Journal ArticleDOI
Identification of novel biomass‐degrading enzymes from genomic dark matter: Populating genomic sequence space with functional annotation
Hailan Piao,Hailan Piao,Jeff Froula,Changbin Du,Tae-Wan Kim,Tae-Wan Kim,Erik R. Hawley,Erik R. Hawley,Stefan Bauer,Zhong Wang,Nathalia Ivanova,Douglas S. Clark,Douglas S. Clark,Hans-Peter Klenk,Matthias Hess +14 more
TLDR
A gene context‐based approach can be used to assign function to genes that are otherwise categorized as “genomic dark matter” and to identify biomass‐degrading enzymes that have little sequence similarity to already known cellulases.Abstract:
Although recent nucleotide sequencing technologies have significantly enhanced our understanding of microbial genomes, the function of ∼35% of genes identified in a genome currently remains unknown. To improve the understanding of microbial genomes and consequently of microbial processes it will be crucial to assign a function to this “genomic dark matter.” Due to the urgent need for additional carbohydrate-active enzymes for improved production of transportation fuels from lignocellulosic biomass, we screened the genomes of more than 5,500 microorganisms for hypothetical proteins that are located in the proximity of already known cellulases. We identified, synthesized and expressed a total of 17 putative cellulase genes with insufficient sequence similarity to currently known cellulases to be identified as such using traditional sequence annotation techniques that rely on significant sequence similarity. The recombinant proteins of the newly identified putative cellulases were subjected to enzymatic activity assays to verify their hydrolytic activity towards cellulose and lignocellulosic biomass. Eleven (65%) of the tested enzymes had significant activity towards at least one of the substrates. This high success rate highlights that a gene context-based approach can be used to assign function to genes that are otherwise categorized as “genomic dark matter” and to identify biomass-degrading enzymes that have little sequence similarity to already known cellulases. The ability to assign function to genes that have no related sequence representatives with functional annotation will be important to enhance our understanding of microbial processes and to identify microbial proteins for a wide range of applications. Biotechnol. Bioeng. 2014;111: 1550–1565. © 2014 Wiley Periodicals, Inc.read more
Citations
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Journal ArticleDOI
Destructuring plant biomass: Focus on fungal and extremophilic cell wall hydrolases
Gea Guerriero,Jean-Francois Hausman,Joseph Strauss,Haluk Ertan,Haluk Ertan,Khawar Sohail Siddiqui +5 more
TL;DR: The present review discusses the current research trends on fungal, as well as extremophilic cell wall hydrolases that can withstand extreme physico-chemical conditions required in efficient industrial processes and suggests further research avenues for improving saccharification.
Journal ArticleDOI
The importance of sourcing enzymes from non-conventional fungi for metabolic engineering and biomass breakdown
TL;DR: Select classes of fungal enzymes that are currently in biotechnological use are discussed, and more basal, non-conventional fungi and their underexploited biomass-degrading mechanisms are explored as promising agents in the transition towards a bio-based society.
Journal ArticleDOI
Defining functional diversity for lignocellulose degradation in a microbial community using multi-omics studies.
Anna M. Alessi,Susannah Bird,Nicola C. Oates,Yi Li,Adam Dowle,Etelvino Henrique Novotny,Eduardo R. deAzevedo,Joseph P. Bennett,Igor Polikarpov,J. Peter W. Young,Simon J. McQueen-Mason,Neil C. Bruce +11 more
TL;DR: A combination of mass spectrometry-based proteomics coupled with metatranscriptomics has enabled the identification of a large number of lignocellulose degrading enzymes that can now be further explored for the development of improved enzyme cocktails for the treatment of plant-based feedstocks.
Journal ArticleDOI
Biocatalysts for biomass deconstruction from environmental genomics.
TL;DR: Recent progress in recovering biological devices from environmental genomes from uncultivated microbial communities are reviewed and how this information can be used to build better biorefining ecosystems are considered.
Journal ArticleDOI
Roles of intestinal Parabacteroides in human health and diseases.
TL;DR: The stability of gut microbiota is essential for the host health and Parabacteroides spp.
References
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