Secretomic analyses of Ruminiclostridium papyrosolvens reveal its enzymatic basis for lignocellulose degradation

Zhenxing Ren,Shasha Wu,Ansgar Poetsch,Chenggang Xu,Wuxin You

doi:10.1186/s13068-019-1522-8

Zhenxing Ren, Shasha Wu + Show 3 more

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https://doi.org/10.1186/s13068-019-1522-8

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Abstract

BackgroundEfficient biotechnological conversion of lignocellulosic biomass to valuable products, such as transportation biofuels, is ecologically attractive, yet requires substantially improved mechanistic understanding and optimization to become economically feasible. Cellulolytic clostridia, such as Ruminiclostridium papyrosolvens (previously Clostridium papyrosolvens), produce a wide variety of carbohydrate-active enzymes (CAZymes) including extracellular multienzyme complexes—cellulosomes with different specificities for enhanced cellulosic biomass degradation. Identification of the secretory components, especially CAZymes, during bacterial growth on lignocellulose and their influence on bacterial catalytic capabilities provide insight into construction of potent cellulase systems of cell factories tuned or optimized for the targeted substrate by matching the type and abundance of enzymes and corresponding transporters.ResultsIn this study, we firstly predicted a total of 174 putative CAZymes from the genome of R. papyrosolvens, including 74 cellulosomal components. To explore profile of secreted proteins involved in lignocellulose degradation, we compared the secretomes of R. papyrosolvens grown on different substrates using label-free quantitative proteomics. CAZymes, extracellular solute-binding proteins (SBPs) of transport systems and proteins involved in spore formation were enriched in the secretome of corn stover for lignocellulose degradation. Furthermore, compared with free CAZymes, complex CAZymes (cellulosomal components) had larger fluctuations in variety and abundance of enzymes among four carbon sources. In particular, cellulosomal proteins encoded by the cip-cel operon and the xyl-doc gene cluster had the highest abundance with corn stover as substrate. Analysis of differential expression of CAZymes revealed a substrate-dependent secretion pattern of CAZymes, which was consistent with their catalytic activity from each secretome determined on different cellulosic substrates. The results suggest that the expression of CAZymes is regulated by the type of substrate in the growth medium.ConclusionsIn the present study, our results demonstrated the complexity of the lignocellulose degradation systems of R. papyrosolvens and showed the potency of its biomass degradation activity. Differential proteomic analyses and activity assays of CAZymes secreted by R. papyrosolvens suggested a distinct environment-sensing strategy for cellulose utilization in which R. papyrosolvens modulated the composition of the CAZymes, especially cellulosome, according to the degradation state of its natural substrate.

Highlights

Efficient biotechnological conversion of lignocellulosic biomass to valuable products, such as transportation biofuels, is ecologically attractive, yet requires substantially improved mechanistic understanding and optimization to become economically feasible
Enzymes involved in the degradation of these polysaccharides are designated carbohydrate-active enzymes (CAZymes) and classified into five distinct groups according to their activities and structural features: glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), glycosyl transferases (GTs) and enzymes with auxiliary activities (AAs), which often display a modular structure with non-catalytic carbohydrate-binding modules (CBMs)
Protein concentrations were measured by the bicinchoninic acid (BCA) assay (Sangon Biotech, Shanghai, China)

Summary

Introduction

Efficient biotechnological conversion of lignocellulosic biomass to valuable products, such as transportation biofuels, is ecologically attractive, yet requires substantially improved mechanistic understanding and optimization to become economically feasible. Cellulolytic clostridia, such as Ruminiclostridium papyrosolvens (previously Clostridium papyrosolvens), produce a wide variety of carbohydrate-active enzymes (CAZymes) including extracellular multienzyme complexes—cellulosomes with different specificities for enhanced cellulosic biomass degradation. The integration is accomplished by the interaction of two complementary module classes, i.e., a cohesin module on the scaffoldin and a dockerin module on each enzymatic subunit [10] These specific characteristics allow the cellulosome to degrade cellulosic substrates effectively. The host cells and their substrate degradation machineries [11,12,13] are being exploited in the production of cellulosic biofuels by a variety of approaches, notably consolidated bioprocessing (CBP; [14])

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