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Identification and characterization of substrate- and product-selective nylon hydrolases
Enzymes can rapidly and selectively hydrolyze diverse natural and anthropogenic polymers, but few have been shown to hydrolyze synthetic polyamides. Here, in this work, we synthesized and characterized a panel of 95 enzymes from the N-terminal nucleophile hydrolase superfamily with 30%–50% pairwise amino acid identity. We found that nearly 40% of the enzymes had substantial nylon hydrolase activity, but there was no relationship between phylogeny and activity, nor any evidence of prior evolutionary selection for nylon hydrolysis. Several newly identified hydrolases showed substrate selectivity, generating up to 20-fold higher product titers with nylon-6,6 versus nylon-6. However, the yield was still less than 1%, necessitating further optimization before potential applications. Finally, we determined the crystal structure and oligomerization state of a nylon-6,6-selective hydrolase to elucidate structural factors that could affect activity and selectivity. These new enzymes provide insights into nylon hydrolase evolution and opportunities for analysis and engineering of improved hydrolases.
Revisiting the activity of two poly(vinyl chloride)- and polyethylene-degrading enzymes
Biocatalytic degradation of non-hydrolyzable plastics is a rapidly growing field of research, driven by the global accumulation of waste. Enzymes capable of cleaving the carbon-carbon bonds in synthetic polymers are highly sought-after as they may provide tools for environmentally friendly plastic recycling. Despite some reports of oxidative enzymes acting on non-hydrolyzable plastics, including polyethylene or poly(vinyl chloride), the notion that these materials are susceptible to efficient enzymatic degradation remains controversial, partly driven by a general lack of studies independently reproducing previous observations. Here, we attempt to replicate two recent studies reporting that deconstruction of polyethylene and poly(vinyl chloride) can be achieved using an insect hexamerin from Galleria mellonella (so-called “Ceres”) or a bacterial catalase-peroxidase from Klebsiella sp., respectively. Reproducing previously described experiments, we do not observe any activity on plastics using multiple reaction conditions and multiple substrate types. Digging deeper into the discrepancies between the previous data and our observations, we show how and why the original experimental results may have been misinterpreted.
Virus-Like Particles (VLPs) as a Platform for Hierarchical Compartmentalization
Hierarchically self-assembled structures are common in biology, but it is often challenging to design and fabricate synthetic analogs. The archetypal cell is defined by hierarchically organized multicompartmentalized structures with boundaries that delineate the interior from exterior environments and is an inspiration for complex functional materials. Here, we have demonstrated an approach to the design and construction of a nested protein cage system that can additionally incorporate the packing of other functional macromolecules and exhibit some of the features of a minimal synthetic cell-like material. We have demonstrated a strategy for controlled co-packaging of subcompartments, ferritin (Fn) cages, together with active cellobiose-hydrolyzing β-glycosidase enzyme macromolecules, CelB, inside the sequestered volume of the bacteriophage P22 capsid. Using controlled in vitro assembly, we were able to modulate the stoichiometry of Fn cages and CelB encapsulated inside the P22 to control the degree of compartmentalization. The co-encapsulated enzyme CelB showed catalytic activity even when packaged at high total macromolecular concentrations comparable to an intracellular environment. Here, this approach could be used as a model to create synthetic protein-based protocells that can confine smaller functionalized proto-organelles and additional macromolecules to support a range of biochemical reactions.
Attraction and Longevity of 2- and 3-Component Food Cone Lures for the Caribbean Fruit Fly, Anastrepha suspensa (Diptera: Tephritidae)
Abstract The Caribbean fruit fly, Anastrepha suspensa (Loew) (Diptera: Tephritidae), is a quarantine pest of Citrus spp. and a production pest of guava and other specialty fruits in Florida. Effective monitoring lures and traps are needed for early pest detection and timely initiation of control measures. As part of a continued effort to identify attractive synthetic lures for the Caribbean fruit fly, we conducted field tests in Homestead, Florida to compare the efficacy and longevity of commercial 2- and 3-component cone lures (2C [ammonium acetate and putrescine], 3C [ammonium acetate, putrescine, and trimethylamine]), the current standards used by regulatory agencies, versus the traditional liquid protein bait consisting of hydrolyzed torula yeast and borax as a positive control. Additional lures were also field-aged and periodically brought into the laboratory to quantify residual chemical contents. Traps baited with the torula yeast-borax mixture captured the highest mean number of A. suspensa, and traps baited with the commercial 2C lures captured more flies than the 3C lures. Traps baited with torula yeast-borax also captured the highest number of nontarget Diptera. Captures with all three treatments were significantly biased toward females. Attractiveness of the 2C lure began to drop after 6–8 wk, and the 3C lure after 5–6 wk. Overall, these data suggest that the 2C cone lure is more attractive to A. suspensa than the 3C cone lure under field conditions in south Florida, and that the 2C lures are attractive for up to 8 wk.
