Biomass Depolymerization projects

Discovery and Characterization of Lignin-Degrading Enzymes

This project is focused on discovering and characterizing new enzymes from soil bacteria that are involved in lignin degradation, thus improving understanding of the relationship between enzyme reactivity and changes in lignin structure. It is exploring the diversity of lignin degradation pathways found in soil samples, which often show high activity towards biomass depolymerization. The group is also focused on development of robust heterologous expression systems for lignin peroxidases, hoping to build a sequence database of bacterialligninases that can add to ongoing metagenomic approaches to gene discovery at the EBI.

project Highlights

2012 Highlights

Our group has been studying the biomass-degrading soil bacterium, Amycolatopsis sp. 75iv2, in order to discover and characterize new enzymes involved in lignin degradation. During 2012, we identified an unusual dye peroxidase (DyP2) from this organism and characterized it using structural and biochemical approaches. This family of enzymes has been previously implicated in the extracellular oxidative degradation of aromatic compounds, including lignin, and DyP2 is a particularly interesting member of this group based on its phylogeny and catalytic reactivity. In the course of these studies, we showed that DyP2 has both peroxidase and manganese peroxidase activity that is orders of magnitude higher than other bacterial DyPs. In addition, we showed that it demonstrates a Mn-dependent oxidase mode of reactivity that expands its substrate scope to include non-phenolic substrates. We further structurally characterized DyP2 and showed that a metal ion, likely Mn, is bound at a discrete site that is approximately 15Å away from the heme active site, which further supports that the Mn is important for its activity.

2011 Highlights

Chang’s group identified several new heme peroxidases from Amycolatopsis sp. 75iv2. They also characterized members of the catalase-peroxidase and DyP families and characterized potential accessory enzymes.

2009 Highlights

(Former Title: New Approaches to Lignin Depolymerization):

Six strains of bacteria were cultured in Miscanthus lignocellulose- and indulin-supplemented media and monitored for extracellular peroxidase activity. All strains showed positive peroxidase activity and produced acid-precipitable polymeric lignin over a negative control. Secreted proteins that showed the most significant lignase activity were analyzed by PAGE for heme-containing proteins, indicative of lignin activity. Two such proteins were identified.

 

Publications

Published in 2012

Identification and Characterization of a Multifunctional Dye Peroxidase from a Lignin-Reactive Bacterium, Margaret Brown, Tiago Barros, and Michelle C. Y. Chang, ACS Chemical Biology, , doi: 10.1012/cb300383y, October 10, 2012.

Published in 2011

Discovery and Characterization of Heme Enzymes from Unsequenced Bacteria: Application to Microbial Lignin Degradation, Margaret Brown, Mark Walker, Toshiki Nakashige, Anthony Iararone, Michelle Chang, Journal of the American Chemical Society, doi: 10.1021/ja203972q, June 14, 2011.

Construction of de Novo Biosynthetic Pathways for Chemical Synthesis Inside Living Cells, Amy Weeks, Michelle C. Y. Chang, Biochemistry, 50(24), pp. 5404-5418, doi: 10.1021/bi200416g, May 17, 2011.

 


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