Adaptive laboratory evolution of Pseudomonas putida KT2440 improves p-coumaric and ferulic acid catabolism and tolerance

• Published in: Metabolic engineering communications Vol. 11; p. e00143
• Main Authors: Mohamed, Elsayed T., Werner, Allison Z., Salvachúa, Davinia, Singer, Christine A., Szostkiewicz, Kiki, Rafael Jiménez-Díaz, Manuel, Eng, Thomas, Radi, Mohammad S., Simmons, Blake A., Mukhopadhyay, Aindrila, Herrgård, Markus J., Singer, Steven W., Beckham, Gregg T., Feist, Adam M.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.12.2020; Elsevier
• Subjects: Adaptive laboratory evolution; BASIC BIOLOGICAL SCIENCES; biofuels; catabolism; epistasis; evolution; ferulic acid; Full Length; genes; growth retardation; Hydroxycinnamic acids; lignin; Microbial lignin conversion; p-coumaric acid; Pseudomonas putida; Pseudomonas putida KT2440; toxicity; transcription (genetics); transporters; TALE; Adaptive laboratory evolution; Microbial lignin conversion; Pseudomonas putida KT2440; FA; Hydroxycinnamic acids; pCA; pCA, p-coumaric acid; TALE, tolerance adaptive laboratory evolution; FA, ferulic acid
• ISSN: 2214-0301; 2214-0301
• DOI: 10.1016/j.mec.2020.e00143

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. [Display omitted] •Pseudomonas putida was evolved in increasing hydroxycinnamic acid concentrations.•The lag phase in high p-coumaric acid concentration was reduced.•The growth rate and tolerance to high ferulic acid concentration was increased.•PP_3350 and ttgB contribute to the observed phenotypes.