The genome sequence of Propionibacterium acidipropionici provides insights into its biotechnological and industrial potential

Abstract

Background: Synthetic biology allows the development of new biochemical pathways for the production of chemicals from renewable sources. One major challenge is the identification of suitable microorganisms to hold these pathways with sufficient robustness and high yield. In this work we analyzed the genome of the propionic acid producer Actinobacteria Propionibacterium acidipropionici (ATCC 4875).

Results: The assembled P. acidipropionici genome has 3,656,170 base pairs (bp) with 68.8% G + C content and a low-copy plasmid of 6,868 bp. We identified 3,336 protein coding genes, approximately 1000 more than P. freudenreichii and P. acnes, with an increase in the number of genes putatively involved in maintenance of genome integrity, as well as the presence of an invertase and genes putatively involved in carbon catabolite repression. In addition, we made an experimental confirmation of the ability of P. acidipropionici to fix CO2, but no phosphoenolpyruvate carboxylase coding gene was found in the genome. Instead, we identified the pyruvate carboxylase gene and confirmed the presence of the corresponding enzyme in proteome analysis as a potential candidate for this activity. Similarly, the phosphate acetyltransferase and acetate kinase genes, which are considered responsible for acetate formation, were not present in the genome. In P. acidipropionici, a similar function seems to be performed by an ADP forming acetate-CoA ligase gene and its corresponding enzyme was confirmed in the proteome analysis.

Conclusions: Our data shows that P. acidipropionici has several of the desired features that are required to become a platform for the production of chemical commodities: multiple pathways for efficient feedstock utilization, ability to fix CO2, robustness, and efficient production of propionic acid, a potential precursor for valuable 3-carbon compounds.

Figure 1

Overview of well-established fermentation processes. Comparison between fermentation processes for production of ethanol, propionic acid and lactic acid. Y, theoretical maximum yield from glucose R, reduction factor.

Figure 2

Comparative protein clustering and GO annotation. A. Venn diagram showing the number of common and unique protein clusters for three Propionibacteria. The values in parentheses represent the number of protein clusters. The values in square brackets represent the number of single proteins (proteins not in clusters). The number of proteins clustered in each group are also indicated, not enclosed and color-coded by organism: values in green represent P. acidipropionici proteins, values in blue represent P. freudenreichii proteins and values in red represent P. acnes proteins. B. Pie chart depicting the result of GO annotation of proteins unique to P. acidipropionici. C. Multi-level pie chart detailing GO annotation of proteins unique to P. acidipropionici. Inner circle represent level 3 terms. Outer circle represent lower level (more specific) terms.

Figure 3

Syntenic dot plot. Dot plot alignment between the chromosome of P. acidipropionici (vertical) against the chromosomes of M. phosphovorus, P. freudenreichii and P. acnes (horizontal) at protein level. The dnaA gene is located at the beginning of all four sequences.

Figure 4

Overview of P. acidipropionici metabolism. Reactions of fermentative pathway are in green while reactions of respiratory pathway are in blue. Reactions described in literature but absent in the genome are in gray dotted lines. Putative reactions for CO₂ fixation are in orange. The total number of transporters in each major category are shown.

Figure 5

Preliminary results of P. acidipropionici experimental batch fermentation with sugarcane juice. Biomass A600 (blue diamond); sucrose (orange circle); glucose (red square); fructose (gray line); propionic acid (blue asterisk); acetic acid (purple cross); succinic acid (green line).

Figure 6

P. acidipropionici culture under CO₂atmosphere.A, Culture under ¹³CO2 (labeled) and B, Culture with CO₂ (unlabeled).