Linking genotype and phenotype in an economically viable propionic acid biosynthesis process

Abstract

BackgroundPropionic acid (PA) is used as a food preservative and increasingly, as a precursor for the synthesis of monomers. PA is produced mainly through hydrocarboxylation of ethylene, also known as the ‘oxo-process’; however, Propionibacterium species are promising biological PA producers natively producing PA as their main fermentation product. However, for fermentation to be competitive, a PA yield of at least 0.6 g/g is required.ResultsA new strain able to reach the required yield was obtained using genome shuffling. To gain insight into the changes leading to the improved phenotype, the genome of the new strain was sequenced, and metabolomics and transcriptomics data were obtained. In combination, the data revealed three key mutations: (i) a mutation in the promoter region of a sugar transporter which enables an increase in the uptake rate of sucrose; (ii) a mutation in a polar amino acid transporter which improves consumption of amino acids and acid tolerance; and (iii) a mutation in a gene annotated as a cytochrome C biogenesis gene, which is likely responsible for the coupling of the Wood–Werkman cycle to ATP production were responsible for the phenotype. The bioprocess was further enhanced with a feeding strategy that achieved 70 g/L of product. The proposed bioprocess is expected to outperform the economics of the current ‘oxo-process’ by 2020.ConclusionsIn this study, using genome shuffling, we obtained a strain capable of producing PA exceeding the commercial needs. The multiomics comparison between the novel strain and the wild type revealed overexpression of amino acid pathways, changes in sucrose transporters and an increased activity in the methylglyoxal and the glucuronate interconversion pathways. The analysis also suggests that a mutation in the cytochrome C biogenesis gene, coupled with ATP production through the Wood–Werkman cycle, may be responsible for the increased PA production.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1222-9) contains supplementary material, which is available to authorized users.

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

“…Several Propionibacterium spp. have been widely explored for propionate production (Gonzalez-Garcia, McCubbin, Navone et al, 2017;Rodriguez et al, 2014), and P. acidipropionici has been identified as the fittest candidate (Gonzalez-Garcia, McCubbin, Navone et al, 2017;Luna-Flores et al, 2018). P. acidipropionici exhibits the highest reported propionate yield on glucose (0.6 g/g), compared with other microorganisms.…”

“…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, ). In contrast, Escherichia coli is easy to engineer and has proven a flexible host for the production of commodity chemicals and fuels (Lee & Kim, ).…”

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

“…At the same time, a 68.8% of decrease of LA yield (3.06 ± 0.82 vs. 1.04 ± 0.17 g•L − 1 ) was obtained. However, there was a 3% increase of AA titer (5.24 ± 0.83 vs. 5.63 ± 0.62 g•L − 1 ), which may be related to the deletion of ldh, which increased carbon flow from pyruvate into the synthesis of LA [21]. The PA production of the mutant II only increased by 3.2%, while the titers of AA and LA were both decreased by more than 70%, which was consistent with the variation tendency of the PA, LA and AA titers of P.…”

“…The ldh and poxB genes, which are main contributors of the by-products acetate and lactate [21], were deleted. Additionally, the methylmalonyl-CoA carboxyltransferase (mmc) gene from P. acidipropionici¸ which controls the carbon flow into the propionate-producing Wood-Werkman cycle [22] was overexpressed.…”

A Pan-Genome Guided Metabolic Network Reconstruction of Five Propionibacterium Species Reveals Extensive Metabolic Diversity

“…Therefore, metabolic reconstructions of five Propionibacterium species were generated through a novel workflow that leverages information from the pan-genomic matrix and its functional pivot (as detailed in the methods section). This included two P. acidipropionici strains, which are the parents of high propionate producing genome-shuffled mutants [ 60 , 65 ] with industrial relevance and to give a sense of intra-species variation. Individual reconstructions were combined to create a genus-level reconstruction.…”