Bilateral BBSRC-FAPESP/ Targeted analysis of microbial lignocellulolytic secretomes - a new approach to enzyme discovery

As fossil fuel supplies dwindle and concerns increase about the environmental impact of chemical waste streams, industrial biotechnologists are exploring ways to use plant based feedstocks in 'biorefineries' to generate biofuels and manufacture polymers, pharmaceuticals and commodity chemicals. The long-term success of biorefining is dependent on the development of economical methods for processing plant biomass to exploit the energy rich polysaccharides in cellulose for fermentation. The complex phenolic polymers present in lignin create a major bottleneck in the deconstruction of plant cell walls, as they are recalcitrant to degradation. Currently biorefineries require the use of acid and steam explosion to treat lignocellulose, which is inefficient and energy dependent, the released cellulose is then digested with a cocktail of cellulases. The costs involved in converting biomass into fermentable sugars currently make cellulosic fermentation too expensive.

While the saccharification of lignocellulose remains a problem for industry, it is carried out effectively in the natural environment by microbial communities. Such communities are found in composting systems and soils. The major challenge in identifying the range of enzymes and other proteins used by communities of microorganisms during lignocellulose degradation lies in the complexity of the process itself. At present the vast majority of microbial biodiversity remains uncharacterised, because less than 1% of microorganisms in most environments are amenable to axenic cultivation, therefore, to date lignocellulose degradation has largely been studied in a few well characterised and culturable microorganisms. The research proposed here is concerned with discovering new enzymes and associated proteins for lignocellulose digestion from rotting cereal straw and sugar cane bagasse, and takes an integrated proteomics and metatranscriptomic approach for their identification. The innovative aspect to our proteomic approach arises from the fact that microbial cells cannot ingest pieces of undigested lignocellulose, but must first convert this material to simple sugars that can then be imported in to the cell, and this requires that they secrete the appropriate digestive enzymes. Thus, the majority of enzymes and accessory proteins involved in lignocellulose mobilisation are distinguished from those involved in housekeeping activities by the fact that they are secreted. The major challenge is that lignocellulose active proteins bind tightly to lignocellulose and require stringent extraction conditions to release them. Similarly, many of the microbes involved in lignocellulose digestion also bind to the substrate and cannot be washed out. The result of this is that if sufficiently stringent extraction is used to get the proteins off the substrate this inevitably leads to cell lysis and contamination of the extract with cellular enzymes; whilst milder extractions only release a small proportion of the target proteins.

To overcome this problem we will use non-invasive extracellular protein tagging to identify secreted enzymes produced by microbial communities. The key to this is the use of a protein affinity tag that cannot cross biological membranes and can therefore only access and tag extracellular proteins. Once the tagging reaction has been quenched, the lignocellulose and microbial culture can be extracted under stringent conditions, with the tagged extracellular proteins simply separated by affinity purification prior to proteomic analysis. Combining the power of extracellular proteomics and metatranscriptomics will allow us to focus in on the proteins critical for lignocellulose deconstruction from microbial communities. This will greatly enhance our ability to identify completely new types of lignocellulose active proteins, both broadening our fundamental understanding of this process, as well as providing novel activities for research and industrial applications.