Luna-Flores, C. H., Nielsen, L.K., and Marcellin, E.*


St Lucia QLD 4072
Australian Institute for Bioengineering and Nanotechnology - The University of Queensland
Brisbane, Queensland, Australia


Propionic acid (PA) is a valuable three-carbon compound traditionally obtained from petrochemical extraction used extensively as a preservative. Biological production of PA has gained interest in recent years. Propionibacterium spp. are promising organisms for the biological production of PA at industrial scale. Propionibacterium spp. produce PA along with other organic acids such as acetate, succinate, and lactate. Current biological conversion of PA using Propionibacterium fermentation suffers from slow growth and low yields which translate into expensive purification costs1. Such limitations can be surpassed using molecular biology tools to eliminate byproducts. However, the best PA producing stains (i.e. Propionibacterium acidipropionici) cannot be rationally engineered, thus limiting rational approaches to less desirable strains. To overcome limitations, non-rational engineering approaches such as random mutagenesis and genome shuffling have been used to optimize production strains for biological PA conversion. In this study, I used genome shuffling to generate a new strain capable of producing PA at an economically favourable yield2. The new strain, named Propionibacterium acidipropionici WGS7, was able to grow at a growth rate of 0.26 h-1, achieved more than 0.60 g/g yield and produced 70 g/L using a fed-batch strategy. To understand the genomic changes leading to the high PA yield, I used genomics, metabolomics, transcriptomics, and proteomics to investigate for the first time mechanisms of genome shuffling and the relevant mutations leading to the improved phenotype. Proteins, metabolites, and RNA were obtained from instrumented fermenters and analysed using SWATH, LCMS, and RNAseq, respectively. Targeted intracellular metabolomics, quantitative SWATH proteomics, and RNAseq were profiled and compared using various approaches including principal component analyses, and linear models in R. Sequencing of the genomes revealed single point recombination events to be responsible for the improved phenotypes and suggested homologous recombination to be the mechanism for genome variation during genome shuffling. Upregulation of unreported mechanisms in Propionibacterium which included the methylglyoxal pathway, the pentose and glucuronate interconversion pathway, and the GABA shunt were linked to the improved yields. Our findings show that increased uptake of sucrose alongside an increase in a polar amino acid uptake rate with the overexpression of the electron transport system rewired the metabolism for enhanced PA production. These changes enhanced the PA generation and reduced the acetic acid synthesis, thus enabling a cost-competitive bioprocess for PA production.

1            L. Liu, Y. Zhu, J. Li, M. Wang, P. Lee, G. Du and J. Chen, Crit. Rev. Biotechnol., 2012, 32, 374–81.

2            B. A. Rodriguez, C. C. Stowers, V. Pham and B. M. Cox, Green Chem., 2014, 16, 1066–1076.

PhD. Carlos Horacio Luna Flores

Australian Institute for Bioengineering and Nanotechnology. Australia.

Phone: 0405343317 E-mail:

Research interests: Systems Biology, Bioprocess, Genomics, Transcriptomics, Proteomics, Metabolomics, Industrial Biotechnology.