skip to main content

Title: Enabling microbial syringol conversion through structure-guided protein engineering
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 KT2440 more » 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
; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
Award ID(s):
Publication Date:
Journal Name:
Proceedings of the National Academy of Sciences
Page Range or eLocation-ID:
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract

    Microbial aromatic catabolism offers a promising approach to convert lignin, a vast source of renewable carbon, into useful products. Aryl-O-demethylation is an essential biochemical reaction to ultimately catabolize coniferyl and sinapyl lignin-derived aromatic compounds, and is often a key bottleneck for both native and engineered bioconversion pathways. Here, we report the comprehensive characterization of a promiscuous P450 aryl-O-demethylase, consisting of a cytochrome P450 protein from the family CYP255A (GcoA) and a three-domain reductase (GcoB) that together represent a new two-component P450 class. Though originally described as converting guaiacol to catechol, we show that this system efficiently demethylates both guaiacol and an unexpectedly wide variety of lignin-relevant monomers. Structural, biochemical, and computational studies of this novel two-component system elucidate the mechanism of its broad substrate specificity, presenting it as a new tool for a critical step in biological lignin conversion.

  2. Pink-pigmented facultative methylotrophs have long been studied for their ability to grow on reduced single-carbon (C 1 ) compounds. The C 1 groups that support methylotrophic growth may come from a variety of sources. Here, we describe a group of Methylobacterium strains that can engage in methoxydotrophy: they can metabolize the methoxy groups from several aromatic compounds that are commonly the product of lignin depolymerization. Furthermore, these organisms can utilize the full aromatic ring as a growth substrate, a phenotype that has rarely been described in Methylobacterium . We demonstrated growth on p -hydroxybenzoate, protocatechuate, vanillate, and ferulate in laboratory culture conditions. We also used comparative genomics to explore the evolutionary history of this trait, finding that the capacity for aromatic catabolism is likely ancestral to two clades of Methylobacterium , but has also been acquired horizontally by closely related organisms. In addition, we surveyed the published metagenome data to find that the most abundant group of aromatic-degrading Methylobacterium in the environment is likely the group related to Methylobacterium nodulans , and they are especially common in soil and root environments. The demethoxylation of lignin-derived aromatic monomers in aerobic environments releases formaldehyde, a metabolite that is a potent cellular toxinmore »but that is also a growth substrate for methylotrophs. We found that, whereas some known lignin-degrading organisms excrete formaldehyde as a byproduct during growth on vanillate, Methylobacterium do not. This observation is especially relevant to our understanding of the ecology and the bioengineering of lignin degradation.« less
  3. Lignin-derivable bisphenols are potential alternatives to bisphenol A (BPA), a suspected endocrine disruptor; however, a greater understanding of structure–activity relationships (SARs) associated with such lignin-derivable building blocks is necessary to move replacement efforts forward. This study focuses on the prediction of bisphenol estrogenic activity (EA) to inform the design of potentially safer BPA alternatives. To achieve this goal, the binding affinities to estrogen receptor alpha (ERα) of lignin-derivable bisphenols were calculated via molecular docking simulations and correlated to median effective concentration (EC 50 ) values using an empirical correlation curve created from known EC 50 values and binding affinities of commercial (bis)phenols. Based on the correlation curve, lignin-derivable bisphenols with binding affinities weaker than ∼−6.0 kcal mol −1 were expected to exhibit no EA, and further analysis suggested that having two methoxy groups on an aromatic ring of the bio-derivable bisphenol was largely responsible for the reduction in binding to ERα. Such dimethoxy aromatics are readily sourced from the depolymerization of hardwood biomass. Additionally, bulkier substituents on the bridging carbon of lignin-bisphenols, like diethyl or dimethoxy, were shown to weaken binding to ERα. And, as the bio-derivable aromatics maintain major structural similarities to BPA, the resultant polymeric materials should possessmore »comparable/equivalent thermal ( e.g. , glass transition temperatures, thermal decomposition temperatures) and mechanical ( e.g. , tensile strength, modulus) properties to those of polymers derived from BPA. Hence, the SARs established in this work can facilitate the development of sustainable polymers that maintain the performance of existing BPA-based materials while simultaneously reducing estrogenic potential.« less
