Engineering topics

Kato, Ryo

Publications and source records attributed to Kato, Ryo.

5 records

DOE OSTI2023

Multiplexed fitness profiling by RB-TnSeq elucidates pathways for lignin-related aromatic catabolism in Sphingobium sp. SYK-6

Bioconversion of lignin-related aromatic compounds relies on robust catabolic pathways in microbes. Sphingobium sp. SYK-6 (SYK-6) is a well-characterized aromatic catabolic organism that has served as a model for microbial lignin conversion, and its utility as a biocatalyst could potentially be further improved by genome-wide metabolic analyses. To this end, we generate a randomly barcoded transposon insertion mutant (RB-TnSeq) library to study gene function in SYK-6. The library is enriched under dozens of enrichment conditions to quantify gene fitness. Several known aromatic catabolic pathways are confirmed, and RB-TnSeq affords additional detail on the genome-wide effects of each enrichment condition. Selected genes are further examined in SYK-6 or Pseudomonas putida KT2440, leading to the identification of new gene functions. The findings from this study further elucidate the metabolism of SYK-6, while also providing targets for future metabolic engineering in this organism or other hosts for the biological valorization of lignin.

09 BIOMASS FUELS↗

DOE OSTI2023

Stereoinversion via Alcohol Dehydrogenases Enables Complete Catabolism of β-1-Type Lignin-Derived Aromatic Isomers

Sphingobium sp. strain SYK-6 is an efficient aromatic catabolic bacterium that can consume all four stereoisomers of 1,2-diguaiacylpropane-1,3-diol (DGPD), which is a ring-opened β-1-type dimer. Recently, LdpA-mediated catabolism of erythro-DGPD was reported in SYK-6, but the catabolic pathway for threo-DGPD was as yet unknown. Here, in this study, we elucidated the catabolism of threo-DGPD, which proceeds through conversion to erythro-DGPD. When threo-DGPD was incubated with SYK-6, the Cα hydroxy groups of threo-DGPD (DGPD I and II) were initially oxidized to produce the Cα carbonyl form (DGPD-keto I and II). This initial oxidation step is catalyzed by Cα-dehydrogenases, which belong to the short-chain dehydrogenase/reductase (SDR) family and are involved in the catabolism of β-O-4-type dimers. Analysis of seven candidate genes revealed that NAD + -dependent LigD and LigL are mainly involved in the conversion of DGPD I and II, respectively. Next, we found that DGPD-keto I and II were reduced to erythro-DGPD (DGPD III and IV) in the presence of NADPH. Genes involved in this reduction were sought from Cα-dehydrogenase and ldpA-neighboring SDR genes. The gene products of SLG_12690 (ldpC) and SLG_12640 (ldpB) catalyzed the NADPH-dependent conversion of DGPD-keto I to DGPD III and DGPD-keto II to DGPD IV, respectively. Mutational analysis further indicated that ldpC and ldpB are predominantly involved in the reduction of DGPD-keto. Together, these results demonstrate that SYK-6 harbors a comprehensive catabolic enzyme system to utilize all four β-1-type stereoisomers through successive oxidation and reduction reactions of the Cα hydroxy group of threo-DGPD with a net stereoinversion using multiple dehydrogenases.

09 BIOMASS FUELS↗

DOE OSTI2023

Biochemical and structural characterization of a sphingomonad diarylpropane lyase for cofactorless deformylation

