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Self-driving labs (SDLs) combine fully automated experiments with artificial intelligence (AI) that decides the next set of experiments. Taken to their ultimate expression, SDLs could usher a new paradigm of scientific research, where the world is probed, interpreted, and explained by machines for human benefit. While there are functioning SDLs in the fields of chemistry and materials science, we contend that synthetic biology provides a unique opportunity since the genome provides a single target for affecting the incredibly wide repertoire of biological cell behavior. However, the level of investment required for the creation of biological SDLs is only warranted if directed toward solving difficult and enabling biological questions. Here, we discuss challenges and opportunities in creating SDLs for synthetic biology.

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 C1 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.

Lignin is an abundant renewable resource that is a promising substrate for upgrading to fuels and chemicals. However, lignin-rich biorefinery streams are often physically and chemically complex, and could benefit substantially from fractionation. In this work, a membrane process was developed to fractionate low molecular weight (LMW) lignin-related compounds (molecular weight (MW) < 1000 Da) from a ligninrich, alkaline pretreated liquor (APL) prepared from pretreatment of corn stover with NaOH. The developed membrane process exhibits up to 98.5% rejection of high molecular weight (HMW) (MW > 1000 Da) species and generates a permeate stream with >80% recovery of LMW lignin-related compounds including aromatic species such as p-coumarate and ferulate, resulting in a 6-fold enrichment in LMW organic compounds relative to the crude APL. Experimental batch data were used to develop a detailed process model of an industrial scale, continuous membrane filtration system. The open-source model has several independent process inputs, such as the concentration of target compounds, feed flow rate, volume recovery, and membrane selectivity. This process model was used to show that the system has a low estimated energy demand (0.75 kW h m-3 permeate) and was used to identify primary cost drivers, including the membrane material cost. These results offer a key step towards a scalable, low energy, and costeffective lignin MW fractionation method with implications for both improving product isolation from lignin and improving carbon yields across the biorefinery.

Pseudomonas putida KT2440 is a promising bacterial chassis for the conversion of lignin-derived aromatic compound mixtures to biofuels and bioproducts. Despite the inherent robustness of this strain, further improvements to aromatic catabolism and toxicity tolerance of P. putida will be required to achieve industrial relevance. Here, tolerance adaptive laboratory evolution (TALE) was employed with increasing concentrations of the hydroxycinnamic acids p-coumaric acid (pCA) and ferulic acid (FA) individually and in combination (pCA ​+ ​FA). The TALE experiments led to evolved P. putida strains with increased tolerance to the targeted acids as compared to wild type. Specifically, a 37 ​h decrease in lag phase in 20 ​g/L pCA and a 2.4-fold increase in growth rate in 30 ​g/L FA was observed. Whole genome sequencing of intermediate and endpoint evolved P. putida populations revealed several expected and non-intuitive genetic targets underlying these aromatic catabolic and toxicity tolerance enhancements. PP_3350 and ttgB were among the most frequently mutated genes, and the beneficial contributions of these mutations were verified via gene knockouts. Deletion of PP_3350, encoding a hypothetical protein, recapitulated improved toxicity tolerance to high concentrations of pCA, but not an improved growth rate in high concentrations of FA. Deletion of ttgB, part of the TtgABC efflux pump, severely inhibited growth in pCA ​+ ​FA TALE-derived strains but did not affect growth in pCA ​+ ​FA in a wild type background, suggesting epistatic interactions. Genes involved in flagellar movement and transcriptional regulation were often mutated in the TALE experiments on multiple substrates, reinforcing ideas of a minimal and deregulated cell as optimal for domesticated growth. Overall, this work demonstrates increased tolerance towards and growth rate at the expense of hydroxycinnamic acids and presents new targets for improving P. putida for microbial lignin valorization.

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 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.

cis,cis-Muconic acid (MA) is a bio-based chemical that can be converted to direct replacement chemicals or performance-advantaged bioproducts. We recently engineered the bacterium Pseudomonas putida KT2440 for the co-utilization of glucose and xylose to produce MA. This study evaluates the effect of additional genetic modifications, media composition, and bioprocess strategy on MA titer, productivity, and yield in bioreactor cultivations. We achieve a MA titer of 47.2 g L−1, a productivity of 0.49 g L−1 h−1, and a yield of 0.50 C-mol C-mol−1 from glucose and xylose supplemented with 5% (v/v) corn steep liquor with a P. putida strain harboring the deletion of gacS. Additionally, we demonstrate efficient MA production from corn stover-derived sugars and scalability to 150 L bioreactors. Techno-economic analysis and life cycle assessment predict that adipic acid, derived from catalytic hydrogenation of MA, can achieve a selling price as low as $2.60 per kg, approaching cost parity and reducing greenhouse gas emissions by up to 80% relative to fossil carbon-based adipic acid. [ABSTRACT FROM AUTHOR]

The separation and purification of bio-based chemicals from conversion processes often contribute substantially to bioprocessing costs, and for many biochemicals produced through fermentation, solventbased liquid--liquid extraction (LLE) is a common separations strategy for in situ product recovery (ISPR). Many in situ LLE-based separations for biochemicals are often challenged by emulsion formation between the immiscible aqueous and organic phases. Typically, membrane contactors have been used to overcome emulsion formation, with the aqueous and organic phases coming into contact in the membrane contactor pores, but these unit operations require a large membrane area to compensate for their limited effective interfacial area. In this study, we show that a hydrophobic polytetrafluoroethylene (PTFE) membrane-based emulsion separator (MBES) enables continuous LLE for the recovery of an exemplary fermentation product, butyric acid, with substantially improved throughput relative to a membrane contactor. With a membrane permeate flux of 290 L m-2 h-1, the overall butyric acid flux of the single-stage MBES system was calculated to be 1450 g m-2 h-1, which is substantially higher than the 9 g m-2 h-1 achievable with a membrane contactor. At an equivalent butyric acid throughput, process modeling estimates that MBES-assisted LLE can enable a 55% and 91% reduction in process costs (the sum of CAPEX and OPEX) and greenhouse gas emissions, respectively, compared to a membrane contactor due to a ~160-fold decrease in the required membrane area. Although membrane fouling from cellular debris led to reduced membrane flux and phase separation efficiency, common fouling mitigation strategies including the incorporation of ultrafiltration and periodic membrane backwashing effectively recovered the membrane performance. Overall, MBES systems can potentially enable continuous LLE processes in bioprocessing separations, including where emulsion formation is a challenge. [ABSTRACT FROM AUTHOR]

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.