Engineering topics
Agee, Alec
Publications and source records attributed to Agee, Alec.
Electrochemical Characterization of Biomolecular Electron Transfer at Conductive Polymer Interfaces
Bio-electrochemical systems (BESs) are promising for renewable energy generation but remain hindered by inefficient electron transfer at electrode surfaces. As the toolbox of bio-anode materials increases, rigorous electrochemical characterization of emerging materials is needed. Here, we holistically characterize the electrochemical interaction of flavin mononucleotide (FMN), an electron shuttle in biological systems and a cofactor for oxidoreductase enzymes, with the bio-inspired mixed conducting polymer poly{3-[6'-(N-methylimidazolium)hexyl]thiophene} (P3HT-Im + ). The behavior of this polymer is compared to the equivalent polymer without the histidine-like imidazolium. We find improved conductivity and charge storage in imidazolium-containing polymers beyond what is explained by differences in the electroactive area. The P3HT-Im + further shows internal charge storage but with negligible faradaic contribution, indicating that charge storage capacity may translate to improved biocatalysis non-intuitive ways. Finally, one-electron transfer is observed between FMN and glassy carbon, while a bio-similar two-electron transfer is observed for the P3HT-Im + . To our knowledge, this is the first example of a concerted two-electron transfer between FMN and an electrode interface, which we attribute to the bio-inspired, histidine-like imidazolium functional groups in the polymer. These studies demonstrate the importance of bio-relevant materials characterization when such materials are deployed in BESs.
Adaptive laboratory evolution of methylotrophic Escherichia coli enables synthesis of all amino acids from methanol-derived carbon
Recent attempts to create synthetic Escherichia coli methylotrophs identified that de novo biosynthesis of amino acids, in the presence of methanol, presents significant challenges in achieving autonomous methylotrophic growth. Previously engineered methanol-dependent strains required co-utilization of stoichiometric amounts of co-substrates and methanol. As such, these strains could not be evolved to grow on methanol alone. In this work, we have explored an alternative approach to enable biosynthesis of all amino acids from methanol-derived carbon in minimal media without stoichiometric coupling. First, we identified that biosynthesis of threonine was limiting the growth of our methylotrophic E. coli. To address this, we performed adaptive laboratory evolution to generate a strain that grew efficiently in minimal medium with methanol and threonine. Methanol assimilation and growth of the evolved strain were analyzed and, interestingly, we found that the evolved strain synthesized all amino acids, including threonine, from methanol-derived carbon. Here, the evolved strain was then further engineered through overexpression of an optimized threonine biosynthetic pathway. We show that the resulting methylotrophic E. coli strain has a methanol-dependent growth phenotype with homoserine as co-substrate. In contrast to previous methanol-dependent strains, co-utilization of homoserine is not stoichiometrically linked to methanol assimilation. As such, future engineering of this strain and successive adaptive evolution could enable autonomous growth on methanol as the sole carbon source.
Regulatory interventions improve the biosynthesis of limiting amino acids from methanol carbon to improve synthetic methylotrophy in Escherichia coli
Synthetic methylotrophy aims to engineer methane and methanol utilization pathways in platform hosts like Escherichia coli for industrial bioprocessing of natural gas and biogas. While recent attempts to engineer synthetic methylotrophs have proved successful, autonomous methylotrophy, that is, the ability to utilize methane or methanol as sole carbon and energy substrates, has not yet been realized. Here, we address an important limitation of autonomous methylotrophy in E. coli: the inability of the organism to synthesize several amino acids when grown on methanol. We targeted global and local amino acid regulatory networks. Those include removal of amino acid allosteric feedback inhibition (argA H15Y , ilvA L447F , hisG E271K , leuA G462D , proB D107N , thrA S345F, trpE S40F ), knockouts of transcriptional repressors (ihfA, metJ); and overexpression of amino acid biosynthetic operons (hisGDCBHAFI, leuABCD, thrABC, trpEDCBA) and transcriptional regulators (crp, purR). Compared to the parent methylotrophic E. coli strain that was unable to synthesize these amino acids from methanol carbon, these strategies resulted in improved biosynthesis of limiting proteinogenic amino acids (histidine, leucine, lysine, methionine, phenylalanine, threonine, tyrosine) from methanol carbon. In several cases, improved amino acid biosynthesis from methanol carbon led to improvements in methylotrophic growth in methanol minimal medium supplemented with a small amount of yeast extract. Here, this study addresses a key limitation currently preventing autonomous methylotrophy in E. coli and possibly other synthetic methylotrophs and provides insight as to how this limitation can be alleviated via global and local regulatory modifications.
Engineering Escherichia coli for methanol-dependent growth on glucose for metabolite production
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Triggering the stringent response enhances synthetic methanol utilization in Escherichia coli
Synthetic methylotrophy aims to engineer methane and methanol utilization pathways in platform hosts like Escherichia coli for industrial bioprocessing of natural gas and biogas. While recent attempts to engineer synthetic methylotrophs have proved successful, autonomous methylotrophy, i.e. the ability to utilize methane or methanol as sole carbon and energy substrates, has not yet been realized. Here in this paper, we address an important limitation of autonomous methylotrophy in E. coli: the inability of the organism to synthesize several amino acids when grown on methanol. By activating the stringent/stress response via ppGpp overproduction, or DksA and RpoS overexpression, we demonstrate improved biosynthesis of proteinogenic amino acids via endogenous upregulation of amino acid synthesis pathway genes. Thus, we were able to achieve biosynthesis of several limiting amino acids from methanol-derived carbon, in contrast to the control methylotrophic E. coli strain. This study addresses a key limitation currently preventing autonomous methylotrophy in E. coli and possibly other synthetic methylotrophs and provides insight as to how this limitation can be alleviated via stringent/stress response activation.