, can greatly contribute to improving production processes and the use of metabolites. This review discussed some works where omic tools have been used to study enzyme production of fungi of the Pleurotus genus.
Download PDF
Full Article
Omic Tools to Study Enzyme Production from Fungi in the Pleurotus genus
Maura Téllez-Téllez,a and Gerardo Díaz-Godínez b,*
Fungi from the Pleurotus genus secrete different enzymes, including laccases, manganese peroxidases, versatile peroxidases, glycosyl hydrolases, peptidases, and esterases/lipases. This genus contains white-rot fungi, which degrade the components of plant materials. The secreted enzymes have great application in the biotechnology field. The general conditions of a fungal culture have a direct effect on the regulation of protein expression, which changes the composition of the transcriptome, proteome, and secretome. Studies have shown that the culture type, either solid or submerged, also changes the transcriptional profiles. The knowledge of the transcriptome and proteome allows one to find valuable enzymes to obtain portable fuels from lignocellulosic materials and provide information oriented to improve the enzymes production through different culture conditions. Additionally, research has been conducted on the Pleurotus genus to better understand its biology. Numerous tools have been used for this purpose, such as classical recombination, genetic engineering, and omic tools. The information generated by the omic sciences (comparative genomics, transcriptomics, proteomics, and metabolomics) and through bioinformatics (massive data analysis), among other things, can greatly contribute to improving production processes and the use of metabolites. This review discussed some works where omic tools have been used to study enzyme production of fungi of the Pleurotus genus.
Keywords: Pleurotus; Transcriptome; Proteome; Secretome; Metabolome; Enzymes
Contact information: a: Laboratory of Mycology, Biological Research Center, Autonomous University of Morelos State, Morelos, Mexico; b: Laboratory of Biotechnology, Research Center for Biological Sciences, Autonomous University of Tlaxcala, Tlaxcala, Mexico;
* Corresponding author: gerardo.diaz@uatx.mx
INTRODUCTION
Fungi have made an enormous contribution to human lives and are of commercial relevance in the production of fermented products, antibiotics, enzymes, pigments, organic acids, etc., which have great applications in the biotechnology field. There is a great diversity of fungi and even more of their metabolites (Ferreira et al. 2016). Among the mushrooms of great importance are those in the genus Pleurotus. Paul Kummer defined the genus Pleurotus (Fries) Kummer (Basidiomycota, Agaricales) in 1871. They are classified as white-rot fungi and are cultivated edible mushrooms. They also have medicinal properties and many environmental and biotechnological applications. The fungi in this genus are the most cultivated mushroom. Their taxonomic classification is complicated because they have many morphological similarities that have been considered part of the taxonomic criteria (Vilgalys et al. 1993; Zervakis and Balis 1996). Recently, the use of molecular tools based on DNA has helped to clarify the taxonomic classification of fungi in the genus Pleurotus (Pawlik et al. 2012; Shnyreva et al. 2012; Avin et al. 2014).
With the help of molecular techniques, researchers are still searching for fungal molecules with biological activities as well as the optimum conditions necessary for their industrial production, the above is expensive and involves a lot of work in different areas of study, due to the wide variety of fungi. Therefore, omic tools can address the functions of numerous genes (functional genomics) (Bunnik and Le Roch 2013), compare genes with another organism (comparative genomics) (Haubold and Wiehe 2004), study expression profiles (transcriptome) (Wang et al. 2009), study expression profiles of proteins (proteome) (Zhu et al. 2003), and study profiles of low molecular weight metabolites present in a cell under a given set of physiological conditions (metabolomics) (Kell et al. 2005). The results obtained through these techniques have contributed greatly to the understanding of the interactions between environmental factors, genetic variants, genetic expression patterns, changes in the concentration of metabolites, etc. This has been an important scientific development and has reduced bioprocessing times and increased yields, while managing to reduce the costs of biotechnological applications. Information generated by omic tools can be analyzed through mathematical and computational models to determine the real behavior of fungal cells in response to some development conditions. This is called systems biology (Fig. 1). These results allow for a better idea of certain biological processes, which can improve the processes or production yields of metabolites of interest.
Fig. 1. Set of molecular tools and techniques that support systems biology
It is known that the successful survival of a species depends mainly upon two criteria: 1) being in a suitable environment and 2) the ability to adapt to new environmental conditions. The first criterion promotes inbreeding that maintains genetic homogeneity within a population, which can be a disadvantage because it allows the expression of mutations. In contrast, the second criterion promotes genetic heterogeneity and genetic recombination. Fungi are advantageous for use as model organisms because they are eukaryotic, which have characteristics that have helped to elucidate many cellular processes (Whiteway and Bachewich 2005). In heterothallic fungi, sexual reproduction is controlled by incompatibility factors. Bifactorial fungi have two incompatibility factors that together control mating competition. These factors are genetically unlinked, and their independent segregation in meiosis leads to the production of four kinds of progeny (Koltin et al. 1972). Laboratory strains typically have stable mating types and are heterothallic. Most wild strains are homothallic, but do not have stable mating types. During mitotic growth, cells can change their mating type (Whiteway and Bachewich 2005).
Pleurotus genus
The genus Pleurotus is bifactorial heterothallic with a tetrapolar system and multiple alleles. Fertilization is only performed between two homocariotic mycelia of different genotypes for two genes or factors (A and B) (Zervakis and Balis 1996). In a fruiting body (dikaryotic), spores are formed with a set of chromosomes (n). Spores give rise to a monokaryotic mycelium when germinating and a dikaryotic mycelium (plasmogamy) through the fusion of two sexually compatible monokaryotic mycelia (different alleles of incompatibility). Ramírez et al. (2000) reported that locus A behaves as one, whereas locus B is a complex of two genes (matBα and matBβ) linked with genetic distances ranging from 17.5 cM to 5.0 cM. Specificities can appear by recombination between the two loci, which occurs in other superior basidiomycetes. Nine different types of mating were found for A and 15 for B, some of which were the result of intra-factorial recombination (Ramírez et al. 2000). A dikaryotic strain is formed when two compatible monokaryotic strains mate, which results in plasmogamy, but not cariogamy. As new hyphae grow, the two nuclei divide synchronously, and each new compartment maintains two nuclei and cariogamy only occurs before the start of sexual reproduction through fusion of the nuclei (Stajich et al. 2009). Hyphae are involved in morphogenesis, its integrity, synthesis, and degradation, based on the environmental and physiological conditions and availability of nutrients. The hyphae from the genus Pleurotus contain two nuclei that are called dikaryons, with each derived from a different father. However, the patterns of gene expression for dikaryons are not well known. Pleurotus is a well-known genus that belongs to the Pleurotaceae family of the order Agaricales. The name Pleurotus comes from the Greek “pleuro”, which means formed laterally or in a lateral position. This is in reference to the position of the stipe compared with that of the pileus. There are many species of this genus, of which some are cultivated to be commercialized and/or consumed. Some of the most representative fungi are P. ostreatus, P. eryngii, P. citrinopileatus, and P. djamor var. roseus (Fig. 2).
There have been major problems in the classification of the genus Pleurotus based only on the morphological characteristics (often not reliable or not blunt due to the influence of environmental conditions) or experiments on compatibility (supported by the concept of biological species) (Zervakis et al. 2001). Molecular tools have provided more precise methodologies for identification, one of which is the printing of DNA fingerprints. Gonzalez and Labarere (2000) related 16 isolates of Pleurotus spp. using the domains V4, V6, and V9 from the rRNA of the small subunit of the mitochondria and related it to its hyphal system.