- The document discusses elucidating transfer hydrogenation mechanisms in non-catalytic lignin depolymerization. The study investigated using formic acid and methyl formate as agents for depolymerizing lignin from sugarcane bagasse. - A time-course study observed the evolution of product quantities and distributions from lignin depolymerization. Using methyl formate and water produced 73% bio-oil containing low molecular weight alkylphenols, with less than 1% char. - The depolymerization was found to occur via a two-stage mechanism involving reactions between lignin and formic acid, methyl formate or carbon monoxide under aqueous conditions. Controlling these reactions maximizes bio-oil yield.

1. Outcomes and Impacts
• Disrupting an organism’s ability to sense nutrients and
regulate transcription and translation will accelerate
the generation of high titer enzyme production strains
Background
• We all live in the fungal digestive tract
• Fungi secrete a significant amount of enzymes which
efficiently decompose plant biomass into its
component building blocks
• Secretion of fungal biomass degrading enzymes is
highly regulated and controlled
Approach
• Understanding how fungi regulate plant biomass
decomposition will allow rational redesign of fungi to
secrete higher titers of enzyme
Protein hyperproduction in fungi by design
Baker (2018) Appl Microbiol Biotechnol, https://doi.org/10.1007/s00253-018-9265-1

2. 0
10
20
30
40
50
60
70
80
0 24 48 72 96 120 144 168
Sugarconcentration(g/L)
Time (h)
Glucose
Xylose
Outcomes and Impacts
• [C2C1Im][OAc] pretreatment of switchgrass has been successfully
scaled up to 40 kg
• Enzymatic hydrolysis of the pretreated switchgrass results in efficient
sugar conversions - 96% glucan and 98% xylan conversion
• The mass flow of the overall process was established and the major
scale-up challenges were identified and discussed
• Efforts are needed in the future to improve transitional processes such
as material transfer, biomass recovery from aqueous IL stream, IL
recycling, and improvement of enzymes tolerance to ILs
Background
• The scalability of ionic liquid (IL) based processes of biomass conversion
and the impact of these solvents on subsequent downstream processes
is still nascent
• Lab-scale process designs may not be straightforward to transfer to a
larger scale, in particular, the pretreatment and downstream conversion
and upgrading processes may require redesign of suitable reactors and
other equipment
Approach
• This study focuses on scaling up the 1-ethyl-3-methylimidazolium
acetate ([C2C1Im][OAc]) pretreatment to a 40 kg batch in a 210 liter
customized pressure reactor followed by enzymatic saccharification at a
50 L stirred tank that was conducted at the ABPDU
Process overview of IL pretreatment and
enzymatic saccharification
Scale-up of biomass conversion using 1-ethyl-3-
methylimidazolium acetate as the solvent
Liang et al. (2018) Green Energy & Environment, DOI: 10.1016/j.gee.2018.07.002
Sugar release during enzymatic saccharification of
[C2C1Im][OAc] pretreated switchgrass

3. Drop-in biofuels offer strategies for meeting
California's 2030 climate mandate
Background
• In 2015, California established a mandate that requires on-road
greenhouse gas (GHG) emissions to be reduced by 40% below
1990 levels by 2030
• Drop-in biofuels are a class of fuels that can be produced from
biomass and blended with either crude oil or finished fuels without
requiring equipment retrofits
Approach
• This paper aims to assess the impacts and resource needs of a
rapid deployment of drop-in biofuel production to meet California’s
2030 GHG reduction target for on-road transportation
• We provide a bottom-up, spatially explicit cost analysis to evaluate
whether California can meet its 2030 GHG reduction target with
drop-in biofuels alone
• This approach is unique in that it considers pathways to mass
commercialization of drop-in biofuels given the current topology of
infrastructure systems
Outcomes and Impacts
• Results indicate that California can meet, and even exceed, its
2030 GHG emissions target for on-road vehicles with drop-in
biofuels alone, but this requires use of biomass resources located
outside the state
• This scale of production would require 58 million metric tons of
biomass feedstock, or 20% of total available biomass residues in
the United States
• Following this pathway would increase national biofuel production
by 30% relative to 2015 production levels
Taptich et al. (2018) Env Res Letters, https://doi.org/10.1088/1748-9326/aadcb2
The scale of drop-in fuel commercialization required to reduce
on-road GHG emissions by 20%–80% from 1990 levels in
California by 2030. Data accounts for the 8.86% GHG reduction
achieved under CARB’s business-as-usual fleet forecast.
(1 MMG = 1 million gallons or 3.79 million liters)

