Simple discovery of bacterial biocatalysts from environmental samples through functional metaproteomics

Abstract

Bacterial biocatalysts play a key role in our transition to a bio-based, post-petroleum economy. However, the discovery of new biocatalysts is currently limited by our ability to analyze genomic information and our capacity of functionally screening for desired activities. Here, we present a simple workflow that combines functional metaproteomics and metagenomics, which facilitates the unmediated and direct discovery of biocatalysts in environmental samples. To identify the entirety of lipolytic biocatalysts in a soil sample contaminated with used cooking oil, we detected all proteins active against a fluorogenic substrate in sample’s metaproteome using a 2D-gel zymogram. Enzymes’ primary structures were then deduced by tryptic in-gel digest and mass spectrometry of the active protein spots, searching against a metagenome database created from the same contaminated soil sample. We then expressed one of the novel biocatalysts heterologously in Escherichia coli and obtained proof of lipolytic activity.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-017-0247-9) contains supplementary material, which is available to authorized users.

Characterization of ML-005, a Novel Metaproteomics-Derived Esterase

“…Through this approach we successfully identified 14 lipolytically active protein spots on a 2D gel derived from the enriched metaproteome of a soil sample harvested from a restaurant’s used cooking oil disposal site. Among those, we identified ML-005, an esterase from a hitherto uncharacterized family, which we could heterologously express in E. coli ( Sukul et al, 2017 ).…”

The Holo-Transcriptome of the Zoantharian Protopalythoa variabilis (Cnidaria: Anthozoa): A Plentiful Source of Enzymes for Potential Application in Green Chemistry, Industrial and Pharmaceutical Biotechnology

“…The identification of industrially relevant enzyme biocatalysts from environmental samples has been concretized by means of metagenomic analysis [ 9 , 35 , 36 ], a combination of metagenomics and metaproteomics technologies [ 37 ], and the combined application of transcriptomics and proteomics [ 38 ]. We based our search on analyzing the P. variabilis holo-transcriptome, providing an insight into the unexplored enzymes and related biosynthesis pathways expressed in this zoantharian-microbiota assemblage.…”

Microbial indicators for soil quality

“…For instance, using metagenomics of microbiomes from industrially-contaminated soil sites in Gujarat (India), Shah et al (2013) identified over 100 different genes for enzymes predicted to be involved in xenobiotic-degradation pathways. Based on these studies, a huge number of potential indicators has become available, however testing of these for robustness regarding the biodegradation potential and activity, and subsequent validation in the context of well-defined soils and metadata, is needed (Shah et al 2013;Sukul et al 2017). …”