Acetylcholinesterase: Structure, dynamics, and interactions with organophosphorus compounds
Acetylcholinesterase (AChE) is an enzyme that hydrolyzes the neurotransmitter acetylcholine (ACh), removing it from the synaptic cleft after the transmission of an electrical signal, making it an essential component of chemical neurotransmission. AChE is a serine hydrolase, containing a catalytic triad of Ser/His/Glu. AChE is a prime target for pharmaceuticals treating a variety of neurological disorders. It is also the target of synthetic organophosphorus (OP) compounds that have been used as pesticides and chemical warfare agents. OP compounds contain a potent leaving group, such as fluorine, and act by forming a covalent adduct with the catalytic serine of the AChE active site. A wealth of structural information is available for AChE, including over 300 structures, including a subset of structures in complex with drugs as well as OP compounds. This review will highlight the interactions between OP compounds and AChE from a structural and computational perspective, with a discussion of access to the active site, as well as side reactions that lead to dealkylation of the OP-catalytic serine adduct, a process known as aging. We conclude that while the majority of the conformational changes needed to accommodate the OP compounds are localized to the acyl loop in the crystal structures, molecular dynamics simulations highlight the potential for a far more dynamic enzyme.
Bio-Based Polyisoprene Can Mitigate Climate Change and Deforestation in Expanding Rubber Production
Biomass is a promising renewable feedstock to produce polyisoprene for the rubber industry. Through metabolic engineering, sugars derived from pretreated and hydrolyzed cellulose and hemicellulose can be directly fermented to isoprene to produce rubber. Here we investigate the life cycle environmental impact of isoprene fermentation to produce bio-polyisoprene from agricultural residues (of Zea mays L.). Results show that the greenhouse gas (GHG) intensity of bio-polyisoprene (−4.59 kg CO2e kg−1) is significantly lower than that of natural rubber (Hevea brasiliensis) and synthetic rubber (−0.79 and 2.41 kg CO2e kg−1, respectively), while supporting a circular biogenic carbon economy. We found the land use intensity of bio-polyisoprene to be 0.25 ha metric ton−1, which is 84% lower than that from rubber tree plantations. We compare the direct fermentation to isoprene results with indirect fermentation to isoprene through the intermediate, methyl butyl ether, where dehydration to isoprene is required. The direct fermentation of isoprene reduces reaction steps and unit operations, an expected outcome when employing process intensification, but our results show additional energy conservation and reduced contribution to climate change. Among the ReCiPe life cycle environmental impact metrics evaluated, air emission related impacts are high for bio-polyisoprene compared to those for natural and synthetic rubber. Those impacts can be reduced with air emission controls during production. All other metrics showed an improvement for bio-polyisoprene compared to natural and synthetic rubber.