Lignin valorization is being intensely pursued via tandem catalytic depolymerization and biological funneling to produce single products. In many lignin depolymerization processes, aromatic dimers and oligomers linked by carbon–carbon bonds remain intact, necessitating the development of enzymes capable of cleaving these compounds to monomers. Recently, the catabolism of erythro -1,2-diguaiacylpropane-1,3-diol ( erythro -DGPD), a ring-opened lignin-derived β-1 dimer, was reported in Novosphingobium aromaticivorans . The first enzyme in this pathway, LdpA (formerly LsdE), is a member of the nuclear transport factor 2 (NTF-2)-like structural superfamily that converts erythro -DGPD to lignostilbene through a heretofore unknown mechanism. In this study, we performed biochemical, structural, and mechanistic characterization of the N. aromaticivorans LdpA and another homolog identified in Sphingobium sp. SYK-6, for which activity was confirmed in vivo. For both enzymes, we first demonstrated that formaldehyde is the C 1 reaction product, and we further demonstrated that both enantiomers of erythro -DGPD were transformed simultaneously, suggesting that LdpA, while diastereomerically specific, lacks enantioselectivity. We also show that LdpA is subject to a severe competitive product inhibition by lignostilbene. Three-dimensional structures of LdpA were determined using X-ray crystallography, including substrate-bound complexes, revealing several residues that were shown to be catalytically essential. We used density functional theory to validate a proposed mechanism that proceeds via dehydroxylation and formation of a quinone methide intermediate that serves as an electron sink for the ensuing deformylation. Overall, this study expands the range of chemistry catalyzed by the NTF-2-like protein family to a prevalent lignin dimer through a cofactorless deformylation reaction.

09 BIOMASS FUELS↗

DOE OSTI2020

Ion-Conducting Thermoresponsive Films Based on Polymer-Grafted Cellulose Nanocrystals

Mechanically robust, thermo-responsive, ion-conducting nanocomposite films are prepared from poly(2-phenylethyl methacrylate) grafted cellulose nanocrystals (MxG-CNC-g-PPMA). One-component nanocomposite films of the polymer grafted nanoparticle (PGN) MxG-CNC-g-PPMA are imbibed with 30 wt% imidazolium-based ionic liquid, to produce flexible ion-conducting films. These films with 1-hexyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (MxG-CNC-g-PPMA/[H]) not only displays remarkable improvements in toughness (>25 times) and tensile strength (>70 times) relative to the corresponding nanocomposites consisting of the ionic liquid imbibed in the two component CNC/PPMA nanocomposite, but also shows higher ionic conductivity than the corresponding neat PPMA with the same wt.% of ionic liquid. Notably, the one-component film containing 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (MxG-CNC-g-PPMA/[E]) exhibits temperature responsive ionic conduction. The ionic conductivity decreases at around 60°C as a consequence of the lower critical solution temperature (LCST) phase transition of the grafted polymer in the ionic liquid, which leads to phase separation. Moreover, holding the MxG-CNC-g-PPMA/[E] film at room temperature for 24 hours returns the film to its original homogenous state. These materials exhibit properties relevant to thermal cutoff safety devices (e.g., thermal fuse) where a reduction in conductivity above a critical temperature is needed.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Ion-Conducting Dynamic Solid Polymer Electrolyte Adhesives

Cross-linked polymer electrolytes containing structurally dynamic disulfide bonds have been synthesized to investigate their combined ion transport and adhesive properties. Dynamic network polymers of varying cross-link densities are synthesized via thiol oxidation of a bisthiol monomer, 2,2'-(ethylenedioxy)diethanethiol, and tetrathiol cross-linker, pentaerythritol tetrakis(3-mercaptopropionate). At optimal loading of lithium bis(trifluoromethane-sulfonyl-imide) (LiTFSI) salt, the ionic conductivities (σ) at 90 °C are about 1 × 10–4 and 1 × 10–5 S/cm at the lowest and highest cross-linking, respectively. Notably, in comparison to the equivalent nondynamic network, the dynamic network shows a positive deviation in σ above 90 °C, which suggests the enhancement of ion transport occurs from the difference in structural relaxation on account of the dissociation of disulfide bonds. Lap shear adhesion and conductivity tests on ITO-coated glass substrates reveal the dynamic network exhibits a higher adhesive shear strength of 0.2 MPa (vs 0.03 MPa for the nondynamic network) and higher σ after the application of external stimulus (UV light or heat). The adhesive strength and σ are stable over multiple debonding/rebonding cycles and, thus, demonstrating the utility of these structurally dynamic networks as solid polymer electrolyte adhesives.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