Bacterial xylose isomerases from the mammal gut Bacteroidetes cluster function in Saccharomyces cerevisiae for effective xylose fermentation.

Bingyin Peng,Shuangcheng Huang,Tingting Liu,Anli Geng

doi:10.1186/s12934-015-0253-1

Bingyin Peng, Shuangcheng Huang + Show 2 more

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https://doi.org/10.1186/s12934-015-0253-1

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Abstract

BackgroundXylose isomerase (XI) catalyzes the conversion of xylose to xylulose, which is the key step for anaerobic ethanolic fermentation of xylose. Very few bacterial XIs can function actively in Saccharomyces cerevisiae. Here, we illustrate a group of XIs that would function for xylose fermentation in S. cerevisiae through phylogenetic analysis, recombinant yeast strain construction, and xylose fermentation.ResultsPhylogenetic analysis of deposited XI sequences showed that XI evolutionary relationship was highly consistent with the bacterial taxonomic orders and quite a few functional XIs in S. cerevisiae were clustered with XIs from mammal gut Bacteroidetes group. An XI from Bacteroides valgutus in this cluster was actively expressed in S. cerevisiae with an activity comparable to the fungal XI from Piromyces sp. Two XI genes were isolated from the environmental metagenome and they were clustered with XIs from environmental Bacteroidetes group. These two XIs could not be expressed in yeast with activity. With the XI from B. valgutus expressed in S. cerevisiae, background yeast strains were optimized by pentose metabolizing pathway enhancement and adaptive evolution in xylose medium. Afterwards, more XIs from the mammal gut Bacteroidetes group, including those from B. vulgatus, Tannerella sp. 6_1_58FAA_CT1, Paraprevotella xylaniphila and Alistipes sp. HGB5, were individually transformed into S. cerevisiae. The known functional XI from Orpinomyces sp. ukk1, a mammal gut fungus, was used as the control. All the resulting recombinant yeast strains were able to ferment xylose. The respiration-deficient strains harboring B. vulgatus and Alistipes sp. HGB5 XI genes respectively obtained specific xylose consumption rate of 0.662 and 0.704 g xylose gcdw−1 h−1, and ethanol specific productivity of 0.277 and 0.283 g ethanol gcdw−1 h−1, much comparable to those obtained by the control strain carrying Orpinomyces sp. ukk1 XI gene.ConclusionsThis study demonstrated that XIs clustered in the mammal gut Bacteroidetes group were able to be expressed functionally in S. cerevisiae and background strain anaerobic adaptive evolution in xylose medium is essential for the screening of functional XIs. The methods outlined in this paper are instructive for the identification of novel XIs that are functional in S. cerevisiae.Electronic supplementary materialThe online version of this article (doi:10.1186/s12934-015-0253-1) contains supplementary material, which is available to authorized users.

Highlights

Xylose isomerase (XI) catalyzes the conversion of xylose to xylulose, which is the key step for anaerobic ethanolic fermentation of xylose
Class I XIs are distinguished from class II XIs by having a shorter N-terminal, and T. thermophilus XI, the first XI actively expressed in S. cerevisiae, belongs to class I
Class II represents a large number of XI families, and the relationship of XIs in phylogenetic tree is highly consistent with the taxonomic orders (Fig. 1)

Summary

Introduction

Xylose isomerase (XI) catalyzes the conversion of xylose to xylulose, which is the key step for anaerobic ethanolic fermentation of xylose. Very few bacterial XIs can function actively in Saccharomyces cerevisiae. Effective conversion of xylose, the second abundant sugar after glucose in lignocellulosic biomass, is necessary to make this process more economically feasible and efficient [1]. Saccharomyces cerevisiae is an attractive host to produce biofuels and industrial chemicals from lignocellulosic biomass due to its robustness and fast fermentation rate [2]. It cannot naturally utilize xylose [3]. Xylose isomerase (XI) naturally catalyzes the bacterial conversion of xylose to xylulose, which is further metabolized to ethanol through central metabolic pathways. The species boundary makes most of eubacterial xylose isomerases fail to be functionally expressed in yeast

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