JBEI Research Highlights - February 2017

1. Understanding factors controlling depolymerization
and polymerization in catalytic degradation of ß-ether
linked model lignin compounds by versatile peroxidase
Outcomes
• In phenolic lignin dimers the VP first produces a neutral
radical via oxidation of the 4-OH position, followed by
polymerization and depolymerization reactions.
• Selection between polymerization and depolymerization
reaction pathways was found to be dependent on the
functional group at the 5 position of the guaiacyl group
(G5).
• The degradation pathway of phenolic β-O-4 was identified
as Cα-aryl cleavage rather than Cα-Cβ.
The effect of H2O2 concentration on the conversion of the
phenolic G-O-4 dimer (red) to monomer (blue) and insoluble
polymer (green) at pH 4.5 (left) and at pH 3.0 (right).
Zeng et al. (2017) ”Understanding factors controlling depolymerization and polymerization in catalytic degradation of
β-ether linked model lignin compounds by versatile peroxidase.” Green Chemistry, DOI: 10.1039/C6GC03379B
Background
• Enzyme catalyzed breakdown of lignin is hindered by the competition
between polymerization and depolymerization reaction pathways.
• Understanding the factors that drive these reactions toward
depolymerization is critical to developing processes for lignin
valorization.
Significance
• New insights into the reaction conditions and structural
features of lignin that facilitate its depolymerization to
smaller fragments
Versatile peroxidase catalyzes both
polymerization and depolymerization of lignin.
Approach
• Analyzed the effects of reaction conditions (pH, addition of H2O2 and
mediators) on the enzymatically catalyzed cleavage of several lignin
β-ether compounds using versatile peroxidase (VP) from B. adusta.
• Performed quantum chemistry calculations of free energy changes of
relevant chemical reactions and of electron spin density distributions
of radical species.
Depolymerization
Repolymerization
G
G S
OCH3
O
HO
OH
O
OCH3
OH
OH
OCH3
O
OCH3

2. Expression of Aspergillus niger CAZymes is
determined by compositional changes in wheat
straw generated by hydrothermal or ionic liquid
pretreatments
Daly et al. (2017) “Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw
generated by hydrothermal or ionic liquid pretreatments.” Biotechnology for Biofuels, DOI: 10.1186/s13068-017-0700-9
Background
• Fungi are major degraders of lignocellulose in nature and are
the main source of the costly enzymes used to saccharify pre-
treated lignocellulose in the production of second-generation
biofuels.
• There is limited understanding of the responses of fungi to
substrates that are pretreated as well as the temporal aspects
of the response.
Approach
• We investigate the response of Aspergillus niger to untreated
and pretreated substrates in a temporally extensive manner,
and are the first to report the fungal response to ionic liquid
pretreated substrates and the response of Aspergilli to
Miscanthus.
Outcomes
• The datasets demonstrate that pretreatment, substrate and
time each have major influence on the fungal responses to
lignocellulose.
• The transcript levels in A. niger correlated with the changes in
substrate composition brought about by the pretreatments
Significance
• Understanding these complex responses of fungi to
pretreated substrates facilitates identification of better
saccharifying enzymes and reduced enzyme production
costs.
a) The number of CAZy genes that encode plant‐polysaccharide active CAZymes
and is significantly induced in cultures with untreated and pretreated straw
compared to the Glu 48 h b) The proportion of transcripts from CAZy genes that
encode plant‐polysaccharide active CAZymes is expressed as FPKM value. c)
Subset of the MFuzz clusters from the clustering of all genes from the KMS
time‐course with number of genes belonging to the indicated categories.