Accelerated discovery of novel glycoside hydrolases using targeted functional profiling and selective pressure on the rumen microbiome

Microbiome

Marisol Baez-Magana¹  Jiangkun Yu²  Le Luo Guan²  Eóin O’Hara²  Kim H. Ominski³  Elena Arutyunova⁴  M. Joanne Lemieux⁴  André L. A. Neves⁵  Tim McAllister⁶  Yutaka Suzuki⁷ 

[1] Centro Multisciplinario de Estudios en Biotecnologia, Facultad de Veterinaria y Zootecnia Universidad Michoacana de San Nicolas de Hidalgo;Department of Agricultural, Food and Nutritional Science, University of Alberta;Department of Animal Science & National Centre for Livestock and the Environment (NCLE), University of Manitoba;Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta;Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen;Lethbridge Research Center, Agriculture and Agri-Food Canada;Research Faculty of Agriculture, Hokkaido University;

关键词: Cattle;    Feed efficiency;    Microbial enzymes;    Rumen microbiota;   

DOI  :  10.1186/s40168-021-01147-1

来源: DOAJ

【 摘 要 】

Abstract Background Carbohydrate-active enzymes (CAZymes) form the most widespread and structurally diverse set of enzymes involved in the breakdown, biosynthesis, or modification of lignocellulose that can be found in living organisms. However, the structural diversity of CAZymes has rendered the targeted discovery of novel enzymes extremely challenging, as these proteins catalyze many different chemical reactions and are sourced by a vast array of microbes. Consequently, many uncharacterized members of CAZyme families of interest have been overlooked by current methodologies (e.g., metagenomic screening) used to discover lignocellulolytic enzymes. Results In the present study, we combined phenotype-based selective pressure on the rumen microbiota with targeted functional profiling to guide the discovery of unknown CAZymes. In this study, we found 61 families of glycoside hydrolases (GH) (out of 182 CAZymes) from protein sequences deposited in the CAZy database—currently associated with more than 20,324 microbial genomes. Phenotype-based selective pressure on the rumen microbiome showed that lignocellulolytic bacteria (e.g., Fibrobacter succinogenes, Butyrivibrio proteoclasticus) and three GH families (e.g., GH11, GH13, GH45) exhibited an increased relative abundance in the rumen of feed efficient cattle when compared to their inefficient counterparts. These results paved the way for the application of targeted functional profiling to screen members of the GH11 and GH45 families against a de novo protein reference database comprised of 1184 uncharacterized enzymes, which led to the identification of 18 putative xylanases (GH11) and three putative endoglucanases (GH45). The biochemical proof of the xylanolytic activity of the newly discovered enzyme validated the computational simulations and demonstrated the stability of the most abundant xylanase. Conclusions These findings contribute to the discovery of novel enzymes for the breakdown, biosynthesis, or modification of lignocellulose and demonstrate that the rumen microbiome is a source of promising enzyme candidates for the biotechnology industry. The combined approaches conceptualized in this study can be adapted to any microbial environment, provided that the targeted microbiome is easy to manipulate and facilitates enrichment for the microbes of interest. Video Abstract

【 授权许可】

Unknown