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Identification and characterization of novel xylose isomerases from a Bos taurus fecal metagenome

  • Ruiqi Tang
  • Peiliang Ye
  • Hal S. Alper
  • Zhanying Liu
  • Xinqing ZhaoEmail author
  • Fengwu Bai
Biotechnologically relevant enzymes and proteins

Abstract

Discovering sugar metabolism genes is of great interest for lignocellulosic biorefinery. Xylose isomerases (XIs) were commonly screened from metagenomes derived from bovine rumen, soil, and other sources. However, so far, XIs and other sugar-utilizing enzymes have not been discovered from fecal metagenomes. In this study, environmental DNA from the fecal samples collected from yellow cattle (Bos taurus) was sequenced and analyzed. In the whole 14.26 Gbp clean data, 92 putative XIs were annotated. After sequence analysis, seven putative XIs were heterologously expressed in Escherichia coli and characterized in vitro. The XIs 58444 and 58960 purified from E. coli exhibited 22% higher enzyme activity when compared with that of the native E. coli XI. The XI 58444, similar to the XI from Lachnospira multipara, exhibited a relatively stable activity profile across different pH conditions. Four XIs were further investigated in budding yeast Saccharomyces cerevisiae after codon optimization. Overexpression of the codon-optimized 58444 enabled S. cerevisiae to utilize 6.4 g/L xylose after 96 h without any other genetic manipulations, which is 56% higher than the control yeast strain overexpressing an optimized XI gene xylA*3 selected by three rounds of mutation. Our results provide evidence that a bovine fecal metagenome is a novel and valuable source of XIs and other industrial enzymes for biotechnology applications.

Keywords

Bovine fecal metagenome Xylose isomerase (XI) Heterologous expression Xylose utilization Saccharomyces cerevisiae 

Notes

Acknowledgments

The authors are grateful to Dr. Bingyin Peng in the University of Queensland for helpful discussion. The assistance in experiments from Juan Xia and Mingming Zhang in Shanghai Jiao Tong University is highly appreciated.

Funding

This work was supported by National Natural Science Foundation of China (No. 21536006) and the joint research grant from the State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University (No. MMLKF19-01).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Ethical statement

This article does not contain any studies involving human participants or animals performed by any of the authors.

Supplementary material

253_2019_10161_MOESM1_ESM.pdf (131 kb)
ESM 1 (PDF 130 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Ruiqi Tang
    • 1
  • Peiliang Ye
    • 1
  • Hal S. Alper
    • 2
  • Zhanying Liu
    • 3
    • 4
  • Xinqing Zhao
    • 1
    Email author
  • Fengwu Bai
    • 1
  1. 1.State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
  2. 2.McKetta Department of Chemical EngineeringThe University of Texas at AustinAustinUSA
  3. 3.School of Chemical EngineeringInner Mongolia University of TechnologyHohhotChina
  4. 4.Center for Conservation and Emission Reductioin in Fermentation IndustryInner MongoliaHohhotChina

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