Proteomic Dissection of the Cellulolytic Machineries Used by Soil-Dwelling Bacteroidetes
Journal article, 2018

ABSTRACT
Bacteria of the phylum Bacteroidetes are regarded as highly efficient carbohydrate metabolizers, but most species are limited to (semi)soluble glycans. The soil Bacteroidetes species Cytophaga hutchinsonii and Sporocytophaga myxococcoides have long been known as efficient cellulose metabolizers, but neither species conforms to known cellulolytic mechanisms. Both species require contact with their substrate but do not encode cellulosomal systems of cell surface-attached enzyme complexes or the polysaccharide utilization loci found in many other Bacteroidetes species. Here, we have fractionated the cellular compartments of each species from cultures growing on crystalline cellulose and pectin, respectively, and analyzed them using label-free quantitative proteomics as well as enzymatic activity assays. The combined results enabled us to highlight enzymes likely to be important for cellulose conversion and to infer their cellular localization. The combined proteomes represent a wide array of putative cellulolytic enzymes and indicate specific and yet highly redundant mechanisms for cellulose degradation. Of the putative endoglucanases, especially enzymes of hitherto-unstudied glycoside hydrolase family, 8 were abundant, indicating an overlooked important role during cellulose metabolism. Furthermore, both species generated a large number of abundant hypothetical proteins during cellulose conversion, providing a treasure trove of targets for future enzymology studies. 

IMPORTANCE
Cellulose is the most abundant renewable polymer on earth, but its recalcitrance limits highly efficient conversion methods for energy-related and material applications. Though microbial cellulose conversion has been studied for decades, recent advances showcased that large knowledge gaps still exist. Bacteria of the phylum Bacteroidetes are regarded as highly efficient carbohydrate metabolizers, but most species are limited to (semi)soluble glycans. A few species, including the soil bacteria C. hutchinsonii and S. myxococcoides, are regarded as cellulose specialists, but their cellulolytic mechanisms are not understood, as they do not conform to the current models for enzymatic cellulose turnover. By unraveling the proteome setups of these two bacteria during growth on both crystalline cellulose and pectin, we have taken a significant step forward in understanding their idiosyncratic mode of cellulose conversion. This report provides a plethora of new enzyme targets for improved biomass conversion.

proteomics

cellulase

carbohydrate-active enzymes

cellulose

soil microbiology

Author

Marcel Taillefer

Chalmers, Biology and Biological Engineering, Industrial Biotechnology

Wallenberg Wood Science Center (WWSC)

Magnus Ø. Arntzen

Norwegian University of Life Sciences

Bernard Henrissat

Centre national de la recherche scientifique (CNRS)

Phillip B. Pope

Norwegian University of Life Sciences

Johan Larsbrink

Wallenberg Wood Science Center (WWSC)

Chalmers, Biology and Biological Engineering, Industrial Biotechnology

mSystems

2379-5077 (eISSN)

Vol. 3 6 1-16 e00240-18

Enzymes for selective decomposition of woody biomass

Knut and Alice Wallenberg Foundation, 2014-01-01 -- 2018-12-31.

Mapping of unstudied cellulose-degrading mechanisms in soil bacteria

Swedish Energy Agency, 2016-01-01 -- 2018-12-31.

Driving Forces

Sustainable development

Subject Categories

Biochemistry and Molecular Biology

Microbiology

Biocatalysis and Enzyme Technology

Areas of Advance

Energy

Life Science Engineering (2010-2018)

Roots

Basic sciences

DOI

10.1128/mSystems.00240-18

More information

Latest update

3/22/2019