Identification of Novel Putative Bacterial Feruloyl Esterases From Anaerobic Ecosystems by Use of Whole-Genome Shotgun Metagenomics and Genome Binning.

Kamyar Mogodiniyai Kasmaei,John Sundh

doi:10.3389/fmicb.2019.02673

Abstract

Feruloyl esterases (FAEs) can reduce the recalcitrance of lignocellulosic biomass to enzymatic hydrolysis, thereby enhancing biorefinery potentials or animal feeding values of the biomass. In addition, ferulic acid, a product of FAE activity, has applications in pharmaceutical and food/beverage industries. It is therefore of great interest to identify new FAEs to enhance understanding about this enzyme family. For this purpose, we used whole-genome shotgun metagenomics and genome binning to explore rumens of dairy cows, large intestines of horses, sediments of freshwater and forest topsoils to identify novel prokaryotic FAEs and trace the responsible microorganisms. A number of prokaryotic genomes were recovered of which, genomes of Clostridiales order and Candidatus Rhabdochlamydia genus showed FAE coding capacities. In total, five sequences were deemed as putative FAE. The BLASTP search against non-redundant protein database of NCBI indicated that these putative FAEs represented novel sequences within this enzyme family. The phylogenetic analysis showed that at least three putative sequences shared evolutionary lineage with FAEs of type A and thus could possess specific activities similar to this type of FAEs, something that is not previously found outside fungal kingdom. We nominate Candidatus Rhabdochlamydia genus as a novel FAE producing taxonomic unit.

Highlights

Production of biofuels and biochemicals from lignocellulosic biomass, a non-food renewable carbon resource, has increasingly become of great importance due to increasing global demands for energy and chemicals, increasing prices of fossil fuels and environmental concerns associated with fossil fuels
These ester bonds in the cell walls of plants can be cleaved with feruloyl esterases (FAEs) (EC 3.1.1.73), member of carboxylic ester hydrolases (EC 3.1.1.-) (Jeske et al, 2019), to reduce complexity of cell wall configuration, thereby enhancing utilization of lignocellulosic biomass (Wong, 2006)
We explored rumens of dairy cows, large intestines of horses, sediments of freshwater and topsoils of forests by means of wholegenome shotgun metagenomics and genome binning to study prokaryotic capacities for FAE production and potential novelty of the predicted FAEs

Summary

Introduction

Production of biofuels and biochemicals from lignocellulosic biomass, a non-food renewable carbon resource, has increasingly become of great importance due to increasing global demands for energy and chemicals, increasing prices of fossil fuels and environmental concerns associated with fossil fuels. In the cell walls of monocots (e.g., grass, cereals), lignin and hemicellulose interconnect, forming a matrix that encrusts the cellulose (Wong, 2006; Rubin, 2008) This configuration creates a complex structure, believed to be the main cause of recalcitrance of lignocellulosic biomass to enzymatic hydrolysis (Rubin, 2008; Pu et al, 2013). The linkage between lignin and hemicellulose is mainly mediated by ferulic acid (FA), forming ester bonds with hemicellulose from the carboxylic side and ether bonds with lignin from the phenolic side of the molecule These ester bonds in the cell walls of plants can be cleaved with feruloyl esterases (FAEs) (EC 3.1.1.73), member of carboxylic ester hydrolases (EC 3.1.1.-) (Jeske et al, 2019), to reduce complexity of cell wall configuration, thereby enhancing utilization of lignocellulosic biomass (Wong, 2006). Several attempts have already been made to improve digestibility of forages in dairy cattle rations by use of FAE producing lactic acid bacteria (Muck et al, 2018)

Methods

Results

Discussion

Conclusion