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

Abstract

BackgroundSynthetic 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).ResultsThe 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.ConclusionsOur 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.

Microbial Propionic Acid Production

“…Targeted genetic engineering of propionibacteria remains challenging for several reasons: propionibacteria have a high GC content, which complicates genetic manipulation and contributes to poor gene annotations [58]; relatively few closed genomes are available [17,18]; a small number of cloning vectors are available [22,59,60]; the ability of strains to readily develop spontaneous antibiotic resistance; thick cell walls; and the presence of strong restriction modification systems which contribute to the low transformation efficiency of propionibacteria [61]. A number of recent studies have reported the modification of P. freudenreichii subsp.…”

Improved Production of Propionic Acid in Propionibacterium jensenii via Combinational Overexpression of Glycerol Dehydrogenase and Malate Dehydrogenase from Klebsiella pneumoniae

“…jensenii produces PA through the dicarboxylic acid pathway, with LA and AA as by-products (16). Several genomes of Propionibacterium have now been sequenced (3,25,(27)(28)(29)(30). However, genetic engineering of these bacteria has not been thoroughly investigated because of the difficulty in transforming Gram-positive bacteria, the various restriction-modification systems of these bacteria, the high GC content in their genomes, and the lack of cloning tools.…”

“…Pyruvate is converted to oxaloacetate and then to malate by malate dehydrogenase (MDH). Fumarate hydratase (FUM) catalyzes the conversion of malate to fumarate, which is converted to PA via a series of intermediates, namely, succinate, succinyl coenzyme A (CoA), methylmalonyl CoA, and propionyl CoA (25). This step is an NADH-consuming pathway.…”

Biochemical and Kinetic Characterization of the Recombinant ADP-Forming Acetyl Coenzyme A Synthetase from the Amitochondriate Protozoan Entamoeba histolytica

“…ACD from the phototrophic Chloroflexus aurantiacus has recently been purified, and the recombinant enzyme was characterized (20). The syntrophs Pelotomaculum thermopropionicum (21) and Syntrophus aciditrophicus (22) and the propionic acid-producing Propionibacterium acidipropionici (23) all lack genes for the PTA-ACK pathway and instead have acd genes. ACD has been identified via proteome analysis of P. acidipropionici cells grown under acetateproducing conditions, but the enzyme has not been purified or characterized (23).…”

“…The syntrophs Pelotomaculum thermopropionicum (21) and Syntrophus aciditrophicus (22) and the propionic acid-producing Propionibacterium acidipropionici (23) all lack genes for the PTA-ACK pathway and instead have acd genes. ACD has been identified via proteome analysis of P. acidipropionici cells grown under acetateproducing conditions, but the enzyme has not been purified or characterized (23). Likewise, the acetate-producing archaea listed above that have ACD lack genes encoding the PTA-ACK pathway.…”