  4. Biomass is abundant, inexpensive and renewable, therefore, it is highly expected to play a significant role in our future energy and chemical landscapes. The US DOE has identified furanic compounds (furfural and 5-(hydroxymethyl)furfural (HMF)) as the top platform building-block chemicals that can be readily derived from biomass sources [1]. Electrocatalytic conversion of these furanic compounds is an emerging route for the sustainable production of valuable chemicals [2, 3]. In my presentation, I will first present our recent mechanistic study of electrocatlytic hydrogenation (ECH) of furfural through a combination of voltammetry, preparative electrolysis, thiol-electrode modifications, and kinetic isotope studies [4]. It is demonstrated that two distinct mechanisms are operable on metallic Cu electrodes in acidic electrolytes: (i) electrocatalytic hydrogenation (ECH) and (ii) direct electroreduction. The contributions of each mechanism to the observed product distribution are clarified by evaluating the requirement for direct chemical interactions with the electrode surface and the role of adsorbed hydrogen. Further analysis reveals that hydrogenation and hydrogenolysis products are generated by parallel ECH pathways. Understanding the underlying mechanisms enables the manipulation of furfural reduction by rationally tuning the electrode potential, electrolyte pH, and furfural concentration to promote selective formation of important bio-based polymer precursors and fuels Wemore »further studied the mechanisms on the Pb electrode, based on the potential regulated ECH and ER products. Isotopic incorporation studies and electrokinetics have confirmed ECH process to alcohol and alkyl product followed different pathways: alcohol was generated from Langmuir Hinshelwood step through surface-bound furfural and hydrogen, which is sensitive to surface structures. In contrast, alkyl product was formed through an Eley–Rideal step via surface-bound furfural and the inner-sphere protons. By modifying the electrode/electrolyte interface, we have elucidated H2O and H3O+ matters in forming alcohol and alkyl products, respectively. Dynamic oscillation studies and electron paramagnetic resonance (EPR) finally confirmed that the alcohol and dimer products shared the same intermediate. The dimer was formed through the intermediate desorption from the surface to form radicals and the self-coupling of two radicals at the bulk electrolyte. Next, I will present electrocatalytic conversion of HMF to two biobased monomers in an H-type electrochemical cell [5]. HMF reduction (hydrogenation) to 2,5-bis(hydroxymethyl)furan (BHMF) was achieved under mild electrolyte conditions and ambient temperature using a Ag/C cathode. Meanwhile, HMF oxidation to 2,5-furandicarboxylic acid (FDCA) with ~100% efficiency was facilitated under the same conditions by a homogeneous nitroxyl radical redox mediator. We recently developed a three-electrode flow cell with an oxide-derived Ag (OD-Ag) cathode and catbon felt anode for paring elecatalytic oxidation and reduction of HMF [6]. The flow cell has a remarkably low cell voltage: from ~7.5 V to ~2.0 V by transferring the electrolysis from the H-type cell to the flow cell. This represents a more than fourfold increase in the energy efficiency at the 10 mA operation. A combined faradaic efficiency of 163% was obtained to BHMF and FDCA. Alternatively, the anodic hydrogen oxidation reaction on platinum further reduced the cell voltage to only ~0.85 V at 10 mA operation. These paired processes have shown potential for integrating renewable electricity and carbon for distributed chemical manufacturing in the future.« less
  5. Stabb, Eric V. (Ed.)
    ABSTRACT Dimethylsulfoniopropionate (DMSP), a key component of the global geochemical sulfur cycle, is a secondary metabolite produced in large quantities by marine phytoplankton and utilized as an osmoprotectant, thermoprotectant, and antioxidant. Marine bacteria can use two pathways to degrade and catabolize DMSP, a demethylation pathway and a cleavage pathway that produces the climate-active gas dimethylsulfide (DMS). Whether marine bacteria can also accumulate DMSP as an osmoprotectant to maintain the turgor pressure of the cell in response to changes in external osmolarity has received little attention. The marine halophile Vibrio parahaemolyticus contains at least six osmolyte transporters, namely four betaine carnitine choline transport (BCCT) carriers (BccT1 to BccT4) and two ATP-binding cassette (ABC) family ProU transporters. In this study, we showed that DMSP is used as an osmoprotectant by V. parahaemolyticus and by several other Vibrio species, including Vibrio cholerae and Vibrio vulnificus . Using a V. parahaemolyticus proU double mutant, we demonstrated that these ABC transporters are not required for DMSP uptake. However, a bccT null mutant lacking all four BCCTs had a growth defect compared to the wild type (WT) in high-salinity medium supplemented with DMSP. Using mutants possessing only one functional BCCT in growth pattern assays, we identifiedmore »two BCCT family transporters, BccT1 and BccT2, that are carriers of DMSP. The only V. parahaemolyticus BccT homolog that V. cholerae and V. vulnificus possess is BccT3, and functional complementation in Escherichia coli MKH13 showed that V. cholerae VcBccT3 could transport DMSP. In V. vulnificus strains, we identified and characterized an additional BCCT family transporter, which we named BccT5, that was also a carrier for DMSP. IMPORTANCE DMSP is present in the marine environment, produced in large quantities by marine phytoplankton as an osmoprotectant, and is an important component of the global geochemical sulfur cycle. This algal osmolyte has not been previously investigated for its role in marine heterotrophic bacterial osmotic stress response. Vibrionaceae species are marine species, many of which are halophiles exemplified by V. parahaemolyticus , a species that possesses at least six transporters for the uptake of osmolytes. Here, we demonstrated that V. parahaemolyticus and other Vibrio species can accumulate DMSP as an osmoprotectant and show that several BCCT family transporters uptake DMSP. These studies suggest that DMSP is a significant bacterial osmoprotectant that may be important for understanding the fate of DMSP in the environment. DMSP is produced and present in coral mucus, and Vibrio species form part of the microbial communities associated with corals. The function of DMSP in these interactions is unclear, but it could be an important driver for these associations, allowing Vibrio proliferation. This work suggests that DMSP likely has a more important role in heterotrophic bacteria ecology than previously appreciated.« less