Functional diversity of carbohydrate-active enzymes enabling a bacterium to ferment plant biomass

PLoS Genet. 2014 Nov 13;10(11):e1004773. doi: 10.1371/journal.pgen.1004773. eCollection 2014 Nov.

Abstract

Microbial metabolism of plant polysaccharides is an important part of environmental carbon cycling, human nutrition, and industrial processes based on cellulosic bioconversion. Here we demonstrate a broadly applicable method to analyze how microbes catabolize plant polysaccharides that integrates carbohydrate-active enzyme (CAZyme) assays, RNA sequencing (RNA-seq), and anaerobic growth screening. We apply this method to study how the bacterium Clostridium phytofermentans ferments plant biomass components including glucans, mannans, xylans, galactans, pectins, and arabinans. These polysaccharides are fermented with variable efficiencies, and diauxies prioritize metabolism of preferred substrates. Strand-specific RNA-seq reveals how this bacterium responds to polysaccharides by up-regulating specific groups of CAZymes, transporters, and enzymes to metabolize the constituent sugars. Fifty-six up-regulated CAZymes were purified, and their activities show most polysaccharides are degraded by multiple enzymes, often from the same family, but with divergent rates, specificities, and cellular localizations. CAZymes were then tested in combination to identify synergies between enzymes acting on the same substrate with different catalytic mechanisms. We discuss how these results advance our understanding of how microbes degrade and metabolize plant biomass.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Wall / metabolism
  • Cellulose / genetics
  • Cellulose / metabolism
  • Cloning, Molecular
  • Clostridium / enzymology*
  • Enzymes / genetics*
  • Enzymes / isolation & purification
  • Enzymes / metabolism
  • Fermentation
  • Glucose / metabolism
  • Humans
  • Plants / metabolism*
  • Polysaccharides / metabolism*
  • Sequence Analysis, RNA
  • Xylose / genetics
  • Xylose / metabolism

Substances

  • Enzymes
  • Polysaccharides
  • Cellulose
  • Xylose
  • Glucose

Grants and funding

This work was funded by the Genoscope-CEA and a CNRS chaire d'excellence to ACT. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.