Synthesis of hydroxycinnamoyl shikimates and their role in monolignol biosynthesis
Hydroxycinnamoyl shikimates were reported in 2005 to be intermediates in monolignol biosynthesis. 3-Hydroxylation of p-coumarate, originally thought to occur via coumarate 3-hydroxylase (C 3 H) from p-coumaric acid or its CoA thioester, was revealed to be via the action of coumaroyl shikimate 3'-hydroxylase (C 3 'H) utilizing p-coumaroyl shikimate as the substrate, itself derived from p-coumaroyl-CoA via hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyltransferase (HCT). The same HCT was conjectured to convert the product, caffeoyl shikimate, to caffeoyl-CoA to continue on the pathway starting with its 3-O-methylation. At least in some plants, however, a more recently discovered caffeoyl shikimate esterase (CSE) enzyme hydrolyzes caffeoyl shikimate to caffeic acid from which it must again produce its CoA thioester to continue on the monolignol biosynthetic pathway. HCT and CSE are therefore monolignol biosynthetic pathway enzymes that have provided new opportunities to misregulate lignification. To facilitate studies into the action and substrate specificity of C 3 H/C 3 'H, HCT, and CSE enzymes, as well as for metabolite authentication and for enzyme characterization, including kinetics, a source of authentic substrates and products was required. A synthetic scheme starting from commercially available shikimic acid and the four key hydroxycinnamic acids (p-coumaric, caffeic, ferulic, and sinapic acid) has been developed to provide this set of hydroxycinnamoyl shikimates for researchers.
pH adjustment increases biofuel production from inhibitory switchgrass hydrolysates
Biofuels derived from renewable and sustainable lignocellulosic biomass, such as switchgrass, offer a promising means to limit greenhouse gas emissions. However, switchgrass grown under drought conditions contains high levels of chemical compounds that inhibit microbial conversion to biofuels. Fermentation of drought switchgrass hydrolysates by engineered Saccharomyces cerevisiae and Zymomonas mobilis results in lower ethanol production than does fermentation of hydrolyzed switchgrass from a typical rainfall year. Here, it is demonstrated that this inhibitory effect can be alleviated by altering the pH of drought switchgrass hydrolysates produced by two different pretreatment methods: Ammonia Fiber Expansion (AFEX) and Soaking in Aqueous Ammonia (SAA). Fermentation rates and biofuel production by Saccharomyces cerevisiae and Zymomonas mobilis were higher at pH 5.8 than at pH 5.0 from all feedstock years and following both pretreatment methods. SAA pretreatment of drought switchgrass furthermore enabled increased fermentation rates and biofuel titers compared to AFEX pretreatment. A synthetic mimic of switchgrass hydrolysate was developed and identified relief from pH-dependent inhibition by lignocellulose-derived inhibitors as the cause of increased biofuel production above a pH of 5.0. These results demonstrate that SAA pretreatment and pH adjustment can significantly improve fermentation and biofuel production from inhibitory feedstocks by industrial microorganisms.
Structural insights into hydrolytic defluorination of difluoroacetate by microbial fluoroacetate dehalogenases
Fluorine forms the strongest single bond to carbon with the highest bond dissociation energy among natural products. However, fluoroacetate dehalogenases (FADs) have been shown to hydrolyze this bond in fluoroacetate under mild reaction conditions. Furthermore, two recent studies demonstrated that the FAD RPA1163 fromRhodopseudomonas palustriscan also accept bulkier substrates. In this study, we explored the substrate promiscuity of microbial FADs and their ability to defluorinate polyfluorinated organic acids. Enzymatic screening of eight purified dehalogenases with reported fluoroacetate defluorination activity revealed significant hydrolytic activity against difluoroacetate in three proteins. Product analysis using liquid chromatography‐mass spectrometry identified glyoxylic acid as the final product of enzymatic DFA defluorination. The crystal structures of DAR3835 fromDechloromonas aromaticaand NOS0089 fromNostocsp. were determined in the apo‐state along with the DAR3835 H274N glycolyl intermediate. Structure‐based site‐directed mutagenesis of DAR3835 demonstrated a key role for the catalytic triad and other active site residues in the defluorination of both fluoroacetate and difluoroacetate. Computational analysis of the dimer structures of DAR3835, NOS0089, and RPA1163 indicated the presence of one substrate access tunnel in each protomer. Moreover, protein‐ligand docking simulations suggested similar catalytic mechanisms for the defluorination of both fluoroacetate and difluoroacetate, with difluoroacetate being defluorinated via two consecutive defluorination reactions producing glyoxylate as the final product. Thus, our findings provide molecular insights into substrate promiscuity and catalytic mechanism of FADs, which are promising biocatalysts for applications in synthetic chemistry and bioremediation of fluorochemicals.