4. TBL10 is required for O-acetylation of pectic
rhamnogalacturonan-l in Arabidopsis thaliana
Background
• Acetylated pectins are abundant in the primary cell wall of plants and
growing evidence suggests they have important roles in plant cell
growth and interaction with the environment
• Despite their importance, genes required for O-acetylation of pectins
have not previously been identified
Approach
• In this study, we showed that TRICHOME BIREFRINGENCE LIKE 10
(AT3G06080) is involved in O-acetylation of pectic RGI
• Two homozygous knock-out mutants of Arabidopsis, tbl10-1 and tbl10-
2, were isolated and shown to exhibit reduced levels of wall-bound
acetyl esters, equivalent of ~50% of the wild-type level in pectin-
enriched fractions derived from leaves
• Further fractionation revealed that the degree of acetylation of the
pectin rhamnogalacturonan-I (RG-I) was reduced in the tbl10 mutant
compared to the wild type, whereas the pectin homogalacturonan
(HG) was unaffected
Outcomes and Impacts
• The degrees of acetylation in hemicelluloses (i.e. xyloglucan, xylan
and mannan) were indistinguishable between the tbl10 mutants and
the wild type
• The mutant plants contained normal trichomes in leaves and exhibited
a similar level of susceptibility to the phytopathogenic microorganisms
Pseudomonas syringae pv. tomato DC3000 and Botrytis cinerea; while
they displayed enhanced tolerance to drought
• These results indicate that TBL10 is an RG-I specific
acetyltransferase, and suggest that O-acetylated RG-I plays a role in
abiotic stress responses in Arabidopsis
Stranne et al. (2018) Plant J, DOI: 10.1111/tpj.14067
Pectin was fractionated into rhamnogalacturonan I (a) and
homogalacturonan (b). The TBL10 acyltransferase is
responsible for acetylation of RGI but not for acetylation of
homogalacturonan.
HSQC 2D-NMR shows that acetylation of xylan and mannan is
unchanged in the tbl10 mutant. Xyloglucan also showed no
change in acetylation in the mutant (not shown). Hence, RGI is
the only polymer that is changed in acetylation in the tbl10
mutants.
Arabidopsis has 46 members
of the TBL family. Clade IV
and V are known to contain
enzymes involved in
hemicellulose acetylation.
TBL10 is in clade I, which is
shown here to be involved in
pectin acetylation.

5. Cell walls have a new family
Background
• The work by Takenaka et al., published in Nature Plants 4(9), 669–
676 (2018), lays the foundation for CAZy-family GT106 through the
characterization of a rhamnosyltransferase involved in building the
backbone of RG-I, the major domain of pectin
• RG-I influences the biomechanical properties of cell walls, thus it
plays a role in the pliable walls of stomata and is critical for the
ability of tension in wood to cause stem bending
Approach
• Takenaka et al. made use of mutants knocked out in transcription
factors that control mucilage production and looked for putative
glycosyltransferase (GT) genes with reduced expression compared
to wild type
• They identified At5g15740, which did not belong to a known CAZy
GT family but had some similarity to GT65 O-fucosyltransferases in
other organisms
• Takenaka et al. then used a biochemical assay they had developed
for RG-I rhamnosyltransferase (RhaT) activity, which itself is an
accomplishment since none of the required substrates are
commercially available, and showed that At5g15740 encodes an
RhaT
Outcomes and Impacts
• They named the new enzyme RRT1 and it was assigned to the new
family GT106. The Arabidopsis genome encodes 34 members of
GT106, four of which are in the same sub-clade as RRT1
• Identification of RRT is a breakthrough in cell wall research and we
predict an accelerated identification of other enzymes involved in
producing RG-I and other cell wall polysaccharides
• The breakthrough by Takenaka et al. is described in the News and
Views article by Scheller and Ulvskov
Ulvskov and Scheller (2018) Nat Plants, 4(9):635-636, DOI: 10.1038/s41477-018-0222-x
Rhamnogalacturonan I
(RGI) is a major
component of plant cell
walls. Unbranched RGI
is abundant in seed
mucilage, as here in
okra. RGI affects the
biomechanical
properties of cell walls.
The biosynthesis of the
complex polymer is
largely unknown.
The newly discovered RRT enzymes belong to a protein family
not previously known to constitute GTs. Members of this new
family GT106 are present in plants but not in any other
organisms. Arabidopsis has 34 members of GT106, many of
which are likely involved in biosynthesis of other polysaccharides
besides RGI.

