05/30/2017

Unlocking the Potential of Fungal Enzymes to Break Down Plant Cell Walls

Biomass-degrading enzyme complexes could improve biofuel production.

The Science

A major bottleneck in biofuel production is the difficulty of breaking down lignocellulose—the primary building block of plant cell walls. A recent study suggests that unlike bacterial enzyme complexes for breaking down lignocellulose, fungal enzyme complexes have a more diverse functionality.

The Impact

The findings highlight the powerful degradation activity of fungal lignocellulose-degrading enzymes, which could be harnessed to develop novel strategies for efficient biofuel production.

Summary

Gut microbes play a major role in helping ruminants such as cows, goats and sheep break down lignocellulose-rich plant matter in their diet. Anaerobic bacteria and fungi inhabiting the ruminant gut have evolved a suite of lignocellulose-degrading enzymes, whose activity supports microbial metabolism while supplying nutrients to ruminants. These enzymes often assemble together in large, multi-protein complexes called cellulosomes, which enhance the ability of gut microbes to degrade lignocellulose by confining all the enzymes in one place. Although bacterial cellulosomes now serve as a standard model for biomass conversion and synthetic biology applications, fungal cellulosomes have not been well characterized due to the lack of genomic and proteomic data, despite their potential value for biofuel and bio-based chemical production. To address this knowledge gap, a collaborative effort by researchers from the University of California, Santa Barbara, the Environmental Molecular Sciences Laboratory ( EMSL); the Department of Energy Joint Genome Institute (DOE JGI); Pacific Northwest National Laboratory; Centre National de la Recherche Scientifique; French National Institute for Agricultural Research; Radboud University; King Abdulaziz University; and the University of California, Berkeley combined next-generation sequencing with functional proteomics to describe the comprehensive set of proteins that play a role in fungal cellulosome assembly. This research was performed under the Facilities Integrating Collaborations for User Science (FICUS) initiative and used resources at DOE JGI and EMSL, which are DOE Office of Science User Facilities. This analysis revealed a new family of genes that likely serves as scaffolding proteins critical for cellulosome assemblies across diverse species of anaerobic gut fungi. Unlike bacterial cellulosomes, which have high species specificity, fungal cellulosomes are likely a composite of enzymes from several species of gut fungi. Although many bacterial and fungal plant biomass-degrading enzymes have shared similarities, the fungal cellulosomes were found to contain additional lignocellulose-degrading enzymes not found in bacterial cellulosomes. These features may not only confer a selective advantage of fungi over bacteria in the ruminant gut, but also impart fungal cellulosomes with great potential for biomass conversion. Taken together, the findings highlight key differences in bacterial and fungal cellulosomes and suggest enzyme connections (known as tethering) play such an important role in plant cell wall degradation.

Principal Investigator(s)

Michelle A. O’Malley
University of California, Santa Barbara
[email protected]

Funding

This work was supported by the U.S. Department of Energy’s Office of Science (Office of Biological and Environmental Research), including support of the Environmental Molecular Sciences Laboratory (EMSL) and the DOE Joint Genome Institute (DOE JGI), DOE Office of Science User Facilities; U.S. Department of Agriculture; National Science Foundation; U.S. Army; University of California, Santa Barbra and Berkeley; and California NanoSystems Institute.

References

C.H. Haitjema, S.P. Gilmore, J.K. Henske, K.V. Solomon, R. de Groot, A. Kuo, S.J. Mondo, A.A. Salamov, K. LaButti, Z. Zhao, J. Chiniquy, K. Barry, H.M. Brewer, S.O. Purvine, A.T. Wright, M. Hainaut, B. Boxma, T. van Alen, J.H.P. Hackstein, B. Henrissat, S.E. Baker, I.V. Grigoriev, and M.A. O’Malley, “A Parts List for Fungal Cellulosomes Revealed by Comparative Genomics.” Nature Microbiology (2017). DOI 10.1038/nmicrobiol.2017.87.