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1. Enabling microbial syringol conversion through structure-guided protein engineering

   https://doi.org/10.1073/pnas.1820001116  

   Machovina, Melodie M. ; Mallinson, Sam J. ; Knott, Brandon C. ; Meyers, Alexander W. ; Garcia-Borràs, Marc ; Bu, Lintao ; Gado, Japheth E. ; Oliver, April ; Schmidt, Graham P. ; Hinchen, Daniel J. ; et al ( January 2019 , Proceedings of the National Academy of Sciences)

   Microbial conversion of aromatic compounds is an emerging and promising strategy for valorization of the plant biopolymer lignin. A critical and often rate-limiting reaction in aromatic catabolism is O -aryl-demethylation of the abundant aromatic methoxy groups in lignin to form diols, which enables subsequent oxidative aromatic ring-opening. Recently, a cytochrome P450 system, GcoAB, was discovered to demethylate guaiacol (2-methoxyphenol), which can be produced from coniferyl alcohol-derived lignin, to form catechol. However, native GcoAB has minimal ability to demethylate syringol (2,6-dimethoxyphenol), the analogous compound that can be produced from sinapyl alcohol-derived lignin. Despite the abundance of sinapyl alcohol-based lignin in plants, no pathway for syringol catabolism has been reported to date. Here we used structure-guided protein engineering to enable microbial syringol utilization with GcoAB. Specifically, a phenylalanine residue (GcoA-F169) interferes with the binding of syringol in the active site, and on mutation to smaller amino acids, efficient syringol O -demethylation is achieved. Crystallography indicates that syringol adopts a productive binding pose in the variant, which molecular dynamics simulations trace to the elimination of steric clash between the highly flexible side chain of GcoA-F169 and the additional methoxy group of syringol. Finally, we demonstrate in vivo syringol turnover in Pseudomonas putida KT2440more »with the GcoA-F169A variant. Taken together, our findings highlight the significant potential and plasticity of cytochrome P450 aromatic O -demethylases in the biological conversion of lignin-derived aromatic compounds.« less
2. Synthetic Biology Tool Development Advances Predictable Gene Expression in the Metabolically Versatile Soil Bacterium Rhodopseudomonas palustris

   https://doi.org/10.3389/fbioe.2022.800734  

   Immethun, Cheryl M. ; Kathol, Mark ; Changa, Taity ; Saha, Rajib ( March 2022 , Frontiers in Bioengineering and Biotechnology)

   Harnessing the unique biochemical capabilities of non-model microorganisms would expand the array of biomanufacturing substrates, process conditions, and products. There are non-model microorganisms that fix nitrogen and carbon dioxide, derive energy from light, catabolize methane and lignin-derived aromatics, are tolerant to physiochemical stresses and harsh environmental conditions, store lipids in large quantities, and produce hydrogen. Model microorganisms often only break down simple sugars and require low stress conditions, but they have been engineered for the sustainable manufacture of numerous products, such as fragrances, pharmaceuticals, cosmetics, surfactants, and specialty chemicals, often by using tools from synthetic biology. Transferring complex pathways has proven to be exceedingly difficult, as the cofactors, cellular conditions, and energy sources necessary for this pathway to function may not be present in the host organism. Utilization of unique biochemical capabilities could also be achieved by engineering the host; although, synthetic biology tools developed for model microbes often do not perform as designed in other microorganisms. The metabolically versatile Rhodopseudomonas palustris CGA009, a purple non-sulfur bacterium, catabolizes aromatic compounds derived from lignin in both aerobic and anaerobic conditions and can use light, inorganic, and organic compounds for its source of energy. R. palustris utilizes three nitrogenase isozymes to fulfillmore »its nitrogen requirements while also generating hydrogen. Furthermore, the bacterium produces two forms of RuBisCo in response to carbon dioxide/bicarbonate availability. While this potential chassis harbors many beneficial traits, stable heterologous gene expression has been problematic due to its intrinsic resistance to many antibiotics and the lack of synthetic biology parts investigated in this microbe. To address these problems, we have characterized gene expression and plasmid maintenance for different selection markers, started a synthetic biology toolbox specifically for the photosynthetic R. palustris , including origins of replication, fluorescent reporters, terminators, and 5′ untranslated regions, and employed the microbe’s endogenous plasmid for exogenous protein production. This work provides essential synthetic biology tools for engineering R. palustris ’ many unique biochemical processes and has helped define the principles for expressing heterologous genes in this promising microbe through a methodology that could be applied to other non-model microorganisms.« less
3. Identifying thermal phase transitions of lignin–solvent mixtures using electrochemical impedance spectroscopy

   https://doi.org/10.1039/C5GC02342D  

   Klett, Adam S. ; Gamble, Jordan A. ; Thies, Mark C. ; Roberts, Mark E. ( January 2016 , Green Chemistry)

