Comparative genomics and transcriptomics analysis‐guided metabolic engineering of Propionibacterium acidipropionici for improved propionic acid production

Abstract

Acid stress induced by the accumulation of organic acids during the fermentation of propionibacteria is a severe limitation in the microbial production of propionic acid (PA). To enhance the acid resistance of strains, the tolerance mechanisms of cells must first be understood. In this study, comparative genomic and transcriptomic analyses were conducted on wild-type and acid-tolerant Propionibacterium acidipropionici to reveal the microbial response of cells to acid stress during fermentation. Combined with the results of previous proteomic and metabolomic studies, several potential acid-resistance mechanisms of P. acidipropionici were analyzed. Energy metabolism and transporter activity of cells were regulated to maintain pH homeostasis by balancing transmembrane transport of protons and ions; redundant protons were eliminated by enhancing the metabolism of certain amino acids for a relatively stable intracellular microenvironment; and protective mechanism of macromolecules were also induced to repair damage to proteins and DNA by acids. Transcriptomic data indicated that the synthesis of acetate and lactate were undesirable in the acid-resistant mutant, the expression of which was 2.21-fold downregulated. In addition, metabolomic data suggested that the accumulation of lactic acid and acetic acid reduced the carbon flow to PA and led to a decrease in pH. On this basis, we propose a metabolic engineering strategy to regulate the synthesis of lactic acid and acetic acid that will reduce by-products significantly and increase the PA yield by 12.2% to 10.31 ± 0.84 g/g DCW. Results of this study provide valuable guidance to understand the response of bacteria to acid stress and to construct microbial cell factories to produce organic acids by combining systems biology technologies with synthetic biology tools.

Engineering Escherichia coli for propionic acid production through the Wood–Werkman cycle

“…Relatively few genetic modification studies have been performed in propionibacteria (Gonzalez‐Garcia, McCubbin, Navone et al ; Guan et al, ; Liu et al, ) due to the limited availability of genetic modification tools. The alternative, random mutagenesis in propionibacteria , has successfully delivered economically viable strains (Luna‐Flores, Stowers, Cox, Nielsen, & Marcellin, ); however, quite often little learning results from random approaches (Jang et al, ).…”

“…The ΔldhA strain did not show a significant increase in propionate production but increased 1-propanol threefold. Interestingly, the ΔldhA knockout in P. acidipropionici reported by Guan et al (2018) showed a detrimental effect on both biomass production and propionate yield associated with an imbalance in the NADH/NAD+ ratio. 1-Propanol production, thus, seems to alleviate this imbalance.…”

Integrating metabolic and evolutionary engineering for enhanced propionic acid production under cross stress: a multi-omics perspective

“…acidipropionici-ΔpoxB-Δldh [17]. A further 37.1% increase of PA titer (28.1 ± 0.96 g•L − 1 vs. 38.7 ± 1.14 g•L − 1 ) and 37.8% increase of PA productivity (0.216 ± 0.006 g…”

“…Liu et al improved the PA titer of P. jensenii by 34.7% by overexpressing phosphoenolpyruvate carboxylase (ppc) and deleting lactate dehydrogenase (ldh) [11]. Guan et al obtained a 12.2% increase of PA by constructing a P. acidipropionici strain with simultaneous deletions of ldh1, ldh2 and pyruvate oxidase (poxB) [17]. However, combining metabolic engineering with laboratory evolution to improve the synthesis of PA has not been published, and may be a successful strategy.…”

Transcriptomics and Proteomics Analyses of the Responses of Propionibacterium acidipropionici to Metabolic and Evolutionary Manipulation

“… Liu et al (2016) improved the PA titer of P. jensenii by 34.7% by overexpressing phosphoenolpyruvate carboxylase ( ppc ) and deleting lactate dehydrogenase ( ldh ). Guan et al (2018) obtained a 12.2% increase of PA by constructing a P. acidipropionici strain with simultaneous deletions of ldh 1, ldh 2 and pox B. Evolutionary engineering, also defined as adaptive laboratory evolution, is a popular approach to develop high-performing strains for industrial application ( Mans et al, 2018 ).…”