6. Commodity chemicals from engineered
modular Type I polyketide synthases
Background
• Reduced polyketides are a subclass of natural products that
have a variety of applications, such as commodity chemicals
and advanced biofuels
• The backbones of these chemically diverse compounds are
made by modular polyketide synthases (PKSs) from simple
metabolites such as malonylcoenzyme A (CoA) and
methylmalonyl-CoA
• The number of extension modules in a given PKS determines
the size of the resultant polyketide produced
Approach
• In this review, we describe experimental protocols and
considerations for modular PKS engineering and two case
studies to produce commodity chemicals by engineered PKSs
• Both structural and fundamental biochemical understanding of
these enzymes are required for efficient production of novel
compounds by engineered PKSs
Outcomes and Impacts
• Controlling noncovalent intermodular interactions gives the
greatest opportunity for generating large numbers of novel
compounds, which would be a major achievement in future
PKS engineering
• PKSs that can produce commodity chemicals have relatively
simple structures and usually require one or two modules, and
require less debugging of the systems
• Production levels need to be increased to 10–100g/L to
compete with the relatively inexpensive means of production
of these chemicals from petroleum
Yuzawa et al. (2018) Methods in Enzymology, Vol. 608, pp. 393-415, DOI: 10.1016/bs.mie.2018.04.027
Precise AT domain swapping of modular polyketide synthases (PKSs).
(A) DEBS module 6 (M6)+TE was used as a model PKS system to
optimize domain boundaries for AT domain swapping. (B) KR-
inactivated LipPks1+TE produces ethyl ketones from various acyl starter
CoAs and methylmalonyl-CoA (left). KR-inactivated, AT-swapped
LipPks1+TE produces methyl ketones from various starter acyl CoAs
and malonyl-CoA.

7. Elucidating transfer hydrogenation mechanisms
in non-catalytic lignin depolymerization
Background
• Lignin undergoes catalytic depolymerization in the presence of
a variety of transfer hydrogenation agents
• The mechanisms for non-catalytic depolymerization of lignin
via transfer hydrogenation are not well understood
Approach
• This study investigates the equilibrium system of formic acid,
methyl formate and carbon monoxide as agents for the
depolymerization of lignin found in sugarcane bagasse
• A time-course study of lignin depolymerization was then
performed to observe the evolution of product quantities and
distributions
Outcomes and Impacts
• In the methyl formate/water system, 73 wt% bio-oil was
produced which contained a significant amount of low
molecular weight alkylphenols, with less than 1 wt% char
produced
• It was found that using either formic acid or methyl formate for
non-catalytic transfer hydrogenation of lignin can produce high
amounts of bio-oil, and can be described as a two-stage
mechanism
• The key parameters for efficient transfer hydrogenation of the
lignin to maximize bio-oil yield appear to involve controlling the
reactions between lignin and formic acid, methyl formate or
carbon monoxide under aqueous conditions
Bouxin et al. (2018) Green Chemistry, DOI: 10.1039/c7gc03239k
Reaction pathways of formic acid and methyl formate equilibrium and
decomposition (a) equilibrium between formic acid and methyl formate;
(b, e) decarboxylation or (c, d) decarbonylation, (f) formaldehyde
decomposition pathways].
Plot of % yields of the lignin depolymerization products (g per 100 g of
the initial lignin) as a function of the experimental conditions; values are
the average of duplicate experiments.