   Lignin is unique among renewable biopolymers in having significant aromatic character, making it potentially attractive for a wide range of uses from coatings to carbon fibers. Recent research has shown that hot acetic acid (AcOH)–water mixtures can be used to recover “ultraclean” lignins of controlled molecular weight from Kraft lignins. A key feature of this discovery is the existence of a region of liquid–liquid equilibrium (LLE), with one phase being rich in the purified lignin and the other rich in solvent. Although visual methods can be used to determine the temperature at which solid lignin melts in the presence of AcOH–water mixtures to form LLE, the phase transition can be seen only at lower AcOH concentrations due to solvent opacity. Thus, an electrochemical impedance spectroscopy (EIS) technique was developed for measuring the phase-transition temperature of a softwood Kraft lignin in AcOH–water mixtures. In electrochemical cells, the resistance to double-layer charging ( i.e. , polarization resistance R p ) is related to the concentration and mobility of free ions in the electrolyte, both of which are affected by the phases present. When the lignin–AcOH–water mixture was heated through the phase transition, R P was found to be a strong function ofmore »temperature, with the maximum in R P corresponding to the transition temperature obtained from visual observation. As the system is heated, acetate ions associate with the solid lignin, forming a liquefied, lignin-rich phase. This association increases the overall impedance of the system, as mobile acetate ions are stripped from the solvent phase and thus are no longer available to adsorb on the polarizing electrode surfaces. The maximum in R P occurs once the new lignin-rich phase has completely formed, and no further association of the lignin polymer with AcOH is possible. Except at sub-ambient temperatures, the phase-transition temperature was a strong function of solvent composition, increasing linearly from 18 °C at 70/30 AcOH/water to 97 °C at 10/90 wt% AcOH/water.« less
4. Predicting lignin depolymerization yields from quantifiable properties using fractionated biorefinery lignins

   https://doi.org/10.1039/C7GC02023F  

   Phongpreecha, Thanaphong ; Hool, Nicholas C. ; Stoklosa, Ryan J. ; Klett, Adam S. ; Foster, Cliff E. ; Bhalla, Aditya ; Holmes, Daniel ; Thies, Mark C. ; Hodge, David B. ( January 2017 , Green Chem.)

   Lignin depolymerization to aromatic monomers with high yields and selectivity is essential for the economic feasibility of many lignin-valorization strategies within integrated biorefining processes. Importantly, the quality and properties of the lignin source play an essential role in impacting the conversion chemistry, yet this relationship between lignin properties and lignin susceptibility to depolymerization is not well established. In this study, we quantitatively demonstrate how the detrimental effect of a pretreatment process on the properties of lignins, particularly β-O-4 content, limit high yields of aromatic monomers using three lignin depolymerization approaches: thioacidolysis, hydrogenolysis, and oxidation. Through pH-based fractionation of alkali-solubilized lignin from hybrid poplar, this study demonstrates that the properties of lignin, namely β-O-4 linkages, phenolic hydroxyl groups, molecular weight, and S/G ratios exhibit strong correlations with each other even after pretreatment. Furthermore, the differences in these properties lead to discernible trends in aromatic monomer yields using the three depolymerization techniques. Based on the interdependency of alkali lignin properties and its susceptibility to depolymerization, a model for the prediction of monomer yields was developed and validated for depolymerization by quantitative thioacidolysis. These results highlight the importance of the lignin properties for their suitability for an ether-cleaving depolymerization process, since the theoreticalmore »monomer yields grows as a second order function of the β-O-4 content. Therefore, this research encourages and provides a reference tool for future studies to identify new methods for lignin-first biomass pretreatment and lignin valorization that emphasize preservation of lignin qualities, apart from focusing on optimization of reaction conditions and catalyst selection.« less
5. Iterative screening methodology enables isolation of strains with improved properties for a FACS-based screen and increased L-DOPA production

   https://doi.org/10.1038/s41598-019-41759-0  

   Savitskaya, Judy ; Protzko, Ryan J. ; Li, Francesca-Zhoufan ; Arkin, Adam P. ; Dueber, John E. ( April 2019 , Scientific Reports)

   Optimizing microbial hosts for the large-scale production of valuable metabolites often requires multiple mutations and modifications to the host’s genome. We describe a three-round screen for increased L-DOPA production inS. cerevisiaeusing FACS enrichment of an enzyme-coupled biosensor for L-DOPA. Multiple rounds of screening were enabled by a single build of a barcodedin vitrotransposon-mediated disruption library. New background strains for screening were built for each iteration using results from previous iterations. The samein vitrotransposon-mediated disruption library was integrated by homologous recombination into new background strains in each round of screening. Compared with creating new transposon insertions in each round, this method takes less time and saves the cost of additional sequencing to characterize transposon insertion sites. In the first two rounds of screening, we identified deletions that improved biosensor compartmentalization and, consequently, improved our ability to screen for L-DOPA production. In a final round, we discovered that deletion of heme oxygenase (HMX1) increases total heme concentration and increases L-DOPA production, using dopamine measurement as a proxy. We further demonstrated that deleting HMX1 may represent a general strategy for P450 function improvement by improving activity of a second P450 enzyme, BM3, which performs a distinct reaction.