Identifying carbohydrate-active enzymes of Cutaneotrichosporon oleaginosus using systems biology

Tobias Fuchs,Mahmoud Masri,Martina Haack,Pariya Shaigani,Jan Lorenzen,Norbert Mehlmer,Dania Awad,Sophia Alice Prem,Thomas B Brueck,Felix Melcher,Zora Selina Rerop

doi:10.1186/s12934-021-01692-2

Tobias Fuchs, Mahmoud Masri + Show 9 more

Open Access

https://doi.org/10.1186/s12934-021-01692-2

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Abstract

BackgroundThe oleaginous yeast Cutaneotrichosporon oleaginosus represents one of the most promising microbial platforms for resource-efficient and scalable lipid production, with the capacity to accept a wide range of carbohydrates encapsulated in complex biomass waste or lignocellulosic hydrolysates. Currently, data related to molecular aspects of the metabolic utilisation of oligomeric carbohydrates are sparse. In addition, comprehensive proteomic information for C. oleaginosus focusing on carbohydrate metabolism is not available.ResultsIn this study, we conducted a systematic analysis of carbohydrate intake and utilisation by C. oleaginosus and investigated the influence of different di- and trisaccharide as carbon sources. Changes in the cellular growth and morphology could be observed, depending on the selected carbon source. The greatest changes in morphology were observed in media containing trehalose. A comprehensive proteomic analysis of secreted, cell wall-associated, and cytoplasmatic proteins was performed, which highlighted differences in the composition and quantity of secreted proteins, when grown on different disaccharides. Based on the proteomic data, we performed a relative quantitative analysis of the identified proteins (using glucose as the reference carbon source) and observed carbohydrate-specific protein distributions. When using cellobiose or lactose as the carbon source, we detected three- and five-fold higher diversity in terms of the respective hydrolases released. Furthermore, the analysis of the secreted enzymes enabled identification of the motif with the consensus sequence LALL[LA]L[LA][LA]AAAAAAA as a potential signal peptide.ConclusionsRelative quantification of spectral intensities from crude proteomic datasets enabled the identification of new enzymes and provided new insights into protein secretion, as well as the molecular mechanisms of carbo-hydrolases involved in the cleavage of the selected carbon oligomers. These insights can help unlock new substrate sources for C. oleaginosus, such as low-cost by-products containing difficult to utilize carbohydrates. In addition, information regarding the carbo-hydrolytic potential of C. oleaginosus facilitates a more precise engineering approach when using targeted genetic approaches. This information could be used to find new and more cost-effective carbon sources for microbial lipid production by the oleaginous yeast C. oleaginosus.

Highlights

The oleaginous yeast Cutaneotrichosporon oleaginosus represents one of the most promising microbial platforms for resource-efficient and scalable lipid production, with the capacity to accept a wide range of carbohydrates encapsulated in complex biomass waste or lignocellulosic hydrolysates
C. oleaginosus cells were cultured on yeast nitrogen base (YNB) plates containing a set of different carbohydrates
C. oleaginosus colonies grown on solid media containing maltose were significantly larger than those grown on media containing glucose, lactose, sucrose, cellobiose, or trehalose (Fig. 2)

Summary

Introduction

The oleaginous yeast Cutaneotrichosporon oleaginosus represents one of the most promising microbial platforms for resource-efficient and scalable lipid production, with the capacity to accept a wide range of carbohydrates encapsulated in complex biomass waste or lignocellulosic hydrolysates. C. oleaginosus features an increased capacity for metabolising diverse and chemically complex carbon sources, including most mono-, di-, and trimeric sugars, as well as glycerol, volatile fatty acids, and lignin-derived aromatics [4,5,6]. This unique attribute provides C. oleaginosus with the metabolic capacity to utilise complex biomass hydrolysates derived from various biomass sources, such as lignocellulose and crude glycerol derived from biodiesel processing, without the need for detoxification. C. oleaginosus can tolerate and even metabolically utilise high concentrations of acetic acid, which is not the case for the model yeast Saccharomyces cerevisiae [1]

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