Worldwide concern about fossil fuel shortage, increased greenhouse gas emission, and air pollution from incomplete combustion have contributed to the search for alternative, sustainable, and clean energy sources [1]. Therefore, developing technologies that use lignocellulosic biomasses as feedstocks for biofuel production is of great interest [1]. Lignocellulosic materials are the most abundant natural renewable resource in the world and are mainly composed of three primary components: cellulose, hemicellulose, and lignin [2]. Significant amounts of these materials are usually produced as by-products from agricultural practices, mainly from several agro-based industries [3].

Considering the large sugarcane production in Brazil, the value-added to the bagasse for producing second-generation (2 G) ethanol is advantageous, increases productivity, and reduces the costs of the sugar and alcohol industry [4]. The application of enzymes to catalyze the depolymerization of cellulose and hemicelluloses from plant biomass into fermentable sugars has been considered the most workable strategy to provide 2 G ethanol with an excellent cost-benefit ratio [5]. However, biomass saccharification shows a significant challenge in this process since the disruption of the complex structure of the plant cell wall requires a varied set of hydrolytic and oxidative enzymes, including cellulases, hemicellulases, ligninases, pectinases, auxiliary enzymes (LPMOs, laccases, catalases, peroxidases) [6], and others non-hydrolytic proteins, such as swollenins [7].

The enzymatic mixtures used in the 2 G ethanol process are produced by microorganisms, especially fungi of the genus Trichoderma and Aspergillus [8]. The enzymes account for most of the 2 G ethanol production costs. However, prospecting new microorganisms as sources of enzymes with high-performance catalytic properties or identifying new enzymes for commercial cocktail supplementation could reduce costs and improve the viability of the process [9].

Chrysoporthe cubensis is a versatile phytopathogenic fungus that grows in different low-cost lignocellulosic substrates [10], [11]. Several studies have demonstrated that C. cubensis cultivated under semi-solid-state fermentation (SSF) using wheat bran as a carbon source showed a remarkable potential for lignocellulolytic enzyme production [12], [13], [14], which exhibited high efficiency for sugarcane bagasse saccharification compared to commercial enzymatic cocktails [15]. Indeed, C. cubensis exhibited high cellulase and hemicellulase production potential when grown under SSF with sugarcane bagasse in natura as a carbon source [11].

Since the crude extracts of this fungus have shown promise for the 2 G bioethanol process, a comparative study of the exoproteomes of C. cubensis grown on wheat bran or sugarcane bagasse could provide qualitative and quantitative information about the cell wall degrading enzymes present in these exoproteomes. The identification of differentially expressed CAZymes by C. cubensis grown in these conditions is essential to get a deeper understanding of the lignocellulose-degrading enzyme system responsible for the unique properties of each C. cubensis extract.

In this study, we identified, quantified, and compared the proteins secreted by C. cubensis after growth in sugarcane bagasse and wheat bran using a high-throughput, quantitative, label-free based LC–ESI–MS/MS proteomic approach. The results allowed us to find the differential proteins secreted by C. cubensis and recognize the specific enzymes in each exoproteome related to plant biomass degradation. Moreover, we tested and compared the performance of these two C. cubensis enzymatic extracts in the saccharification of sugarcane bagasse. This study contributed to the knowledge of the biotechnological potential of C. cubensis concerning its capability to secrete plant cell wall degrading enzymes in response to the carbon sources present in the culture medium and to identify differentially secreted proteins as promising targets for future industrial application, mainly aimed at supplementing commercial enzyme mixtures.