Insights into Thermophilic Plant Biomass Hydrolysis from Caldicellulosiruptor Systems Biology

Abstract

Plant polysaccharides continue to serve as a promising feedstock for bioproduct fermentation. However, the recalcitrant nature of plant biomass requires certain key enzymes, including cellobiohydrolases, for efficient solubilization of polysaccharides. Thermostable carbohydrate-active enzymes are sought for their stability and tolerance to other process parameters. Plant biomass degrading microbes found in biotopes like geothermally heated water sources, compost piles, and thermophilic digesters are a common source of thermostable enzymes. While traditional thermophilic enzyme discovery first focused on microbe isolation followed by functional characterization, metagenomic sequences are negating the initial need for species isolation. Here, we summarize the current state of knowledge about the extremely thermophilic genus Caldicellulosiruptor, including genomic and metagenomic analyses in addition to recent breakthroughs in enzymology and genetic manipulation of the genus. Ten years after completing the first Caldicellulosiruptor genome sequence, the tools required for systems biology of this non-model environmental microorganism are in place.

Keywords: Caldicellulosiruptor; enzyme synergy; extreme thermophile; genomics; systems biology; thermostable enzymes.

Figure 1

Global sites where members of the genus Caldicellulosiruptor have been isolated or detected. Locations are approximate to country or territory from peer-reviewed literature (see Table 2). Open diamonds, 16S rRNA gene sequencing; open circles, meta-omics identification; closed squares, Caldicellulosiruptor spp. genomic sequencing.

Figure 2

Progress on the generation of data and tools required for Caldicellulosiruptor strain development. Maturing research areas are shaded in light gray, nascent research areas are shaded in light green. Tools and data discussed in this review are listed in dark gray rectangles, tools that require further development for strain development are highlighted in the blue ovals. Image modified from strategies illustrated by Yan and Fong [135].